request from: hawk checking if we should skip the build started at: Mon Jan 21 12:30:36 2019 fetching http://src.tld-linux.org/~buildertidev//srpms/a3c64fa2-a85b-48af-a9da-e32fc23bc7d7/R-3.5.2-1.src.rpm fetched 30200918 bytes, 236020.3 K/s installing srpm: R-3.5.2-1.src.rpm + install -d /tmp/B.61K3e5/BUILD /tmp/B.61K3e5/RPMS + LC_ALL=en_US.UTF-8 + rpm -qp --changelog R-3.5.2-1.src.rpm * Mon Jan 21 2019 TLD Linux - For complete changelog see: http://git.tld-linux.org/?p=packages/R.git;a=log;h=master * Mon Jan 21 2019 Marcin Krol 2001c6b - updated to 3.5.2, note: requires configured /etc/localtime to build * Fri Mar 16 2018 Jakub Bogusz 967c8b5 - updated to 3.4.3 + rpm -Uhv --nodeps --define '_topdir /tmp/B.61K3e5' --define '_specdir %{_topdir}' --define '_sourcedir %{_specdir}' --define '_rpmdir %{_topdir}/RPMS' --define '_builddir %{_topdir}/BUILD' R-3.5.2-1.src.rpm R ################################################## + rm -f R-3.5.2-1.src.rpm + install -m 700 -d /tmp/B.61K3e5/BUILD/tmp + TMPDIR=/tmp/B.61K3e5/BUILD/tmp + exec nice -n 19 rpmbuild -bp --short-circuit --nodeps --define '_topdir /tmp/B.61K3e5' --define '_specdir %{_topdir}' --define '_sourcedir %{_specdir}' --define '_rpmdir %{_topdir}/RPMS' --define '_builddir %{_topdir}/BUILD' --target x86_64-tld-linux --define 'prep exit 0' /tmp/B.61K3e5/R.spec Building target platforms: x86_64-tld-linux checking BuildConflict-ing packages no BuildConflicts found checking BR rpm: Building target platforms: x86_64-tld-linux no BR needed building RPM using: set -ex; : build-id: a3c64fa2-a85b-48af-a9da-e32fc23bc7d7; TMPDIR=/tmp/B.61K3e5/BUILD/tmp exec nice -n 19 rpmbuild -bb --define '_smp_mflags -j4' --define '_tld_builder 1' --define '_topdir /tmp/B.61K3e5' --define '_specdir %{_topdir}' --define '_sourcedir %{_specdir}' --define '_rpmdir %{_topdir}/RPMS' --define '_builddir %{_topdir}/BUILD' --target x86_64-tld-linux /tmp/B.61K3e5/R.spec + : build-id: a3c64fa2-a85b-48af-a9da-e32fc23bc7d7 + TMPDIR=/tmp/B.61K3e5/BUILD/tmp + exec nice -n 19 rpmbuild -bb --define '_smp_mflags -j4' --define '_tld_builder 1' --define '_topdir /tmp/B.61K3e5' --define '_specdir %{_topdir}' --define '_sourcedir %{_specdir}' --define '_rpmdir %{_topdir}/RPMS' --define '_builddir %{_topdir}/BUILD' --target x86_64-tld-linux /tmp/B.61K3e5/R.spec Building target platforms: x86_64-tld-linux Executing(%prep): env -i TMP=/home/users/builder/tmp HOME=/home/users/builder PATH=/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/users/builder/bin TMPDIR=/tmp/B.61K3e5/BUILD/tmp /bin/sh -e /tmp/B.61K3e5/BUILD/tmp/rpm-tmp.19732 + umask 022 + cd /tmp/B.61K3e5/BUILD + cd /tmp/B.61K3e5/BUILD + rm -rf R-3.5.2 + /usr/bin/gzip -dc /tmp/B.61K3e5/R-3.5.2.tar.gz + /bin/tar -xf - + STATUS=0 + '[' 0 -ne 0 ']' + cd R-3.5.2 + /bin/id -u + '[' 10001 '=' 0 ']' + true . + /bin/chmod -Rf -Rf a+rX,u+w,g-w,o-w . + exit 0 Executing(%build): env -i TMP=/home/users/builder/tmp HOME=/home/users/builder PATH=/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/users/builder/bin TMPDIR=/tmp/B.61K3e5/BUILD/tmp /bin/sh -e /tmp/B.61K3e5/BUILD/tmp/rpm-tmp.19732 TMP=/home/users/builder/tmp HOME=/home/users/builder PATH=/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/users/builder/bin TMPDIR=/tmp/B.61K3e5/BUILD/tmp + umask 022 + cd /tmp/B.61K3e5/BUILD + cd R-3.5.2 + aclocal -I m4 + autoconf + install -d build + cd build + .././configure 'LDFLAGS=-Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc ' 'CFLAGS=-O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 ' 'CXXFLAGS=-O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 ' 'FFLAGS=-O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 ' 'FCFLAGS=-O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 ' 'CPPFLAGS=' 'CC=x86_64-tld-linux-gcc' 'CXX=x86_64-tld-linux-g++' '--host=x86_64-tld-linux' '--build=x86_64-tld-linux' '--prefix=/usr' '--exec-prefix=/usr' '--bindir=/usr/bin' '--sbindir=/usr/sbin' '--sysconfdir=/etc' '--datadir=/usr/share' '--includedir=/usr/include' '--libdir=/usr/lib64' '--libexecdir=/usr/lib64' '--localstatedir=/var' '--sharedstatedir=/var/lib' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--x-libraries=/usr/lib64' 'F77=gfortran' 'FC=gfortran' --enable-R-shlib --enable-largefile --with-internal-tzcode --with-ICU --with-blas --with-cairo --with-jpeglib --with-lapack --with-libpng --with-readline --with-recommended-packages --with-system-tre --with-tcltk '--with-tcl-config=/usr/lib/tclConfig.sh' '--with-tk-config=/usr/lib/tkConfig.sh' --with-x checking build system type... x86_64-tld-linux-gnu checking host system type... x86_64-tld-linux-gnu loading site script '.././config.site' checking for pwd... /bin/pwd checking whether builddir is srcdir... no checking whether ln -s works... yes checking for ar... ar checking for a BSD-compatible install... /usr/bin/install -c checking for sed... /bin/sed checking for which... /usr/bin/which checking for less... /usr/bin/less checking for gtar... /usr/bin/gtar checking for tex... /usr/bin/tex checking for pdftex... /usr/bin/pdftex checking for pdflatex... /usr/bin/pdflatex checking for makeindex... no checking for texi2any... /usr/bin/texi2any checking whether texi2any version is at least 5.1... yes checking for ginstall-info... no checking for install-info... no checking for texi2dvi... /usr/bin/texi2dvi checking for kpsewhich... /usr/bin/kpsewhich checking for latex inconsolata package... missing configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally checking for unzip... /usr/bin/unzip checking for zip... /usr/bin/zip checking for gzip... /usr/bin/gzip checking for bzip2... /usr/bin/bzip2 checking for firefox... no checking for mozilla... no checking for galeon... no checking for opera... no checking for xdg-open... no checking for kfmclient... no checking for gnome-moz-remote... no checking for open... /usr/bin/open using default browser ... /usr/bin/open checking for acroread... no checking for acroread4... no checking for xdg-open... no checking for evince... no checking for xpdf... no checking for gv... no checking for gnome-gv... no checking for ggv... no checking for okular... no checking for kpdf... no checking for open... /usr/bin/open checking for working aclocal... found checking for working autoconf... found checking for working autoheader... found checking for bison... bison -y checking for notangle... false checking for realpath... /usr/bin/realpath checking for pkg-config... /usr/bin/pkg-config checking for x86_64-tld-linux-gcc... x86_64-tld-linux-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether x86_64-tld-linux-gcc accepts -g... yes checking for x86_64-tld-linux-gcc option to accept ISO C89... none needed checking how to run the C preprocessor... x86_64-tld-linux-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether x86_64-tld-linux-gcc needs -traditional... no checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking how to run the C preprocessor... x86_64-tld-linux-gcc -E defining F77 to be gfortran checking for x86_64-tld-linux-g77... gfortran checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes checking whether we are using the GNU C++ compiler... yes checking whether x86_64-tld-linux-g++ accepts -g... yes checking whether x86_64-tld-linux-g++ -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 can compile C++ code... yes checking how to run the C++ preprocessor... x86_64-tld-linux-g++ -E checking whether __attribute__((visibility())) is supported... yes checking whether x86_64-tld-linux-gcc accepts -fvisibility... yes checking whether x86_64-tld-linux-g++ accepts -fvisibility... yes checking whether gfortran accepts -fvisibility... yes checking for x86_64-tld-linux-gcc... x86_64-tld-linux-gcc checking whether we are using the GNU Objective C compiler... yes checking whether x86_64-tld-linux-gcc accepts -g... yes checking for Objective C++ compiler... trying some possibilities checking whether x86_64-tld-linux-g++ can compile ObjC++... no no working ObjC++ compiler found checking how to print strings... print -r checking for a sed that does not truncate output... (cached) /bin/sed checking for fgrep... /bin/grep -F checking for ld used by x86_64-tld-linux-gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-tld-linux-gnu file names to x86_64-tld-linux-gnu format... func_convert_file_noop checking how to convert x86_64-tld-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for x86_64-tld-linux-objdump... no checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for x86_64-tld-linux-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... print -r -- checking for x86_64-tld-linux-ar... (cached) ar checking for archiver @FILE support... @ checking for x86_64-tld-linux-strip... no checking for strip... strip checking for x86_64-tld-linux-ranlib... no checking for ranlib... ranlib checking for mawk... mawk checking command to parse /usr/bin/nm -B output from x86_64-tld-linux-gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for x86_64-tld-linux-mt... no checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if x86_64-tld-linux-gcc supports -fno-rtti -fno-exceptions... no checking for x86_64-tld-linux-gcc option to produce PIC... -fPIC -DPIC checking if x86_64-tld-linux-gcc PIC flag -fPIC -DPIC works... yes checking if x86_64-tld-linux-gcc static flag -static works... yes checking if x86_64-tld-linux-gcc supports -c -o file.o... yes checking if x86_64-tld-linux-gcc supports -c -o file.o... (cached) yes checking whether the x86_64-tld-linux-gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... x86_64-tld-linux-g++ -E checking for ld used by x86_64-tld-linux-g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the x86_64-tld-linux-g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for x86_64-tld-linux-g++ option to produce PIC... -fPIC -DPIC checking if x86_64-tld-linux-g++ PIC flag -fPIC -DPIC works... yes checking if x86_64-tld-linux-g++ static flag -static works... yes checking if x86_64-tld-linux-g++ supports -c -o file.o... yes checking if x86_64-tld-linux-g++ supports -c -o file.o... (cached) yes checking whether the x86_64-tld-linux-g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for gfortran option to produce PIC... -fPIC checking if gfortran PIC flag -fPIC works... yes checking if gfortran static flag -static works... no checking if gfortran supports -c -o file.o... yes checking if gfortran supports -c -o file.o... (cached) yes checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for cos in -lm... yes checking for sin in -lm... yes checking for dlopen in -ldl... yes checking readline/history.h usability... yes checking readline/history.h presence... yes checking for readline/history.h... yes checking readline/readline.h usability... yes checking readline/readline.h presence... yes checking for readline/readline.h... yes checking for rl_callback_read_char in -lreadline... yes checking for history_truncate_file... yes checking whether rl_callback_sigcleanup exists and is declared... yes checking whether rl_completion_matches exists and is declared... yes checking whether rl_resize_terminal exists and is declared... yes checking whether rl_sort_completion_matches exists and is declared... yes checking for ANSI C header files... (cached) yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for sys/wait.h that is POSIX.1 compatible... yes checking for dlfcn.h... (cached) yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking glob.h usability... yes checking glob.h presence... yes checking for glob.h... yes checking grp.h usability... yes checking grp.h presence... yes checking for grp.h... yes checking pwd.h usability... yes checking pwd.h presence... yes checking for pwd.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for strings.h... (cached) yes checking sys/resource.h usability... yes checking sys/resource.h presence... yes checking for sys/resource.h... yes checking sys/select.h usability... yes checking sys/select.h presence... yes checking for sys/select.h... yes checking sys/socket.h usability... yes checking sys/socket.h presence... yes checking for sys/socket.h... yes checking for sys/stat.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sys/times.h usability... yes checking sys/times.h presence... yes checking for sys/times.h... yes checking sys/utsname.h usability... yes checking sys/utsname.h presence... yes checking for sys/utsname.h... yes checking for unistd.h... (cached) yes checking utime.h usability... yes checking utime.h presence... yes checking for utime.h... yes checking arpa/inet.h usability... yes checking arpa/inet.h presence... yes checking for arpa/inet.h... yes checking dl.h usability... no checking dl.h presence... no checking for dl.h... no checking elf.h usability... yes checking elf.h presence... yes checking for elf.h... yes checking features.h usability... yes checking features.h presence... yes checking for features.h... yes checking floatingpoint.h usability... no checking floatingpoint.h presence... no checking for floatingpoint.h... no checking langinfo.h usability... yes checking langinfo.h presence... yes checking for langinfo.h... yes checking netdb.h usability... yes checking netdb.h presence... yes checking for netdb.h... yes checking netinet/in.h usability... yes checking netinet/in.h presence... yes checking for netinet/in.h... yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking stdalign.h usability... yes checking stdalign.h presence... yes checking for stdalign.h... yes checking errno.h usability... yes checking errno.h presence... yes checking for errno.h... yes checking for inttypes.h... (cached) yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking locale.h usability... yes checking locale.h presence... yes checking for locale.h... yes checking stdarg.h usability... yes checking stdarg.h presence... yes checking for stdarg.h... yes checking stdbool.h usability... yes checking stdbool.h presence... yes checking for stdbool.h... yes checking for stdint.h... (cached) yes checking for string.h... (cached) yes checking whether setjmp.h is POSIX.1 compatible... yes checking whether sigsetjmp is declared... yes checking whether siglongjmp is declared... yes checking for GNU C library with version >= 2... yes checking return type of signal handlers... void checking for uint64_t... yes checking for int64_t... yes checking for int_fast64_t... yes checking for pid_t... yes checking for size_t... yes checking whether SIZE_MAX is declared... yes checking for blkcnt_t... yes checking for type of socket length... socklen_t * checking for stack_t... yes checking for intptr_t... yes checking for uintptr_t... yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for x86_64-tld-linux-gcc option to accept ISO C99... none needed checking for x86_64-tld-linux-gcc option to accept ISO Standard C... (cached) none needed checking for inline... inline checking size of int... 4 checking size of long... 8 checking size of long long... 8 checking size of double... 8 checking size of size_t... 8 checking size of long double... 16 checking whether we can compute C Make dependencies... yes, using $(CC) -MM checking whether x86_64-tld-linux-gcc supports -c -o FILE.lo... yes checking for x86_64-tld-linux-gcc option to support OpenMP... -fopenmp checking how to get verbose linking output from gfortran... -v checking for Fortran 77 libraries of gfortran... -L/usr/lib64/gcc/x86_64-tld-linux/8.2.0 -L/usr/lib64/gcc/x86_64-tld-linux/8.2.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-tld-linux/8.2.0/../../.. -lgfortran -lm -lquadmath checking how to get verbose linking output from x86_64-tld-linux-gcc... -v checking for C libraries of x86_64-tld-linux-gcc... -L/usr/lib64/gcc/x86_64-tld-linux/8.2.0 -L/usr/lib64/gcc/x86_64-tld-linux/8.2.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-tld-linux/8.2.0/../../.. -lgcc_s checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore checking whether gfortran appends underscores to external names... yes checking whether gfortran appends extra underscores to external names... no checking whether mixed C/Fortran code can be run... yes checking whether gfortran and x86_64-tld-linux-gcc agree on int and double... yes checking whether gfortran and x86_64-tld-linux-gcc agree on double complex... yes checking for gfortran option to support OpenMP... -fopenmp checking whether x86_64-tld-linux-g++ accepts -M for generating dependencies... yes checking for x86_64-tld-linux-g++ option to support OpenMP... -fopenmp checking whether we can compute ObjC Make dependencies... yes, using x86_64-tld-linux-gcc -MM checking for ObjC runtime library... -lobjc checking for ObjC runtime style... unknown checking whether x86_64-tld-linux-gcc accepts -fobjc-exceptions... yes checking whether C runtime needs -D__NO_MATH_INLINES... no checking for xmkmf... /usr/bin/xmkmf checking whether x86_64-tld-linux-g++ supports C++98 features with -std=gnu++98... yes checking whether x86_64-tld-linux-g++ supports C++11 features with -std=gnu++11... yes checking whether x86_64-tld-linux-g++ supports C++14 features with -std=gnu++14... yes checking whether x86_64-tld-linux-g++ supports C++17 features with -std=gnu++17... yes checking for option providing pthread_kill... none required checking whether POSIX threads are supported... yes checking for off_t... yes checking for working alloca.h... yes checking for alloca... yes checking whether alloca is declared... yes checking whether expm1 exists and is declared... yes checking whether hypot exists and is declared... yes checking whether log1p exists and is declared... yes checking whether log1pl exists and is declared... yes checking whether log2 exists and is declared... yes checking whether log10 exists and is declared... yes checking whether nearbyint exists and is declared... yes checking whether nearbyintl exists and is declared... yes checking whether powl exists and is declared... yes checking whether rintl exists and is declared... yes checking whether va_copy exists and is declared... yes checking for isblank... yes checking sunmath.h usability... no checking sunmath.h presence... no checking for sunmath.h... no checking for cospi in -lsunmath... no checking for atanpi... no checking for atan2pi... no checking for cospi... no checking for exp10... yes checking for pown... no checking for sinpi... no checking for tanpi... no checking for __cospi... no checking for __sinpi... no checking for __tanpi... no checking for fseeko... yes checking for ftello... yes checking for matherr... no checking whether fcntl exists and is declared... yes checking whether getgrgid exists and is declared... yes checking whether getpwuid exists and is declared... yes checking whether kill exists and is declared... yes checking whether sigaction exists and is declared... yes checking whether sigaltstack exists and is declared... yes checking whether sigemptyset exists and is declared... yes checking whether fdopen exists and is declared... yes checking whether popen exists and is declared... yes checking whether getline exists and is declared... yes checking whether select exists and is declared... yes checking whether setenv exists and is declared... yes checking whether unsetenv exists and is declared... yes checking whether getrlimit exists and is declared... yes checking whether setrlimit exists and is declared... yes checking whether getrusage exists and is declared... yes checking whether getpriority exists and is declared... yes checking whether chmod exists and is declared... yes checking whether mkfifo exists and is declared... yes checking whether stat exists and is declared... yes checking whether umask exists and is declared... yes checking whether gettimeofday exists and is declared... yes checking whether utimes exists and is declared... yes checking whether times exists and is declared... yes checking whether gmtime_r exists and is declared... yes checking whether localtime_r exists and is declared... yes checking whether nl_langinfo exists and is declared... yes checking whether access exists and is declared... yes checking whether chdir exists and is declared... yes checking whether execv exists and is declared... yes checking whether ftruncate exists and is declared... yes checking whether getcwd exists and is declared... yes checking whether geteuid exists and is declared... yes checking whether getuid exists and is declared... yes checking whether link exists and is declared... yes checking whether readlink exists and is declared... yes checking whether symlink exists and is declared... yes checking whether sysconf exists and is declared... yes checking whether sched_setaffinity exists and is declared... yes checking whether sched_getaffinity exists and is declared... yes checking whether utime exists and is declared... yes checking whether utimensat exists and is declared... yes checking for clock_gettime in -lrt... yes checking whether clock_gettime exists and is declared... yes checking whether timespec_get exists and is declared... yes checking for putenv... yes checking whether putenv is declared... yes checking for vasprintf... yes checking whether vasprintf is declared... yes checking for mempcpy... yes checking for realpath... yes checking whether realpath is declared... yes checking whether glob exists and is declared... yes checking for dladdr... yes checking for dlsym... yes checking whether dladdr is declared... yes checking whether dlsym is declared... yes checking whether RTLD_DEFAULT is declared... yes checking whether RTLD_NEXT is declared... yes checking thread.h usability... no checking thread.h presence... no checking for thread.h... no checking whether thr_stksegment exists and is declared... no checking for isnan... yes checking whether isfinite is declared... yes checking whether isnan is declared... yes checking whether you have IEEE 754 floating-point arithmetic... yes checking whether putenv("FOO") can unset an environment variable... yes checking whether putenv("FOO=") can unset an environment variable... no checking for nl_langinfo and CODESET... yes checking for mkdtemp... yes checking for strdup... yes checking for strncasecmp... yes checking whether mkdtemp is declared... yes checking whether strdup is declared... yes checking whether strncasecmp is declared... yes checking for library containing connect... none required checking for library containing gethostbyname... none required checking for library containing xdr_string... none required checking for working calloc... yes checking for working isfinite... yes checking for working log1p... yes checking whether ftell works correctly on files opened for append... yes checking for working sigaction... yes checking complex.h usability... yes checking complex.h presence... yes checking for complex.h... yes checking for double complex... yes checking whether C99 double complex is supported... yes checking whether cabs exists and is declared... yes checking whether carg exists and is declared... yes checking whether cexp exists and is declared... yes checking whether clog exists and is declared... yes checking whether csqrt exists and is declared... yes checking whether cpow exists and is declared... yes checking whether ccos exists and is declared... yes checking whether csin exists and is declared... yes checking whether ctan exists and is declared... yes checking whether cacos exists and is declared... yes checking whether casin exists and is declared... yes checking whether catan exists and is declared... yes checking whether ccosh exists and is declared... yes checking whether csinh exists and is declared... yes checking whether ctanh exists and is declared... yes checking for working ctanh... yes checking whether 'struct tm' includes tm_zone... yes checking whether 'struct tm' includes tm_gmtoff... yes checking for dgemm_... no checking for ATL_xerbla in -latlas... no checking for dgemm_ in -lblas... yes checking for dgemm_ in -ldgemm... no checking for dgemm_ in -lblas... (cached) yes checking for dgemm_ in -lessl... no checking for dgemm_ in -lblas... (cached) yes checking whether double complex BLAS can be used... yes checking whether the BLAS is complete... yes checking for dpstrf_... no checking for dpstrf_ in -llapack... yes checking iconv.h usability... yes checking iconv.h presence... yes checking for iconv.h... yes checking for iconv... yes checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... yes checking whether iconv accepts "CP1252"... yes checking for iconvlist... no checking for iconv... yes checking for iconv declaration... extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft); checking wchar.h usability... yes checking wchar.h presence... yes checking for wchar.h... yes checking wctype.h usability... yes checking wctype.h presence... yes checking for wctype.h... yes checking whether mbrtowc exists and is declared... yes checking whether wcrtomb exists and is declared... yes checking whether wcscoll exists and is declared... yes checking whether wcsftime exists and is declared... yes checking whether wcstod exists and is declared... yes checking whether mbstowcs exists and is declared... yes checking whether wcstombs exists and is declared... yes checking whether wctrans exists and is declared... yes checking whether iswblank exists and is declared... yes checking whether wctype exists and is declared... yes checking whether iswctype exists and is declared... yes checking for wctrans_t... yes checking for mbstate_t... yes checking for ICU... yes checking for X... libraries /usr/lib64, headers checking whether -R must be followed by a space... neither works checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking X11/Intrinsic.h usability... yes checking X11/Intrinsic.h presence... yes checking for X11/Intrinsic.h... yes checking for XtToolkitInitialize in -lXt... yes using X11 ... yes checking for KeySym... yes checking X11/Xmu/Atoms.h usability... yes checking X11/Xmu/Atoms.h presence... yes checking for X11/Xmu/Atoms.h... yes checking for XmuInternAtom in -lXmu... yes checking whether pkg-config knows about cairo and pango... yes checking whether cairo including pango is >= 1.2 and works... yes checking for /usr/lib/tclConfig.sh... /usr/lib/tclConfig.sh checking for /usr/lib/tkConfig.sh... /usr/lib/tkConfig.sh checking tcl.h usability... yes checking tcl.h presence... yes checking for tcl.h... yes checking tk.h usability... yes checking tk.h presence... yes checking for tk.h... yes checking whether compiling/linking Tcl/Tk code works... yes checking for BSD networking... yes checking rpc/types.h usability... yes checking rpc/types.h presence... yes checking for rpc/types.h... yes checking for rpc/xdr.h... yes checking for XDR support... yes checking for inflateInit2_ in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking if zlib version >= 1.2.5... yes checking whether zlib support suffices... yes checking mmap support for zlib... yes checking for BZ2_bzlibVersion in -lbz2... yes checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes checking if bzip2 version >= 1.0.6... yes checking whether bzip2 support suffices... yes checking for lzma_version_number in -llzma... yes checking lzma.h usability... yes checking lzma.h presence... yes checking for lzma.h... yes checking if lzma version >= 5.0.3... yes checking for pcre_fullinfo in -lpcre... yes checking pcre.h usability... yes checking pcre.h presence... yes checking for pcre.h... yes checking pcre/pcre.h usability... no checking pcre/pcre.h presence... no checking for pcre/pcre.h... no checking if PCRE version >= 8.20, < 10.0 and has UTF-8 support... yes checking if PCRE version >= 8.32... yes checking whether PCRE support suffices... yes checking pcre2.h usability... yes checking pcre2.h presence... yes checking for pcre2.h... yes checking for pcre2_compile_8 in -lpcre2-8... yes checking for tre_regncompb in -ltre... no checking for curl-config... /usr/bin/curl-config checking libcurl version ... 7.63.0 checking curl/curl.h usability... yes checking curl/curl.h presence... yes checking for curl/curl.h... yes checking if libcurl is version 7 and >= 7.22.0... yes checking if libcurl supports https... yes checking if jpeglib version >= 6b... yes checking for jpeg_destroy_compress in -ljpeg... yes checking if libpng version >= 1.2.7... yes checking for png_create_write_struct in -lpng... yes checking tiffio.h usability... yes checking tiffio.h presence... yes checking for tiffio.h... yes checking for TIFFOpen in -ltiff... yes checking whether leap seconds are treated according to POSIX... yes checking for inline... inline checking for sys/time.h... (cached) yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for struct stat.st_atim.tv_nsec... yes checking whether struct stat.st_atim is of type struct timespec... yes checking for setitimer... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking whether KERN_USRSTACK sysctl is supported... no checking for visible __lib_stack_end... yes checking for lpr... no checking for lp... no checking for paperconf... /usr/bin/paperconf checking for x86_64-tld-linux-gfortran... gfortran checking whether we are using the GNU Fortran compiler... yes checking whether gfortran accepts -g... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for gfortran option to produce PIC... -fPIC checking if gfortran PIC flag -fPIC works... yes checking if gfortran static flag -static works... no checking if gfortran supports -c -o file.o... yes checking if gfortran supports -c -o file.o... (cached) yes checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for Fortran flag to compile .f90 files... none checking for Fortran flag to compile .f95 files... none checking for gfortran option to support OpenMP... -fopenmp checking for recommended packages... yes checking whether NLS is requested... yes Configuring src/extra/intl directory checking for a thread-safe mkdir -p... /bin/mkdir -p checking whether we are using the GNU C Library 2 or newer... yes checking for x86_64-tld-linux-ranlib... ranlib checking for simple visibility declarations... yes checking for stdint.h... yes checking for getpagesize... yes checking for working mmap... yes checking whether integer division by zero raises SIGFPE... yes checking for inttypes.h... yes checking for unsigned long long int... yes checking for inttypes.h... (cached) yes checking whether the inttypes.h PRIxNN macros are broken... no checking for ld used by x86_64-tld-linux-gcc... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking for shared library run path origin... done checking whether imported symbols can be declared weak... yes checking for multithread API to use... none checking argz.h usability... yes checking argz.h presence... yes checking for argz.h... yes checking for inttypes.h... (cached) yes checking for limits.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for getcwd... yes checking for getegid... yes checking for geteuid... yes checking for getgid... yes checking for getuid... yes checking for mempcpy... (cached) yes checking for munmap... yes checking for stpcpy... yes checking for strcasecmp... yes checking for strdup... (cached) yes checking for strtoul... yes checking for tsearch... yes checking for argz_count... yes checking for argz_stringify... yes checking for argz_next... yes checking for __fsetlocking... yes checking whether feof_unlocked is declared... yes checking whether fgets_unlocked is declared... yes checking for iconv... (cached) yes checking for iconv declaration... (cached) extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft); checking for NL_LOCALE_NAME macro... yes checking for bison... bison checking version of bison... 3.2.4, ok checking for long long int... yes checking for long double... yes checking for wchar_t... yes checking for wint_t... yes checking for intmax_t... yes checking whether printf() supports POSIX/XSI format strings... yes checking whether we are using the GNU C Library 2.1 or newer... yes checking for stdint.h... (cached) yes checking for SIZE_MAX... yes checking for stdint.h... (cached) yes checking for CFPreferencesCopyAppValue... no checking for CFLocaleCopyCurrent... no checking for ptrdiff_t... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for asprintf... yes checking for fwprintf... yes checking for putenv... (cached) yes checking for setenv... yes checking for setlocale... yes checking for snprintf... yes checking for wcslen... yes checking whether _snprintf is declared... no checking whether _snwprintf is declared... no checking whether getc_unlocked is declared... yes checking for nl_langinfo and CODESET... (cached) yes checking for LC_MESSAGES... yes checking for CFPreferencesCopyAppValue... (cached) no checking for CFLocaleCopyCurrent... (cached) no checking whether included gettext is requested... no checking for GNU gettext in libc... yes checking whether to use NLS... yes checking where the gettext function comes from... libc Finished configuring src/extra/intl directory checking whether OpenMP SIMD reduction is supported... yes using as R_SHELL for scripts ... /bin/sh configure: creating ./config.status config.status: creating Makeconf config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/html/Makefile config.status: creating doc/manual/Makefile config.status: creating etc/Makefile config.status: creating etc/Makeconf config.status: creating etc/Renviron config.status: creating etc/javaconf config.status: creating etc/ldpaths config.status: creating m4/Makefile config.status: creating po/Makefile config.status: creating share/Makefile config.status: creating src/Makefile config.status: creating src/appl/Makefile config.status: creating src/extra/Makefile config.status: creating src/extra/blas/Makefile config.status: creating src/extra/intl/Makefile config.status: creating src/extra/tre/Makefile config.status: creating src/extra/tzone/Makefile config.status: creating src/extra/xdr/Makefile config.status: creating src/include/Makefile config.status: creating src/include/Rmath.h0 config.status: creating src/include/R_ext/Makefile config.status: creating src/library/Recommended/Makefile config.status: creating src/library/Makefile config.status: creating src/library/base/DESCRIPTION config.status: creating src/library/base/Makefile config.status: creating src/library/compiler/DESCRIPTION config.status: creating src/library/compiler/Makefile config.status: creating src/library/datasets/DESCRIPTION config.status: creating src/library/datasets/Makefile config.status: creating src/library/graphics/DESCRIPTION config.status: creating src/library/graphics/Makefile config.status: creating src/library/graphics/src/Makefile config.status: creating src/library/grDevices/DESCRIPTION config.status: creating src/library/grDevices/Makefile config.status: creating src/library/grDevices/src/Makefile config.status: creating src/library/grDevices/src/cairo/Makefile config.status: creating src/library/grid/DESCRIPTION config.status: creating src/library/grid/Makefile config.status: creating src/library/grid/src/Makefile config.status: creating src/library/methods/DESCRIPTION config.status: creating src/library/methods/Makefile config.status: creating src/library/methods/src/Makefile config.status: creating src/library/parallel/DESCRIPTION config.status: creating src/library/parallel/Makefile config.status: creating src/library/parallel/src/Makefile config.status: creating src/library/profile/Makefile config.status: creating src/library/stats/DESCRIPTION config.status: creating src/library/stats/Makefile config.status: creating src/library/stats/src/Makefile config.status: creating src/library/stats4/DESCRIPTION config.status: creating src/library/stats4/Makefile config.status: creating src/library/splines/DESCRIPTION config.status: creating src/library/splines/Makefile config.status: creating src/library/splines/src/Makefile config.status: creating src/library/tcltk/DESCRIPTION config.status: creating src/library/tcltk/Makefile config.status: creating src/library/tcltk/src/Makefile config.status: creating src/library/tools/DESCRIPTION config.status: creating src/library/tools/Makefile config.status: creating src/library/tools/src/Makefile config.status: creating src/library/translations/DESCRIPTION config.status: creating src/library/translations/Makefile config.status: creating src/library/utils/DESCRIPTION config.status: creating src/library/utils/Makefile config.status: creating src/library/utils/src/Makefile config.status: creating src/main/Makefile config.status: creating src/modules/Makefile config.status: creating src/modules/X11/Makefile config.status: creating src/modules/internet/Makefile config.status: creating src/modules/lapack/Makefile config.status: creating src/nmath/Makefile config.status: creating src/nmath/standalone/Makefile config.status: creating src/scripts/Makefile config.status: creating src/scripts/R.sh config.status: creating src/scripts/Rcmd config.status: creating src/scripts/f77_f2c config.status: creating src/scripts/javareconf config.status: creating src/scripts/mkinstalldirs config.status: creating src/scripts/pager config.status: creating src/scripts/rtags config.status: creating src/unix/Makefile config.status: creating tests/Makefile config.status: creating tests/Embedding/Makefile config.status: creating tests/Examples/Makefile config.status: creating tools/Makefile config.status: creating src/include/config.h config.status: executing libtool commands config.status: executing stamp-h commands R is now configured for x86_64-tld-linux-gnu Source directory: ../. Installation directory: /usr C compiler: x86_64-tld-linux-gcc -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 Fortran 77 compiler: gfortran -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 Default C++ compiler: x86_64-tld-linux-g++ -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 C++98 compiler: x86_64-tld-linux-g++ -std=gnu++98 -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 C++11 compiler: x86_64-tld-linux-g++ -std=gnu++11 -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 C++14 compiler: x86_64-tld-linux-g++ -std=gnu++14 -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 C++17 compiler: x86_64-tld-linux-g++ -std=gnu++17 -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 Fortran 90/95 compiler: gfortran -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 Obj-C compiler: x86_64-tld-linux-gcc -g -O2 -fobjc-exceptions Interfaces supported: X11, tcltk External libraries: readline, BLAS(generic), LAPACK(generic), curl Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU Options enabled: shared R library, R profiling Capabilities skipped: Options not enabled: shared BLAS, memory profiling Recommended packages: yes configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally + /usr/bin/make -j4 -j1 make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/m4' make[1]: Nothing to be done for 'R'. make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/m4' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tools' make[1]: Nothing to be done for 'R'. make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tools' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/html' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/html' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/html' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/html' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc' make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/etc' make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/etc' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/share' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/share' mkdir -p -- ../share/R mkdir -p -- ../share/dictionaries mkdir -p -- ../share/encodings mkdir -p -- ../share/java mkdir -p -- ../share/licenses mkdir -p -- ../share/make mkdir -p -- ../share/Rd mkdir -p -- ../share/Rd/macros mkdir -p -- ../share/sh mkdir -p -- ../share/texmf mkdir -p -- ../share/texmf/bibtex/bib mkdir -p -- ../share/texmf/bibtex/bst mkdir -p -- ../share/texmf/tex/latex make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/share' make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/share' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/scripts' creating src/scripts/R.fe make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/scripts' mkdir -p -- ../../bin make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/scripts' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/scripts' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/include' mkdir -p -- ../../include make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/include/R_ext' mkdir -p -- ../../../include/R_ext make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/include/R_ext' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/include' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tre' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tre' making regcomp.d from ../../../.././src/extra/tre/regcomp.c making regerror.d from ../../../.././src/extra/tre/regerror.c making regexec.d from ../../../.././src/extra/tre/regexec.c making tre-ast.d from ../../../.././src/extra/tre/tre-ast.c making tre-compile.d from ../../../.././src/extra/tre/tre-compile.c making tre-match-approx.d from ../../../.././src/extra/tre/tre-match-approx.c making tre-match-backtrack.d from ../../../.././src/extra/tre/tre-match-backtrack.c making tre-match-parallel.d from ../../../.././src/extra/tre/tre-match-parallel.c making tre-mem.d from ../../../.././src/extra/tre/tre-mem.c making tre-parse.d from ../../../.././src/extra/tre/tre-parse.c making tre-stack.d from ../../../.././src/extra/tre/tre-stack.c making xmalloc.d from ../../../.././src/extra/tre/xmalloc.c make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tre' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tre' x86_64-tld-linux-gcc -I../../../.././src/extra/tre -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/extra/tre/regcomp.c -o regcomp.o x86_64-tld-linux-gcc -I../../../.././src/extra/tre -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/extra/tre/regerror.c -o regerror.o x86_64-tld-linux-gcc -I../../../.././src/extra/tre -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/extra/tre/regexec.c -o regexec.o x86_64-tld-linux-gcc -I../../../.././src/extra/tre -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/extra/tre/tre-ast.c -o tre-ast.o x86_64-tld-linux-gcc -I../../../.././src/extra/tre -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/extra/tre/tre-compile.c -o tre-compile.o x86_64-tld-linux-gcc -I../../../.././src/extra/tre -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/extra/tre/tre-match-approx.c -o tre-match-approx.o x86_64-tld-linux-gcc -I../../../.././src/extra/tre -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/extra/tre/tre-match-backtrack.c -o tre-match-backtrack.o x86_64-tld-linux-gcc -I../../../.././src/extra/tre -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/extra/tre/tre-match-parallel.c -o tre-match-parallel.o x86_64-tld-linux-gcc -I../../../.././src/extra/tre -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/extra/tre/tre-mem.c -o tre-mem.o x86_64-tld-linux-gcc -I../../../.././src/extra/tre -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/extra/tre/tre-parse.c -o tre-parse.o x86_64-tld-linux-gcc -I../../../.././src/extra/tre -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/extra/tre/tre-stack.c -o tre-stack.o x86_64-tld-linux-gcc -I../../../.././src/extra/tre -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/extra/tre/xmalloc.c -o xmalloc.o ar -cr libtre.a regcomp.o regerror.o regexec.o tre-ast.o tre-compile.o tre-match-approx.o tre-match-backtrack.o tre-match-parallel.o tre-mem.o tre-parse.o tre-stack.o xmalloc.o ranlib libtre.a make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tre' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tre' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tzone' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tzone' making localtime.d from ../../../.././src/extra/tzone/localtime.c making strftime.d from ../../../.././src/extra/tzone/strftime.c make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tzone' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tzone' x86_64-tld-linux-gcc -I. -I../../../src/include -I../../../.././src/include -I../../../.././src/extra/tzone -I../../../.././src/main -DHAVE_CONFIG_H -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/extra/tzone/localtime.c -o localtime.o x86_64-tld-linux-gcc -I. -I../../../src/include -I../../../.././src/include -I../../../.././src/extra/tzone -I../../../.././src/main -DHAVE_CONFIG_H -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/extra/tzone/strftime.c -o strftime.o ar -cr libtz.a localtime.o strftime.o make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tzone' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tzone' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/appl' making integrate.d from ../../.././src/appl/integrate.c making interv.d from ../../.././src/appl/interv.c making maxcol.d from ../../.././src/appl/maxcol.c making optim.d from ../../.././src/appl/optim.c making pretty.d from ../../.././src/appl/pretty.c making uncmin.d from ../../.././src/appl/uncmin.c make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/appl' x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/integrate.c -o integrate.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/interv.c -o interv.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/maxcol.c -o maxcol.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/optim.c -o optim.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/pretty.c -o pretty.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/uncmin.c -o uncmin.o gfortran -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/dchdc.f -o dchdc.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/dpbfa.f -o dpbfa.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/dpbsl.f -o dpbsl.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/dpoco.f -o dpoco.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/dpodi.f -o dpodi.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/dpofa.f -o dpofa.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/dposl.f -o dposl.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/dqrdc.f -o dqrdc.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/dqrdc2.f -o dqrdc2.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/dqrls.f -o dqrls.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/dqrsl.f -o dqrsl.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/dqrutl.f -o dqrutl.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/dsvdc.f -o dsvdc.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/dtrco.f -o dtrco.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/appl/dtrsl.f -o dtrsl.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran ar -cr libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o ranlib libappl.a make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/appl' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/appl' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/nmath' making mlutils.d from ../../.././src/nmath/mlutils.c making d1mach.d from ../../.././src/nmath/d1mach.c making i1mach.d from ../../.././src/nmath/i1mach.c making fmax2.d from ../../.././src/nmath/fmax2.c making fmin2.d from ../../.././src/nmath/fmin2.c making fprec.d from ../../.././src/nmath/fprec.c making fround.d from ../../.././src/nmath/fround.c making ftrunc.d from ../../.././src/nmath/ftrunc.c making sign.d from ../../.././src/nmath/sign.c making fsign.d from ../../.././src/nmath/fsign.c making imax2.d from ../../.././src/nmath/imax2.c making imin2.d from ../../.././src/nmath/imin2.c making chebyshev.d from ../../.././src/nmath/chebyshev.c making log1p.d from ../../.././src/nmath/log1p.c making lgammacor.d from ../../.././src/nmath/lgammacor.c making gammalims.d from ../../.././src/nmath/gammalims.c making stirlerr.d from ../../.././src/nmath/stirlerr.c making bd0.d from ../../.././src/nmath/bd0.c making gamma.d from ../../.././src/nmath/gamma.c making lgamma.d from ../../.././src/nmath/lgamma.c making gamma_cody.d from ../../.././src/nmath/gamma_cody.c making beta.d from ../../.././src/nmath/beta.c making lbeta.d from ../../.././src/nmath/lbeta.c making polygamma.d from ../../.././src/nmath/polygamma.c making cospi.d from ../../.././src/nmath/cospi.c making bessel_i.d from ../../.././src/nmath/bessel_i.c making bessel_j.d from ../../.././src/nmath/bessel_j.c making bessel_k.d from ../../.././src/nmath/bessel_k.c making bessel_y.d from ../../.././src/nmath/bessel_y.c making choose.d from ../../.././src/nmath/choose.c making snorm.d from ../../.././src/nmath/snorm.c making sexp.d from ../../.././src/nmath/sexp.c making dgamma.d from ../../.././src/nmath/dgamma.c making pgamma.d from ../../.././src/nmath/pgamma.c making qgamma.d from ../../.././src/nmath/qgamma.c making rgamma.d from ../../.././src/nmath/rgamma.c making dbeta.d from ../../.././src/nmath/dbeta.c making pbeta.d from ../../.././src/nmath/pbeta.c making qbeta.d from ../../.././src/nmath/qbeta.c making rbeta.d from ../../.././src/nmath/rbeta.c making dunif.d from ../../.././src/nmath/dunif.c making punif.d from ../../.././src/nmath/punif.c making qunif.d from ../../.././src/nmath/qunif.c making runif.d from ../../.././src/nmath/runif.c making dnorm.d from ../../.././src/nmath/dnorm.c making pnorm.d from ../../.././src/nmath/pnorm.c making qnorm.d from ../../.././src/nmath/qnorm.c making rnorm.d from ../../.././src/nmath/rnorm.c making dlnorm.d from ../../.././src/nmath/dlnorm.c making plnorm.d from ../../.././src/nmath/plnorm.c making qlnorm.d from ../../.././src/nmath/qlnorm.c making rlnorm.d from ../../.././src/nmath/rlnorm.c making df.d from ../../.././src/nmath/df.c making pf.d from ../../.././src/nmath/pf.c making qf.d from ../../.././src/nmath/qf.c making rf.d from ../../.././src/nmath/rf.c making dnf.d from ../../.././src/nmath/dnf.c making dt.d from ../../.././src/nmath/dt.c making pt.d from ../../.././src/nmath/pt.c making qt.d from ../../.././src/nmath/qt.c making rt.d from ../../.././src/nmath/rt.c making dnt.d from ../../.././src/nmath/dnt.c making dchisq.d from ../../.././src/nmath/dchisq.c making pchisq.d from ../../.././src/nmath/pchisq.c making qchisq.d from ../../.././src/nmath/qchisq.c making rchisq.d from ../../.././src/nmath/rchisq.c making rnchisq.d from ../../.././src/nmath/rnchisq.c making dbinom.d from ../../.././src/nmath/dbinom.c making pbinom.d from ../../.././src/nmath/pbinom.c making qbinom.d from ../../.././src/nmath/qbinom.c making rbinom.d from ../../.././src/nmath/rbinom.c making rmultinom.d from ../../.././src/nmath/rmultinom.c making dcauchy.d from ../../.././src/nmath/dcauchy.c making pcauchy.d from ../../.././src/nmath/pcauchy.c making qcauchy.d from ../../.././src/nmath/qcauchy.c making rcauchy.d from ../../.././src/nmath/rcauchy.c making dexp.d from ../../.././src/nmath/dexp.c making pexp.d from ../../.././src/nmath/pexp.c making qexp.d from ../../.././src/nmath/qexp.c making rexp.d from ../../.././src/nmath/rexp.c making dgeom.d from ../../.././src/nmath/dgeom.c making pgeom.d from ../../.././src/nmath/pgeom.c making qgeom.d from ../../.././src/nmath/qgeom.c making rgeom.d from ../../.././src/nmath/rgeom.c making dhyper.d from ../../.././src/nmath/dhyper.c making phyper.d from ../../.././src/nmath/phyper.c making qhyper.d from ../../.././src/nmath/qhyper.c making rhyper.d from ../../.././src/nmath/rhyper.c making dnbinom.d from ../../.././src/nmath/dnbinom.c making pnbinom.d from ../../.././src/nmath/pnbinom.c making qnbinom.d from ../../.././src/nmath/qnbinom.c making rnbinom.d from ../../.././src/nmath/rnbinom.c making dpois.d from ../../.././src/nmath/dpois.c making ppois.d from ../../.././src/nmath/ppois.c making qpois.d from ../../.././src/nmath/qpois.c making rpois.d from ../../.././src/nmath/rpois.c making dweibull.d from ../../.././src/nmath/dweibull.c making pweibull.d from ../../.././src/nmath/pweibull.c making qweibull.d from ../../.././src/nmath/qweibull.c making rweibull.d from ../../.././src/nmath/rweibull.c making dlogis.d from ../../.././src/nmath/dlogis.c making plogis.d from ../../.././src/nmath/plogis.c making qlogis.d from ../../.././src/nmath/qlogis.c making rlogis.d from ../../.././src/nmath/rlogis.c making dnchisq.d from ../../.././src/nmath/dnchisq.c making pnchisq.d from ../../.././src/nmath/pnchisq.c making qnchisq.d from ../../.././src/nmath/qnchisq.c making dnbeta.d from ../../.././src/nmath/dnbeta.c making pnbeta.d from ../../.././src/nmath/pnbeta.c making qnbeta.d from ../../.././src/nmath/qnbeta.c making pnf.d from ../../.././src/nmath/pnf.c making pnt.d from ../../.././src/nmath/pnt.c making qnf.d from ../../.././src/nmath/qnf.c making qnt.d from ../../.././src/nmath/qnt.c making ptukey.d from ../../.././src/nmath/ptukey.c making qtukey.d from ../../.././src/nmath/qtukey.c making toms708.d from ../../.././src/nmath/toms708.c making wilcox.d from ../../.././src/nmath/wilcox.c making signrank.d from ../../.././src/nmath/signrank.c make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/nmath' x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/mlutils.c -o mlutils.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/d1mach.c -o d1mach.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/i1mach.c -o i1mach.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/fmax2.c -o fmax2.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/fmin2.c -o fmin2.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/fprec.c -o fprec.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/fround.c -o fround.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/ftrunc.c -o ftrunc.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/sign.c -o sign.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/fsign.c -o fsign.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/imax2.c -o imax2.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/imin2.c -o imin2.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/chebyshev.c -o chebyshev.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/log1p.c -o log1p.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/lgammacor.c -o lgammacor.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/gammalims.c -o gammalims.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/stirlerr.c -o stirlerr.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/bd0.c -o bd0.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/gamma.c -o gamma.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/lgamma.c -o lgamma.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/gamma_cody.c -o gamma_cody.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/beta.c -o beta.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/lbeta.c -o lbeta.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/polygamma.c -o polygamma.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/cospi.c -o cospi.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/bessel_i.c -o bessel_i.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/bessel_j.c -o bessel_j.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/bessel_k.c -o bessel_k.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/bessel_y.c -o bessel_y.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/choose.c -o choose.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/snorm.c -o snorm.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/sexp.c -o sexp.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dgamma.c -o dgamma.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/pgamma.c -o pgamma.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qgamma.c -o qgamma.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/rgamma.c -o rgamma.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dbeta.c -o dbeta.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/pbeta.c -o pbeta.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qbeta.c -o qbeta.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/rbeta.c -o rbeta.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dunif.c -o dunif.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/punif.c -o punif.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qunif.c -o qunif.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/runif.c -o runif.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dnorm.c -o dnorm.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/pnorm.c -o pnorm.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qnorm.c -o qnorm.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/rnorm.c -o rnorm.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dlnorm.c -o dlnorm.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/plnorm.c -o plnorm.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qlnorm.c -o qlnorm.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/rlnorm.c -o rlnorm.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/df.c -o df.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/pf.c -o pf.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qf.c -o qf.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/rf.c -o rf.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dnf.c -o dnf.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dt.c -o dt.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/pt.c -o pt.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qt.c -o qt.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/rt.c -o rt.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dnt.c -o dnt.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dchisq.c -o dchisq.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/pchisq.c -o pchisq.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qchisq.c -o qchisq.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/rchisq.c -o rchisq.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/rnchisq.c -o rnchisq.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dbinom.c -o dbinom.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/pbinom.c -o pbinom.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qbinom.c -o qbinom.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/rbinom.c -o rbinom.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/rmultinom.c -o rmultinom.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dcauchy.c -o dcauchy.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/pcauchy.c -o pcauchy.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qcauchy.c -o qcauchy.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/rcauchy.c -o rcauchy.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dexp.c -o dexp.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/pexp.c -o pexp.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qexp.c -o qexp.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/rexp.c -o rexp.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dgeom.c -o dgeom.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/pgeom.c -o pgeom.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qgeom.c -o qgeom.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/rgeom.c -o rgeom.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dhyper.c -o dhyper.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/phyper.c -o phyper.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qhyper.c -o qhyper.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/rhyper.c -o rhyper.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dnbinom.c -o dnbinom.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/pnbinom.c -o pnbinom.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qnbinom.c -o qnbinom.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/rnbinom.c -o rnbinom.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dpois.c -o dpois.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/ppois.c -o ppois.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qpois.c -o qpois.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/rpois.c -o rpois.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dweibull.c -o dweibull.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/pweibull.c -o pweibull.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qweibull.c -o qweibull.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/rweibull.c -o rweibull.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dlogis.c -o dlogis.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/plogis.c -o plogis.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qlogis.c -o qlogis.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/rlogis.c -o rlogis.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dnchisq.c -o dnchisq.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/pnchisq.c -o pnchisq.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qnchisq.c -o qnchisq.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/dnbeta.c -o dnbeta.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/pnbeta.c -o pnbeta.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qnbeta.c -o qnbeta.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/pnf.c -o pnf.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/pnt.c -o pnt.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qnf.c -o qnf.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qnt.c -o qnt.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/ptukey.c -o ptukey.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/qtukey.c -o qtukey.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/toms708.c -o toms708.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/wilcox.c -o wilcox.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/nmath/signrank.c -o signrank.o ar -cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o ranlib libnmath.a make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/nmath' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/nmath' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/unix' config.status: creating src/unix/Makefile making Rembedded.d from ../../.././src/unix/Rembedded.c making dynload.d from ../../.././src/unix/dynload.c making system.d from ../../.././src/unix/system.c making sys-unix.d from ../../.././src/unix/sys-unix.c making sys-std.d from ../../.././src/unix/sys-std.c making X11.d from ../../.././src/unix/X11.c make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/unix' x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/unix/Rembedded.c -o Rembedded.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/unix/dynload.c -o dynload.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/unix/system.c -o system.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/unix/sys-unix.c -o sys-unix.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/unix/sys-std.c -o sys-std.o x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/unix/X11.c -o X11.o ar -cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o ranlib libunix.a make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/unix' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/unix' x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -DR_HOME='"/tmp/B.61K3e5/BUILD/R-3.5.2/build"' \ -o Rscript ../../.././src/unix/Rscript.c make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/unix' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/unix' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' config.status: creating src/main/Makefile making CommandLineArgs.d from ../../.././src/main/CommandLineArgs.c making Rdynload.d from ../../.././src/main/Rdynload.c making Renviron.d from ../../.././src/main/Renviron.c making RNG.d from ../../.././src/main/RNG.c making agrep.d from ../../.././src/main/agrep.c making altrep.d from ../../.././src/main/altrep.c making apply.d from ../../.././src/main/apply.c making arithmetic.d from ../../.././src/main/arithmetic.c making array.d from ../../.././src/main/array.c making attrib.d from ../../.././src/main/attrib.c making bind.d from ../../.././src/main/bind.c making builtin.d from ../../.././src/main/builtin.c making character.d from ../../.././src/main/character.c making coerce.d from ../../.././src/main/coerce.c making colors.d from ../../.././src/main/colors.c making complex.d from ../../.././src/main/complex.c making connections.d from ../../.././src/main/connections.c making context.d from ../../.././src/main/context.c making cum.d from ../../.././src/main/cum.c making dcf.d from ../../.././src/main/dcf.c making datetime.d from ../../.././src/main/datetime.c making debug.d from ../../.././src/main/debug.c making deparse.d from ../../.././src/main/deparse.c making devices.d from ../../.././src/main/devices.c making dotcode.d from ../../.././src/main/dotcode.c making dounzip.d from ../../.././src/main/dounzip.c making dstruct.d from ../../.././src/main/dstruct.c making duplicate.d from ../../.././src/main/duplicate.c making edit.d from ../../.././src/main/edit.c making engine.d from ../../.././src/main/engine.c making envir.d from ../../.././src/main/envir.c making errors.d from ../../.././src/main/errors.c making eval.d from ../../.././src/main/eval.c making format.d from ../../.././src/main/format.c making gevents.d from ../../.././src/main/gevents.c making gram.d from ../../.././src/main/gram.c making gram-ex.d from ../../.././src/main/gram-ex.c making graphics.d from ../../.././src/main/graphics.c making grep.d from ../../.././src/main/grep.c making identical.d from ../../.././src/main/identical.c making inlined.d from ../../.././src/main/inlined.c making inspect.d from ../../.././src/main/inspect.c making internet.d from ../../.././src/main/internet.c making iosupport.d from ../../.././src/main/iosupport.c making lapack.d from ../../.././src/main/lapack.c making list.d from ../../.././src/main/list.c making localecharset.d from ../../.././src/main/localecharset.c making logic.d from ../../.././src/main/logic.c making main.d from ../../.././src/main/main.c making mapply.d from ../../.././src/main/mapply.c making match.d from ../../.././src/main/match.c making memory.d from ../../.././src/main/memory.c making names.d from ../../.././src/main/names.c making objects.d from ../../.././src/main/objects.c making options.d from ../../.././src/main/options.c making paste.d from ../../.././src/main/paste.c making platform.d from ../../.././src/main/platform.c making plot.d from ../../.././src/main/plot.c making plot3d.d from ../../.././src/main/plot3d.c making plotmath.d from ../../.././src/main/plotmath.c making print.d from ../../.././src/main/print.c making printarray.d from ../../.././src/main/printarray.c making printvector.d from ../../.././src/main/printvector.c making printutils.d from ../../.././src/main/printutils.c making qsort.d from ../../.././src/main/qsort.c making radixsort.d from ../../.././src/main/radixsort.c making random.d from ../../.././src/main/random.c making raw.d from ../../.././src/main/raw.c making registration.d from ../../.././src/main/registration.c making relop.d from ../../.././src/main/relop.c making rlocale.d from ../../.././src/main/rlocale.c making saveload.d from ../../.././src/main/saveload.c making scan.d from ../../.././src/main/scan.c making seq.d from ../../.././src/main/seq.c making serialize.d from ../../.././src/main/serialize.c making sort.d from ../../.././src/main/sort.c making source.d from ../../.././src/main/source.c making split.d from ../../.././src/main/split.c making sprintf.d from ../../.././src/main/sprintf.c making startup.d from ../../.././src/main/startup.c making subassign.d from ../../.././src/main/subassign.c making subscript.d from ../../.././src/main/subscript.c making subset.d from ../../.././src/main/subset.c making summary.d from ../../.././src/main/summary.c making sysutils.d from ../../.././src/main/sysutils.c making times.d from ../../.././src/main/times.c making unique.d from ../../.././src/main/unique.c making util.d from ../../.././src/main/util.c making version.d from ../../.././src/main/version.c making g_alab_her.d from ../../.././src/main/g_alab_her.c making g_cntrlify.d from ../../.././src/main/g_cntrlify.c making g_fontdb.d from ../../.././src/main/g_fontdb.c making g_her_glyph.d from ../../.././src/main/g_her_glyph.c making Rmain.d from ../../.././src/main/Rmain.c making alloca.d from ../../.././src/main/alloca.c making mkdtemp.d from ../../.././src/main/mkdtemp.c making strdup.d from ../../.././src/main/strdup.c making strncasecmp.d from ../../.././src/main/strncasecmp.c make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/CommandLineArgs.c -o CommandLineArgs.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/Rdynload.c -o Rdynload.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/Renviron.c -o Renviron.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/RNG.c -o RNG.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/agrep.c -o agrep.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/altrep.c -o altrep.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/apply.c -o apply.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/arithmetic.c -o arithmetic.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/array.c -o array.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/attrib.c -o attrib.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/bind.c -o bind.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/builtin.c -o builtin.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/character.c -o character.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/coerce.c -o coerce.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/colors.c -o colors.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/complex.c -o complex.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/connections.c -o connections.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/context.c -o context.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/cum.c -o cum.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/dcf.c -o dcf.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/datetime.c -o datetime.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/debug.c -o debug.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/deparse.c -o deparse.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/devices.c -o devices.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/dotcode.c -o dotcode.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/dounzip.c -o dounzip.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/dstruct.c -o dstruct.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/duplicate.c -o duplicate.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/edit.c -o edit.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/engine.c -o engine.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/envir.c -o envir.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/errors.c -o errors.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/eval.c -o eval.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/format.c -o format.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/gevents.c -o gevents.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/gram.c -o gram.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/gram-ex.c -o gram-ex.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/graphics.c -o graphics.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/grep.c -o grep.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/identical.c -o identical.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/inlined.c -o inlined.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/inspect.c -o inspect.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/internet.c -o internet.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/iosupport.c -o iosupport.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/lapack.c -o lapack.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/list.c -o list.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/localecharset.c -o localecharset.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/logic.c -o logic.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/main.c -o main.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/mapply.c -o mapply.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/match.c -o match.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/memory.c -o memory.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/names.c -o names.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/objects.c -o objects.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/options.c -o options.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/paste.c -o paste.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/platform.c -o platform.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/plot.c -o plot.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/plot3d.c -o plot3d.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/plotmath.c -o plotmath.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/print.c -o print.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/printarray.c -o printarray.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/printvector.c -o printvector.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/printutils.c -o printutils.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/qsort.c -o qsort.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/radixsort.c -o radixsort.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/random.c -o random.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/raw.c -o raw.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/registration.c -o registration.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/relop.c -o relop.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/rlocale.c -o rlocale.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/saveload.c -o saveload.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/scan.c -o scan.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/seq.c -o seq.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/serialize.c -o serialize.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/sort.c -o sort.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/source.c -o source.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/split.c -o split.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/sprintf.c -o sprintf.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/startup.c -o startup.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/subassign.c -o subassign.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/subscript.c -o subscript.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/subset.c -o subset.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/summary.c -o summary.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/sysutils.c -o sysutils.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/times.c -o times.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/unique.c -o unique.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/util.c -o util.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/version.c -o version.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/g_alab_her.c -o g_alab_her.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/g_cntrlify.c -o g_cntrlify.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/g_fontdb.c -o g_fontdb.o x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/g_her_glyph.c -o g_her_glyph.o gfortran -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/xxxpr.f -o xxxpr.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran x86_64-tld-linux-gcc -shared -fopenmp -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o altrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/tre/libtre.a ../extra/tzone/libtz.a -lblas -lgfortran -lm -lquadmath -lreadline -lpcre2-8 -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' mkdir -p -- /tmp/B.61K3e5/BUILD/R-3.5.2/build/bin/exec mkdir -p -- /tmp/B.61K3e5/BUILD/R-3.5.2/build/lib make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/Rmain.c -o Rmain.o x86_64-tld-linux-gcc -Wl,--export-dynamic -fopenmp -L"../../lib" -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o R.bin Rmain.o -lR make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/internet' making Rhttpd.d from ../../../.././src/modules/internet/Rhttpd.c making Rsock.d from ../../../.././src/modules/internet/Rsock.c making internet.d from ../../../.././src/modules/internet/internet.c making libcurl.d from ../../../.././src/modules/internet/libcurl.c making nanoftp.d from ../../../.././src/modules/internet/nanoftp.c making nanohttp.d from ../../../.././src/modules/internet/nanohttp.c making sock.d from ../../../.././src/modules/internet/sock.c making sockconn.d from ../../../.././src/modules/internet/sockconn.c make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/internet' x86_64-tld-linux-gcc -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/modules/internet/Rhttpd.c -o Rhttpd.o x86_64-tld-linux-gcc -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/modules/internet/Rsock.c -o Rsock.o x86_64-tld-linux-gcc -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/modules/internet/internet.c -o internet.o x86_64-tld-linux-gcc -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/modules/internet/libcurl.c -o libcurl.o x86_64-tld-linux-gcc -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/modules/internet/nanoftp.c -o nanoftp.o x86_64-tld-linux-gcc -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/modules/internet/nanohttp.c -o nanohttp.o x86_64-tld-linux-gcc -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/modules/internet/sock.c -o sock.o x86_64-tld-linux-gcc -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -fvisibility=hidden -c ../../../.././src/modules/internet/sockconn.c -o sockconn.o x86_64-tld-linux-gcc -shared -L"../../../lib" -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o nanoftp.o nanohttp.o sock.o sockconn.o -lcurl -lcares -lnghttp2 -lidn2 -lrtmp -lz -lssl -lcrypto -lssh2 -lssh2 -lpsl -lssl -lcrypto -lgssapi -lldap -llber -lbrotlidec -lz -lR make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/internet' mkdir -p -- /tmp/B.61K3e5/BUILD/R-3.5.2/build/modules make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/internet' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/internet' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/internet' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/lapack' making Lapack.d from ../../../.././src/modules/lapack/Lapack.c make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/lapack' x86_64-tld-linux-gcc -I. -I../../../src/include -I../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../.././src/modules/lapack/Lapack.c -o Lapack.o x86_64-tld-linux-gcc -shared -L"../../../lib" -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o lapack.so Lapack.o -lR -llapack -lblas -lgfortran -lm -lquadmath make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/lapack' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/lapack' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/lapack' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/lapack' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/X11' making devX11.d from ../../../.././src/modules/X11/devX11.c making rotated.d from ../../../.././src/modules/X11/rotated.c making rbitmap.d from ../../../.././src/modules/X11/rbitmap.c make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/X11' x86_64-tld-linux-gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../.././src/include -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng16 -I../../../.././src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../.././src/modules/X11/devX11.c -o devX11.o x86_64-tld-linux-gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../.././src/include -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng16 -I../../../.././src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../.././src/modules/X11/rotated.c -o rotated.o x86_64-tld-linux-gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../.././src/include -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng16 -I../../../.././src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../.././src/modules/X11/rbitmap.c -o rbitmap.o x86_64-tld-linux-gcc -shared -L"../../../lib" -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o R_X11.so devX11.o rotated.o rbitmap.o -ltiff -ljpeg -lpng16 -lz -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -lX11 -lXext -L/usr/lib64 -lX11 -lXt -lXmu -lR -lm x86_64-tld-linux-gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../.././src/include -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng16 -I../../../.././src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../.././src/modules/X11/dataentry.c -o dataentry.o x86_64-tld-linux-gcc -shared -L"../../../lib" -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -lX11 -lXext -L/usr/lib64 -lX11 -lXt -lXmu -lR -lm make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/X11' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/X11' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/X11' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/X11' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' mkdir -p -- ../../library make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/profile' building system startup profile mkdir -p -- ../../../library/base/R make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/profile' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/translations' building package 'translations' mkdir -p -- ../../../library/translations make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/translations' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/translations' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/translations' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/base' building package 'base' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/base' mkdir -p -- ../../../library/base/demo make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/base' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/base' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' building package 'tools' mkdir -p -- ../../../library/tools make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' mkdir -p -- ../../../library/tools/R make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools/src' making text.d from ../../../../.././src/library/tools/src/text.c making init.d from ../../../../.././src/library/tools/src/init.c making Rmd5.d from ../../../../.././src/library/tools/src/Rmd5.c making md5.d from ../../../../.././src/library/tools/src/md5.c making signals.d from ../../../../.././src/library/tools/src/signals.c making install.d from ../../../../.././src/library/tools/src/install.c making getfmts.d from ../../../../.././src/library/tools/src/getfmts.c making http.d from ../../../../.././src/library/tools/src/http.c making gramLatex.d from ../../../../.././src/library/tools/src/gramLatex.c making gramRd.d from ../../../../.././src/library/tools/src/gramRd.c x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/tools/src/text.c -o text.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/tools/src/init.c -o init.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/tools/src/Rmd5.c -o Rmd5.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/tools/src/md5.c -o md5.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/tools/src/signals.c -o signals.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/tools/src/install.c -o install.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/tools/src/getfmts.c -o getfmts.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/tools/src/http.c -o http.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/tools/src/gramLatex.c -o gramLatex.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/tools/src/gramRd.c -o gramRd.o x86_64-tld-linux-gcc -shared -L../../../../lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o -L../../../../lib -lR make[6]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[6]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools/src' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' installing 'sysdata.rda' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/compiler' building package 'compiler' mkdir -p -- ../../../library/compiler make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/compiler' mkdir -p -- ../../../library/compiler/R make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/compiler' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/compiler' byte-compiling package 'compiler' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/compiler' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/compiler' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/base' byte-compiling package 'base' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/base' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' byte-compiling package 'tools' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' building package 'utils' mkdir -p -- ../../../library/utils mkdir -p -- ../../../library/utils/doc make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' mkdir -p -- ../../../library/utils/R mkdir -p -- ../../../library/utils/Sweave mkdir -p -- ../../../library/utils/misc make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils/src' making init.d from ../../../../.././src/library/utils/src/init.c making io.d from ../../../../.././src/library/utils/src/io.c making size.d from ../../../../.././src/library/utils/src/size.c making sock.d from ../../../../.././src/library/utils/src/sock.c making stubs.d from ../../../../.././src/library/utils/src/stubs.c making utils.d from ../../../../.././src/library/utils/src/utils.c x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/utils/src/init.c -o init.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/utils/src/io.c -o io.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/utils/src/size.c -o size.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/utils/src/sock.c -o sock.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/utils/src/stubs.c -o stubs.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/utils/src/utils.c -o utils.o x86_64-tld-linux-gcc -shared -L../../../../lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o utils.so init.o io.o size.o sock.o stubs.o utils.o -L../../../../lib -lR make[6]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils/src' mkdir -p -- ../../../../library/utils/libs make[6]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils/src' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' installing 'sysdata.rda' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' byte-compiling package 'utils' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices' building package 'grDevices' mkdir -p -- ../../../library/grDevices make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices' mkdir -p -- ../../../library/grDevices/R mkdir -p -- ../../../library/grDevices/afm mkdir -p -- ../../../library/grDevices/enc mkdir -p -- ../../../library/grDevices/icc make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices' make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src' making axis_scales.d from ../../../../.././src/library/grDevices/src/axis_scales.c making chull.d from ../../../../.././src/library/grDevices/src/chull.c making devices.d from ../../../../.././src/library/grDevices/src/devices.c making init.d from ../../../../.././src/library/grDevices/src/init.c making stubs.d from ../../../../.././src/library/grDevices/src/stubs.c making colors.d from ../../../../.././src/library/grDevices/src/colors.c making devCairo.d from ../../../../.././src/library/grDevices/src/devCairo.c making devPicTeX.d from ../../../../.././src/library/grDevices/src/devPicTeX.c making devPS.d from ../../../../.././src/library/grDevices/src/devPS.c making devQuartz.d from ../../../../.././src/library/grDevices/src/devQuartz.c x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grDevices/src/axis_scales.c -o axis_scales.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grDevices/src/chull.c -o chull.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grDevices/src/devices.c -o devices.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grDevices/src/init.c -o init.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grDevices/src/stubs.c -o stubs.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grDevices/src/colors.c -o colors.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grDevices/src/devCairo.c -o devCairo.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grDevices/src/devPicTeX.c -o devPicTeX.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grDevices/src/devPS.c -o devPS.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grDevices/src/devQuartz.c -o devQuartz.o x86_64-tld-linux-gcc -shared -L../../../../lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR make[6]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src' mkdir -p -- ../../../../library/grDevices/libs make[7]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src/cairo' making cairoBM.d from ../../../../../.././src/library/grDevices/src/cairo/cairoBM.c make[8]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src/cairo' make[9]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src/cairo' x86_64-tld-linux-gcc -I. -I../../../../../src/include -I../../../../../.././src/include -I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng16 -I../../../../../.././src/modules/X11 -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../../.././src/library/grDevices/src/cairo/cairoBM.c -o cairoBM.o x86_64-tld-linux-gcc -shared -L"../../../../../lib" -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff -ljpeg -lpng16 -lz -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -L"../../../../../lib" -lR -lm make[9]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src/cairo' make[8]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src/cairo' make[7]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src/cairo' make[6]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices' byte-compiling package 'grDevices' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics' building package 'graphics' mkdir -p -- ../../../library/graphics make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics' mkdir -p -- ../../../library/graphics/R make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics' make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics/src' making init.d from ../../../../.././src/library/graphics/src/init.c making base.d from ../../../../.././src/library/graphics/src/base.c making graphics.d from ../../../../.././src/library/graphics/src/graphics.c making par.d from ../../../../.././src/library/graphics/src/par.c making plot.d from ../../../../.././src/library/graphics/src/plot.c making plot3d.d from ../../../../.././src/library/graphics/src/plot3d.c making stem.d from ../../../../.././src/library/graphics/src/stem.c x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/graphics/src/init.c -o init.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/graphics/src/base.c -o base.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/graphics/src/graphics.c -o graphics.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/graphics/src/par.c -o par.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/graphics/src/plot.c -o plot.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/graphics/src/plot3d.c -o plot3d.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I../../../../.././src/main -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/graphics/src/stem.c -o stem.o x86_64-tld-linux-gcc -shared -L../../../../lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR make[6]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics/src' mkdir -p -- ../../../../library/graphics/libs make[6]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics/src' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics' byte-compiling package 'graphics' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats' building package 'stats' mkdir -p -- ../../../library/stats make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats' mkdir -p -- ../../../library/stats/R make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats' make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats/src' making init.d from ../../../../.././src/library/stats/src/init.c making kmeans.d from ../../../../.././src/library/stats/src/kmeans.c making ansari.d from ../../../../.././src/library/stats/src/ansari.c making bandwidths.d from ../../../../.././src/library/stats/src/bandwidths.c making chisqsim.d from ../../../../.././src/library/stats/src/chisqsim.c making d2x2xk.d from ../../../../.././src/library/stats/src/d2x2xk.c making fexact.d from ../../../../.././src/library/stats/src/fexact.c making kendall.d from ../../../../.././src/library/stats/src/kendall.c making ks.d from ../../../../.././src/library/stats/src/ks.c making line.d from ../../../../.././src/library/stats/src/line.c making smooth.d from ../../../../.././src/library/stats/src/smooth.c making prho.d from ../../../../.././src/library/stats/src/prho.c making swilk.d from ../../../../.././src/library/stats/src/swilk.c making ksmooth.d from ../../../../.././src/library/stats/src/ksmooth.c making loessc.d from ../../../../.././src/library/stats/src/loessc.c making monoSpl.d from ../../../../.././src/library/stats/src/monoSpl.c making isoreg.d from ../../../../.././src/library/stats/src/isoreg.c making Srunmed.d from ../../../../.././src/library/stats/src/Srunmed.c making dblcen.d from ../../../../.././src/library/stats/src/dblcen.c making distance.d from ../../../../.././src/library/stats/src/distance.c making hclust-utils.d from ../../../../.././src/library/stats/src/hclust-utils.c making nls.d from ../../../../.././src/library/stats/src/nls.c making rWishart.d from ../../../../.././src/library/stats/src/rWishart.c making HoltWinters.d from ../../../../.././src/library/stats/src/HoltWinters.c making PPsum.d from ../../../../.././src/library/stats/src/PPsum.c making arima.d from ../../../../.././src/library/stats/src/arima.c making burg.d from ../../../../.././src/library/stats/src/burg.c making filter.d from ../../../../.././src/library/stats/src/filter.c making mAR.d from ../../../../.././src/library/stats/src/mAR.c making pacf.d from ../../../../.././src/library/stats/src/pacf.c making starma.d from ../../../../.././src/library/stats/src/starma.c making port.d from ../../../../.././src/library/stats/src/port.c making family.d from ../../../../.././src/library/stats/src/family.c making sbart.d from ../../../../.././src/library/stats/src/sbart.c making approx.d from ../../../../.././src/library/stats/src/approx.c making loglin.d from ../../../../.././src/library/stats/src/loglin.c making lowess.d from ../../../../.././src/library/stats/src/lowess.c making massdist.d from ../../../../.././src/library/stats/src/massdist.c making splines.d from ../../../../.././src/library/stats/src/splines.c making lm.d from ../../../../.././src/library/stats/src/lm.c making complete_cases.d from ../../../../.././src/library/stats/src/complete_cases.c making cov.d from ../../../../.././src/library/stats/src/cov.c making deriv.d from ../../../../.././src/library/stats/src/deriv.c making fft.d from ../../../../.././src/library/stats/src/fft.c making fourier.d from ../../../../.././src/library/stats/src/fourier.c making model.d from ../../../../.././src/library/stats/src/model.c making optim.d from ../../../../.././src/library/stats/src/optim.c making optimize.d from ../../../../.././src/library/stats/src/optimize.c making integrate.d from ../../../../.././src/library/stats/src/integrate.c making random.d from ../../../../.././src/library/stats/src/random.c making distn.d from ../../../../.././src/library/stats/src/distn.c making zeroin.d from ../../../../.././src/library/stats/src/zeroin.c making rcont.d from ../../../../.././src/library/stats/src/rcont.c making influence.d from ../../../../.././src/library/stats/src/influence.c x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/init.c -o init.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/kmeans.c -o kmeans.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/ansari.c -o ansari.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/bandwidths.c -o bandwidths.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/chisqsim.c -o chisqsim.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/d2x2xk.c -o d2x2xk.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/fexact.c -o fexact.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/kendall.c -o kendall.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/ks.c -o ks.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/line.c -o line.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/smooth.c -o smooth.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/prho.c -o prho.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/swilk.c -o swilk.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/ksmooth.c -o ksmooth.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/loessc.c -o loessc.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/monoSpl.c -o monoSpl.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/isoreg.c -o isoreg.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/Srunmed.c -o Srunmed.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/dblcen.c -o dblcen.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/distance.c -o distance.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/hclust-utils.c -o hclust-utils.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/nls.c -o nls.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/rWishart.c -o rWishart.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/HoltWinters.c -o HoltWinters.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/PPsum.c -o PPsum.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/arima.c -o arima.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/burg.c -o burg.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/filter.c -o filter.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/mAR.c -o mAR.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/pacf.c -o pacf.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/starma.c -o starma.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/port.c -o port.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/family.c -o family.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/sbart.c -o sbart.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/approx.c -o approx.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/loglin.c -o loglin.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/lowess.c -o lowess.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/massdist.c -o massdist.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/splines.c -o splines.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/lm.c -o lm.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/complete_cases.c -o complete_cases.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/cov.c -o cov.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/deriv.c -o deriv.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/fft.c -o fft.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/fourier.c -o fourier.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/model.c -o model.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/optim.c -o optim.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/optimize.c -o optimize.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/integrate.c -o integrate.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/random.c -o random.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/distn.c -o distn.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/zeroin.c -o zeroin.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/rcont.c -o rcont.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/influence.c -o influence.o gfortran -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/bsplvd.f -o bsplvd.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/bvalue.f -o bvalue.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/bvalus.f -o bvalus.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/loessf.f -o loessf.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/ppr.f -o ppr.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/qsbart.f -o qsbart.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/sgram.f -o sgram.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/sinerp.f -o sinerp.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/sslvrg.f -o sslvrg.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/stxwx.f -o stxwx.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/hclust.f -o hclust.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/kmns.f -o kmns.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/eureka.f -o eureka.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/stl.f -o stl.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -msse2 -mfpmath=sse -c ../../../../.././src/library/stats/src/portsrc.f -o portsrc.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/stats/src/lminfl.f -o lminfl.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran x86_64-tld-linux-gcc -shared -L../../../../lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o complete_cases.o cov.o deriv.o fft.o fourier.o model.o optim.o optimize.o integrate.o random.o distn.o zeroin.o rcont.o influence.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L../../../../lib -lR make[6]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats/src' mkdir -p -- ../../../../library/stats/libs make[6]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats/src' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats' byte-compiling package 'stats' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/datasets' building package 'datasets' mkdir -p -- ../../../library/datasets make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/datasets' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/datasets' mkdir -p -- ../../../library/datasets/data make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/datasets' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods' building package 'methods' mkdir -p -- ../../../library/methods make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods' mkdir -p -- ../../../library/methods/R make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods' make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods/src' making do_substitute_direct.d from ../../../../.././src/library/methods/src/do_substitute_direct.c making init.d from ../../../../.././src/library/methods/src/init.c making methods_list_dispatch.d from ../../../../.././src/library/methods/src/methods_list_dispatch.c making slot.d from ../../../../.././src/library/methods/src/slot.c making class_support.d from ../../../../.././src/library/methods/src/class_support.c making tests.d from ../../../../.././src/library/methods/src/tests.c making utils.d from ../../../../.././src/library/methods/src/utils.c x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/methods/src/do_substitute_direct.c -o do_substitute_direct.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/methods/src/init.c -o init.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/methods/src/methods_list_dispatch.c -o methods_list_dispatch.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/methods/src/slot.c -o slot.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/methods/src/class_support.c -o class_support.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/methods/src/tests.c -o tests.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/methods/src/utils.c -o utils.o x86_64-tld-linux-gcc -shared -L../../../../lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR make[6]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods/src' mkdir -p -- ../../../../library/methods/libs make[6]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods/src' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods' byte-compiling 'methods' initializing class and method definitions ... done make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid' building package 'grid' mkdir -p -- ../../../library/grid mkdir -p -- ../../../library/grid/doc make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid' mkdir -p -- ../../../library/grid/R make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid' make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid/src' making gpar.d from ../../../../.././src/library/grid/src/gpar.c making grid.d from ../../../../.././src/library/grid/src/grid.c making just.d from ../../../../.././src/library/grid/src/just.c making layout.d from ../../../../.././src/library/grid/src/layout.c making matrix.d from ../../../../.././src/library/grid/src/matrix.c making register.d from ../../../../.././src/library/grid/src/register.c making state.d from ../../../../.././src/library/grid/src/state.c making unit.d from ../../../../.././src/library/grid/src/unit.c making util.d from ../../../../.././src/library/grid/src/util.c making viewport.d from ../../../../.././src/library/grid/src/viewport.c x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grid/src/gpar.c -o gpar.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grid/src/grid.c -o grid.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grid/src/just.c -o just.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grid/src/layout.c -o layout.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grid/src/matrix.c -o matrix.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grid/src/register.c -o register.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grid/src/state.c -o state.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grid/src/unit.c -o unit.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grid/src/util.c -o util.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grid/src/viewport.c -o viewport.o x86_64-tld-linux-gcc -shared -L../../../../lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o grid.so gpar.o grid.o just.o layout.o matrix.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR make[6]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid/src' mkdir -p -- ../../../../library/grid/libs make[6]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid/src' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid' byte-compiling package 'grid' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines' building package 'splines' mkdir -p -- ../../../library/splines make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines' mkdir -p -- ../../../library/splines/R make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines' make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines/src' making splines.d from ../../../../.././src/library/splines/src/splines.c x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/splines/src/splines.c -o splines.o x86_64-tld-linux-gcc -shared -L../../../../lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o splines.so splines.o -L../../../../lib -lR make[6]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines/src' mkdir -p -- ../../../../library/splines/libs make[6]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines/src' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines' byte-compiling package 'splines' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats4' building package 'stats4' mkdir -p -- ../../../library/stats4 make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats4' mkdir -p -- ../../../library/stats4/R make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats4' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats4' byte-compiling package 'stats4' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats4' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats4' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk' building package 'tcltk' mkdir -p -- ../../../library/tcltk/R make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk' mkdir -p -- ../../../library/tcltk/exec make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk/src' making init.d from ../../../../.././src/library/tcltk/src/init.c making tcltk.d from ../../../../.././src/library/tcltk/src/tcltk.c making tcltk_unix.d from ../../../../.././src/library/tcltk/src/tcltk_unix.c x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/include -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/tcltk/src/init.c -o init.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/include -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/tcltk/src/tcltk.c -o tcltk.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/include -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/tcltk/src/tcltk_unix.c -o tcltk_unix.o x86_64-tld-linux-gcc -shared -L../../../../lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib64 -ltcl8.6 -L/usr/lib64 -ltk8.6 -L/usr/lib64 -lX11 -lXss -lXext -lm -L../../../../lib -lR make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk/src' mkdir -p -- ../../../../library/tcltk/libs make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk/src' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk' byte-compiling package 'tcltk' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel' building package 'parallel' mkdir -p -- ../../../library/parallel mkdir -p -- ../../../library/parallel/doc make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel' mkdir -p -- ../../../library/parallel/R make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel' make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel/src' making init.d from ../../../../.././src/library/parallel/src/init.c making rngstream.d from ../../../../.././src/library/parallel/src/rngstream.c making fork.d from ../../../../.././src/library/parallel/src/fork.c x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/parallel/src/init.c -o init.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/parallel/src/rngstream.c -o rngstream.o x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/parallel/src/fork.c -o fork.o x86_64-tld-linux-gcc -shared -L../../../../lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR make[6]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel/src' mkdir -p -- ../../../../library/parallel/libs make[6]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel/src' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel' byte-compiling package 'parallel' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/base' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/base' installing parsed NAMESPACE files make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make[1]: Nothing to be done for 'R'. make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' you should 'make docs' now ... make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc' creating doc/NEWS creating doc/NEWS.pdf make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual' creating doc/manual/R-FAQ.html creating doc/manual/version.texi creating doc/manual/R-admin.html creating doc/manual/R-data.html creating doc/manual/R-exts.html make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual' mkdir -p -- ../../doc/manual/images make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual' creating doc/manual/R-intro.html creating doc/manual/R-ints.html creating doc/manual/R-lang.html make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/html' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/html' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual' make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' installing parsed Rd make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 compiler parallel make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' building/updating package metadata ... make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' writing package indices make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/Recommended' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/Recommended' begin installing recommended package MASS * installing *source* package 'MASS' ... ** package 'MASS' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmpBnCE0N/R.INSTALL21e946d19a8d/MASS/src' x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c MASS.c -o MASS.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c lqs.c -o lqs.o x86_64-tld-linux-gcc -shared -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o MASS.so MASS.o lqs.o -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -lR make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmpBnCE0N/R.INSTALL21e946d19a8d/MASS/src' installing to /tmp/B.61K3e5/BUILD/R-3.5.2/build/library/MASS/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (MASS) begin installing recommended package lattice * installing *source* package 'lattice' ... ** package 'lattice' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmpPwxdxr/R.INSTALL220e142945a6/lattice/src' x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c init.c -o init.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c threeDplot.c -o threeDplot.o x86_64-tld-linux-gcc -shared -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o lattice.so init.o threeDplot.o -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -lR make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmpPwxdxr/R.INSTALL220e142945a6/lattice/src' installing to /tmp/B.61K3e5/BUILD/R-3.5.2/build/library/lattice/libs ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (lattice) begin installing recommended package Matrix * installing *source* package 'Matrix' ... ** package 'Matrix' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src' x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c CHMfactor.c -o CHMfactor.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c Csparse.c -o Csparse.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c TMatrix_as.c -o TMatrix_as.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c Tsparse.c -o Tsparse.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c init.c -o init.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c Mutils.c -o Mutils.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c chm_common.c -o chm_common.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c cs.c -o cs.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c cs_utils.c -o cs_utils.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c dense.c -o dense.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c dgCMatrix.c -o dgCMatrix.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c dgTMatrix.c -o dgTMatrix.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c dgeMatrix.c -o dgeMatrix.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c dpoMatrix.c -o dpoMatrix.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c dppMatrix.c -o dppMatrix.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c dsCMatrix.c -o dsCMatrix.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c dsyMatrix.c -o dsyMatrix.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c dspMatrix.c -o dspMatrix.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c dtCMatrix.c -o dtCMatrix.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c dtTMatrix.c -o dtTMatrix.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c dtrMatrix.c -o dtrMatrix.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c dtpMatrix.c -o dtpMatrix.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c factorizations.c -o factorizations.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ldense.c -o ldense.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c lgCMatrix.c -o lgCMatrix.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c sparseQR.c -o sparseQR.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c abIndex.c -o abIndex.o make[4]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/CHOLMOD' ( cd Lib ; /usr/bin/make clean ) make[5]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/CHOLMOD/Lib' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/CHOLMOD/Lib' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/CHOLMOD' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/COLAMD' ( cd Source ; /usr/bin/make clean ) make[5]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/COLAMD/Source' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/COLAMD/Source' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/COLAMD' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/AMD' ( cd Source ; /usr/bin/make clean ) make[5]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/AMD/Source' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/AMD/Source' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/AMD' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/SuiteSparse_config' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/SuiteSparse_config' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/CHOLMOD' ( cd Lib ; /usr/bin/make -f "/tmp/B.61K3e5/BUILD/R-3.5.2/build/etc/Makeconf" -f Makefile ) make[5]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/CHOLMOD/Lib' x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Core/cholmod_aat.c -o cholmod_aat.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Core/cholmod_add.c -o cholmod_add.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Core/cholmod_band.c -o cholmod_band.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Core/cholmod_common.c -o cholmod_common.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Core/cholmod_complex.c -o cholmod_complex.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Core/cholmod_copy.c -o cholmod_copy.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Core/cholmod_dense.c -o cholmod_dense.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Core/cholmod_error.c -o cholmod_error.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Core/cholmod_factor.c -o cholmod_factor.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Core/cholmod_memory.c -o cholmod_memory.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Core/cholmod_sparse.c -o cholmod_sparse.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Core/cholmod_transpose.c -o cholmod_transpose.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Core/cholmod_triplet.c -o cholmod_triplet.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Core/cholmod_version.c -o cholmod_version.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Check/cholmod_check.c -o cholmod_check.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Check/cholmod_read.c -o cholmod_read.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Check/cholmod_write.c -o cholmod_write.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Modify/cholmod_updown.c -o cholmod_updown.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_super_symbolic.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Core/cholmod_aat.c -o cholmod_l_aat.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Core/cholmod_add.c -o cholmod_l_add.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Core/cholmod_band.c -o cholmod_l_band.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Core/cholmod_common.c -o cholmod_l_common.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Core/cholmod_complex.c -o cholmod_l_complex.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Core/cholmod_copy.c -o cholmod_l_copy.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Core/cholmod_dense.c -o cholmod_l_dense.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Core/cholmod_error.c -o cholmod_l_error.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Core/cholmod_factor.c -o cholmod_l_factor.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Core/cholmod_memory.c -o cholmod_l_memory.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Core/cholmod_sparse.c -o cholmod_l_sparse.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Core/cholmod_transpose.c -o cholmod_l_transpose.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Core/cholmod_triplet.c -o cholmod_l_triplet.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Core/cholmod_version.c -o cholmod_l_version.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Check/cholmod_check.c -o cholmod_l_check.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Check/cholmod_read.c -o cholmod_l_read.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Check/cholmod_write.c -o cholmod_l_write.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Modify/cholmod_updown.c -o cholmod_l_updown.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -DDLONG -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o ar -rucs ../../CHOLMOD.a cholmod_aat.o cholmod_add.o cholmod_band.o cholmod_change_factor.o cholmod_common.o cholmod_complex.o cholmod_copy.o cholmod_dense.o cholmod_error.o cholmod_factor.o cholmod_memory.o cholmod_sparse.o cholmod_transpose.o cholmod_triplet.o cholmod_version.o cholmod_check.o cholmod_read.o cholmod_write.o cholmod_amd.o cholmod_analyze.o cholmod_colamd.o cholmod_etree.o cholmod_factorize.o cholmod_postorder.o cholmod_rcond.o cholmod_resymbol.o cholmod_rowcolcounts.o cholmod_rowfac.o cholmod_solve.o cholmod_spsolve.o cholmod_drop.o cholmod_horzcat.o cholmod_norm.o cholmod_scale.o cholmod_sdmult.o cholmod_ssmult.o cholmod_submatrix.o cholmod_vertcat.o cholmod_symmetry.o cholmod_rowadd.o cholmod_rowdel.o cholmod_updown.o cholmod_super_numeric.o cholmod_super_solve.o cholmod_super_symbolic.o cholmod_l_aat.o cholmod_l_add.o cholmod_l_band.o cholmod_l_change_factor.o cholmod_l_common.o cholmod_l_complex.o cholmod_l_copy.o cholmod_l_dense.o cholmod_l_error.o cholmod_l_factor.o cholmod_l_memory.o cholmod_l_sparse.o cholmod_l_transpose.o cholmod_l_triplet.o cholmod_l_version.o cholmod_l_check.o cholmod_l_read.o cholmod_l_write.o cholmod_l_amd.o cholmod_l_analyze.o cholmod_l_colamd.o cholmod_l_etree.o cholmod_l_factorize.o cholmod_l_postorder.o cholmod_l_rcond.o cholmod_l_resymbol.o cholmod_l_rowcolcounts.o cholmod_l_rowfac.o cholmod_l_solve.o cholmod_l_spsolve.o cholmod_l_drop.o cholmod_l_horzcat.o cholmod_l_norm.o cholmod_l_scale.o cholmod_l_sdmult.o cholmod_l_ssmult.o cholmod_l_submatrix.o cholmod_l_vertcat.o cholmod_l_symmetry.o cholmod_l_rowadd.o cholmod_l_rowdel.o cholmod_l_updown.o cholmod_l_super_numeric.o cholmod_l_super_solve.o cholmod_l_super_symbolic.o make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/CHOLMOD/Lib' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/CHOLMOD' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/COLAMD' ( cd Source ; /usr/bin/make -f "/tmp/B.61K3e5/BUILD/R-3.5.2/build/etc/Makeconf" -f Makefile lib ) make[5]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/COLAMD/Source' x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c colamd_global.c -o colamd_global.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c colamd.c -o colamd.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDLONG -c colamd.c -o colamd_l.o ar -rucs ../../COLAMD.a colamd_global.o colamd.o colamd_l.o make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/COLAMD/Source' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/COLAMD' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/AMD' ( cd Source ; /usr/bin/make -f "/tmp/B.61K3e5/BUILD/R-3.5.2/build/etc/Makeconf" -f Makefile lib ) make[5]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/AMD/Source' x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDINT -c amd_1.c -o amd_i_1.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDLONG -c amd_1.c -o amd_l_1.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDINT -c amd_2.c -o amd_i_2.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDLONG -c amd_2.c -o amd_l_2.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDINT -c amd_order.c -o amd_i_order.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDLONG -c amd_order.c -o amd_l_order.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDINT -c amd_control.c -o amd_i_control.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDLONG -c amd_control.c -o amd_l_control.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDINT -c amd_info.c -o amd_i_info.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDLONG -c amd_info.c -o amd_l_info.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDINT -c amd_global.c -o amd_i_global.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -I../Include -DDLONG -c amd_global.c -o amd_l_global.o ar -rucs ../../AMD.a amd_i_aat.o amd_l_aat.o amd_i_1.o amd_l_1.o amd_i_2.o amd_l_2.o amd_i_postorder.o amd_l_postorder.o amd_i_post_tree.o amd_l_post_tree.o amd_i_defaults.o amd_l_defaults.o amd_i_order.o amd_l_order.o amd_i_control.o amd_l_control.o amd_i_info.o amd_l_info.o amd_i_valid.o amd_l_valid.o amd_i_preprocess.o amd_l_preprocess.o amd_i_dump.o amd_l_dump.o amd_i_global.o amd_l_global.o make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/AMD/Source' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/AMD' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/SuiteSparse_config' x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -DNTIMER -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c SuiteSparse_config.c -o SuiteSparse_config.o ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src/SuiteSparse_config' x86_64-tld-linux-gcc -shared -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lblas -lgfortran -lm -lquadmath -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -lR make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmphFOEqJ/R.INSTALL22355c4bb884/Matrix/src' installing to /tmp/B.61K3e5/BUILD/R-3.5.2/build/library/Matrix/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for 'chol2inv' from 'base' in package 'Matrix' (from the saved implicit definition) Creating a generic function for 'chol2inv' from package 'base' in package 'Matrix' Creating a generic function for 'diag' from package 'base' in package 'Matrix' Creating a generic function for 'drop' from package 'base' in package 'Matrix' Creating a generic function for 'cov2cor' from package 'stats' in package 'Matrix' Creating a generic function for 'unname' from package 'base' in package 'Matrix' Creating a generic function for 'norm' from package 'base' in package 'Matrix' Creating a generic function for 'rcond' from 'base' in package 'Matrix' (from the saved implicit definition) Creating a generic function for 'rcond' from package 'base' in package 'Matrix' in method for 'coerce' with signature '"matrix.csr","dgRMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"dgRMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csc","dgCMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"dgCMatrix","matrix.csc"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.coo","dgTMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"dgTMatrix","matrix.coo"': no definition for class "matrix.coo" in method for 'coerce' with signature '"dsparseMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csr","dgCMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","dgCMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csr","RsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csc","CsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.coo","TsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csr","CsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","CsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","TsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","TsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"CsparseMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"CsparseMatrix","matrix.coo"': no definition for class "matrix.coo" in method for 'coerce' with signature '"CsparseMatrix","matrix.csc"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","Matrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","Matrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","Matrix"': no definition for class "matrix.csc" Creating a generic function for 'colSums' from package 'base' in package 'Matrix' Creating a generic function for 'colMeans' from package 'base' in package 'Matrix' Creating a generic function for 'rowSums' from package 'base' in package 'Matrix' Creating a generic function for 'rowMeans' from package 'base' in package 'Matrix' in method for 'colSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'rowSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'colMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'rowMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix" Creating a generic function for 'zapsmall' from package 'base' in package 'Matrix' Creating a generic function for 'diag<-' from package 'base' in package 'Matrix' Creating a generic function for 'crossprod' from package 'base' in package 'Matrix' Creating a generic function for 'tcrossprod' from package 'base' in package 'Matrix' Creating a generic function for 'which' from package 'base' in package 'Matrix' in method for 'coerce' with signature '"graphAM","sparseMatrix"': no definition for class "graphAM" in method for 'coerce' with signature '"graph","CsparseMatrix"': no definition for class "graph" in method for 'coerce' with signature '"graph","Matrix"': no definition for class "graph" in method for 'coerce' with signature '"graphNEL","CsparseMatrix"': no definition for class "graphNEL" in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no definition for class "graphNEL" in method for 'coerce' with signature '"sparseMatrix","graph"': no definition for class "graph" in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no definition for class "graphNEL" in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL" Creating a generic function for 'qr.R' from package 'base' in package 'Matrix' Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix' Creating a generic function for 'qr.coef' from package 'base' in package 'Matrix' Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix' Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix' Creating a generic function for 'toeplitz' from package 'stats' in package 'Matrix' ** help *** installing help indices ** building package indices Loading required package: Matrix ** installing vignettes ** testing if installed package can be loaded * DONE (Matrix) begin installing recommended package nlme * installing *source* package 'nlme' ... ** package 'nlme' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmpIWE80Y/R.INSTALL26387dc219b3/nlme/src' gfortran -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c chol.f -o chol.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c corStruct.c -o corStruct.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c gnls.c -o gnls.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c init.c -o init.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c matrix.c -o matrix.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c nlOptimizer.c -o nlOptimizer.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c nlme.c -o nlme.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c nlmefit.c -o nlmefit.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c pdMat.c -o pdMat.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fvisibility=hidden -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c pythag.c -o pythag.o gfortran -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c rs.f -o rs.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran x86_64-tld-linux-gcc -shared -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -lgfortran -lm -lquadmath -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -lR make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmpIWE80Y/R.INSTALL26387dc219b3/nlme/src' installing to /tmp/B.61K3e5/BUILD/R-3.5.2/build/library/nlme/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (nlme) begin installing recommended package survival * installing *source* package 'survival' ... ** package 'survival' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/Rtmpaz13Rf/R.INSTALL268753f054f7/survival/src' x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c agexact.c -o agexact.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c agfit4.c -o agfit4.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c agfit5.c -o agfit5.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c agmart.c -o agmart.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c agmart2.c -o agmart2.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c agmart3.c -o agmart3.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c agscore.c -o agscore.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c agsurv3.c -o agsurv3.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c agsurv4.c -o agsurv4.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c agsurv5.c -o agsurv5.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c chinv2.c -o chinv2.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c chinv3.c -o chinv3.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c cholesky2.c -o cholesky2.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c cholesky3.c -o cholesky3.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c cholesky5.c -o cholesky5.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c chsolve2.c -o chsolve2.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c chsolve3.c -o chsolve3.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c chsolve5.c -o chsolve5.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c concordance1.c -o concordance1.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c concordance3.c -o concordance3.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c cox_Rcallback.c -o cox_Rcallback.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c coxcount1.c -o coxcount1.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c coxdetail.c -o coxdetail.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c coxexact.c -o coxexact.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c coxfit5.c -o coxfit5.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c coxfit6.c -o coxfit6.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c coxmart.c -o coxmart.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c coxmart2.c -o coxmart2.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c coxph_wtest.c -o coxph_wtest.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c coxsafe.c -o coxsafe.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c coxscho.c -o coxscho.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c coxscore.c -o coxscore.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c dmatrix.c -o dmatrix.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c doloop.c -o doloop.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c finegray.c -o finegray.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c gchol.c -o gchol.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c init.c -o init.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c norisk.c -o norisk.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c pyears1.c -o pyears1.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c pyears2.c -o pyears2.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c pyears3b.c -o pyears3b.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c pystep.c -o pystep.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c survConcordance.c -o survConcordance.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c survdiff2.c -o survdiff2.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c survfit4.c -o survfit4.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c survfitci.c -o survfitci.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c survpenal.c -o survpenal.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c survreg6.c -o survreg6.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c survreg7.c -o survreg7.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c survregc1.c -o survregc1.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c survregc2.c -o survregc2.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c survsplit.c -o survsplit.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c tmerge.c -o tmerge.o x86_64-tld-linux-gcc -shared -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart2.o agmart3.o agscore.o agsurv3.o agsurv4.o agsurv5.o chinv2.o chinv3.o cholesky2.o cholesky3.o cholesky5.o chsolve2.o chsolve3.o chsolve5.o concordance1.o concordance3.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit5.o coxfit6.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore.o dmatrix.o doloop.o finegray.o gchol.o init.o norisk.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -lR make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/Rtmpaz13Rf/R.INSTALL268753f054f7/survival/src' installing to /tmp/B.61K3e5/BUILD/R-3.5.2/build/library/survival/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (survival) begin installing recommended package boot * installing *source* package 'boot' ... ** package 'boot' successfully unpacked and MD5 sums checked ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (boot) begin installing recommended package cluster * installing *source* package 'cluster' ... ** package 'cluster' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmpEouPbV/R.INSTALL279977a438b4/cluster/src' x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c clara.c -o clara.o gfortran -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c daisy.f -o daisy.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c dysta.f -o dysta.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c fanny.c -o fanny.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c init.c -o init.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c mona.c -o mona.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c pam.c -o pam.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c sildist.c -o sildist.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c spannel.c -o spannel.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c twins.c -o twins.o x86_64-tld-linux-gcc -shared -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -lgfortran -lm -lquadmath -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -lR make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmpEouPbV/R.INSTALL279977a438b4/cluster/src' installing to /tmp/B.61K3e5/BUILD/R-3.5.2/build/library/cluster/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (cluster) begin installing recommended package codetools * installing *source* package 'codetools' ... ** package 'codetools' successfully unpacked and MD5 sums checked ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (codetools) begin installing recommended package foreign * installing *source* package 'foreign' ... ** package 'foreign' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/RtmpkSWCOq/R.INSTALL27ed51f0e506/foreign/src' x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c R_systat.c -o R_systat.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c Rdbfread.c -o Rdbfread.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c Rdbfwrite.c -o Rdbfwrite.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c SASxport.c -o SASxport.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c avl.c -o avl.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c dbfopen.c -o dbfopen.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c file-handle.c -o file-handle.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c format.c -o format.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c init.c -o init.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c minitab.c -o minitab.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c pfm-read.c -o pfm-read.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c sfm-read.c -o sfm-read.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c spss.c -o spss.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c stataread.c -o stataread.o x86_64-tld-linux-gcc -shared -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o foreign.so R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -lR make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/RtmpkSWCOq/R.INSTALL27ed51f0e506/foreign/src' installing to /tmp/B.61K3e5/BUILD/R-3.5.2/build/library/foreign/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (foreign) begin installing recommended package KernSmooth * installing *source* package 'KernSmooth' ... ** package 'KernSmooth' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/Rtmp2leLhH/R.INSTALL28446eb44c8d/KernSmooth/src' gfortran -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c blkest.f -o blkest.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c cp.f -o cp.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c dgedi.f -o dgedi.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c dgefa.f -o dgefa.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c dgesl.f -o dgesl.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c init.c -o init.o gfortran -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c linbin.f -o linbin.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c linbin2D.f -o linbin2D.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c locpoly.f -o locpoly.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c rlbin.f -o rlbin.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c sdiag.f -o sdiag.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran gfortran -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c sstdiag.f -o sstdiag.o f951: Warning: command line option '-Wformat=1' is valid for C/C++/ObjC/ObjC++ but not for Fortran x86_64-tld-linux-gcc -shared -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -lR make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/Rtmp2leLhH/R.INSTALL28446eb44c8d/KernSmooth/src' installing to /tmp/B.61K3e5/BUILD/R-3.5.2/build/library/KernSmooth/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (KernSmooth) begin installing recommended package rpart * installing *source* package 'rpart' ... ** package 'rpart' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/Rtmpn8gPI0/R.INSTALL2880ab796d9/rpart/src' x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c anova.c -o anova.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c anovapred.c -o anovapred.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c branch.c -o branch.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c bsplit.c -o bsplit.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c choose_surg.c -o choose_surg.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c fix_cp.c -o fix_cp.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c free_tree.c -o free_tree.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c gini.c -o gini.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c graycode.c -o graycode.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c init.c -o init.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c insert_split.c -o insert_split.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c make_cp_list.c -o make_cp_list.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c make_cp_table.c -o make_cp_table.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c mysort.c -o mysort.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c nodesplit.c -o nodesplit.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c partition.c -o partition.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c poisson.c -o poisson.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c pred_rpart.c -o pred_rpart.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c print_tree.c -o print_tree.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c rpart.c -o rpart.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c rpart_callback.c -o rpart_callback.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c rpartexp.c -o rpartexp.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c rpartexp2.c -o rpartexp2.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c rpcountup.c -o rpcountup.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c rpmatrix.c -o rpmatrix.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c rundown.c -o rundown.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c rundown2.c -o rundown2.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c surrogate.c -o surrogate.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c usersplit.c -o usersplit.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c xpred.c -o xpred.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c xval.c -o xval.o x86_64-tld-linux-gcc -shared -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o rpart.so anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -lR make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/Rtmpn8gPI0/R.INSTALL2880ab796d9/rpart/src' installing to /tmp/B.61K3e5/BUILD/R-3.5.2/build/library/rpart/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (rpart) begin installing recommended package class * installing *source* package 'class' ... ** package 'class' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/Rtmptsjv1H/R.INSTALL291919c51986/class/src' x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c class.c -o class.o x86_64-tld-linux-gcc -shared -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o class.so class.o -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -lR make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/Rtmptsjv1H/R.INSTALL291919c51986/class/src' installing to /tmp/B.61K3e5/BUILD/R-3.5.2/build/library/class/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (class) begin installing recommended package nnet * installing *source* package 'nnet' ... ** package 'nnet' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/Rtmp96BhaB/R.INSTALL29346419308c/nnet/src' x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c nnet.c -o nnet.o x86_64-tld-linux-gcc -shared -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o nnet.so nnet.o -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -lR make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/Rtmp96BhaB/R.INSTALL29346419308c/nnet/src' installing to /tmp/B.61K3e5/BUILD/R-3.5.2/build/library/nnet/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (nnet) begin installing recommended package spatial * installing *source* package 'spatial' ... ** package 'spatial' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/Rtmp1jgKXK/R.INSTALL294f67465f/spatial/src' x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c init.c -o init.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c krc.c -o krc.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c pps.c -o pps.o x86_64-tld-linux-gcc -shared -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o spatial.so init.o krc.o pps.o -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -lR make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/Rtmp1jgKXK/R.INSTALL294f67465f/spatial/src' installing to /tmp/B.61K3e5/BUILD/R-3.5.2/build/library/spatial/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (spatial) begin installing recommended package mgcv * installing *source* package 'mgcv' ... ** package 'mgcv' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/Rtmp8qycQ7/R.INSTALL29726fb9e8ed/mgcv/src' x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c coxph.c -o coxph.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c discrete.c -o discrete.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c gdi.c -o gdi.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c init.c -o init.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c magic.c -o magic.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c mat.c -o mat.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c matrix.c -o matrix.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c mgcv.c -o mgcv.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c misc.c -o misc.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c mvn.c -o mvn.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c qp.c -o qp.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c soap.c -o soap.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c sparse-smooth.c -o sparse-smooth.o x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c tprs.c -o tprs.o x86_64-tld-linux-gcc -shared -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o mgcv.so coxph.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o qp.o soap.o sparse-smooth.o tprs.o -llapack -lblas -lgfortran -lm -lquadmath -fopenmp -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -lR make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/Rtmp8qycQ7/R.INSTALL29726fb9e8ed/mgcv/src' installing to /tmp/B.61K3e5/BUILD/R-3.5.2/build/library/mgcv/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (mgcv) make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/Recommended' make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/Recommended' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' building/updating vignettes for package 'grid' ... building/updating vignettes for package 'parallel' ... building/updating vignettes for package 'utils' ... make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build' configuring Java ... Java interpreter : /usr/bin/java Java version : 1.8.0_181 Java home path : /usr/lib64/jvm/icedtea8-3.9.0/jre Java compiler : /usr/bin/javac Java headers gen.: /usr/bin/javah Java archive tool: /usr/bin/jar trying to compile and link a JNI program detected JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64 -ljvm make[2]: Entering directory '/tmp/B.61K3e5/BUILD/tmp/Rjavareconf.EylhTW' x86_64-tld-linux-gcc -I"/tmp/B.61K3e5/BUILD/R-3.5.2/build/include" -DNDEBUG -I/usr/lib64/jvm/icedtea8-3.9.0/jre/../include -I/usr/lib64/jvm/icedtea8-3.9.0/jre/../include/linux -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c conftest.c -o conftest.o x86_64-tld-linux-gcc -shared -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o conftest.so conftest.o -L/usr/lib64/jvm/icedtea8-3.9.0/jre/lib/amd64 -ljvm -L/tmp/B.61K3e5/BUILD/R-3.5.2/build/lib -lR make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/tmp/Rjavareconf.EylhTW' JAVA_HOME : /usr/lib64/jvm/icedtea8-3.9.0/jre Java library path: $(JAVA_HOME)/lib/amd64 JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux JNI linker flags : -L$(JAVA_HOME)/lib/amd64 -ljvm Updating Java configuration in /tmp/B.61K3e5/BUILD/R-3.5.2/build Done. make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build' + /usr/bin/make -j4 check make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests/Examples' Testing examples for package 'base' Testing examples for package 'tools' comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ... OK Testing examples for package 'utils' Testing examples for package 'grDevices' comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.save' ... OK Testing examples for package 'graphics' comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.save' ... OK Testing examples for package 'stats' comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.save' ... NOTE 17463c17463 < assertCondition: caught "error" --- > assertCondition: caught 'error' Testing examples for package 'datasets' comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.save' ... OK Testing examples for package 'methods' Testing examples for package 'grid' comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.save' ... OK Testing examples for package 'splines' comparing 'splines-Ex.Rout' to 'splines-Ex.Rout.save' ... OK Testing examples for package 'stats4' comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.save' ... OK Testing examples for package 'tcltk' Testing examples for package 'compiler' Testing examples for package 'parallel' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests/Examples' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. running strict specific tests make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' running code in '../.././tests/eval-etc.R' ... OK comparing 'eval-etc.Rout' to '../.././tests/eval-etc.Rout.save' ... OK running code in '../.././tests/simple-true.R' ... OK comparing 'simple-true.Rout' to '../.././tests/simple-true.Rout.save' ... OK running code in '../.././tests/arith-true.R' ... OK comparing 'arith-true.Rout' to '../.././tests/arith-true.Rout.save' ... OK running code in '../.././tests/arith.R' ... OK comparing 'arith.Rout' to '../.././tests/arith.Rout.save' ... OK running code in '../.././tests/lm-tests.R' ... OK comparing 'lm-tests.Rout' to '../.././tests/lm-tests.Rout.save' ... OK running code in '../.././tests/ok-errors.R' ... OK comparing 'ok-errors.Rout' to '../.././tests/ok-errors.Rout.save' ... OK running code in '../.././tests/method-dispatch.R' ... OK comparing 'method-dispatch.Rout' to '../.././tests/method-dispatch.Rout.save' ... OK running code in '../.././tests/any-all.R' ... OK comparing 'any-all.Rout' to '../.././tests/any-all.Rout.save' ... OK running code in '../.././tests/d-p-q-r-tests.R' ... OK comparing 'd-p-q-r-tests.Rout' to '../.././tests/d-p-q-r-tests.Rout.save' ... OK make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' running sloppy specific tests make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' running code in '../.././tests/complex.R' ... OK comparing 'complex.Rout' to '../.././tests/complex.Rout.save' ... OK running code in '../.././tests/eval-etc-2.R' ... OK comparing 'eval-etc-2.Rout' to '../.././tests/eval-etc-2.Rout.save' ... OK running code in '../.././tests/print-tests.R' ... OK comparing 'print-tests.Rout' to '../.././tests/print-tests.Rout.save' ... OK running code in '../.././tests/lapack.R' ... OK comparing 'lapack.Rout' to '../.././tests/lapack.Rout.save' ... OK running code in '../.././tests/datasets.R' ... OK comparing 'datasets.Rout' to '../.././tests/datasets.Rout.save' ... OK running code in '../.././tests/datetime.R' ... OK comparing 'datetime.Rout' to '../.././tests/datetime.Rout.save' ... OK running code in '../.././tests/iec60559.R' ... OK comparing 'iec60559.Rout' to '../.././tests/iec60559.Rout.save' ... OK make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' checking Sys.timezone ... make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' running code in '../.././tests/timezone.R' ... OK make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. running regression tests ... make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' running code in '../.././tests/array-subset.R' ... OK running code in '../.././tests/reg-tests-1a.R' ... OK running code in '../.././tests/reg-tests-1b.R' ... OK running code in '../.././tests/reg-tests-1c.R' ... OK running code in '../.././tests/reg-tests-1d.R' ... OK running code in '../.././tests/reg-tests-2.R' ... OK comparing 'reg-tests-2.Rout' to '../.././tests/reg-tests-2.Rout.save' ... OK running code in '../.././tests/reg-examples1.R' ... OK running code in '../.././tests/reg-examples2.R' ... OK running code in '../.././tests/reg-packages.R' ... OK running code in '../.././tests/p-qbeta-strict-tst.R' ... OK running code in '../.././tests/r-strict-tst.R' ... OK running code in '../.././tests/reg-IO.R' ... OK comparing 'reg-IO.Rout' to '../.././tests/reg-IO.Rout.save' ... OK running code in '../.././tests/reg-IO2.R' ... OK comparing 'reg-IO2.Rout' to '../.././tests/reg-IO2.Rout.save' ... OK running code in '../.././tests/reg-plot.R' ... OK comparing 'reg-plot.pdf' to '../.././tests/reg-plot.pdf.save' ... OK running code in '../.././tests/reg-S4-examples.R' ... OK running code in '../.././tests/reg-BLAS.R' ... OK make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' running code in '../.././tests/reg-tests-3.R' ... OK comparing 'reg-tests-3.Rout' to '../.././tests/reg-tests-3.Rout.save' ... OK running code in '../.././tests/reg-examples3.R' ... OK comparing 'reg-examples3.Rout' to '../.././tests/reg-examples3.Rout.save' ... OK running tests of plotting Latin-1 expect failure or some differences if not in a Latin-1 or UTF-8 locale running code in '../.././tests/reg-plot-latin1.R' ... FAILED running code in '../.././tests/reg-S4.R' ... OK comparing 'reg-S4.Rout' to '../.././tests/reg-S4.Rout.save' ... OK make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. running tests of Internet functions make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' running code in '../.././tests/internet.R' ... OK comparing 'internet.Rout' to '../.././tests/internet.Rout.save' ...8,10c8,247 < Warning message: < In nsl("cran.r-project.org") : < nsl() was unable to resolve host 'cran.r-project.org' --- > > > > # test do_download (and "record" #{packages}): > > ap <- available.packages(contrib.url("http://cran.r-project.org")) > > ## IGNORE_RDIFF_END > > > > # test url connections on http > > zz <- url("http://cran.r-project.org/") > > readLines(zz) > [1] "" > [2] "" > [3] "" > [4] "The Comprehensive R Archive Network" > [5] "" > [6] "" > [7] "" > [8] "" > [9] "" > [10] "" > [11] "" > [12] "" > [13] "" > [14] "" > [15] "" > [16] "" > [17] "" > [18] "<h1>The Comprehensive R Archive Network</h1>" > [19] "" > [20] "Your browser seems not to support frames," > [21] "here is the <A href=\"navbar.html\">contents page</A> of CRAN." > [22] "" > [23] "" > > close(zz) > > > > # and via read.table, test http and ftp. > > > > read.table("http://www.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat") > V1 V2 V3 V4 V5 > 1 1 307 930 36.58 0 > 2 2 307 940 36.73 0 > 3 3 307 950 36.93 0 > 4 4 307 1000 37.15 0 > 5 5 307 1010 37.23 0 > 6 6 307 1020 37.24 0 > 7 7 307 1030 37.24 0 > 8 8 307 1040 36.90 0 > 9 9 307 1050 36.95 0 > 10 10 307 1100 36.89 0 > 11 11 307 1110 36.95 0 > 12 12 307 1120 37.00 0 > 13 13 307 1130 36.90 0 > 14 14 307 1140 36.99 0 > 15 15 307 1150 36.99 0 > 16 16 307 1200 37.01 0 > 17 17 307 1210 37.04 0 > 18 18 307 1220 37.04 0 > 19 19 307 1230 37.14 0 > 20 20 307 1240 37.07 0 > 21 21 307 1250 36.98 0 > 22 22 307 1300 37.01 0 > 23 23 307 1310 36.97 0 > 24 24 307 1320 36.97 0 > 25 25 307 1330 37.12 0 > 26 26 307 1340 37.13 0 > 27 27 307 1350 37.14 0 > 28 28 307 1400 37.15 0 > 29 29 307 1410 37.17 0 > 30 30 307 1420 37.12 0 > 31 31 307 1430 37.12 0 > 32 32 307 1440 37.17 0 > 33 33 307 1450 37.28 0 > 34 34 307 1500 37.28 0 > 35 35 307 1510 37.44 0 > 36 36 307 1520 37.51 0 > 37 37 307 1530 37.64 0 > 38 38 307 1540 37.51 0 > 39 39 307 1550 37.98 1 > 40 40 307 1600 38.02 1 > 41 41 307 1610 38.00 1 > 42 42 307 1620 38.24 1 > 43 43 307 1630 38.10 1 > 44 44 307 1640 38.24 1 > 45 45 307 1650 38.11 1 > 46 46 307 1700 38.02 1 > 47 47 307 1710 38.11 1 > 48 48 307 1720 38.01 1 > 49 49 307 1730 37.91 1 > 50 50 307 1740 37.96 1 > 51 51 307 1750 38.03 1 > 52 52 307 1800 38.17 1 > 53 53 307 1810 38.19 1 > 54 54 307 1820 38.18 1 > 55 55 307 1830 38.15 1 > 56 56 307 1840 38.04 1 > 57 57 307 1850 37.96 1 > 58 58 307 1900 37.84 1 > 59 59 307 1910 37.83 1 > 60 60 307 1920 37.84 1 > 61 61 307 1930 37.74 1 > 62 62 307 1940 37.76 1 > 63 63 307 1950 37.76 1 > 64 64 307 2000 37.64 1 > 65 65 307 2010 37.63 1 > 66 66 307 2020 38.06 1 > 67 67 307 2030 38.19 1 > 68 68 307 2040 38.35 1 > 69 69 307 2050 38.25 1 > 70 70 307 2100 37.86 1 > 71 71 307 2110 37.95 1 > 72 72 307 2120 37.95 1 > 73 73 307 2130 37.76 1 > 74 74 307 2140 37.60 1 > 75 75 307 2150 37.89 1 > 76 76 307 2200 37.86 1 > 77 77 307 2210 37.71 1 > 78 78 307 2220 37.78 1 > 79 79 307 2230 37.82 1 > 80 80 307 2240 37.76 1 > 81 81 307 2250 37.81 1 > 82 82 307 2300 37.84 1 > 83 83 307 2310 38.01 1 > 84 84 307 2320 38.10 1 > 85 85 307 2330 38.15 1 > 86 86 307 2340 37.92 1 > 87 87 307 2350 37.64 1 > 88 88 308 0 37.70 1 > 89 89 308 10 37.46 1 > 90 90 308 20 37.41 1 > 91 91 308 30 37.46 1 > 92 92 308 40 37.56 1 > 93 93 308 50 37.55 1 > 94 94 308 100 37.75 1 > 95 95 308 110 37.76 1 > 96 96 308 120 37.73 1 > 97 97 308 130 37.77 1 > 98 98 308 140 38.01 1 > 99 99 308 150 38.04 1 > 100 100 308 200 38.07 1 > > read.table("ftp://ftp.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat") > V1 V2 V3 V4 V5 > 1 1 307 930 36.58 0 > 2 2 307 940 36.73 0 > 3 3 307 950 36.93 0 > 4 4 307 1000 37.15 0 > 5 5 307 1010 37.23 0 > 6 6 307 1020 37.24 0 > 7 7 307 1030 37.24 0 > 8 8 307 1040 36.90 0 > 9 9 307 1050 36.95 0 > 10 10 307 1100 36.89 0 > 11 11 307 1110 36.95 0 > 12 12 307 1120 37.00 0 > 13 13 307 1130 36.90 0 > 14 14 307 1140 36.99 0 > 15 15 307 1150 36.99 0 > 16 16 307 1200 37.01 0 > 17 17 307 1210 37.04 0 > 18 18 307 1220 37.04 0 > 19 19 307 1230 37.14 0 > 20 20 307 1240 37.07 0 > 21 21 307 1250 36.98 0 > 22 22 307 1300 37.01 0 > 23 23 307 1310 36.97 0 > 24 24 307 1320 36.97 0 > 25 25 307 1330 37.12 0 > 26 26 307 1340 37.13 0 > 27 27 307 1350 37.14 0 > 28 28 307 1400 37.15 0 > 29 29 307 1410 37.17 0 > 30 30 307 1420 37.12 0 > 31 31 307 1430 37.12 0 > 32 32 307 1440 37.17 0 > 33 33 307 1450 37.28 0 > 34 34 307 1500 37.28 0 > 35 35 307 1510 37.44 0 > 36 36 307 1520 37.51 0 > 37 37 307 1530 37.64 0 > 38 38 307 1540 37.51 0 > 39 39 307 1550 37.98 1 > 40 40 307 1600 38.02 1 > 41 41 307 1610 38.00 1 > 42 42 307 1620 38.24 1 > 43 43 307 1630 38.10 1 > 44 44 307 1640 38.24 1 > 45 45 307 1650 38.11 1 > 46 46 307 1700 38.02 1 > 47 47 307 1710 38.11 1 > 48 48 307 1720 38.01 1 > 49 49 307 1730 37.91 1 > 50 50 307 1740 37.96 1 > 51 51 307 1750 38.03 1 > 52 52 307 1800 38.17 1 > 53 53 307 1810 38.19 1 > 54 54 307 1820 38.18 1 > 55 55 307 1830 38.15 1 > 56 56 307 1840 38.04 1 > 57 57 307 1850 37.96 1 > 58 58 307 1900 37.84 1 > 59 59 307 1910 37.83 1 > 60 60 307 1920 37.84 1 > 61 61 307 1930 37.74 1 > 62 62 307 1940 37.76 1 > 63 63 307 1950 37.76 1 > 64 64 307 2000 37.64 1 > 65 65 307 2010 37.63 1 > 66 66 307 2020 38.06 1 > 67 67 307 2030 38.19 1 > 68 68 307 2040 38.35 1 > 69 69 307 2050 38.25 1 > 70 70 307 2100 37.86 1 > 71 71 307 2110 37.95 1 > 72 72 307 2120 37.95 1 > 73 73 307 2130 37.76 1 > 74 74 307 2140 37.60 1 > 75 75 307 2150 37.89 1 > 76 76 307 2200 37.86 1 > 77 77 307 2210 37.71 1 > 78 78 307 2220 37.78 1 > 79 79 307 2230 37.82 1 > 80 80 307 2240 37.76 1 > 81 81 307 2250 37.81 1 > 82 82 307 2300 37.84 1 > 83 83 307 2310 38.01 1 > 84 84 307 2320 38.10 1 > 85 85 307 2330 38.15 1 > 86 86 307 2340 37.92 1 > 87 87 307 2350 37.64 1 > 88 88 308 0 37.70 1 > 89 89 308 10 37.46 1 > 90 90 308 20 37.41 1 > 91 91 308 30 37.46 1 > 92 92 308 40 37.56 1 > 93 93 308 50 37.55 1 > 94 94 308 100 37.75 1 > 95 95 308 110 37.76 1 > 96 96 308 120 37.73 1 > 97 97 308 130 37.77 1 > 98 98 308 140 38.01 1 > 99 99 308 150 38.04 1 > 100 100 308 200 38.07 1 > > OK make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' + /usr/bin/make -j4 docs pdf info make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual' creating doc/manual/version.tex make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/m4' make[1]: Nothing to be done for 'R'. make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/m4' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual' /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I../../.././doc/manual ../../.././doc/manual/R-FAQ.texi make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tools' make[1]: Nothing to be done for 'R'. make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tools' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/html' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/html' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/html' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/html' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc' make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/etc' make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/etc' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/share' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/share' collecting LaTeX docs for package 'tools' ... make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/share' make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/share' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/scripts' creating src/scripts/R.fe make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/scripts' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/scripts' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/scripts' collecting LaTeX docs for package 'base' ... make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/include' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/include/R_ext' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/include/R_ext' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/include' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tre' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tre' make[4]: 'Makedeps' is up to date. make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tre' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tre' make[4]: 'libtre.a' is up to date. make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tre' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tre' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tzone' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tzone' make[4]: 'Makedeps' is up to date. make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tzone' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tzone' make[4]: 'libtz.a' is up to date. make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tzone' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tzone' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/appl' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/appl' make[3]: 'libappl.a' is up to date. make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/appl' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/appl' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/nmath' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/nmath' make[3]: 'libnmath.a' is up to date. make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/nmath' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/nmath' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/unix' Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX .config.status: creating src/unix/Makefile make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/unix' make[3]: 'libunix.a' is up to date. make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/unix' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/unix' x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -DR_HOME='"/tmp/B.61K3e5/BUILD/R-3.5.2/build"' \ -o Rscript ../../.././src/unix/Rscript.c ..make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/unix' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/unix' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' ..config.status: creating src/main/Makefile make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/serialize.c -o serialize.o . collecting LaTeX docs for package 'utils' ... .creating doc/manual/version.texi Converting parsed Rd's to LaTeX /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I../../.././doc/manual ../../.././doc/manual/R-admin.texi ..............x86_64-tld-linux-gcc -I../../.././src/extra -I. -I../../src/include -I../../.././src/include -I../../.././src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../.././src/main/version.c -o version.o .x86_64-tld-linux-gcc -shared -fopenmp -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o altrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/tre/libtre.a ../extra/tzone/libtz.a -lblas -lgfortran -lm -lquadmath -lreadline -lpcre2-8 -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n ..make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' /tmp/B.61K3e5/BUILD/R-3.5.2/build/lib/libR.so is unchanged make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' /tmp/B.61K3e5/BUILD/R-3.5.2/build/bin/exec/R is unchanged make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/internet' .make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/internet' make[4]: 'internet.so' is up to date. make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/internet' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/internet' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/lapack' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/lapack' make[4]: 'lapack.so' is up to date. make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/lapack' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/lapack' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/X11' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/X11' make[4]: 'R_X11.so' is up to date. make[4]: 'R_de.so' is up to date. make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/X11' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/X11' /tmp/B.61K3e5/BUILD/R-3.5.2/build/modules/R_X11.so is unchanged /tmp/B.61K3e5/BUILD/R-3.5.2/build/modules/R_de.so is unchanged make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/X11' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/X11' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/profile' building system startup profile make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/profile' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/translations' building package 'translations' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/translations' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/translations' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/translations' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/base' building package 'base' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/base' all.R is unchanged make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/base' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/base' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' building package 'tools' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' all.R is unchanged make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools/src' ..make[6]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[6]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools/src' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' installing 'sysdata.rda' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/compiler' building package 'compiler' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/compiler' all.R is unchanged .make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/compiler' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/compiler' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/compiler' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/compiler' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/base' make[3]: Nothing to be done for 'mklazycomp'. make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/base' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' make[3]: Nothing to be done for 'mklazycomp'. make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tools' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' building package 'utils' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' all.R is unchanged .make[4]: Nothing to be done for 'iconvlist'. make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils/src' .make[6]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[6]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils/src' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' installing 'sysdata.rda' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/utils' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices' building package 'grDevices' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices' all.R is unchanged .make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices' make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src' x86_64-tld-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../.././src/include -DHAVE_CONFIG_H -fpic -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -c ../../../../.././src/library/grDevices/src/devPS.c -o devPS.o collecting LaTeX docs for package 'grDevices' ... Converting parsed Rd's to LaTeX ..../usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I../../.././doc/manual ../../.././doc/manual/R-data.texi ....... /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I../../.././doc/manual ../../.././doc/manual/R-exts.texi .collecting LaTeX docs for package 'graphics' ... .Converting parsed Rd's to LaTeX ................x86_64-tld-linux-gcc -shared -L../../../../lib -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR .make[6]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[7]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src/cairo' make[8]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src/cairo' make[9]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src/cairo' make[9]: 'cairo.so' is up to date. make[9]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src/cairo' make[8]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src/cairo' make[7]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src/cairo' make[6]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices' .. .collecting LaTeX docs for package 'stats' ... .make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grDevices' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics' building package 'graphics' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics' all.R is unchanged .make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics' make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics/src' make[6]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[6]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics/src' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/graphics' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats' building package 'stats' Converting parsed Rd's to LaTeX make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats' all.R is unchanged .make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats' make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats/src' make[6]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[6]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats/src' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/datasets' building package 'datasets' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/datasets' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/datasets' .....make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/datasets' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods' building package 'methods' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods' all.R is unchanged ..make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods' make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods/src' make[6]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[6]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods/src' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods' make[4]: Nothing to be done for 'RfilesLazy'. make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/methods' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid' building package 'grid' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid' all.R is unchanged .make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid' make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid/src' make[6]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[6]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid/src' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/grid' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines' building package 'splines' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines' all.R is unchanged .make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines' .make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines/src' make[6]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[6]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines/src' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/splines' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats4' building package 'stats4' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats4' all.R is unchanged make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats4' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats4' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats4' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/stats4' .make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk' building package 'tcltk' all.R is unchanged make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk' .make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk/src' make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk/src' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/tcltk' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel' building package 'parallel' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel' all.R is unchanged make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel' make[5]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel/src' make[6]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[6]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel/src' make[5]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel/src' make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel' make[4]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/parallel' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/base' .make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library/base' installing parsed NAMESPACE files make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make[1]: Nothing to be done for 'R'. make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual' creating doc/manual/R-admin.html collecting LaTeX docs for package 'datasets' ... ..Converting parsed Rd's to LaTeX ............/usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I../../.././doc/manual ../../.././doc/manual/R-intro.texi . creating doc/manual/R-data.html .collecting LaTeX docs for package 'methods' ... ..Converting parsed Rd's to LaTeX .creating doc/manual/R-exts.html .........../usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I../../.././doc/manual ../../.././doc/manual/R-ints.texi ........ .collecting LaTeX docs for package 'grid' ... Converting parsed Rd's to LaTeX ../usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I../../.././doc/manual ../../.././doc/manual/R-lang.texi ....... .. collecting LaTeX docs for package 'splines' ... collecting LaTeX docs for package 'stats4' ... creating doc/manual/R-intro.html Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX .. collecting LaTeX docs for package 'tcltk' ... collecting LaTeX docs for package 'compiler' ... Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual' make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc' creating doc/manual/R-ints.html . collecting LaTeX docs for package 'MASS' ... collecting LaTeX docs for package 'parallel' ... Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX ... collecting LaTeX docs for package 'lattice' ... ..Converting parsed Rd's to LaTeX creating doc/manual/R-lang.html ..collecting LaTeX docs for package 'Matrix' ... ...Converting parsed Rd's to LaTeX ............make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/html' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/html' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual' make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' installing parsed Rd make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' . base stats collecting LaTeX docs for package 'nlme' ... utils . methods . graphics grDevices datasets Converting parsed Rd's to LaTeX grid tools .. tcltk splines stats4 compiler parallel make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' building/updating package metadata ... ... .collecting LaTeX docs for package 'survival' ... make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' writing package indices make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' ...Converting parsed Rd's to LaTeX .............. .collecting LaTeX docs for package 'boot' ... .make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' .make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' collecting LaTeX docs for package 'cluster' ... ..Converting parsed Rd's to LaTeX .Converting parsed Rd's to LaTeX .......... .collecting LaTeX docs for package 'codetools' ... ....Converting parsed Rd's to LaTeX .. collecting LaTeX docs for package 'foreign' ... .....Converting parsed Rd's to LaTeX collecting LaTeX docs for package 'KernSmooth' ... ... Converting parsed Rd's to LaTeX collecting LaTeX docs for package 'rpart' ... . collecting LaTeX docs for package 'class' ... collecting LaTeX docs for package 'nnet' ... .Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX .Converting parsed Rd's to LaTeX .. collecting LaTeX docs for package 'spatial' ... .collecting LaTeX docs for package 'mgcv' ... . TEXINPUTS="../../.././doc/manual:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf ../../.././doc/manual/R-FAQ.texi .Converting parsed Rd's to LaTeX Converting parsed Rd's to LaTeX ... .TEXINPUTS="../../.././doc/manual:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf ../../.././doc/manual/R-admin.texi This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros,. cross references, insertions, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/usr/share/texmf-dist/tex/texinfo/txi-en.tex) [1{/usr/share/texmf/fonts/map/pd ftex/updmap/pdftex.map}] [-1] Chapter 1 Cross reference values unknown; you must run TeX again. Chapter 2 [1] [2] [3] [4] [5] Underfull \hbox (badness 3158) in paragraph at lines 528--541 []@textrm Debian pack-ages, main-tained by Dirk Ed-del-buet-tel, have long been part of Underfull \hbox (badness 3769) in paragraph at lines 562--564 []@textrm See [][]@texttt https://CRAN.R-project.org/bin/linux/suse/README.html [][][] @textrm for in-for-ma-tion [6] Underfull \hbox (badness 10000) in paragraph at lines 624--627 []@textrm John M. Cham-bers (2008), ``Soft-ware for Data Anal-y-sis: Pro- Underfull \hbox (badness 8132) in paragraph at lines 624--627 @textrm gram-ming with R''. Springer, New York, ISBN 978-0-387-75935-7, Underfull \hbox (badness 10000) in paragraph at lines 632--635 []@textrm Robert Gen-tle-man (2008), ``R Pro-gram-ming for Bioin-for-mat-ics'' . Underfull \hbox (badness 7379) in paragraph at lines 632--635 @textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7, Underfull \hbox (badness 2846) in paragraph at lines 651--654 []@textrm William N. Ven-ables and Brian D. Rip-ley (2002), ``Mod-ern Ap-plied Underfull \hbox (badness 10000) in paragraph at lines 651--654 @textrm Statis-tics with S'' (4th edi-tion). Springer, ISBN 0-387-95457-0, [7] [8] Overfull \hbox (59.99986pt too wide) in paragraph at lines 792--797 @textrm and is mir-rored daily to many sites around the world. See [][]@texttt https://CRAN.R-project.org/mirrors.html[][][] [9] Chapter 3 [10] [11TEXINPUTS="../../.././doc/manual:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf ../../.././doc/manual/R-data.texi ] [12] [13] [14] [15] [16] [17] Overfull \hbox (11.28497pt too wide) in paragraph at lines 1524--1527 []@textrm See also [][]@texttt https://en.wikipedia.org/wiki/R_programming_lang uage#Commercialized_ Chapter 4 [18] [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [37]entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: [38 pdf, fonts,]. [39] page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, [40 macros, cross references, insertions,] (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, [41 and turning on texinfo input format.) (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)] Underfull \hbox (badness 6559) in paragraph at lines 3389--3397 []@textrm When R trans-fers files over @reducedrm HTTP @textrm (e.g., us-ing th e @texttt install.packages()[] @textrm or Underfull \hbox (badness 10000) in paragraph at lines 3389--3397 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the Underfull \hbox (badness 3364) in paragraph at lines 3389--3397 @textrm `@texttt download.file.method[]@textrm '[] op-tion. There are sev-eral meth-ods avail-able and the [42) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi) [1]{/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map Chapter 8 [43] Chapter 9 [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 3628--3636 [][]@texttt https://en.wikipedia.org/wiki/Reproducibility[][][]@textrm ) the pr ob-lem, prefer-ably the Chapter 10 [46] [47] [48] ) (see the transcript file for additional information) [13< /usr/share/texmf-dist/fonts/type1/bluesky/cm/cmmi7.pfb] Underfull \hbox (badness 7685) in paragraph at lines 1293--1297 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [14] Underfull \hbox (badness 10000) in paragraph at lines 1425--1431 @textrm ics li-braries built by Si-mon Ur-banek at [][]@texttt https://www.rfor ge.net/Cairo/files/ Underfull \hbox (badness 10000) in paragraph at lines 1447--1453 @textrm The first should be un-com-mented and the sec-ond set to the top-level di- Underfull \hbox (badness 10000) in paragraph at lines 1447--1453 @textrm rec-tory of a suit-ably pack-aged bi-nary build of ICU, for ex-am-ple t hat at Underfull \hbox (badness 10000) in paragraph at lines 1447--1453 [][]@texttt https://www.stats.ox.ac.uk/pub/Rtools/goodies/ICU_531.zip[][][]@tex trm . De-pend-ing on [15] Underfull \hbox (badness 2582) in paragraph at lines 1510--1514 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make check- Underfull \hbox (badness 10000) in paragraph at lines 1547--1549 [][][]@smallrm Suitable dis-tri-bu-tions in-clude Straw-berry Perl, [][]@smallt t http://strawberryperl.com/[][][] @smallrm and Ac-tivePerl, [16] [17] Chapter 4 [18] Underfull \hbox (badness 10000) in paragraph at lines 1763--1767 []@textrm Installers for R-patched and R-devel are usu-ally avail-able from Underfull \hbox (badness 3872) in paragraph at lines 1763--1767 [][]@texttt https://r.research.att.com[][][]@textrm . (Some of these pack-ages are un-signed: to in-stall Underfull \hbox (badness 10000) in paragraph at lines 1791--1796 []@textrm Various parts of the build re-quire XQuartz to be in-stalled: see Underfull \hbox (badness 3009) in paragraph at lines 1791--1796 [][]@texttt https://xquartz.macosforge.org/[][][]@textrm . These in-clude the @ textbf tcltk @textrm pack-age and the @texttt X11[] Underfull \hbox (badness 2111) in paragraph at lines 1791--1796 @textrm de-vice: at-tempt-ing to use these with-out XQuartz will re-mind you. A lso for the Underfull \hbox (badness 10000) in paragraph at lines 1843--1847 @texttt library/mac/releasenotes/MacOSX/WhatsNewInOSX/Articles/MacOSX10_9.html[ ][][]@textrm ) which [19] Underfull \hbox (badness 10000) in paragraph at lines 1859--1861 @textrm (see [][]@texttt https://developer.apple.com/library/mac/releasenotes/ MacOSX/ Underfull \hbox (badness 3668) in paragraph at lines 1888--1900 []@textrm The in-stal-la-tion con-sists of up to four Ap-ple pack-ages:$[]$ @te xttt org.r-project.R.el- Underfull \hbox (badness 10000) in paragraph at lines 1888--1900 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [20] Chapter 5 [21] Chapter 6> [22]< /usr/share/texmf-dist/fonts/type1/bluesky/cm/cmti10.pfb> [25 [26] [27] [28.] Output written on R-FAQ.pdf (50 pages, 332285 bytes). Transcript written on R-FAQ.log. Underfull \hbox (badness 3907) in paragraph at lines 2626--2634 []@textrm Utilities such as @texttt install.packages[] @textrm can be pointed a t any @reducedrm CRAN@textrm -style repos-i-tory, Underfull \hbox (badness 2158) in paragraph at lines 2626--2634 @textrm such as [][]@texttt http://www.stats.ox.ac.uk/pub/RWin[][][]@textrm : t his must be an URL scheme that [29] [30] Chapter 7 [31] [32] [33] Chapter 8 [34] Chapter 9 [35] [36] [37] Appendix A [38] [39] Overfull \hbox (27.8098pt too wide) in paragraph at lines 3355--3355 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] Underfull \hbox (badness 6927) in paragraph at lines 3376--3382 [][][]@smallrm Such as @keyrm GNU @smalltt tar[] @smallrm 1.15 or later, @small tt bsdtar[] @smallrm (from [][]@smalltt https://github.com/libarchive/libarchiv e/[][][]@smallrm , Underfull \hbox (badness 2277) in paragraph at lines 3376--3382 @smallrm as used as @smalltt tar[] @smallrm by FreeBSD and macOS 10.6 and later ) or @smalltt tar[] @smallrm from the Heir-loom Toolch-est [40]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. Underfull \hbox (badness 10000) in paragraph at lines 3480--3482 [][][]@smallrm also known as @smalltt ttf-mscorefonts-installer[] @smallrm in t he De-bian/Ubuntu world: see also Underfull \hbox (badness 2409) in paragraph at lines 3477--3495 @textrm avail-able at [][]@texttt https://fedorahosted.org/liberation-fonts/[][ ][]@textrm ,$[]$ which cover the Latin, [41]entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: Underfull \hbox (badness 3078) in paragraph at lines 3551--3557 []@textrm The @texttt bitmap[] @textrm and @texttt dev2bitmap[] @textrm de-vice s and func-tion @texttt embedFonts()[] @textrm use ghost-script [42 pdf,] fonts, [43] page headings, tables, conditionals,This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. indexing, sectioning, [44 toc, environments,] defuns, macros, cross references, insertions, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization,entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: Underfull \hbox (badness 5077) in paragraph at lines 3793--3798 []@textrm Debian/Ubuntu sys-tems pro-vide a system-specific way to switch the B LAS in [45 formatting, and turning on texinfo input format. pdf,)] fonts, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex) [46) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi) [1]{/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map page headings, tables, [47 conditionals, indexing, sectioning,] toc, environments, defuns, macros, cross references, Appendix B [48 insertions, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> )] localization, [49] formatting, and turning on texinfo input format.) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-FAQ.aux [50] [51] [52) (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)]}] [1{/usr/share/texmf/fonts/map/pd ftex/updmap/pdftex.map [2 [53] [-1] (Acknowledgements)] Underfull \hbox (badness 5119) in paragraph at lines 4545--4549 []@textrm Other vari-ables of-ten set by @texttt configure[] @textrm in-clude ` @texttt MAIN_LDFLAGS[]@textrm '[], `@texttt SAFE_FFLAGS[]@textrm '[], [54] Underfull \hbox (badness 10000) in paragraph at lines 4598--4602 [][][]@smallrm The links there have proved dif-fi-cult to ac-cess, in which cas e ei-ther point an FTP Underfull \hbox (badness 10000) in paragraph at lines 4598--4602 @smallrm client at [][]@smalltt ftp://www.eecs.harvard.edu/pub/nr/[][][] @small rm or grab the copy made avail-able at Appendix C Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL[][]| Chapter 1 [55 [1]] [56] Cross reference values unknown; you must run TeX again. [57 [2]] [58 [3]] [4 Underfull \hbox (badness 10000) in paragraph at lines 1--4896 []@textrm R has been built with Linux `@texttt ix86[]@textrm '[] and `@texttt x 86_64[]@textrm '[] C and C@texttt ++ @textrm com-pil-ers Underfull \hbox (badness 10000) in paragraph at lines 1--4896 @textrm ([][]@texttt http://clang.llvm.org[][][]@textrm ) based on the Clang fr ont-ends, in-voked by @texttt CC=clang [59]] Overfull \hbox (56.55324pt too wide) in paragraph at lines 5036--5036 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] [60] Chapter 2} [5] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-FAQ.toc Overfull \hbox (50.80455pt too wide) in paragraph at lines 5042--5042 []@texttt CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.s dk/usr/include"[] Underfull \hbox (badness 10000) in paragraph at lines 5052--5056 []@textrm An X sub-system is re-quired un-less con-fig-ur-ing us-ing `@texttt - -without-x[]@textrm '[]: see Underfull \hbox (badness 2221) in paragraph at lines 5052--5056 [][]@texttt https://xquartz.macosforge.org/[][][]@textrm . R's @texttt configur e[] @textrm script can be told to look for Underfull \hbox (badness 10000) in paragraph at lines 5096--5105 []@textrm There are in-stallers$[]$ for For-tran com-pil-ers for El Cap-i-tan a nd Sierra at [61]] [6 Underfull \hbox (badness 4595) in paragraph at lines 5121--5132 []@textrm Current @reducedrm CRAN @textrm bi-nary dis-tri-bu-tions use the buil d of @texttt clang[] @textrm 6.0.0 con-tained in Underfull \hbox (badness 10000) in paragraph at lines 5121--5132 [][]@texttt https://cran.r-project.org/bin/macosx/tools/clang-6.0.0.pkg[][][]@t extrm . Other re-cent Overfull \hbox (56.55324pt too wide) in paragraph at lines 5134--5134 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] Overfull \hbox (85.29668pt too wide) in paragraph at lines 5172--5172 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [62]] [-1 [7]] Underfull \hbox (badness 10000) in paragraph at lines 5215--5225 []@textrm The T[]X im-ple-men-ta-tion used by the de-vel-op-ers is Mac-TeX Underfull \hbox (badness 2600) in paragraph at lines 5215--5225 @textrm ([][]@texttt https://www.tug.org/mactex/[][][]@textrm ): the full in-st al-la-tion is about 5GB, but a smaller [63] [8 [-2 [64]]] [9] Underfull \hbox (badness 3428) in paragraph at lines 5453--5457 @textrm than other plat-forms. This makes it de-sir-able to build PCRE with the op-tion [65) [-3]] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-FAQ.toc [10) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-FAQ.toc [66] Chapter 3 [11]] [67) Chapter 1] [12 Underfull \hbox (badness 10000) in paragraph at lines 5680--5684 []@textrm Note that paths such as `@texttt /opt/csw/lib[]@textrm '[], `@texttt /usr/local/lib/amd64[]@textrm '[] and Underfull \hbox (badness 5050) in paragraph at lines 5680--5684 @textrm `@texttt /opt/csw/lib/amd64[]@textrm '[] may need to be in the []@textt t LD_LIBRARY_PATH[] @textrm dur-ing con-fig-u-ra- [68] Chapter 2] [1] Underfull \hbox (badness 2088) in paragraph at lines 1104--1112 []@textrm Octave is a nu-mer-i-cal lin-ear al-ge-bra sys-tem ([][]@texttt http: //www.octave.org[][][]@textrm ), and func-tion Chapter 4 [2 [13]] Underfull \hbox (badness 2111) in paragraph at lines 5781--5786 []@textrm The re-cent WU test-ing was done us-ing com-pil-ers from both the @re ducedrm GNU @textrm Com-piler [69] [3 Underfull \hbox (badness 3058) in paragraph at lines 1196--1202 @textrm data-bases and even text files (pos-si-bly com-pressed). Open Data-base Con-nec-tiv-ity [14]] [70] [15 Underfull \hbox (badness 4492) in paragraph at lines 5906--5912 @textrm PACK code to avoid com-pu-ta-tions en-tirely in extended-precision reg- is-ters, so file Appendix D [71] [4]] [72 [5]] Underfull \hbox (badness 10000) in paragraph at lines 1355--1359 []@textrm Package [][]@textbf RMongo[][] @textrm pro-vides an R in-ter-face to a Java client for `Mon-goDB' Underfull \hbox (badness 10000) in paragraph at lines 1355--1359 @textrm ([][]@texttt https://en.wikipedia.org/wiki/MongoDB[][][]@textrm ) data- bases, which are queried us-ing [16] Underfull \hbox (badness 5302) in paragraph at lines 6112--6115 []@textrm You may need to set the en-vi-ron-ment vari-able @texttt CYGWIN[] @te xtrm to a value in-clud-ing [73 Underfull \hbox (badness 3158) in paragraph at lines 528--541 []@textrm Debian pack-ages, main-tained by Dirk Ed-del-buet-tel, have long been part of Underfull \hbox (badness 3769) in paragraph at lines 562--564 []@textrm See [][]@texttt https://CRAN.R-project.org/bin/linux/suse/README.html [][][] @textrm for in-for-ma-tion [6]] (Function and variable index) [74 Underfull \hbox (badness 10000) in paragraph at lines 624--627 []@textrm John M. Cham-bers (2008), ``Soft-ware for Data Anal-y-sis: Pro- Underfull \hbox (badness 8132) in paragraph at lines 624--627 @textrm gram-ming with R''. Springer, New York, ISBN 978-0-387-75935-7, Underfull \hbox (badness 10000) in paragraph at lines 632--635 []@textrm Robert Gen-tle-man (2008), ``R Pro-gram-ming for Bioin-for-mat-ics'' . Underfull \hbox (badness 7379) in paragraph at lines 632--635 @textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7, Underfull \hbox (badness 2846) in paragraph at lines 651--654 []@textrm William N. Ven-ables and Brian D. Rip-ley (2002), ``Mod-ern Ap-plied Underfull \hbox (badness 10000) in paragraph at lines 651--654 @textrm Statis-tics with S'' (4th edi-tion). Springer, ISBN 0-387-95457-0, [7] (Concept index) Underfull \hbox (badness 3690) in paragraph at lines 1417--1421 []@textrm These are con-ve-nient in-ter-faces to read/write/test/delete ta-bles in the data-base. [17] [75] (Environment variable index) [76]] [77] ) (see the transcript file for additional information)< [8/usr/share/texmf-dist/font s/type1/bluesky/cm/cmb10.pfb]> Overfull \hbox (59.99986pt too wide) in paragraph at lines 792--797 @textrm and is mir-rored daily to many sites around the world. See [][]@texttt https://CRAN.R-project.org/mirrors.html[][][] [9] [20] [14 [22 [15]] Output written on R-admin.pdf (80 pages, 469482 bytes). Transcript written on R-admin.log. [16 [23]] [17] Underfull \hbox (badness 2150) in paragraph at lines 2094--2098 []@textrm A sum-mary of all the con-nec-tions cur-rently opened by the user can be found by [24 Overfull \hbox (11.28497pt too wide) in paragraph at lines 1524--1527 []@textrm See also [][]@texttt https://en.wikipedia.org/wiki/R_programming_lang uage#Commercialized_ Chapter 4 [18]] Chapter 8 [25 [19]] Underfull \hbox (badness 3815) in paragraph at lines 2239--2241 []@textrm The ear-lier low-level in-ter-face is given by func-tions @texttt mak e.socket[]@textrm , @texttt read.socket[]@textrm , Chapter 9 [26 Chapter 5 [20]] Underfull \hbox (badness 2012) in paragraph at lines 2278--2287 []@textrm If you do not have Ex-cel, many other pro-grams are able to read such spread- Underfull \hbox (badness 7326) in paragraph at lines 2278--2287 @textrm sheets and ex-port in a text for-mat on both Win-dows and Unix, for ex- am- Underfull \hbox (badness 10000) in paragraph at lines 2278--2287 @textrm ple Gnu-meric ([][]@texttt http://www.gnome.org/projects/gnumeric/[][][ ]@textrm ) and OpenOf-fice Appendix A [27 [21]] Overfull \hbox (38.37012pt too wide) in paragraph at lines 2363--2366 @textrm B. D. Rip-ley (2001) Con-nec-tions. @textit R News@textrm , @textbf 1/1 @textrm , 16--7. [][]@texttt https://www.r-project.org/doc/Rnews/Rnews_ (Function and variable index) [28] (Concept index) [29] [30] [22 ) (see the transcript file for additional information) [24 Chapter 6 [25 [26 Chapter 7 [28] Output written on R-data.pdf (33 pages, 236004 bytes). Transcript written on R-data.log. [29] [30] [31] [32] [33] [34This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. ] [35]entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, [36] [37] page headings, tables, conditionals, indexing, sectioning, toc, [38 environments,] defuns, macros, cross references, insertions, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) [39 localization,] formatting, and turning on texinfo input format.) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-admin.aux [40] [41]) Underfull \hbox (badness 6559) in paragraph at lines 3389--3397 []@textrm When R trans-fers files over @reducedrm HTTP @textrm (e.g., us-ing th e @texttt install.packages()[] @textrm or Underfull \hbox (badness 10000) in paragraph at lines 3389--3397 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the Underfull \hbox (badness 3364) in paragraph at lines 3389--3397 @textrm `@texttt download.file.method[]@textrm '[] op-tion. There are sev-eral meth-ods avail-able and the [42 (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)] Chapter 8 [43.]) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi) [1{/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map Chapter 9 [44] [45This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. ] Underfull \hbox (badness 10000) in paragraph at lines 3628--3636 [][]@texttt https://en.wikipedia.org/wiki/Reproducibility[][][]@textrm ) the pr ob-lem, prefer-ably the Chapter 10 [46] [47] [48]entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: ) (see the transcript file for additional information)< /usr/share/texmf-dist/fonts/type1/bluesky/cm/cmmi7.pfb conditionals, indexing,>< sectioning,/usr/share/texmf-dist/f onts/type1/bluesky/cm/cmr10.pfb toc, environments,> defuns, macros, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex )> localization,}<]/usr/share/texmf-dist/fonts/type1/blu esky/cm/cmsltt10.pfb formatting, and turning on texinfo input format.) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-data.aux [2>] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-admin.toc< /usr/share/texmf-dist/fonts/type1/bluesky/cm/cmti10.pfb> (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi) [-2 Output written on R-FAQ.pdf (52 pages, 384663 bytes). Transcript written on R-FAQ.log. ]) [-3] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-admin.toc) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-admin.toc) Chapter 1 Underfull \hbox (badness 10000) in paragraph at lines 152--157 []@textrm The tar-balls are avail-able from [][]@texttt https://stat.ethz.ch/R/ daily[][][]@textrm . Down-load Underfull \hbox (badness 4303) in paragraph at lines 180--186 @textrm to check out `@texttt r-devel[]@textrm '[] into di-rec-tory @textsl pat h @textrm (which will be cre-ated if nec-es-sary). Underfull \hbox (badness 2181) in paragraph at lines 180--186 @textrm The al-pha, beta and RC ver-sions of an up-com-ing @textsl x.y.0 @textr m re-lease are avail-able from [1] Chapter 2 [2]}] [2] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-data.toc [3] [-1] [4) [-2] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-data.toc) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-data.toc]) (Acknowledgements) [5] Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL[][]| Chapter 1 [1] [6] [7 [2]] [8 [3]] [4 Underfull \hbox (badness 2932) in paragraph at lines 835--845 []@textrm When sub-architectures are used the ver-sion of @texttt Rscript[] @te xtrm in e.g. `@texttt /usr/bin[]@textrm '[] will Underfull \hbox (badness 6775) in paragraph at lines 835--845 @textrm be the last in-stalled, but architecture-specific ver-sions will be ava il-able in e.g. [9]] Underfull \hbox (badness 10000) in paragraph at lines 927--932 []@textrm One that may be use-ful when work-ing on R it-self is the op-tion Underfull \hbox (badness 10000) in paragraph at lines 927--932 @textrm `@texttt --disable-byte-compiled-packages[]@textrm '[], which en-sures that the base and rec-om- [10] Chapter 2 [5] [11] [6 Chapter 3 [12]] [7]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [13] [8] Underfull \hbox (badness 7685) in paragraph at lines 1293--1297 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [14entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi [9 (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]:]] pdf, fonts, Underfull \hbox (badness 10000) in paragraph at lines 1425--1431 @textrm ics li-braries built by Si-mon Ur-banek at [][]@texttt https://www.rfor ge.net/Cairo/files/ Underfull \hbox (badness 10000) in paragraph at lines 1447--1453 @textrm The first should be un-com-mented and the sec-ond set to the top-level di- Underfull \hbox (badness 10000) in paragraph at lines 1447--1453 @textrm rec-tory of a suit-ably pack-aged bi-nary build of ICU, for ex-am-ple t hat at Underfull \hbox (badness 10000) in paragraph at lines 1447--1453 [][]@texttt https://www.stats.ox.ac.uk/pub/Rtools/goodies/ICU_531.zip[][][]@tex trm . De-pend-ing on [15 [10]] Chapter 3 [11] page headings, Underfull \hbox (badness 2582) in paragraph at lines 1510--1514 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make check- Underfull \hbox (badness 10000) in paragraph at lines 1547--1549 [][][]@smallrm Suitable dis-tri-bu-tions in-clude Straw-berry Perl, [][]@smallt t http://strawberryperl.com/[][][] @smallrm and Ac-tivePerl, [16 tables, conditionals, indexing,] sectioning, toc, environments, [17 defuns, [12 macros,] cross references, insertions, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex] This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, Chapter 4 [18 Underfull \hbox (badness 2088) in paragraph at lines 1104--1112 []@textrm Octave is a nu-mer-i-cal lin-ear al-ge-bra sys-tem ([][]@texttt http: //www.octave.org[][][]@textrm ), and func-tion Chapter 4 [13]] formatting, and turning on texinfo input format.) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-FAQ.aux Underfull \hbox (badness 3058) in paragraph at lines 1196--1202 @textrm data-bases and even text files (pos-si-bly com-pressed). Open Data-base Con-nec-tiv-ity [14 Underfull \hbox (badness 10000) in paragraph at lines 1763--1767 []@textrm Installers for R-patched and R-devel are usu-ally avail-able from Underfull \hbox (badness 3872) in paragraph at lines 1763--1767 [][]@texttt https://r.research.att.com[][][]@textrm . (Some of these pack-ages are un-signed: to in-stall Underfull \hbox (badness 10000) in paragraph at lines 1791--1796 []@textrm Various parts of the build re-quire XQuartz to be in-stalled: see Underfull \hbox (badness 3009) in paragraph at lines 1791--1796 [][]@texttt https://xquartz.macosforge.org/[][][]@textrm . These in-clude the @ textbf tcltk @textrm pack-age and the @texttt X11[] Underfull \hbox (badness 2111) in paragraph at lines 1791--1796 @textrm de-vice: at-tempt-ing to use these with-out XQuartz will re-mind you. A lso for the Underfull \hbox (badness 10000) in paragraph at lines 1843--1847 @texttt library/mac/releasenotes/MacOSX/WhatsNewInOSX/Articles/MacOSX10_9.html[ ][][]@textrm ) which [19]] [15] Underfull \hbox (badness 10000) in paragraph at lines 1859--1861 @textrm (see [][]@texttt https://developer.apple.com/library/mac/releasenotes/ MacOSX/ Underfull \hbox (badness 3668) in paragraph at lines 1888--1900 []@textrm The in-stal-la-tion con-sists of up to four Ap-ple pack-ages:$[]$ @te xttt org.r-project.R.el- Underfull \hbox (badness 10000) in paragraph at lines 1888--1900 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [20] Chapter 5 [21] Chapter 6 [22]) Underfull \hbox (badness 10000) in paragraph at lines 1355--1359 []@textrm Package [][]@textbf RMongo[][] @textrm pro-vides an R in-ter-face to a Java client for `Mon-goDB' Underfull \hbox (badness 10000) in paragraph at lines 1355--1359 @textrm ([][]@texttt https://en.wikipedia.org/wiki/MongoDB[][][]@textrm ) data- bases, which are queried us-ing [16 (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)] [1{/usr/share/texmf/fonts/map/pd ftex/updmap/pdftex.map [23 Underfull \hbox (badness 3690) in paragraph at lines 1417--1421 []@textrm These are con-ve-nient in-ter-faces to read/write/test/delete ta-bles in the data-base. [17]] [24 [18]] Chapter 5 [19] [25] Underfull \hbox (badness 3098) in paragraph at lines 1755--1761 @textrm to @reducedrm NASA@textrm 's HDF5 (Hi-er-ar-chi-cal Data For-mat, see [ ][]@texttt https://www.hdfgroup.org/HDF5/[][][]@textrm ) Underfull \hbox (badness 10000) in paragraph at lines 1755--1761 @textrm and to UCAR's netCDF data files (net-work Com-mon Data Form, see Underfull \hbox (badness 2111) in paragraph at lines 1781--1794 @textrm been adopted for the 'Xbase' fam-ily of data-bases, cov-er-ing dBase, C lip-per, Fox-Pro Underfull \hbox (badness 3098) in paragraph at lines 1781--1794 @textrm (see for ex-am-ple [][]@texttt http://www.digitalpreservation.gov/forma ts/fdd/fdd000325.shtml[][][] Chapter 6 [20 [26]] [27] Chapter 7 [21] [28]} [22] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-FAQ.toc Underfull \hbox (badness 3907) in paragraph at lines 2626--2634 []@textrm Utilities such as @texttt install.packages[] @textrm can be pointed a t any @reducedrm CRAN@textrm -style repos-i-tory, Underfull \hbox (badness 2158) in paragraph at lines 2626--2634 @textrm such as [][]@texttt http://www.stats.ox.ac.uk/pub/RWin[][][]@textrm : t his must be an URL scheme that [29]] [23 [30] [-1] Chapter 7 [31]] Underfull \hbox (badness 2150) in paragraph at lines 2094--2098 []@textrm A sum-mary of all the con-nec-tions cur-rently opened by the user can be found by [24] [32. Chapter 8] [25 [-2]] [33 Underfull \hbox (badness 3815) in paragraph at lines 2239--2241 []@textrm The ear-lier low-level in-ter-face is given by func-tions @texttt mak e.socket[]@textrm , @texttt read.socket[]@textrm , Chapter 9 [26]] Chapter 8 [34)] [-3] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-FAQ.toc) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-FAQ.toc Chapter 9 [35 Underfull \hbox (badness 2012) in paragraph at lines 2278--2287 []@textrm If you do not have Ex-cel, many other pro-grams are able to read such spread- Underfull \hbox (badness 7326) in paragraph at lines 2278--2287 @textrm sheets and ex-port in a text for-mat on both Win-dows and Unix, for ex- am- Underfull \hbox (badness 10000) in paragraph at lines 2278--2287 @textrm ple Gnu-meric ([][]@texttt http://www.gnome.org/projects/gnumeric/[][][ ]@textrm ) and OpenOf-fice Appendix A [27]] Overfull \hbox (38.37012pt too wide) in paragraph at lines 2363--2366 @textrm B. D. Rip-ley (2001) Con-nec-tions. @textit R News@textrm , @textbf 1/1 @textrm , 16--7. [][]@texttt https://www.r-project.org/doc/Rnews/Rnews_ (Function and variable index) [36 [28])] Chapter 1 (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-data.vrs [37] Appendix A [38] Chapter 2 [1] [2] [39 [29 [3]]]) [4 (Concept index) [30]] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-data.cps Overfull \hbox (27.8098pt too wide) in paragraph at lines 3355--3355 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] Underfull \hbox (badness 6927) in paragraph at lines 3376--3382 [][][]@smallrm Such as @keyrm GNU @smalltt tar[] @smallrm 1.15 or later, @small tt bsdtar[] @smallrm (from [][]@smalltt https://github.com/libarchive/libarchiv e/[][][]@smallrm , Underfull \hbox (badness 2277) in paragraph at lines 3376--3382 @smallrm as used as @smalltt tar[] @smallrm by FreeBSD and macOS 10.6 and later ) or @smalltt tar[] @smallrm from the Heir-loom Toolch-est [40 [5]]) [31 Underfull \hbox (badness 10000) in paragraph at lines 3480--3482 [][][]@smallrm also known as @smalltt ttf-mscorefonts-installer[] @smallrm in t he De-bian/Ubuntu world: see also Underfull \hbox (badness 2409) in paragraph at lines 3477--3495 @textrm avail-able at [][]@texttt https://fedorahosted.org/liberation-fonts/[][ ][]@textrm ,$[]$ which cover the Latin, [41 Underfull \hbox (badness 3158) in paragraph at lines 528--541 []@textrm Debian pack-ages, main-tained by Dirk Ed-del-buet-tel, have long been part of Underfull \hbox (badness 3769) in paragraph at lines 562--564 []@textrm See [][]@texttt https://CRAN.R-project.org/bin/linux/suse/README.html [][][] @textrm for in-for-ma-tion [6]]] ) (see the transcript file for additional information) Underfull \hbox (badness 3078) in paragraph at lines 3551--3557 []@textrm The @texttt bitmap[] @textrm and @texttt dev2bitmap[] @textrm de-vice s and func-tion @texttt embedFonts()[] @textrm use ghost-script [42]] [10] [11] [13 [46]] [14] Output written on R-data.pdf (35 pages, 302991 bytes). Transcript written on R-data.log. [47] [15] Appendix B [16 [48]] [17] [49 Overfull \hbox (11.28497pt too wide) in paragraph at lines 1524--1527 []@textrm See also [][]@texttt https://en.wikipedia.org/wiki/R_programming_lang uage#Commercialized_ Chapter 4 [18]] [19 [50]] Chapter 5 [20] [51] [21 [52]] [22] Underfull \hbox (badness 5119) in paragraph at lines 4545--4549 []@textrm Other vari-ables of-ten set by @texttt configure[] @textrm in-clude ` @texttt MAIN_LDFLAGS[]@textrm '[], `@texttt SAFE_FFLAGS[]@textrm '[], [53] Underfull \hbox (badness 10000) in paragraph at lines 4598--4602 [][][]@smallrm The links there have proved dif-fi-cult to ac-cess, in which cas e ei-ther point an FTP Underfull \hbox (badness 10000) in paragraph at lines 4598--4602 @smallrm client at [][]@smalltt ftp://www.eecs.harvard.edu/pub/nr/[][][] @small rm or grab the copy made avail-able at Appendix C [54] [23] [55 [24]] Chapter 6 [25 [56]] [26 [57]] Chapter 7 [27] Underfull \hbox (badness 10000) in paragraph at lines 1--4896 []@textrm R has been built with Linux `@texttt ix86[]@textrm '[] and `@texttt x 86_64[]@textrm '[] C and C@texttt ++ @textrm com-pil-ers Underfull \hbox (badness 10000) in paragraph at lines 1--4896 @textrm ([][]@texttt http://clang.llvm.org[][][]@textrm ) based on the Clang fr ont-ends, in-voked by @texttt CC=clang [58] [28] Overfull \hbox (56.55324pt too wide) in paragraph at lines 5036--5036 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] [59 [29]] Overfull \hbox (50.80455pt too wide) in paragraph at lines 5042--5042 []@texttt CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.s dk/usr/include"[] Underfull \hbox (badness 10000) in paragraph at lines 5052--5056 []@textrm An X sub-system is re-quired un-less con-fig-ur-ing us-ing `@texttt - -without-x[]@textrm '[]: see Underfull \hbox (badness 2221) in paragraph at lines 5052--5056 [][]@texttt https://xquartz.macosforge.org/[][][]@textrm . R's @texttt configur e[] @textrm script can be told to look for Underfull \hbox (badness 10000) in paragraph at lines 5096--5105 []@textrm There are in-stallers$[]$ for For-tran com-pil-ers for El Cap-i-tan a nd Sierra at [60] [30] Underfull \hbox (badness 4595) in paragraph at lines 5121--5132 []@textrm Current @reducedrm CRAN @textrm bi-nary dis-tri-bu-tions use the buil d of @texttt clang[] @textrm 6.0.0 con-tained in Underfull \hbox (badness 10000) in paragraph at lines 5121--5132 [][]@texttt https://cran.r-project.org/bin/macosx/tools/clang-6.0.0.pkg[][][]@t extrm . Other re-cent Overfull \hbox (56.55324pt too wide) in paragraph at lines 5134--5134 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] Overfull \hbox (85.29668pt too wide) in paragraph at lines 5172--5172 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [61] [31] Underfull \hbox (badness 10000) in paragraph at lines 5215--5225 []@textrm The T[]X im-ple-men-ta-tion used by the de-vel-op-ers is Mac-TeX Underfull \hbox (badness 2600) in paragraph at lines 5215--5225 @textrm ([][]@texttt https://www.tug.org/mactex/[][][]@textrm ): the full in-st al-la-tion is about 5GB, but a smaller [62] [32] [63] [33] Underfull \hbox (badness 3428) in paragraph at lines 5453--5457 @textrm than other plat-forms. This makes it de-sir-able to build PCRE with the op-tion [64] [34] [65] [66 [35]]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [36 Underfull \hbox (badness 10000) in paragraph at lines 5680--5684 []@textrm Note that paths such as `@texttt /opt/csw/lib[]@textrm '[], `@texttt /usr/local/lib/amd64[]@textrm '[] and Underfull \hbox (badness 5050) in paragraph at lines 5680--5684 @textrm `@texttt /opt/csw/lib/amd64[]@textrm '[] may need to be in the []@textt t LD_LIBRARY_PATH[] @textrm dur-ing con-fig-u-ra- [67]] [37 Underfull \hbox (badness 2111) in paragraph at lines 5781--5786 []@textrm The re-cent WU test-ing was done us-ing com-pil-ers from both the @re ducedrm GNU @textrm Com-piler [68entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]:]] pdf, fonts, [38 [69]] Underfull \hbox (badness 4492) in paragraph at lines 5906--5912 @textrm PACK code to avoid com-pu-ta-tions en-tirely in extended-precision reg- is-ters, so file Appendix D [70 [39] page headings, tables,] conditionals, indexing, sectioning, toc, [71 environments, defuns,] macros, cross references, insertions, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, [40 formatting, and turning on texinfo input format.]) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-data.aux Underfull \hbox (badness 5302) in paragraph at lines 6112--6115 []@textrm You may need to set the en-vi-ron-ment vari-able @texttt CYGWIN[] @te xtrm to a value in-clud-ing [72] [41 (Function and variable index). [73]] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-admin.vrs)) (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex (Concept index)) [74] Underfull \hbox (badness 6559) in paragraph at lines 3389--3397 []@textrm When R trans-fers files over @reducedrm HTTP @textrm (e.g., us-ing th e @texttt install.packages()[] @textrm or Underfull \hbox (badness 10000) in paragraph at lines 3389--3397 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the Underfull \hbox (badness 3364) in paragraph at lines 3389--3397 @textrm `@texttt download.file.method[]@textrm '[] op-tion. There are sev-eral meth-ods avail-able and the [42 (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-admin.cps] Chapter 8 [43]) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi) [1){/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map (Environment variable index) [75] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-admin.ens Chapter 9 [44] [45)] [76 Underfull \hbox (badness 10000) in paragraph at lines 3628--3636 [][]@texttt https://en.wikipedia.org/wiki/Reproducibility[][][]@textrm ) the pr ob-lem, prefer-ably the Chapter 10 [46]] [47] ) (see the transcript file for additional information)pdfTeX warning (dest): name {77} has been referenced but does not exist, replaced by a fixed one >>< /usr/share/texmf-dist/fonts/type1/bluesky/cm/cmmi7.pfb>>}>])> [-2> (Acknowledgements)< /usr/share/texmf-dist/fonts/type1/bluesky/cm/cmti10.pfb>] Output written on R-FAQ.pdf (52 pages, 384666 bytes). Transcript written on R-FAQ.log. [2] [3] [4] Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11] [12] Underfull \hbox (badness 2088) in paragraph at lines 1104--1112 []@textrm Octave is a nu-mer-i-cal lin-ear al-ge-bra sys-tem ([][]@texttt http: //www.octave.org[][][]@textrm ), and func-tion Chapter 4 [13] Underfull \hbox (badness 3058) in paragraph at lines 1196--1202 @textrm data-bases and even text files (pos-si-bly com-pressed). Open Data-base Con-nec-tiv-ity [14] [15] Underfull \hbox (badness 10000) in paragraph at lines 1355--1359 []@textrm Package [][]@textbf RMongo[][] @textrm pro-vides an R in-ter-face to a Java client for `Mon-goDB' Underfull \hbox (badness 10000) in paragraph at lines 1355--1359 @textrm ([][]@texttt https://en.wikipedia.org/wiki/MongoDB[][][]@textrm ) data- bases, which are queried us-ing [16] Underfull \hbox (badness 3690) in paragraph at lines 1417--1421 []@textrm These are con-ve-nient in-ter-faces to read/write/test/delete ta-bles in the data-base. [17] [18] Chapter 5 [19] Underfull \hbox (badness 3098) in paragraph at lines 1755--1761 @textrm to @reducedrm NASA@textrm 's HDF5 (Hi-er-ar-chi-cal Data For-mat, see [ ][]@texttt https://www.hdfgroup.org/HDF5/[][][]@textrm ) Underfull \hbox (badness 10000) in paragraph at lines 1755--1761 @textrm and to UCAR's netCDF data files (net-work Com-mon Data Form, see Underfull \hbox (badness 2111) in paragraph at lines 1781--1794 @textrm been adopted for the 'Xbase' fam-ily of data-bases, cov-er-ing dBase, C lip-per, Fox-Pro Underfull \hbox (badness 3098) in paragraph at lines 1781--1794 @textrm (see for ex-am-ple [][]@texttt http://www.digitalpreservation.gov/forma ts/fdd/fdd000325.shtml[][][] Chapter 6 [20]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. Chapter 7 [21]entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, [22] [23 page headings,] tables, conditionals, indexing, sectioning, toc, environments, Underfull \hbox (badness 2150) in paragraph at lines 2094--2098 []@textrm A sum-mary of all the con-nec-tions cur-rently opened by the user can be found by [24 defuns, macros, cross references,] insertions,TEXINPUTS="../../.././doc/manual:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf ../../.././doc/manual/R-exts.texi (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, Chapter 8 [25 formatting, and turning on texinfo input format.) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-admin.aux] Underfull \hbox (badness 3815) in paragraph at lines 2239--2241 []@textrm The ear-lier low-level in-ter-face is given by func-tions @texttt mak e.socket[]@textrm , @texttt read.socket[]@textrm , Chapter 9 [26] Underfull \hbox (badness 2012) in paragraph at lines 2278--2287 []@textrm If you do not have Ex-cel, many other pro-grams are able to read such spread- Underfull \hbox (badness 7326) in paragraph at lines 2278--2287 @textrm sheets and ex-port in a text for-mat on both Win-dows and Unix, for ex- am- Underfull \hbox (badness 10000) in paragraph at lines 2278--2287 @textrm ple Gnu-meric ([][]@texttt http://www.gnome.org/projects/gnumeric/[][][ ]@textrm ) and OpenOf-fice Appendix A [27] Overfull \hbox (38.37012pt too wide) in paragraph at lines 2363--2366 @textrm B. D. Rip-ley (2001) Con-nec-tions. @textit R News@textrm , @textbf 1/1 @textrm , 16--7. [][]@texttt https://www.r-project.org/doc/Rnews/Rnews_ (Function and variable index) [28)] (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-data.vrs (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi) [1{/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map [29]) (Concept index) [30] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-data.cps) [31] ) (see the transcript file for additional information)}] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-admin.toc [-2] Output written on R-data.pdf (35 pages, 302989 bytes). Transcript written on R-data.log. ) [-3] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-admin.toc) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-admin.toc) Chapter 1 Underfull \hbox (badness 10000) in paragraph at lines 152--157 []@textrm The tar-balls are avail-able from [][]@texttt https://stat.ethz.ch/R/ daily[][][]@textrm . Down-load Underfull \hbox (badness 4303) in paragraph at lines 180--186 @textrm to check out `@texttt r-devel[]@textrm '[] into di-rec-tory @textsl pat h @textrm (which will be cre-ated if nec-es-sary). Underfull \hbox (badness 2181) in paragraph at lines 180--186 @textrm The al-pha, beta and RC ver-sions of an up-com-ing @textsl x.y.0 @textr m re-lease are avail-able from [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] Underfull \hbox (badness 2932) in paragraph at lines 835--845 []@textrm When sub-architectures are used the ver-sion of @texttt Rscript[] @te xtrm in e.g. `@texttt /usr/bin[]@textrm '[] will Underfull \hbox (badness 6775) in paragraph at lines 835--845 @textrm be the last in-stalled, but architecture-specific ver-sions will be ava il-able in e.g. [9] Underfull \hbox (badness 10000) in paragraph at lines 927--932 []@textrm One that may be use-ful when work-ing on R it-self is the op-tion Underfull \hbox (badness 10000) in paragraph at lines 927--932 @textrm `@texttt --disable-byte-compiled-packages[]@textrm '[], which en-sures that the base and rec-om- [10] [11] Chapter 3 [12] [13] Underfull \hbox (badness 7685) in paragraph at lines 1293--1297 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [14] Underfull \hbox (badness 10000) in paragraph at lines 1425--1431 @textrm ics li-braries built by Si-mon Ur-banek at [][]@texttt https://www.rfor ge.net/Cairo/files/ Underfull \hbox (badness 10000) in paragraph at lines 1447--1453 @textrm The first should be un-com-mented and the sec-ond set to the top-level di- Underfull \hbox (badness 10000) in paragraph at lines 1447--1453 @textrm rec-tory of a suit-ably pack-aged bi-nary build of ICU, for ex-am-ple t hat at Underfull \hbox (badness 10000) in paragraph at lines 1447--1453 [][]@texttt https://www.stats.ox.ac.uk/pub/Rtools/goodies/ICU_531.zip[][][]@tex trm . De-pend-ing on [15] Underfull \hbox (badness 2582) in paragraph at lines 1510--1514 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make check- Underfull \hbox (badness 10000) in paragraph at lines 1547--1549 [][][]@smallrm Suitable dis-tri-bu-tions in-clude Straw-berry Perl, [][]@smallt t http://strawberryperl.com/[][][] @smallrm and Ac-tivePerl, [16] [17] Chapter 4 [18] Underfull \hbox (badness 10000) in paragraph at lines 1763--1767 []@textrm Installers for R-patched and R-devel are usu-ally avail-able from Underfull \hbox (badness 3872) in paragraph at lines 1763--1767 [][]@texttt https://r.research.att.com[][][]@textrm . (Some of these pack-ages are un-signed: to in-stall Underfull \hbox (badness 10000) in paragraph at lines 1791--1796 []@textrm Various parts of the build re-quire XQuartz to be in-stalled: see Underfull \hbox (badness 3009) in paragraph at lines 1791--1796 [][]@texttt https://xquartz.macosforge.org/[][][]@textrm . These in-clude the @ textbf tcltk @textrm pack-age and the @texttt X11[] Underfull \hbox (badness 2111) in paragraph at lines 1791--1796 @textrm de-vice: at-tempt-ing to use these with-out XQuartz will re-mind you. A lso for the Underfull \hbox (badness 10000) in paragraph at lines 1843--1847 @texttt library/mac/releasenotes/MacOSX/WhatsNewInOSX/Articles/MacOSX10_9.html[ ][][]@textrm ) which [19] Underfull \hbox (badness 10000) in paragraph at lines 1859--1861 @textrm (see [][]@texttt https://developer.apple.com/library/mac/releasenotes/ MacOSX/ Underfull \hbox (badness 3668) in paragraph at lines 1888--1900 []@textrm The in-stal-la-tion con-sists of up to four Ap-ple pack-ages:$[]$ @te xttt org.r-project.R.el- Underfull \hbox (badness 10000) in paragraph at lines 1888--1900 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [20] Chapter 5 [21] Chapter 6 [22]make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual' [23] [24] [25]make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual' [26.]TEXINPUTS="../../.././doc/manual:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf ../../.././doc/manual/R-ints.texi [27] [28] Underfull \hbox (badness 3907) in paragraph at lines 2626--2634 []@textrm Utilities such as @texttt install.packages[] @textrm can be pointed a t any @reducedrm CRAN@textrm -style repos-i-tory, Underfull \hbox (badness 2158) in paragraph at lines 2626--2634 @textrm such as [][]@texttt http://www.stats.ox.ac.uk/pub/RWin[][][]@textrm : t his must be an URL scheme that [29] [30] Chapter 7 [31] [32] [33] Chapter 8 [34] Chapter 9 [35] [36] [37] Appendix A [38] [39] Overfull \hbox (27.8098pt too wide) in paragraph at lines 3355--3355 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] Underfull \hbox (badness 6927) in paragraph at lines 3376--3382 [][][]@smallrm Such as @keyrm GNU @smalltt tar[] @smallrm 1.15 or later, @small tt bsdtar[] @smallrm (from [][]@smalltt https://github.com/libarchive/libarchiv e/[][][]@smallrm , Underfull \hbox (badness 2277) in paragraph at lines 3376--3382 @smallrm as used as @smalltt tar[] @smallrm by FreeBSD and macOS 10.6 and later ) or @smalltt tar[] @smallrm from the Heir-loom Toolch-est [40] Underfull \hbox (badness 10000) in paragraph at lines 3480--3482 [][][]@smallrm also known as @smalltt ttf-mscorefonts-installer[] @smallrm in t he De-bian/Ubuntu world: see also Underfull \hbox (badness 2409) in paragraph at lines 3477--3495 @textrm avail-able at [][]@texttt https://fedorahosted.org/liberation-fonts/[][ ][]@textrm ,$[]$ which cover the Latin, [41] Underfull \hbox (badness 3078) in paragraph at lines 3551--3557 []@textrm The @texttt bitmap[] @textrm and @texttt dev2bitmap[] @textrm de-vice s and func-tion @texttt embedFonts()[] @textrm use ghost-script [42] [43] [44] Underfull \hbox (badness 5077) in paragraph at lines 3793--3798 []@textrm Debian/Ubuntu sys-tems pro-vide a system-specific way to switch the B LAS in [45] [46] [47] Appendix B [48] [49] [50] [51]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [52] Underfull \hbox (badness 5119) in paragraph at lines 4545--4549 []@textrm Other vari-ables of-ten set by @texttt configure[] @textrm in-clude ` @texttt MAIN_LDFLAGS[]@textrm '[], `@texttt SAFE_FFLAGS[]@textrm '[], [53]entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: Underfull \hbox (badness 10000) in paragraph at lines 4598--4602 [][][]@smallrm The links there have proved dif-fi-cult to ac-cess, in which cas e ei-ther point an FTP Underfull \hbox (badness 10000) in paragraph at lines 4598--4602 @smallrm client at [][]@smalltt ftp://www.eecs.harvard.edu/pub/nr/[][][] @small rm or grab the copy made avail-able at Appendix C [54 pdf,] fonts, [55] [56 page headings, tables,] conditionals, indexing, sectioning, toc, environments, [57 defuns, macros, cross references,] insertions, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Underfull \hbox (badness 10000) in paragraph at lines 1--4896 []@textrm R has been built with Linux `@texttt ix86[]@textrm '[] and `@texttt x 86_64[]@textrm '[] C and C@texttt ++ @textrm com-pil-ers Underfull \hbox (badness 10000) in paragraph at lines 1--4896 @textrm ([][]@texttt http://clang.llvm.org[][][]@textrm ) based on the Clang fr ont-ends, in-voked by @texttt CC=clang [58 (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)] Overfull \hbox (56.55324pt too wide) in paragraph at lines 5036--5036 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] [59) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi) [1]{/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map Overfull \hbox (50.80455pt too wide) in paragraph at lines 5042--5042 []@texttt CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.s dk/usr/include"[] Underfull \hbox (badness 10000) in paragraph at lines 5052--5056 []@textrm An X sub-system is re-quired un-less con-fig-ur-ing us-ing `@texttt - -without-x[]@textrm '[]: see Underfull \hbox (badness 2221) in paragraph at lines 5052--5056 [][]@texttt https://xquartz.macosforge.org/[][][]@textrm . R's @texttt configur e[] @textrm script can be told to look for Underfull \hbox (badness 10000) in paragraph at lines 5096--5105 []@textrm There are in-stallers$[]$ for For-tran com-pil-ers for El Cap-i-tan a nd Sierra at [60] Underfull \hbox (badness 4595) in paragraph at lines 5121--5132 []@textrm Current @reducedrm CRAN @textrm bi-nary dis-tri-bu-tions use the buil d of @texttt clang[] @textrm 6.0.0 con-tained in Underfull \hbox (badness 10000) in paragraph at lines 5121--5132 [][]@texttt https://cran.r-project.org/bin/macosx/tools/clang-6.0.0.pkg[][][]@t extrm . Other re-cent Overfull \hbox (56.55324pt too wide) in paragraph at lines 5134--5134 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] Overfull \hbox (85.29668pt too wide) in paragraph at lines 5172--5172 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [61] Underfull \hbox (badness 10000) in paragraph at lines 5215--5225 []@textrm The T[]X im-ple-men-ta-tion used by the de-vel-op-ers is Mac-TeX Underfull \hbox (badness 2600) in paragraph at lines 5215--5225 @textrm ([][]@texttt https://www.tug.org/mactex/[][][]@textrm ): the full in-st al-la-tion is about 5GB, but a smaller [62] [63] Underfull \hbox (badness 3428) in paragraph at lines 5453--5457 @textrm than other plat-forms. This makes it de-sir-able to build PCRE with the op-tion [64] [65]. [66]}] [2] Underfull \hbox (badness 10000) in paragraph at lines 5680--5684 []@textrm Note that paths such as `@texttt /opt/csw/lib[]@textrm '[], `@texttt /usr/local/lib/amd64[]@textrm '[] and Underfull \hbox (badness 5050) in paragraph at lines 5680--5684 @textrm `@texttt /opt/csw/lib/amd64[]@textrm '[] may need to be in the []@textt t LD_LIBRARY_PATH[] @textrm dur-ing con-fig-u-ra- [67 [-1] (Acknowledgements) Chapter 1] [1] Cross reference values unknown; you must run TeX again. Underfull \hbox (badness 2111) in paragraph at lines 5781--5786 []@textrm The re-cent WU test-ing was done us-ing com-pil-ers from both the @re ducedrm GNU @textrm Com-piler [68 [2]] [69 Underfull \hbox (badness 4660) in paragraph at lines 280--283 []@textrm For the con-ven-tions for files `@texttt NEWS[]@textrm '[] and `@text tt ChangeLog[]@textrm '[] in the @reducedrm GNU @textrm project see [3] Underfull \hbox (badness 4492) in paragraph at lines 5906--5912 @textrm PACK code to avoid com-pu-ta-tions en-tirely in extended-precision reg- is-ters, so file Appendix D [70]] Underfull \hbox (badness 10000) in paragraph at lines 370--380 [][]@texttt https://www.debian.org/doc/debian-policy/index.html#document-ch-con trolfields[][][]@textrm : [4] [71] [5] Underfull \hbox (badness 5302) in paragraph at lines 6112--6115 []@textrm You may need to set the en-vi-ron-ment vari-able @texttt CYGWIN[] @te xtrm to a value in-clud-ing [72 Underfull \hbox (badness 10000) in paragraph at lines 493--496 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6]] (Function and variable index) [73] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-admin.vrs) (Concept index) [74] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-admin.cps Underfull \hbox (badness 10000) in paragraph at lines 626--639 @textrm Lit-er-a-ture Clas-si-fi-ca-tion Sys-tem, [][]@texttt https://www.aeawe b.org/econlit/jelCodes.php[][][]@textrm , Underfull \hbox (badness 10000) in paragraph at lines 626--639 @textrm or `@texttt Classification/MSC[]@textrm '[] or `@texttt Classification/ MSC-2010[]@textrm '[] (the Math-e-mat-ics Sub-ject [7]) (Environment variable index) [75] [8 (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-admin.ens] [9)] [76] [10 ) (see the transcript file for additional information) Underfull \hbox (badness 2376) in paragraph at lines 1009--1016 @textrm this is OK if that con-di-tion-ing is done in ex-am-ples/tests/vignette s, al-though us-ing [11 [12 [13] [16] Output written on R-admin.pdf (81 pages, 552375 bytes). Transcript written on R-admin.log. Underfull \hbox (badness 10000) in paragraph at lines 1439--1446 @textrm `@texttt RnavGraph/inst/tcl[]@textrm '[], `@texttt RProtoBuf/inst/pytho n[]@textrm '[] and `@texttt emdbook/inst/BUGS[]@textrm '[] and Underfull \hbox (badness 5288) in paragraph at lines 1476--1480 @textrm then down-load the sources from [][]@texttt https://sourceforge.net/pro jects/tcllib/files/ [17] [18] [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 1871--1876 []@textrm [@texttt libRlapack[] @textrm in-cludes all the double-precision LA- PACK rou-tines which Underfull \hbox (badness 2875) in paragraph at lines 1871--1876 @textrm were cur-rent in 2003: a list of which rou-tines are in-cluded is in f ile [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 2063--2065 [][][][][]@smalltt http://www.openmp.org/[][][]@smallrm , [][]@smalltt https:// en.wikipedia.org/wiki/OpenMP[][][]@smallrm , [][]@smalltt https://computing.lln l.gov/ [23] [24] [25] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2271--2271 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2273--2273 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [26]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [27] [28]entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: Underfull \hbox (badness 10000) in paragraph at lines 2527--2529 [][][]@smallrm The changes are linked from [][]@smalltt https://isocpp.org/std/ standing-documents/ [29 pdf, fonts,] [30] page headings, Overfull \hbox (39.30717pt too wide) in paragraph at lines 2654--2654 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] Underfull \hbox (badness 10000) in paragraph at lines 2702--2708 [][][]@smallrm See [][]@smalltt https://isocpp.org/std/standing-documents/sd-6- sg10-feature-test-recommendations[][][] @smallrm or [31 tables, conditionals,] indexing, sectioning, toc, environments, defuns, [32 macros, cross references, insertions,] (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, [33 formatting, and turning on texinfo input format.) (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)] [34) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi) [1{/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map] [35] [36] Underfull \hbox (badness 2809) in paragraph at lines 3204--3210 @textrm (or set the en-vi-ron-ment vari-able @texttt _R_BUILD_KEEP_EMPTY_DIRS_[ ] @textrm to `@texttt TRUE[]@textrm '[], or have a [37] [38] Underfull \hbox (badness 4556) in paragraph at lines 3441--3449 @textrm Others you may see are @texttt \VignettePackage[] @textrm (cur-rently i g-nored), @texttt \VignetteDepends[] Underfull \hbox (badness 2617) in paragraph at lines 3441--3449 @textrm pack-age in-stal-la-tion time to cre-ate the saved data frame `@texttt Meta/vignette.rds[]@textrm '[], but Underfull \hbox (badness 3579) in paragraph at lines 3441--3449 @textrm The @texttt \VignetteEngine[] @textrm state-ment is de-scribed in [][]$ @textsy h$@textrm un-de-fined$@textsy i$ @textrm [Non-Sweave vi-gnettes], [39] [40}] [2]] [-1] Chapter 1 [41 [1]]TEXINPUTS="../../.././doc/manual:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf ../../.././doc/manual/R-lang.texi [42 [2]] [3 [43]] [4 [44]] [45 [5]] [6] [46] [7 [47]] [8] Underfull \hbox (badness 10000) in paragraph at lines 4264--4284 @textrm at [][]@texttt http://pubs.opengroup.org/onlinepubs/9699919799/utiliti es/make.html[][][]@textrm ; [48 [9]] [49 [10]] [50 [11]] [51. [12]] [13 Overfull \hbox (32.24495pt too wide) in paragraph at lines 4635--4635 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4637--4637 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4638--4638 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] [52]] Underfull \hbox (badness 3826) in paragraph at lines 4641--4648 @textrm Java 9 changed the for-mat of this string (which used to be some-thing like Overfull \hbox (55.2397pt too wide) in paragraph at lines 4653--4653 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [53 [14]] [54 [15]] [55 Overfull \hbox (27.8098pt too wide) in paragraph at lines 1455--1455 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 1456--1456 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 1457--1457 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (137.03487pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [16]] [56] [17 [57]] [18 Underfull \hbox (badness 3826) in paragraph at lines 5081--5084 []@textrm Some (but not all) ex-ten-sions are listed at [][]@texttt https://gc c.gnu.org/onlinedocs/ Underfull \hbox (badness 10000) in paragraph at lines 5081--5084 @texttt gcc/C-Extensions.html[][][] @textrm and [][]@texttt https://gcc.gnu.or g/onlinedocs/gcc/C_002b_ [58]] [59] [19 Overfull \hbox (32.24495pt too wide) in paragraph at lines 5284--5284 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [60]] [20 [61]] [21 [62]] Chapter 2 [22] [23 [63]] [24] [64 [25]] Chapter 2 [65 Underfull \hbox (badness 3108) in paragraph at lines 2324--2329 []@textrm Some prim-i-tives are re-garded as lan-guage el-e-ments (the cur-rent ones are listed [26]] Chapter 3 [27] [66] [28] [67 Chapter 4 [29]] [68 [30]] Chapter 5 [69 [31]] Chapter 6 [32] [70] Underfull \hbox (badness 10000) in paragraph at lines 2719--2722 @texttt ~paul/R/basegraph.html[][][] @textrm and [][]@texttt https://www.stat.a uckland.ac.nz/~paul/R/ [33] [71] [34] [72] [35] [36 Underfull \hbox (badness 2707) in paragraph at lines 6409--6415 []@textrm Packages may have an over-view help page with an @texttt \alias[] @te xtttsl pkg-name@texttt -package[]@textrm , e.g. Underfull \hbox (badness 3635) in paragraph at lines 6416--6422 []@textrm Skeletons of doc-u-men-ta-tion for a pack-age can be gen-er-ated us-i ng the func-tion [73]] [37] Underfull \hbox (badness 4467) in paragraph at lines 3216--3220 []@textrm The in-ter-pre-ta-tion of the line tex-ture (@texttt par("lty"[]@text rm ) is de-scribed in the header [38 [74]] [39] [75 [40]] [76 [41]] Underfull \hbox (badness 6428) in paragraph at lines 3519--3523 []@textrm The base sys-tem state is con-tained in @texttt baseSystemState[] @te xtrm struc-ture de-fined in [42 Underfull \hbox (badness 10000) in paragraph at lines 6806--6813 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and Underfull \hbox (badness 3919) in paragraph at lines 6806--6813 @texttt \figure{@textttsl filename@texttt }{@textttsl alternate text@texttt }[] @textrm . This will in-clude a copy of the fig-ure in [77]] Chapter 7 [43] [78 Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 []@texttt R.app[] @textrm re-lies on `@texttt libR.dylib[]@textrm '[] be-ing in a spe-cific place, and hence on Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm R hav-ing been built and in-stalled as a Mac macOS `frame-work'. Specif - Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm i-cally, it uses `@texttt /Library/Frameworks/R.framework/R[]@textrm '[ ]. This is a sym-bolic Underfull \hbox (badness 3679) in paragraph at lines 3631--3640 @textrm link, as frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu -ally re-solves to Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm `@texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib /libR.dylib[]@textrm '[], [44]] Chapter 8 [45] Underfull \hbox (badness 10000) in paragraph at lines 6983--6989 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text @textrm part of [79] [46] [80] Underfull \hbox (badness 2326) in paragraph at lines 3852--3857 []@textrm Allows turn-ing off @texttt checkFF()[] @textrm test-ing. If set to `@texttt registration[]@textrm '[], checks Underfull \hbox (badness 10000) in paragraph at lines 3852--3857 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [47] Underfull \hbox (badness 10000) in paragraph at lines 7125--7129 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file Underfull \hbox (badness 4686) in paragraph at lines 7125--7129 @textrm `@texttt share/Rd/macros/system.Rd[]@textrm '[] of the R source or home di-rec-tory, and these will [81] [48] [82 [49]] Overfull \hbox (3.59178pt too wide) in paragraph at lines 7295--7298 []@textrm Another is the Eclipse IDE with the Stat-ET plu-gin ([][]@texttt http ://www.walware.de/goto/statet[][][]@textrm ), Underfull \hbox (badness 3029) in paragraph at lines 7302--7304 []@textrm Some R front-ends pro-vide edit-ing sup-port for `@texttt .Rd[]@textr m '[] files, for ex-am-ple RStu-dio Chapter 3 [83] [50 [84]] [85] [51] [86 [52]] Chapter 9 Underfull \hbox (badness 2443) in paragraph at lines 7653--7656 []@textrm Data frames are slower than ma-tri-ces and this is an ex-am-ple of wh y. Us-ing Underfull \hbox (badness 10000) in paragraph at lines 7676--7681 []@textrm Options in-clude us-ing @texttt sprof[] @textrm for a shared ob-ject, and @texttt oprofile[] @textrm (see Underfull \hbox (badness 4927) in paragraph at lines 7676--7681 [][]@texttt http://oprofile.sourceforge.net/[][][]@textrm ) and @texttt perf[] @textrm (see [][]@texttt https://perf.wiki.kernel.org/ [87 [53]] [88] [54 [89]] Chapter 10 [55] [90 Chapter 11 [56]] Overfull \hbox (213.15503pt too wide) in paragraph at lines 7896--7901 [][]@texttt https://developer.apple.com/library/content/documentation/Developer Tools/Conceptual/InstrumentsUserGuide/index.html[][][]@textrm ). Chapter 4 [91] Chapter 12 [57] [92] [58 [93]] (Function and variable index) [59] [94 (Concept index) [60]] [61] ) (see the transcript file for additional information)]]]] Underfull \hbox (badness 4913) in paragraph at lines 8584--8587 [][][]@smallrm installed on some Linux sys-tems as @smalltt asan_symbolize[]@sm allrm , and ob-tain-able from [][]@smalltt https://llvm.org/ Underfull \hbox (badness 10000) in paragraph at lines 8584--8587 @smalltt svn/llvm-project/compiler-rt/trunk/lib/asan/scripts/asan_symbolize.py[ ][][]@smallrm : it makes use of Underfull \hbox (badness 10000) in paragraph at lines 8624--8629 []@textrm For op-tions avail-able @textit via @textrm the en-vi-ron-ment vari-a ble @texttt ASAN_OPTIONS[] @textrm see Underfull \hbox (badness 10000) in paragraph at lines 8624--8629 [][]@texttt https://code.google.com/p/address-sanitizer/wiki/AddressSanitizerFL ags[][][]@textrm . Underfull \hbox (badness 10000) in paragraph at lines 8640--8644 []@textrm Recent ver-sions$[]$ added the flag `@texttt -fsanitize-address-use-a fter-scope[]@textrm '[]: see [100] Output written on R-ints.pdf (64 pages, 355426 bytes). Transcript written on R-ints.log. Overfull \hbox (56.55324pt too wide) in paragraph at lines 8688--8688 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8716--8718 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by Underfull \hbox (badness 6542) in paragraph at lines 8754--8759 []@textrm See [][]@texttt https://gcc.gnu.org/onlinedocs/gcc/Instrumentation-Op tions.html[][][] @textrm (or the [101] Underfull \hbox (badness 10000) in paragraph at lines 8777--8781 []@textrm From GCC 8 @texttt signed-integer-overflow[] @textrm is no longer a d e-fault part of Underfull \hbox (badness 10000) in paragraph at lines 8777--8781 @textrm `@texttt -fsanitize=undefined[]@textrm '[], but can be spec-i-fied sep- a-rately. It adds op-tions Underfull \hbox (badness 5878) in paragraph at lines 8804--8808 []@textrm For more de-tails on the topic see [][]@texttt http://blog.regehr.org /archives/213[][][] @textrm and Underfull \hbox (badness 10000) in paragraph at lines 8818--8825 []@textrm Recent ver-sions of @texttt clang[] @textrm on `@texttt x86_64[]@text rm '[] Linux have `Thread-San-i-tizer' Underfull \hbox (badness 4441) in paragraph at lines 8818--8825 @textrm ([][]@texttt https://code.google.com/p/thread-sanitizer/[][][]@textrm ) , a `data race de-tec-tor for C/C@texttt ++ Overfull \hbox (50.80455pt too wide) in paragraph at lines 8847--8847 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [102] [103.] [104] [105] Chapter 5 [106] [107] [108] [109] [110] [111]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [112] Underfull \hbox (badness 4505) in paragraph at lines 9749--9754 @textrm Without or with reg-is-tra-tion, these will both work. If @texttt R_ini t_mypkg[] @textrm calls @texttt R_ [113]entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, [114] [115] page headings, tables, Overfull \hbox (30.03963pt too wide) in paragraph at lines 9995--9995 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [116 conditionals, indexing,] sectioning, toc, environments, defuns, macros, cross references, insertions, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex [117 This is `epsf.tex' v2.7.4 <14 February 2011> ) localization,] formatting, and turning on texinfo input format.) (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex) [118) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi)] [1{/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map [119] [120] Overfull \hbox (61.1125pt too wide) in paragraph at lines 10435--10437 [][][]@smallrm For ex-am-ple, `@smalltt _GLIBCXX_USE_CXX11_ABI[]@smallrm '[] in @smalltt g++[] @smallrm 5.1 and later: [][]@smalltt https://gcc.gnu.org/online docs/libstdc++/manual/using_ [121] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10574--10574 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [122This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. ] [123entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]:] pdf, fonts, [124]}] [2] [-1] Chapter 1 [125 page headings, tables, Chapter 2] [1 conditionals, indexing,] sectioning, toc, environments, defuns, macros, cross references, [126 [2 insertions, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex]] This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, Cross reference values unknown; you must run TeX again. formatting, [127 and turning on texinfo input format.) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.aux] [128] Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [129] [130) (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi] (/usr/share/texmf-dist/tex/texinfo/txi-en.tex) [4 Underfull \hbox (badness 2781) in paragraph at lines 11325--11327 [][][]@smallrm You can as-sign a @smallit copy @smallrm of the ob-ject in the e n-vi-ron-ment frame @smalltt rho[] @smallrm us-ing @smalltt defineVar(symbol, [131]) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi)] [1{/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map Underfull \hbox (badness 10000) in paragraph at lines 11407--11409 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [132 [5]] [133] [134] [6] [135] [136 [7]] [137] Chapter 3 [8] [138] [139] [9 [140]] [141] [10] [142] [11 [143]]}] [12 [2] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.toc] Underfull \hbox (badness 10000) in paragraph at lines 12415--12420 []@textrm A toy ex-am-ple of the use of weak ref-er-ences can be found at Underfull \hbox (badness 10000) in paragraph at lines 12415--12420 [][]@texttt https://homepage.stat.uiowa.edu/~luke/R/references/weakfinex.html[] [][]@textrm , but Overfull \hbox (22.06111pt too wide) in paragraph at lines 12440--12440 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [144] [13 [145] [-1] Chapter 6 [14 [146]]] [147) [15 [-2]]] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.toc) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.toc [148 [16]]) Chapter 1 [17] [1 [149 [18]]] [19] [2 [150]] [20 [3 [151]]] Chapter 4 [21] [4] [152] [5 [22]] [6] [23 [153]] [7] [24 [8] [154] Chapter 5 [25]] [9] [26] [10 [27]] [155 [11 [28]]] [156 [12] [29]] [157 [13]] [14 [158 [30]]] Chapter 6 [31] Warning: unbalanced parentheses in @def... [15 [32]] [159] [33 Overfull \hbox (27.8098pt too wide) in paragraph at lines 1455--1455 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 1456--1456 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 1457--1457 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (137.03487pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [16]] [34 [160] [17]] [35] [161] [18 [36]] [162 [37]] [19 Underfull \hbox (badness 2689) in paragraph at lines 14107--14113 []@textrm The vis-i-bil-ity mech-a-nism is not avail-able on Win-dows, but ther e is an equally [163] [38]] Chapter 7 [39] [20 [164]] Underfull \hbox (badness 10000) in paragraph at lines 14235--14241 []@textrm The graph-ics sys-tems are ex-posed in head-ers `@texttt R_ext/Graphi csEngine.h[]@textrm '[], Underfull \hbox (badness 3240) in paragraph at lines 14235--14241 @textrm `@texttt R_ext/GraphicsDevice.h[]@textrm '[] (which it in-cludes) and ` @texttt R_ext/QuartzDevice.h[]@textrm '[]. Fa-cil-i- Chapter 7 [165] [21 [166] Chapter 2 Chapter 8] [22 [40] Chapter 8] [167 [41]] [23] Chapter 9 [42 [168]] [169] [43] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14647--14647 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [170 Chapter 10 [44]] [24] Overfull \hbox (33.55849pt too wide) in paragraph at lines 14706--14706 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [171] [45 [25]] [172] Underfull \hbox (badness 10000) in paragraph at lines 4342--4344 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46] Underfull \hbox (badness 3108) in paragraph at lines 2324--2329 []@textrm Some prim-i-tives are re-garded as lan-guage el-e-ments (the cur-rent ones are listed [26 [173] [47.] Underfull \hbox (badness 10000) in paragraph at lines 14949--14956 @texttt internet/nanoftp.c[]@textrm '[], `@texttt src/modules/internet/nanohtt p.c[]@textrm '[] and `@texttt src/modules/ [174] [48] Underfull \hbox (badness 10000) in paragraph at lines 15073--15078 []@textrm Another (D)COM server, @texttt RDCOMServer[]@textrm , may be avail-a ble from Omega-hat, [175] Chapter 3 [27] [49]] [176] [28 Underfull \hbox (badness 6284) in paragraph at lines 15209--15216 @textrm may be avail-able from the Win-dows Reg-istry: it will be in @texttt H KEY_LOCAL_ Underfull \hbox (badness 10000) in paragraph at lines 15209--15216 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and Underfull \hbox (badness 3769) in paragraph at lines 15209--15216 @texttt HKEY_CURRENT_USER\Software\R-core\R\InstallPath[] @textrm oth-er-wise, if se-lected dur-ing [177 [50]]] [178 (Function and Variable Index) [51]] (Function and variable index) (Concept Index) [52 [179]] Appendix A [53] (Concept index) [180 [54]] [181] ) (see the transcript file for additional information)]>> Chapter 5 [31>> Chapter 6>>>]>> [35 [36 Underfull \hbox (badness 4467) in paragraph at lines 3216--3220 []@textrm The in-ter-pre-ta-tion of the line tex-ture (@texttt par("lty"[]@text rm ) is de-scribed in the header [38] Output written on R-exts.pdf (184 pages, 924436 bytes). Transcript written on R-exts.log. [39] [40] [41] Underfull \hbox (badness 6428) in paragraph at lines 3519--3523 []@textrm The base sys-tem state is con-tained in @texttt baseSystemState[] @te xtrm struc-ture de-fined in [42] Chapter 7 [43] Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 []@texttt R.app[] @textrm re-lies on `@texttt libR.dylib[]@textrm '[] be-ing in a spe-cific place, and hence on Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm R hav-ing been built and in-stalled as a Mac macOS `frame-work'. Specif - Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm i-cally, it uses `@texttt /Library/Frameworks/R.framework/R[]@textrm '[ ]. This is a sym-bolic Underfull \hbox (badness 3679) in paragraph at lines 3631--3640 @textrm link, as frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu -ally re-solves to Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm `@texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib /libR.dylib[]@textrm '[], [44] Chapter 8 [45] [46] Underfull \hbox (badness 2326) in paragraph at lines 3852--3857 []@textrm Allows turn-ing off @texttt checkFF()[] @textrm test-ing. If set to `@texttt registration[]@textrm '[], checks Underfull \hbox (badness 10000) in paragraph at lines 3852--3857 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [47] [48] [49] [50] [51] [52] Chapter 9 [53] [54] Chapter 10 [55] Chapter 11 [56]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. Chapter 12 [57] [58entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]:] pdf, (Function and variable index) [59 fonts,] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.vrs page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, [60 formatting, and turning on texinfo input format.) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.aux]) (Concept index) [61] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.cps) [62This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. ) (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)] ) (see the transcript file for additional information) tables, sectioning, defuns, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex )> localization, Output written on R-ints.pdf (66 pages, 442582 bytes). Transcript written on R-ints.log. }] [2] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.toc [-1) (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi] (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi) [1{/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map [-2].) [-3] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.toc) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.toc) Chapter 1 Chapter 2 [1] [2]}] Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3 [2] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-exts.toc] [-1 [4]] [5] [-2] [6] [7] [-3 Chapter 3 [8]] [9) [-4]] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-exts.toc [10) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-exts.toc]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [11] [12) (Acknowledgements)] Chapter 1 [1]entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, [2 [13]] [14] Underfull \hbox (badness 4660) in paragraph at lines 280--283 []@textrm For the con-ven-tions for files `@texttt NEWS[]@textrm '[] and `@text tt ChangeLog[]@textrm '[] in the @reducedrm GNU @textrm project see [3 page headings, tables, conditionals, indexing,] sectioning, toc, environments, [15 defuns, Underfull \hbox (badness 10000) in paragraph at lines 370--380 [][]@texttt https://www.debian.org/doc/debian-policy/index.html#document-ch-con trolfields[][][]@textrm : [4 macros, cross references,] insertions,] (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, [5 [16 formatting, and turning on texinfo input format.) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.aux]] [17 Underfull \hbox (badness 10000) in paragraph at lines 493--496 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6]] [18] [19) Underfull \hbox (badness 10000) in paragraph at lines 626--639 @textrm Lit-er-a-ture Clas-si-fi-ca-tion Sys-tem, [][]@texttt https://www.aeawe b.org/econlit/jelCodes.php[][][]@textrm , Underfull \hbox (badness 10000) in paragraph at lines 626--639 @textrm or `@texttt Classification/MSC[]@textrm '[] or `@texttt Classification/ MSC-2010[]@textrm '[] (the Math-e-mat-ics Sub-ject [7] (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)]) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi [20) [1 [8{/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map]] Chapter 4 [21] [9] [22 [10]] [23 Underfull \hbox (badness 2376) in paragraph at lines 1009--1016 @textrm this is OK if that con-di-tion-ing is done in ex-am-ples/tests/vignette s, al-though us-ing [11]] [24 [12] Chapter 5] [25] [26 [13}]] [2] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.toc] [27] [14] [-1 [28 [15]]] [29] Underfull \hbox (badness 10000) in paragraph at lines 1439--1446 @textrm `@texttt RnavGraph/inst/tcl[]@textrm '[], `@texttt RProtoBuf/inst/pytho n[]@textrm '[] and `@texttt emdbook/inst/BUGS[]@textrm '[] and [16) [-2 [30]] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.toc]) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.toc Chapter 6 [31] Underfull \hbox (badness 5288) in paragraph at lines 1476--1480 @textrm then down-load the sources from [][]@texttt https://sourceforge.net/pro jects/tcllib/files/ [17) Chapter 1 [32]] [18] [33 [1]] [19 [34]] [2] [35 [20]] [3 [36] Underfull \hbox (badness 10000) in paragraph at lines 1871--1876 []@textrm [@texttt libRlapack[] @textrm in-cludes all the double-precision LA- PACK rou-tines which Underfull \hbox (badness 2875) in paragraph at lines 1871--1876 @textrm were cur-rent in 2003: a list of which rou-tines are in-cluded is in f ile [21]] [37 [4] [22]] [38 Underfull \hbox (badness 10000) in paragraph at lines 2063--2065 [][][][][]@smalltt http://www.openmp.org/[][][]@smallrm , [][]@smalltt https:// en.wikipedia.org/wiki/OpenMP[][][]@smallrm , [][]@smalltt https://computing.lln l.gov/ [23] [5 Chapter 7 [39]]] [24] [6] [25] Chapter 8 [40 [7] [41] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2271--2271 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2273--2273 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [26]] [27] [8 Chapter 9] [42 [28]] [9] [43 Underfull \hbox (badness 10000) in paragraph at lines 2527--2529 [][][]@smallrm The changes are linked from [][]@smalltt https://isocpp.org/std/ standing-documents/ [29]] Chapter 10 [44 [10] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2654--2654 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [30]] [11 Underfull \hbox (badness 10000) in paragraph at lines 2702--2708 [][][]@smallrm See [][]@smalltt https://isocpp.org/std/standing-documents/sd-6- sg10-feature-test-recommendations[][][] @smallrm or [31 [45]]] [12 [32 Underfull \hbox (badness 10000) in paragraph at lines 4342--4344 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46]]] [13 [33 [47]]] [14 [48 [34]]] [49] [15 [35]] [50] Overfull \hbox (27.8098pt too wide) in paragraph at lines 1455--1455 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 1456--1456 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 1457--1457 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (137.03487pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [16 (Function and Variable Index) [51 Underfull \hbox (badness 2809) in paragraph at lines 3204--3210 @textrm (or set the en-vi-ron-ment vari-able @texttt _R_BUILD_KEEP_EMPTY_DIRS_[ ] @textrm to `@texttt TRUE[]@textrm '[], or have a [36]] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.vrs]. [17 [37]] [18 [38 [52]]] Underfull \hbox (badness 4556) in paragraph at lines 3441--3449 @textrm Others you may see are @texttt \VignettePackage[] @textrm (cur-rently i g-nored), @texttt \VignetteDepends[] [39) (Concept Index)] [19 [53]] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.cps [40] [20] [41 [21]] Chapter 2 [22]) Appendix A [54 [42 [23]] [24]] [43 [55] [25]] ) (see the transcript file for additional information) [45] [28 [46] [47]] Underfull \hbox (badness 10000) in paragraph at lines 4264--4284 @textrm at [][]@texttt http://pubs.opengroup.org/onlinepubs/9699919799/utiliti es/make.html[][][]@textrm ; [48] Underfull \hbox (badness 10000) in paragraph at lines 2719--2722 @texttt ~paul/R/basegraph.html[][][] @textrm and [][]@texttt https://www.stat.a uckland.ac.nz/~paul/R/ [33 [49]] Output written on R-lang.pdf (60 pages, 408510 bytes). Transcript written on R-lang.log. [34 [50]] [35] [51 [36]] [37] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4635--4635 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4637--4637 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4638--4638 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Underfull \hbox (badness 3826) in paragraph at lines 4641--4648 @textrm Java 9 changed the for-mat of this string (which used to be some-thing like [52] Underfull \hbox (badness 4467) in paragraph at lines 3216--3220 []@textrm The in-ter-pre-ta-tion of the line tex-ture (@texttt par("lty"[]@text rm ) is de-scribed in the header [38] Overfull \hbox (55.2397pt too wide) in paragraph at lines 4653--4653 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [53] [39] [54 [40]] [55] [41 [56]] Underfull \hbox (badness 6428) in paragraph at lines 3519--3523 []@textrm The base sys-tem state is con-tained in @texttt baseSystemState[] @te xtrm struc-ture de-fined in [42 Underfull \hbox (badness 3826) in paragraph at lines 5081--5084 []@textrm Some (but not all) ex-ten-sions are listed at [][]@texttt https://gc c.gnu.org/onlinedocs/ Underfull \hbox (badness 10000) in paragraph at lines 5081--5084 @texttt gcc/C-Extensions.html[][][] @textrm and [][]@texttt https://gcc.gnu.or g/onlinedocs/gcc/C_002b_ [57] Chapter 7 [43]] [58] Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 []@texttt R.app[] @textrm re-lies on `@texttt libR.dylib[]@textrm '[] be-ing in a spe-cific place, and hence on Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm R hav-ing been built and in-stalled as a Mac macOS `frame-work'. Specif - Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm i-cally, it uses `@texttt /Library/Frameworks/R.framework/R[]@textrm '[ ]. This is a sym-bolic Underfull \hbox (badness 3679) in paragraph at lines 3631--3640 @textrm link, as frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu -ally re-solves to Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm `@texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib /libR.dylib[]@textrm '[], [44] [59] Chapter 8 [45] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5284--5284 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [60] [46 [61]] [62] Underfull \hbox (badness 2326) in paragraph at lines 3852--3857 []@textrm Allows turn-ing off @texttt checkFF()[] @textrm test-ing. If set to `@texttt registration[]@textrm '[], checks Underfull \hbox (badness 10000) in paragraph at lines 3852--3857 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [47] [63] [48] [64] [49 Chapter 2] [65]PDF/LaTeX documentation: full reference index ... [66 [50]] [67] [51] [68] [52] [69] Chapter 9 [53] [70] [54 [71This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. ]] Chapter 10 [55] Chapter 11 [56] [72 Chapter 12 [57]]entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]:This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) %&-line parsing enabled. pdf, [58 fonts, Underfull \hbox (badness 2707) in paragraph at lines 6409--6415 []@textrm Packages may have an over-view help page with an @texttt \alias[] @te xtttsl pkg-name@texttt -package[]@textrm , e.g. Underfull \hbox (badness 3635) in paragraph at lines 6416--6422 []@textrm Skeletons of doc-u-men-ta-tion for a pack-age can be gen-er-ated us-i ng the func-tion [73]] (Function and variable index) [59]entering extended mode (./fullrefman.tex (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.vrs LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, german-x-2008-06-18, ngerman-x-2008-06-18, ancientgreek, ibycus, ar abic, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danish, dutc h, esperanto, estonian, farsi, finnish, french, galician, german, ngerman, mono greek, greek, hungarian, icelandic, indonesian, interlingua, irish, italian, la tin, mongolian, mongolian2a, bokmal, nynorsk, polish, portuguese, romanian, rus sian, sanskrit, serbian, slovak, slovenian, spanish, swedish, turkish, ukenglis h, ukrainian, uppersorbian, welsh, loaded. (/usr/share/texmf-dist/tex/latex/base/book.cls [74 Document Class: book 2005/09/16 v1.4f Standard LaTeX document class (/usr/share/texmf-dist/tex/latex/base/bk10.clo page headings,]) tables, conditionals, indexing, sectioning, toc, environments, defuns,) (../../.././share/texmf/tex/latex/Rd.sty (/usr/share/texmf-dist/tex/latex/base/ifthen.sty macros,) cross references, [75 (/usr/share/texmf-dist/tex/latex/tools/longtable.sty insertions, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex)] This is `epsf.tex' v2.7.4 <14 February 2011> ) (/usr/share/texmf-dist/tex/latex/tools/bm.sty localization,) (/usr/share/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texmf-dist/tex/latex/tools/verbatim.sty) formatting, (/usr/share/texmf/tex/latex/latex2html/url.sty and turning on texinfo input format.)) (/usr/share/texmf-dist/tex/latex/base/textcomp.sty (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex) [60 [76] (/usr/share/texmf-dist/tex/latex/base/ts1enc.def) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi) [1){/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map)] Underfull \hbox (badness 10000) in paragraph at lines 6806--6813 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and Underfull \hbox (badness 3919) in paragraph at lines 6806--6813 @texttt \figure{@textttsl filename@texttt }{@textttsl alternate text@texttt }[] @textrm . This will in-clude a copy of the fig-ure in [77] (/usr/share/texmf-dist/tex/latex/base/fontenc.sty) (Concept index) [78 [61]] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.cps Underfull \hbox (badness 10000) in paragraph at lines 6983--6989 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text @textrm part of [79]) (/usr/share/texmf-dist/tex/latex/base/t1enc.def [62 [80]] Underfull \hbox (badness 10000) in paragraph at lines 7125--7129 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file Underfull \hbox (badness 4686) in paragraph at lines 7125--7129 @textrm `@texttt share/Rd/macros/system.Rd[]@textrm '[] of the R source or home di-rec-tory, and these will [81] [82 ) (see the transcript file for additional information)<]/usr/share/texmf-dist/font s/type1/bluesky/cm/cmb10.pfb Overfull \hbox (3.59178pt too wide) in paragraph at lines 7295--7298 []@textrm Another is the Eclipse IDE with the Stat-ET plu-gin ([][]@texttt http ://www.walware.de/goto/statet[][][]@textrm ), Underfull \hbox (badness 3029) in paragraph at lines 7302--7304 []@textrm Some R front-ends pro-vide edit-ing sup-port for `@texttt .Rd[]@textr m '[] files, for ex-am-ple RStu-dio Chapter 3 [83)>] [86 (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.toc]]] [94 Underfull \hbox (badness 10000) in paragraph at lines 8278--8287 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [96 [-2] [97]] Output written on R-ints.pdf (66 pages, 442582 bytes). Transcript written on R-ints.log. Underfull \hbox (badness 10000) in paragraph at lines 8502--8508 []@texttt valgrind[] @textrm is good at spot-ting the use of unini-tial-ized va l-ues: use op-tion [98)] [-3] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.toc Underfull \hbox (badness 10000) in paragraph at lines 8541--8551 @textrm See [][]@texttt https://clang.llvm.org/docs/UsersManual.html#controllin g-code-generation[][][]@textrm , Underfull \hbox (badness 2478) in paragraph at lines 8541--8551 [][]@texttt https://clang.llvm.org/docs/AddressSanitizer.html[][][] @textrm and [][]@texttt https://code.google.com/ Overfull \hbox (39.30319pt too wide) in paragraph at lines 8555--8556 [][][]@smallrm see [][]@smalltt http://llvm.org/devmtg/2014-04/PDFs/LightningTa lks/EuroLLVM%202014%20--%20container%20overflow.pdf[][][]@smallrm .| Underfull \hbox (badness 4913) in paragraph at lines 8584--8587 [][][]@smallrm installed on some Linux sys-tems as @smalltt asan_symbolize[]@sm allrm , and ob-tain-able from [][]@smalltt https://llvm.org/ Underfull \hbox (badness 10000) in paragraph at lines 8584--8587 @smalltt svn/llvm-project/compiler-rt/trunk/lib/asan/scripts/asan_symbolize.py[ ][][]@smallrm : it makes use of [99) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.toc] Underfull \hbox (badness 10000) in paragraph at lines 8624--8629 []@textrm For op-tions avail-able @textit via @textrm the en-vi-ron-ment vari-a ble @texttt ASAN_OPTIONS[] @textrm see Underfull \hbox (badness 10000) in paragraph at lines 8624--8629 [][]@texttt https://code.google.com/p/address-sanitizer/wiki/AddressSanitizerFL ags[][][]@textrm . Underfull \hbox (badness 10000) in paragraph at lines 8640--8644 []@textrm Recent ver-sions$[]$ added the flag `@texttt -fsanitize-address-use-a fter-scope[]@textrm '[]: see [100) Chapter 1] Chapter 2 [1] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8688--8688 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8716--8718 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by Underfull \hbox (badness 6542) in paragraph at lines 8754--8759 []@textrm See [][]@texttt https://gcc.gnu.org/onlinedocs/gcc/Instrumentation-Op tions.html[][][] @textrm (or the Underfull \hbox (badness 10000) in paragraph at lines 8777--8781 []@textrm From GCC 8 @texttt signed-integer-overflow[] @textrm is no longer a d e-fault part of Underfull \hbox (badness 10000) in paragraph at lines 8777--8781 @textrm `@texttt -fsanitize=undefined[]@textrm '[], but can be spec-i-fied sep- a-rately. It adds op-tions [101]tar: R-ints.aux: Cannot stat: No such file or directory tar: Exiting with failure status due to previous errors [2] Underfull \hbox (badness 5878) in paragraph at lines 8804--8808 []@textrm For more de-tails on the topic see [][]@texttt http://blog.regehr.org /archives/213[][][] @textrm and Underfull \hbox (badness 10000) in paragraph at lines 8818--8825 []@textrm Recent ver-sions of @texttt clang[] @textrm on `@texttt x86_64[]@text rm '[] Linux have `Thread-San-i-tizer' Underfull \hbox (badness 4441) in paragraph at lines 8818--8825 @textrm ([][]@texttt https://code.google.com/p/thread-sanitizer/[][][]@textrm ) , a `data race de-tec-tor for C/C@texttt ++ Overfull \hbox (50.80455pt too wide) in paragraph at lines 8847--8847 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [102 Cross reference values unknown; you must run TeX again.] [103] [104 Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3]] [105] Chapter 5 [106] [4 [107]] [108] [5] [109] [110 [6]] [111] [7] Chapter 3 [112 [8]] Underfull \hbox (badness 4505) in paragraph at lines 9749--9754 @textrm Without or with reg-is-tra-tion, these will both work. If @texttt R_ini t_mypkg[] @textrm calls @texttt R_ [113] [9] [114] [10] [115] [11 Overfull \hbox (30.03963pt too wide) in paragraph at lines 9995--9995 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [116]] [12 [117]] [118 [13] [119]] [120 [14]] Overfull \hbox (61.1125pt too wide) in paragraph at lines 10435--10437 [][][]@smallrm For ex-am-ple, `@smalltt _GLIBCXX_USE_CXX11_ABI[]@smallrm '[] in @smalltt g++[] @smallrm 5.1 and later: [][]@smalltt https://gcc.gnu.org/online docs/libstdc++/manual/using_ [121]) (/usr/share/texmf-dist/tex/latex/psnfss/times.sty [15] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10574--10574 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [122] [16 [123]]) (/usr/share/texmf-dist/tex/latex/graphics/color.sty [124 (/usr/share/texmf/tex/latex/config/color.cfg [17)This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. (/usr/share/texmf-dist/tex/latex/pdftex-def/pdftex.def]])) (/usr/share/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texmf-dist/tex/latex/graphics/keyval.sty) [18 [125 (/usr/share/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texmf-dist/tex/generic/ifxetex/ifxetex.sty)] (/usr/share/texmf-dist/tex/latex/oberdiek/hycolor.sty] (/usr/share/texmf-dist/tex/latex/oberdiek/xcolor-patch.sty) [19)entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex] Loading texinfo [version 2008-04-18.10]: (/usr/share/texmf-dist/tex/latex/hyperref/pd1enc.def pdf, fonts, [126] [20)] [127 (/usr/share/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texmf-dist/tex/generic/oberdiek/infwarerr.sty Chapter 4) [21)]] page headings, [128 tables,] conditionals, indexing, sectioning, (/usr/share/texmf/tex/latex/config/hyperref.cfg) (/usr/share/texmf-dist/tex/latex/oberdiek/kvoptions.sty [129 toc,] [22 environments,) defuns,] macros, cross references, insertions, [130 (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex Implicit mode ON; LaTeX internals redefined (/usr/share/texmf-dist/tex/generic/oberdiek/bitset.sty (/usr/share/texmf-dist/tex/generic/oberdiek/intcalc.sty] This is `epsf.tex' v2.7.4 <14 February 2011> ) localization,) (/usr/share/texmf-dist/tex/generic/oberdiek/bigintcalc.sty (/usr/share/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty) [23 formatting, Underfull \hbox (badness 2781) in paragraph at lines 11325--11327 [][][]@smallrm You can as-sign a @smallit copy @smallrm of the ob-ject in the e n-vi-ron-ment frame @smalltt rho[] @smallrm us-ing @smalltt defineVar(symbol, [131 and turning on texinfo input format.)) (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi] (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)]) Underfull \hbox (badness 10000) in paragraph at lines 11407--11409 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [132 (/usr/share/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi)) [24 [1]{/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map] (/usr/share/texmf-dist/tex/generic/oberdiek/atbegshi.sty [133 Chapter 5 [25])] [134] [26] [135) *hyperref using default driver hpdftex* (/usr/share/texmf-dist/tex/latex/hyperref/hpdftex.def] [27 [136)]] Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 366. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 366. ) [137 (/usr/share/texmf-dist/tex/latex/base/inputenc.sty] (/usr/share/texmf-dist/tex/latex/base/utf8.def (/usr/share/texmf-dist/tex/latex/base/t1enc.dfu [138 [28]]) (/usr/share/texmf-dist/tex/latex/base/ot1enc.dfu [139) (/usr/share/texmf-dist/tex/latex/base/omsenc.dfu]) (/usr/share/texmf-dist/tex/latex/base/ts1enc.dfu [29 [140])))] (/usr/share/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texmf-dist/tex/latex/graphics/trig.sty) [141 (/usr/share/texmf/tex/latex/config/graphics.cfg)] [30))] (/usr/share/texmf-dist/tex/latex/base/makeidx.sty Chapter 6) [31] Writing index file fullrefman.idx No file fullrefman.aux. (/usr/share/texmf-dist/tex/latex/base/ts1cmr.fd [142) (/usr/share/texmf-dist/tex/latex/psnfss/t1ptm.fd] [32 [143]]}] [2 Underfull \hbox (badness 10000) in paragraph at lines 12415--12420 []@textrm A toy ex-am-ple of the use of weak ref-er-ences can be found at Underfull \hbox (badness 10000) in paragraph at lines 12415--12420 [][]@texttt https://homepage.stat.uiowa.edu/~luke/R/references/weakfinex.html[] [][]@textrm , but Overfull \hbox (22.06111pt too wide) in paragraph at lines 12440--12440 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [144] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.toc [33]] [145 [34] Chapter 6 [146]] [-1 [147 [35]]] [148] [36]) [149 [-2 [37]]] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.toc [150) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.toc] [38 [151])] Chapter 7 Chapter 1 [39]) [152] [1] [153 Chapter 8] [40 [2] [41]] [154] Chapter 9 [3 [42]] [4 [43 [155]]] [156 Chapter 10 [44]] [5 [157]] [158 [45] [6] Warning: unbalanced parentheses in @def...] [159 Underfull \hbox (badness 10000) in paragraph at lines 4342--4344 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46]] [7 [160]] [47] [8 [161]] [162 [48] [9]] Underfull \hbox (badness 2689) in paragraph at lines 14107--14113 []@textrm The vis-i-bil-ity mech-a-nism is not avail-able on Win-dows, but ther e is an equally [163] [49 [164] [10] Underfull \hbox (badness 10000) in paragraph at lines 14235--14241 []@textrm The graph-ics sys-tems are ex-posed in head-ers `@texttt R_ext/Graphi csEngine.h[]@textrm '[], Underfull \hbox (badness 3240) in paragraph at lines 14235--14241 @textrm `@texttt R_ext/GraphicsDevice.h[]@textrm '[] (which it in-cludes) and ` @texttt R_ext/QuartzDevice.h[]@textrm '[]. Fa-cil-i- Chapter 7 [165]] [166 [50] Chapter 8] [167] [11 (Function and Variable Index) [51] [168]] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.vrs [169] [12 Overfull \hbox (22.06111pt too wide) in paragraph at lines 14647--14647 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [170]] Overfull \hbox (33.55849pt too wide) in paragraph at lines 14706--14706 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [171 [13] [172] [52] [173] [14]] Underfull \hbox (badness 10000) in paragraph at lines 14949--14956 @texttt internet/nanoftp.c[]@textrm '[], `@texttt src/modules/internet/nanohtt p.c[]@textrm '[] and `@texttt src/modules/ [174]) (Concept Index) [53 Underfull \hbox (badness 10000) in paragraph at lines 15073--15078 []@textrm Another (D)COM server, @texttt RDCOMServer[]@textrm , may be avail-a ble from Omega-hat, [175] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.cps] [15 [176]] Underfull \hbox (badness 6284) in paragraph at lines 15209--15216 @textrm may be avail-able from the Win-dows Reg-istry: it will be in @texttt H KEY_LOCAL_ Underfull \hbox (badness 10000) in paragraph at lines 15209--15216 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and Underfull \hbox (badness 3769) in paragraph at lines 15209--15216 @texttt HKEY_CURRENT_USER\Software\R-core\R\InstallPath[] @textrm oth-er-wise, if se-lected dur-ing [177] [178 Overfull \hbox (27.8098pt too wide) in paragraph at lines 1455--1455 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 1456--1456 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 1457--1457 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (137.03487pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [16] (Function and variable index) [179]] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-exts.vrs) [17 Appendix A [54] [180 [18]]] [55] ) (see the transcript file for additional information) [181 [19] [183] [25) [184]] Output written on R-lang.pdf (60 pages, 412690 bytes). Transcript written on R-lang.log. Underfull \hbox (badness 3108) in paragraph at lines 2324--2329 []@textrm Some prim-i-tives are re-garded as lan-guage el-e-ments (the cur-rent ones are listed [26] Chapter 3 [27] [28] Chapter 4 [29] [30] Chapter 5 [31 ) (see the transcript file for additional information) Chapter 6] [36 Underfull \hbox (badness 4467) in paragraph at lines 3216--3220 []@textrm The in-ter-pre-ta-tion of the line tex-ture (@texttt par("lty"[]@text rm ) is de-scribed in the header [38] [40 Output written on R-exts.pdf (190 pages, 1100694 bytes). Transcript written on R-exts.log. ] [41] Underfull \hbox (badness 6428) in paragraph at lines 3519--3523 []@textrm The base sys-tem state is con-tained in @texttt baseSystemState[] @te xtrm struc-ture de-fined in [42] Chapter 7 [43]tar: R-exts.aux: Cannot stat: No such file or directory tar: Exiting with failure status due to previous errors Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 []@texttt R.app[] @textrm re-lies on `@texttt libR.dylib[]@textrm '[] be-ing in a spe-cific place, and hence on Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm R hav-ing been built and in-stalled as a Mac macOS `frame-work'. Specif - Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm i-cally, it uses `@texttt /Library/Frameworks/R.framework/R[]@textrm '[ ]. This is a sym-bolic Underfull \hbox (badness 3679) in paragraph at lines 3631--3640 @textrm link, as frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu -ally re-solves to Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm `@texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib /libR.dylib[]@textrm '[], [44] Chapter 8 [45] [46] Underfull \hbox (badness 2326) in paragraph at lines 3852--3857 []@textrm Allows turn-ing off @texttt checkFF()[] @textrm test-ing. If set to `@texttt registration[]@textrm '[], checks Underfull \hbox (badness 10000) in paragraph at lines 3852--3857 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [47]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [48]entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: [49] pdf, fonts, [50] page headings, tables, conditionals, indexing, sectioning, [51 toc, environments,] defuns, macros, cross references, insertions, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex [52 This is `epsf.tex' v2.7.4 <14 February 2011> ) localization,] formatting, and turning on texinfo input format.) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.aux Chapter 9 [53] [54] Chapter 10 [55] Chapter 11 [56] Chapter 12 [57] [58) (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi] (/usr/share/texmf-dist/tex/texinfo/txi-en.tex) (Function and variable index) [59]) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.vrs (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi) (/usr/share/texmf-dist/tex/context/base/supp-pdf.tex [1{/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.mapThis is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texmf-dist/tex/latex/oberdiek/refcount.sty))entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, (/usr/share/texmf-dist/tex/latex/psnfss/t1phv.fd [60 page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros,] cross references, insertions, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex) This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.)) (Concept index) (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi [61 (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi)] [1{/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-ints.cps) [62] ) (see the transcript file for additional information) [2] [-1 (./version.tex) (/usr/share/texmf-dist/tex/latex/psnfss/ts1ptm.fd])] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.toc) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.toc [1 Output written on R-ints.pdf (66 pages, 442582 bytes). Transcript written on R-ints.log. [-3) Chapter 1] Chapter 2 [1]) [-4 [2]] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-exts.toc) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-exts.toc Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3]) (Acknowledgements) Chapter 1 [1] Cross reference values unknown; you must run TeX again. [2] [4] Underfull \hbox (badness 4660) in paragraph at lines 280--283 []@textrm For the con-ven-tions for files `@texttt NEWS[]@textrm '[] and `@text tt ChangeLog[]@textrm '[] in the @reducedrm GNU @textrm project see [3] [5 Underfull \hbox (badness 10000) in paragraph at lines 370--380 [][]@texttt https://www.debian.org/doc/debian-policy/index.html#document-ch-con trolfields[][][]@textrm : [4]] [5 [6]] Underfull \hbox (badness 10000) in paragraph at lines 493--496 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7]{/usr/share/texmf/fonts/ma p/pdftex/updmap/pdftex.map Chapter 3 [8] Underfull \hbox (badness 10000) in paragraph at lines 626--639 @textrm Lit-er-a-ture Clas-si-fi-ca-tion Sys-tem, [][]@texttt https://www.aeawe b.org/econlit/jelCodes.php[][][]@textrm , Underfull \hbox (badness 10000) in paragraph at lines 626--639 @textrm or `@texttt Classification/MSC[]@textrm '[] or `@texttt Classification/ MSC-2010[]@textrm '[] (the Math-e-mat-ics Sub-ject [7] [9 [8]] [10 [9]] [11] [10 [12]] Underfull \hbox (badness 2376) in paragraph at lines 1009--1016 @textrm this is OK if that con-di-tion-ing is done in ex-am-ples/tests/vignette s, al-though us-ing [11 [13]] [14] [12] [15}] [13] [16] [14 [17]] [18 [15] [19]] [16 [20]] Chapter 4 [21] Underfull \hbox (badness 10000) in paragraph at lines 1439--1446 @textrm `@texttt RnavGraph/inst/tcl[]@textrm '[], `@texttt RProtoBuf/inst/pytho n[]@textrm '[] and `@texttt emdbook/inst/BUGS[]@textrm '[] and Underfull \hbox (badness 5288) in paragraph at lines 1476--1480 @textrm then down-load the sources from [][]@texttt https://sourceforge.net/pro jects/tcllib/files/ [17] [22 [18]] [19 [23]] [24 [20]] Chapter 5 [25] [26 Underfull \hbox (badness 10000) in paragraph at lines 1871--1876 []@textrm [@texttt libRlapack[] @textrm in-cludes all the double-precision LA- PACK rou-tines which Underfull \hbox (badness 2875) in paragraph at lines 1871--1876 @textrm were cur-rent in 2003: a list of which rou-tines are in-cluded is in f ile [21]] [27 [22]] Underfull \hbox (badness 10000) in paragraph at lines 2063--2065 [][][][][]@smalltt http://www.openmp.org/[][][]@smallrm , [][]@smalltt https:// en.wikipedia.org/wiki/OpenMP[][][]@smallrm , [][]@smalltt https://computing.lln l.gov/ [23 [28]] [24 [29]] [30 [25] Chapter 6 [31]] [32TEXINPUTS="../../.././doc/manual:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf ../../.././doc/manual/R-intro.texi ] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2271--2271 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2273--2273 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [26] [33] [1]] [27 [2] [34]] [1 [28] [2] (./base-pkg.tex] [35 Chapter 1. (/usr/share/texmf-dist/tex/latex/psnfss/t1pcr.fd Underfull \hbox (badness 10000) in paragraph at lines 2527--2529 [][][]@smallrm The changes are linked from [][]@smalltt https://isocpp.org/std/ standing-documents/ [29] [36]] [37 [30)]] [38] Chapter 7 [39 Overfull \hbox (39.30717pt too wide) in paragraph at lines 2654--2654 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] Underfull \hbox (badness 10000) in paragraph at lines 2702--2708 [][][]@smallrm See [][]@smalltt https://isocpp.org/std/standing-documents/sd-6- sg10-feature-test-recommendations[][][] @smallrm or [31]] [32 Chapter 8 [40]] [41] [33 Chapter 9 [42]] [34 [43]] Chapter 10 [44] [35] [45] [36 Underfull \hbox (badness 10000) in paragraph at lines 4342--4344 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46]] Underfull \hbox (badness 4595) in paragraph at lines 40--43 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [3 [47 Underfull \hbox (badness 2809) in paragraph at lines 3204--3210 @textrm (or set the en-vi-ron-ment vari-able @texttt _R_BUILD_KEEP_EMPTY_DIRS_[ ] @textrm to `@texttt TRUE[]@textrm '[], or have a [37]] [48] [49] [38] [50] Underfull \hbox (badness 4556) in paragraph at lines 3441--3449 @textrm Others you may see are @texttt \VignettePackage[] @textrm (cur-rently i g-nored), @texttt \VignetteDepends[] Underfull \hbox (badness 2617) in paragraph at lines 3441--3449 @textrm pack-age in-stal-la-tion time to cre-ate the saved data frame `@texttt Meta/vignette.rds[]@textrm '[], but Underfull \hbox (badness 3579) in paragraph at lines 3441--3449 @textrm The @texttt \VignetteEngine[] @textrm state-ment is de-scribed in [][]$ @textsy h$@textrm un-de-fined$@textsy i$ @textrm [Non-Sweave vi-gnettes], [39 (Function and Variable Index) [51]] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.vrs [40] [52 [41]]) (Concept Index) [53] [42 (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.cps] [43]) [44 Appendix A [54] [45]] [55 [46]] ) (see the transcript file for additional information)] [51] Output written on R-lang.pdf (60 pages, 408510 bytes). Transcript written on R-lang.log. Overfull \hbox (32.24495pt too wide) in paragraph at lines 4635--4635 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4637--4637 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4638--4638 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] [52] Underfull \hbox (badness 3826) in paragraph at lines 4641--4648 @textrm Java 9 changed the for-mat of this string (which used to be some-thing like Overfull \hbox (55.2397pt too wide) in paragraph at lines 4653--4653 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [53] [54] [55] [56] [57] Underfull \hbox (badness 3826) in paragraph at lines 5081--5084 []@textrm Some (but not all) ex-ten-sions are listed at [][]@texttt https://gc c.gnu.org/onlinedocs/ Underfull \hbox (badness 10000) in paragraph at lines 5081--5084 @texttt gcc/C-Extensions.html[][][] @textrm and [][]@texttt https://gcc.gnu.or g/onlinedocs/gcc/C_002b_ [58] [59] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5284--5284 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [60] [61] [62] [63] [64] Chapter 2 [65] [66] [67] [68] [69] [70] [71]] [72] Underfull \hbox (badness 2707) in paragraph at lines 6409--6415 []@textrm Packages may have an over-view help page with an @texttt \alias[] @te xtttsl pkg-name@texttt -package[]@textrm , e.g. Underfull \hbox (badness 3635) in paragraph at lines 6416--6422 []@textrm Skeletons of doc-u-men-ta-tion for a pack-age can be gen-er-ated us-i ng the func-tion [73] [74] Underfull \hbox (badness 4168) in paragraph at lines 94--99 []\T1/pcr/m/n/10 .Devices \T1/ptm/m/n/10 is a [][]pairlist[][][] of length-one char-ac-ter vec-tors. The first en-try is al-ways [4 [75]] [76] Underfull \hbox (badness 10000) in paragraph at lines 6806--6813 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and Underfull \hbox (badness 3919) in paragraph at lines 6806--6813 @texttt \figure{@textttsl filename@texttt }{@textttsl alternate text@texttt }[] @textrm . This will in-clude a copy of the fig-ure in [77]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. Underfull \hbox (badness 10000) in paragraph at lines 135--141 []\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1/ptm/m/n/10 such that Underfull \hbox (badness 10000) in paragraph at lines 135--141 \T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . It equals \T1/pcr/m/n/10 double.base ^ ulp.digits \T1/ptm/m/n/10 if ei- Underfull \hbox (badness 6236) in paragraph at lines 135--141 \T1/ptm/m/n/10 ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m /n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er-wise, Underfull \hbox (badness 10000) in paragraph at lines 135--141 \T1/ptm/m/n/10 it is \T1/pcr/m/n/10 (double.base ^ double.ulp.digits) / 2\T1/pt m/m/n/10 . Nor-mally Underfull \hbox (badness 10000) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1 /ptm/m/n/10 such that \T1/pcr/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 4328) in paragraph at lines 141--149 \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/pcr/m/n/10 (double.base ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-ma lly Underfull \hbox (badness 10000) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ- Underfull \hbox (badness 10000) in paragraph at lines 152--159 \T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) * [5] [78]entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: [6 pdf,] Underfull \hbox (badness 10000) in paragraph at lines 6983--6989 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text @textrm part of [79 fonts,] [80] page headings, tables, conditionals, indexing, [7 sectioning,] Underfull \hbox (badness 10000) in paragraph at lines 7125--7129 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file Underfull \hbox (badness 4686) in paragraph at lines 7125--7129 @textrm `@texttt share/Rd/macros/system.Rd[]@textrm '[] of the R source or home di-rec-tory, and these will [81 toc, environments,] defuns, macros, cross references, insertions, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, [82 formatting, and turning on texinfo input format.) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.aux Underfull \hbox (badness 10000) in paragraph at lines 339--342 [][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys. info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar, [8] Overfull \hbox (3.59178pt too wide) in paragraph at lines 7295--7298 []@textrm Another is the Eclipse IDE with the Stat-ET plu-gin ([][]@texttt http ://www.walware.de/goto/statet[][][]@textrm ), Underfull \hbox (badness 3029) in paragraph at lines 7302--7304 []@textrm Some R front-ends pro-vide edit-ing sup-port for `@texttt .Rd[]@textr m '[] files, for ex-am-ple RStu-dio Chapter 3 [83]] [84] Underfull \hbox (badness 2359) in paragraph at lines 386--389 []\T1/ptm/m/n/10 logical: should \T1/pcr/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [9] [85] [10 [86)] (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)]) Underfull \hbox (badness 2443) in paragraph at lines 7653--7656 []@textrm Data frames are slower than ma-tri-ces and this is an ex-am-ple of wh y. Us-ing Underfull \hbox (badness 10000) in paragraph at lines 7676--7681 []@textrm Options in-clude us-ing @texttt sprof[] @textrm for a shared ob-ject, and @texttt oprofile[] @textrm (see Underfull \hbox (badness 4927) in paragraph at lines 7676--7681 [][]@texttt http://oprofile.sourceforge.net/[][][]@textrm ) and @texttt perf[] @textrm (see [][]@texttt https://perf.wiki.kernel.org/ [87 (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi)] [1{/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map Underfull \hbox (badness 1072) in paragraph at lines 534--540 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [11 [88]] [89] [90] Overfull \hbox (213.15503pt too wide) in paragraph at lines 7896--7901 [][]@texttt https://developer.apple.com/library/content/documentation/Developer Tools/Conceptual/InstrumentsUserGuide/index.html[][][]@textrm ). Chapter 4 [91] [12] [92] [93] (/usr/share/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [94 [13]] [95] Underfull \hbox (badness 10000) in paragraph at lines 8278--8287 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [96 [14]] [97]}] [98 [2] [15 (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.toc]] Underfull \hbox (badness 10000) in paragraph at lines 8502--8508 []@texttt valgrind[] @textrm is good at spot-ting the use of unini-tial-ized va l-ues: use op-tion Underfull \hbox (badness 10000) in paragraph at lines 8541--8551 @textrm See [][]@texttt https://clang.llvm.org/docs/UsersManual.html#controllin g-code-generation[][][]@textrm , Underfull \hbox (badness 2478) in paragraph at lines 8541--8551 [][]@texttt https://clang.llvm.org/docs/AddressSanitizer.html[][][] @textrm and [][]@texttt https://code.google.com/ Overfull \hbox (39.30319pt too wide) in paragraph at lines 8555--8556 [][][]@smallrm see [][]@smalltt http://llvm.org/devmtg/2014-04/PDFs/LightningTa lks/EuroLLVM%202014%20--%20container%20overflow.pdf[][][]@smallrm .| [99] [-1 Overfull \hbox (0.78088pt too wide) in paragraph at lines 860--860 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [16] Underfull \hbox (badness 4913) in paragraph at lines 8584--8587 [][][]@smallrm installed on some Linux sys-tems as @smalltt asan_symbolize[]@sm allrm , and ob-tain-able from [][]@smalltt https://llvm.org/ Underfull \hbox (badness 10000) in paragraph at lines 8584--8587 @smalltt svn/llvm-project/compiler-rt/trunk/lib/asan/scripts/asan_symbolize.py[ ][][]@smallrm : it makes use of Underfull \hbox (badness 10000) in paragraph at lines 8624--8629 []@textrm For op-tions avail-able @textit via @textrm the en-vi-ron-ment vari-a ble @texttt ASAN_OPTIONS[] @textrm see Underfull \hbox (badness 10000) in paragraph at lines 8624--8629 [][]@texttt https://code.google.com/p/address-sanitizer/wiki/AddressSanitizerFL ags[][][]@textrm . Underfull \hbox (badness 10000) in paragraph at lines 8640--8644 []@textrm Recent ver-sions$[]$ added the flag `@texttt -fsanitize-address-use-a fter-scope[]@textrm '[]: see [100]] [17 Overfull \hbox (56.55324pt too wide) in paragraph at lines 8688--8688 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8716--8718 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by Underfull \hbox (badness 6542) in paragraph at lines 8754--8759 []@textrm See [][]@texttt https://gcc.gnu.org/onlinedocs/gcc/Instrumentation-Op tions.html[][][] @textrm (or the [101]] [-2] Underfull \hbox (badness 10000) in paragraph at lines 8777--8781 []@textrm From GCC 8 @texttt signed-integer-overflow[] @textrm is no longer a d e-fault part of Underfull \hbox (badness 10000) in paragraph at lines 8777--8781 @textrm `@texttt -fsanitize=undefined[]@textrm '[], but can be spec-i-fied sep- a-rately. It adds op-tions Underfull \hbox (badness 5878) in paragraph at lines 8804--8808 []@textrm For more de-tails on the topic see [][]@texttt http://blog.regehr.org /archives/213[][][] @textrm and Underfull \hbox (badness 10000) in paragraph at lines 8818--8825 []@textrm Recent ver-sions of @texttt clang[] @textrm on `@texttt x86_64[]@text rm '[] Linux have `Thread-San-i-tizer' Underfull \hbox (badness 4441) in paragraph at lines 8818--8825 @textrm ([][]@texttt https://code.google.com/p/thread-sanitizer/[][][]@textrm ) , a `data race de-tec-tor for C/C@texttt ++ Overfull \hbox (50.80455pt too wide) in paragraph at lines 8847--8847 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [102] [18) [-3] [103]] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.toc) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-lang.toc [104] [19 [105])] Chapter 1This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. Chapter 5 [106] Chapter 2 [1] [107 Underfull \hbox (badness 1838) in paragraph at lines 1147--1150 []\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [20 [2entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]:]]] pdf, fonts, [108] [21] [109 Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] page headings,] tables, [22 conditionals, indexing, [110] sectioning,] toc, environments, defuns, macros, cross references, insertions, [111 (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex [4 This is `epsf.tex' v2.7.4 <14 February 2011> ) localization,]] [23 formatting, and turning on texinfo input format.]) (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex [112)] [5 Underfull \hbox (badness 4505) in paragraph at lines 9749--9754 @textrm Without or with reg-is-tra-tion, these will both work. If @texttt R_ini t_mypkg[] @textrm calls @texttt R_ [113) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi)] [1]{/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map Underfull \hbox (badness 5862) in paragraph at lines 1381--1387 []\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m /n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I t is guar-an-teed that [24] [114 [6]] [115] [25 [7 Overfull \hbox (30.03963pt too wide) in paragraph at lines 9995--9995 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [116]]] Chapter 3 [8] [117] [26 [9]] [118 [10]] [119] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1639--1639 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] Underfull \hbox (badness 3168) in paragraph at lines 1656--1663 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , set-ting row n ames and con-vert-ing col-umn names Underfull \hbox (badness 3128) in paragraph at lines 1656--1663 \T1/ptm/m/n/10 (to syn-tac-tic names: see [][]\T1/pcr/m/n/10 make.names[][][]\T 1/ptm/m/n/10 ) is op-tional. Note that all Underfull \hbox (badness 6094) in paragraph at lines 1656--1663 \T1/ptm/m/n/10 of \T1/phv/m/n/10 R\T1/ptm/m/n/10 's \T1/ptm/b/n/10 base \T1/ptm /m/n/10 pack-age \T1/pcr/m/n/10 as.data.frame() \T1/ptm/m/n/10 meth-ods use \T1 /pcr/m/n/10 optional Underfull \hbox (badness 10000) in paragraph at lines 1656--1663 \T1/ptm/m/n/10 only for col-umn names treat-ment, ba-si-cally with the mean-ing of Underfull \hbox (badness 10000) in paragraph at lines 1656--1663 [][]\T1/pcr/m/n/10 data.frame[][][](*, check.names = !optional)\T1/ptm/m/n/10 . See also the [27 [11]] [120] [12]}] Underfull \hbox (badness 1303) in paragraph at lines 1667--1670 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [28 [2 Overfull \hbox (61.1125pt too wide) in paragraph at lines 10435--10437 [][][]@smallrm For ex-am-ple, `@smalltt _GLIBCXX_USE_CXX11_ABI[]@smallrm '[] in @smalltt g++[] @smallrm 5.1 and later: [][]@smalltt https://gcc.gnu.org/online docs/libstdc++/manual/using_ [121]] [13 [-1] (Preface)]] Cross reference values unknown; you must run TeX again. Chapter 1 [1] [14] [2 Overfull \hbox (16.31242pt too wide) in paragraph at lines 10574--10574 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [122 Underfull \hbox (badness 10000) in paragraph at lines 1785--1787 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 Date \T1/ptm/m/n/10 ob-ject, or some-thing wh ich can be co-erced by [29] [15]]] [3 [30] [16 [123]]] [4 Overfull \hbox (112.38031pt too wide) in paragraph at lines 1922--1922 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31 [17]] [124]] [18 [125 [5] [19]]] Chapter 2 [6] Overfull \hbox (19.13934pt too wide) in paragraph at lines 1957--1959 []\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e nv[][][](x, parent = emptyenv()) Underfull \hbox (badness 10000) in paragraph at lines 1960--1962 []\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an [32] [126 [20]] [7 [127 Chapter 4 [21]]] [33 [128]] [8 [22 [129]]] Underfull \hbox (badness 10000) in paragraph at lines 2120--2122 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [130] [9 [23]] Underfull \hbox (badness 2781) in paragraph at lines 11325--11327 [][][]@smallrm You can as-sign a @smallit copy @smallrm of the ob-ject in the e n-vi-ron-ment frame @smalltt rho[] @smallrm us-ing @smalltt defineVar(symbol, [131 [35] [10] [24 Underfull \hbox (badness 10000) in paragraph at lines 11407--11409 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [132]]] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2233--2233 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [36 Chapter 5] [11 [25] [133]] Chapter 3 [12] [134 [26]] [135 [13] [37 [27]]] [136] [137 [14] [28] Chapter 4 [138 [15 Underfull \hbox (badness 1107) in paragraph at lines 2366--2368 []\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1 0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see [38]]]] [139 [29] [16 [140]]] [141 [30 Chapter 5 [39 [17]]]] Chapter 6 [31] [142 [32]] [18] Overfull \hbox (36.78088pt too wide) in paragraph at lines 2533--2533 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse(substitute(what), backt ick=FALSE), [40 [143 [33 [19]]]] [34 Underfull \hbox (badness 10000) in paragraph at lines 12415--12420 []@textrm A toy ex-am-ple of the use of weak ref-er-ences can be found at Underfull \hbox (badness 10000) in paragraph at lines 12415--12420 [][]@texttt https://homepage.stat.uiowa.edu/~luke/R/references/weakfinex.html[] [][]@textrm , but Overfull \hbox (22.06111pt too wide) in paragraph at lines 12440--12440 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [144]] [20] [35] [41 [145]] [36 Chapter 6 [146]] [21] [37] [147 [42]] [38] Chapter 7 [39] [22 [148]] Underfull \hbox (badness 5878) in paragraph at lines 2698--2703 []\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to \T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at- Underfull \hbox (badness 10000) in paragraph at lines 2698--2703 \T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting [43] [23] [149 Chapter 8 [40]] [41] [44 [24 [150]] Chapter 9 [42] Chapter 6] [25] [151 [43]] [26 [45]] Chapter 10 [44] [152] [27] [45 [46]] [28] Underfull \hbox (badness 10000) in paragraph at lines 4342--4344 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46 Chapter 7] [29] [153] [47 [47 [30]]] [48 [154 [31]] [48] Chapter 8 [32]] [49] [49 [50 [33]]] (Function and Variable Index) [50 [56 Underfull \hbox (badness 2689) in paragraph at lines 14107--14113 []@textrm The vis-i-bil-ity mech-a-nism is not avail-able on Win-dows, but ther e is an equally [163 [165 Chapter 8 [167 [168] Output written on R-lang.pdf (60 pages, 408511 bytes). Transcript written on R-lang.log. [169 [59]] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14647--14647 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [170] Overfull \hbox (102.78088pt too wide) in paragraph at lines 3897--3897 [] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [60] Overfull \hbox (33.55849pt too wide) in paragraph at lines 14706--14706 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [171] [61 [172]] [173] [62 Underfull \hbox (badness 10000) in paragraph at lines 14949--14956 @texttt internet/nanoftp.c[]@textrm '[], `@texttt src/modules/internet/nanohtt p.c[]@textrm '[] and `@texttt src/modules/ [174]] Underfull \hbox (badness 10000) in paragraph at lines 15073--15078 []@textrm Another (D)COM server, @texttt RDCOMServer[]@textrm , may be avail-a ble from Omega-hat, [175 [63]] [176] Underfull \hbox (badness 6284) in paragraph at lines 15209--15216 @textrm may be avail-able from the Win-dows Reg-istry: it will be in @texttt H KEY_LOCAL_ Underfull \hbox (badness 10000) in paragraph at lines 15209--15216 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and Underfull \hbox (badness 3769) in paragraph at lines 15209--15216 @texttt HKEY_CURRENT_USER\Software\R-core\R\InstallPath[] @textrm oth-er-wise, if se-lected dur-ing [177] Underfull \hbox (badness 4927) in paragraph at lines 4136--4140 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an ob-ject Underfull \hbox (badness 2012) in paragraph at lines 4136--4140 \T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or [64 [178]] (Function and variable index) [179] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-exts.vrs [65]> [34] [72>]] [76] Output written on R-exts.pdf (190 pages, 1108748 bytes). Transcript written on R-exts.log. [77] [78] [79] [80] Underfull \hbox (badness 10000) in paragraph at lines 5285--5293 []\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [81] [82] [83] [84] [85] [86]> [35] [87 [36]] [37] [38] Chapter 9 [39] [98]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [40] Underfull \hbox (badness 10000) in paragraph at lines 6580--6583 []\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is Underfull \hbox (badness 2057) in paragraph at lines 6580--6583 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T 1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/ 10 host [99 Chapter 10 [41]]entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, [42] [100] [43 page headings,] tables, conditionals, indexing, sectioning, toc, environments, [44 Underfull \hbox (badness 1248) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it Underfull \hbox (badness 10000) in paragraph at lines 6782--6784 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from [101 defuns, macros,] cross references, insertions,] (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, [45] formatting, and turning on texinfo input format.) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-exts.aux [46] [47] Underfull \hbox (badness 1067) in paragraph at lines 6824--6831 \T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar ds . freedesktop . org / clipboards-[]spec / [102] [48] [103 [49]] Chapter 11 [50] Underfull \vbox (badness 10000) has occurred while \output is active [104] [51] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7016--7016 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [105] [52] [53) Underfull \hbox (badness 1231) in paragraph at lines 7141--7147 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [106] (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)] [54) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi) [1]{/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map [107] [55] [56] [108] [57] [58] [109 [59]] [60] [61] Underfull \hbox (badness 10000) in paragraph at lines 7352--7354 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [110 Chapter 12 [62]] [63] [64]}] [111 [2]] [65 (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-exts.toc] [66] [67] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7497--7497 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] Underfull \hbox (badness 4595) in paragraph at lines 7539--7542 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [112 [68 [-1]] [69]] [70] [71] ] [72] [73] [74 Underfull \hbox (badness 10000) in paragraph at lines 626--639 @textrm Lit-er-a-ture Clas-si-fi-ca-tion Sys-tem, [][]@texttt https://www.aeawe b.org/econlit/jelCodes.php[][][]@textrm , Underfull \hbox (badness 10000) in paragraph at lines 626--639 @textrm or `@texttt Classification/MSC[]@textrm '[] or `@texttt Classification/ MSC-2010[]@textrm '[] (the Math-e-mat-ics Sub-ject [7] [75]] Underfull \hbox (badness 10000) in paragraph at lines 6412--6415 @textrm and these can be ac-cessed from R via the pack-age [][]@textbf rggobi[] []@textrm , de-scribed at Chapter 13 [76] [122 [8]] [77] Chapter 14 [78] [9 [79]] Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as `@texttt \\server\dir1\dir2\file[]@t extrm '[] and Underfull \hbox (badness 5189) in paragraph at lines 6647--6652 @textrm `@texttt \\?\UNC\server\dir1\dir2\file[]@textrm '[]) are not sup-porte d, but they may work in [80 [123] Underfull \hbox (badness 10000) in paragraph at lines 6724--6728 []@textrm There is some con-fu-sion be-tween @texttt xz[] @textrm and @texttt l zma[] @textrm com-pres-sion (see Underfull \hbox (badness 10000) in paragraph at lines 6724--6728 [][]@texttt https://en.wikipedia.org/wiki/Xz[][][] @textrm and [][]@texttt http s://en.wikipedia.org/wiki/LZMA[][][]@textrm ): Appendix A [81]] [10 [82]] [83] Underfull \hbox (badness 10000) in paragraph at lines 8358--8370 \T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n /10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8358--8370 \T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59", tz = "UTC") \T1/ptm/m/n/10 will give [124 Appendix B [84]] Underfull \hbox (badness 2376) in paragraph at lines 1009--1016 @textrm this is OK if that con-di-tion-ing is done in ex-am-ples/tests/vignette s, al-though us-ing [11 Underfull \hbox (badness 2635) in paragraph at lines 7023--7029 @textrm `@texttt --no-site-file[]@textrm '[] was given. The name of this file is taken from the value Underfull \hbox (badness 2158) in paragraph at lines 7023--7029 @textrm of the @texttt R_PROFILE[] @textrm en-vi-ron-ment vari-able. If that v ari-able is un-set, the de-fault [85]] [86] [87 [125]] [12 Underfull \hbox (badness 4752) in paragraph at lines 7295--7307 []@textrm In ad-di-tion, you can use op-tions `@texttt --arch=[]@textrm '[], `@ texttt --no-environ[]@textrm '[], `@texttt --no-init-file[]@textrm '[], [88]] [89] [90] Appendix C [91 [126] [13] [92]] Appendix D [93] Appendix E [94] Appendix F [14 [95] [96] Underfull \hbox (badness 5802) in paragraph at lines 8585--8589 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10 reads the file byte-by-byte. This al-lows a Underfull \hbox (badness 10000) in paragraph at lines 8620--8621 [][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy / index . [127] ) (see the transcript file for additional information) [22] [133] [32]] [35 Underfull \hbox (badness 1603) in paragraph at lines 9266--9269 []\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t er-mi-nant if [136]] Output written on R-intro.pdf (99 pages, 555471 bytes). Transcript written on R-intro.log. Underfull \hbox (badness 2809) in paragraph at lines 3204--3210 @textrm (or set the en-vi-ron-ment vari-able @texttt _R_BUILD_KEEP_EMPTY_DIRS_[ ] @textrm to `@texttt TRUE[]@textrm '[], or have a [36] [37 [137]] [38] [138 Underfull \hbox (badness 4556) in paragraph at lines 3441--3449 @textrm Others you may see are @texttt \VignettePackage[] @textrm (cur-rently i g-nored), @texttt \VignetteDepends[] [39]] [40] [139 [41]] [140] [42] [141] [43] [44 [142]] [45] [143] [46] [144] [47] Underfull \hbox (badness 10000) in paragraph at lines 4264--4284 @textrm at [][]@texttt http://pubs.opengroup.org/onlinepubs/9699919799/utiliti es/make.html[][][]@textrm ; [48] Underfull \hbox (badness 1917) in paragraph at lines 9872--9877 []\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has [145] [49] [50 Overfull \hbox (36.7804pt too wide) in paragraph at lines 9927--9927 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE RS)))) # recycling[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9928--9928 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [146]] [51 [147]] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4635--4635 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4637--4637 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4638--4638 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Underfull \hbox (badness 3826) in paragraph at lines 4641--4648 @textrm Java 9 changed the for-mat of this string (which used to be some-thing like [52] Underfull \hbox (badness 1168) in paragraph at lines 10030--10035 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by Underfull \hbox (badness 10000) in paragraph at lines 10069--10075 []\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m /n/10 .. \T1/ptm/m/n/10 and ba-si-cally the same as Underfull \hbox (badness 5403) in paragraph at lines 10076--10079 []\T1/pcr/m/n/10 ...length() \T1/ptm/m/n/10 re-turns the num-ber of ex-pres-sio ns in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . This is the same as [148] Overfull \hbox (55.2397pt too wide) in paragraph at lines 4653--4653 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [53] [149] [54] [150] [55] Underfull \hbox (badness 2828) in paragraph at lines 10235--10239 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 10235--10239 \T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr /m/n/10 https : / / en . wikipedia . org / wiki / Double _ Overfull \hbox (42.78088pt too wide) in paragraph at lines 10268--10268 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [151] [56] [152]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. Underfull \hbox (badness 3826) in paragraph at lines 5081--5084 []@textrm Some (but not all) ex-ten-sions are listed at [][]@texttt https://gc c.gnu.org/onlinedocs/ Underfull \hbox (badness 10000) in paragraph at lines 5081--5084 @texttt gcc/C-Extensions.html[][][] @textrm and [][]@texttt https://gcc.gnu.or g/onlinedocs/gcc/C_002b_ [57 [153]] [58] [154entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]:] [59 pdf, fonts,] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5284--5284 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [60 Overfull \hbox (9.78043pt too wide) in paragraph at lines 10483--10483 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [155]] page headings, [61 Underfull \hbox (badness 1629) in paragraph at lines 10557--10561 []\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re -sult of lazy-loading (when [156 tables, conditionals,] indexing,] sectioning, toc, environments, [62 defuns, Underfull \hbox (badness 2150) in paragraph at lines 10658--10661 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [157] macros,] cross references, insertions, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, [63 Underfull \hbox (badness 3690) in paragraph at lines 10672--10680 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10 anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for Underfull \hbox (badness 10000) in paragraph at lines 10681--10683 []\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent to but faster than Underfull \hbox (badness 3735) in paragraph at lines 10701--10708 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [158 formatting, and turning on texinfo input format.]) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-intro.aux] [159] [64] [160] Chapter 2 [65] [66] Underfull \hbox (badness 10000) in paragraph at lines 10897--10900 []\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use [161] [67]) (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex) [68]) [162 (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi) [69 [1]{/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map] [70] [163] [71] [72] [164] Underfull \hbox (badness 2707) in paragraph at lines 6409--6415 []@textrm Packages may have an over-view help page with an @texttt \alias[] @te xtttsl pkg-name@texttt -package[]@textrm , e.g. Underfull \hbox (badness 3635) in paragraph at lines 6416--6422 []@textrm Skeletons of doc-u-men-ta-tion for a pack-age can be gen-er-ated us-i ng the func-tion [73] [165] [74] [75]} [166] [2]] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-intro.toc [76] [167 [-1] Underfull \hbox (badness 10000) in paragraph at lines 6806--6813 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and Underfull \hbox (badness 3919) in paragraph at lines 6806--6813 @texttt \figure{@textttsl filename@texttt }{@textttsl alternate text@texttt }[] @textrm . This will in-clude a copy of the fig-ure in [77]] [168 [78] [-2]] [169 Underfull \hbox (badness 10000) in paragraph at lines 6983--6989 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text @textrm part of [79]] [-3 [80]]) [-4 Underfull \hbox (badness 10000) in paragraph at lines 7125--7129 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file Underfull \hbox (badness 4686) in paragraph at lines 7125--7129 @textrm `@texttt share/Rd/macros/system.Rd[]@textrm '[] of the R source or home di-rec-tory, and these will [81] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-intro.toc]) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-intro.toc Underfull \hbox (badness 5288) in paragraph at lines 11594--11596 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of Underfull \hbox (badness 3039) in paragraph at lines 11604--11609 []\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10 dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10 and [170] [82]) Overfull \hbox (3.59178pt too wide) in paragraph at lines 7295--7298 []@textrm Another is the Eclipse IDE with the Stat-ET plu-gin ([][]@texttt http ://www.walware.de/goto/statet[][][]@textrm ), Underfull \hbox (badness 3029) in paragraph at lines 7302--7304 []@textrm Some R front-ends pro-vide edit-ing sup-port for `@texttt .Rd[]@textr m '[] files, for ex-am-ple RStu-dio Chapter 3 (Preface) [83] Chapter 1 [1] [84] [2 Underfull \hbox (badness 10000) in paragraph at lines 11664--11666 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [171 [85]]] [86 [3]] Underfull \hbox (badness 2443) in paragraph at lines 7653--7656 []@textrm Data frames are slower than ma-tri-ces and this is an ex-am-ple of wh y. Us-ing Underfull \hbox (badness 10000) in paragraph at lines 7676--7681 []@textrm Options in-clude us-ing @texttt sprof[] @textrm for a shared ob-ject, and @texttt oprofile[] @textrm (see Underfull \hbox (badness 4927) in paragraph at lines 7676--7681 [][]@texttt http://oprofile.sourceforge.net/[][][]@textrm ) and @texttt perf[] @textrm (see [][]@texttt https://perf.wiki.kernel.org/ [87] [172 [88] [4] [89]] [90] Overfull \hbox (213.15503pt too wide) in paragraph at lines 7896--7901 [][]@texttt https://developer.apple.com/library/content/documentation/Developer Tools/Conceptual/InstrumentsUserGuide/index.html[][][]@textrm ). Chapter 4 [91] Underfull \hbox (badness 4569) in paragraph at lines 11781--11785 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11781--11785 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [173 [92]] [5 [93]] Chapter 2 [6] [94 [174]] [95] Underfull \hbox (badness 10000) in paragraph at lines 8278--8287 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [96] [7 [97]] Underfull \hbox (badness 10000) in paragraph at lines 11896--11898 []\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/ m/n/10 where \T1/ptm/m/n/10 as Underfull \hbox (badness 2790) in paragraph at lines 11939--11941 []\T1/pcr/m/n/10 get0(): \T1/ptm/m/n/10 The object---as from [][]\T1/pcr/m/n/10 get[][][](x, *)\T1/ptm/m/n/10 --- if \T1/pcr/m/n/10 exists(x, *) \T1/ptm/m/n/1 0 is true, oth-er-wise [175 Underfull \hbox (badness 10000) in paragraph at lines 8502--8508 []@texttt valgrind[] @textrm is good at spot-ting the use of unini-tial-ized va l-ues: use op-tion [98]] [8 Underfull \hbox (badness 10000) in paragraph at lines 8541--8551 @textrm See [][]@texttt https://clang.llvm.org/docs/UsersManual.html#controllin g-code-generation[][][]@textrm , Underfull \hbox (badness 2478) in paragraph at lines 8541--8551 [][]@texttt https://clang.llvm.org/docs/AddressSanitizer.html[][][] @textrm and [][]@texttt https://code.google.com/ Overfull \hbox (39.30319pt too wide) in paragraph at lines 8555--8556 [][][]@smallrm see [][]@smalltt http://llvm.org/devmtg/2014-04/PDFs/LightningTa lks/EuroLLVM%202014%20--%20container%20overflow.pdf[][][]@smallrm .| Underfull \hbox (badness 4913) in paragraph at lines 8584--8587 [][][]@smallrm installed on some Linux sys-tems as @smalltt asan_symbolize[]@sm allrm , and ob-tain-able from [][]@smalltt https://llvm.org/ Underfull \hbox (badness 10000) in paragraph at lines 8584--8587 @smalltt svn/llvm-project/compiler-rt/trunk/lib/asan/scripts/asan_symbolize.py[ ][][]@smallrm : it makes use of [99]] Underfull \hbox (badness 10000) in paragraph at lines 8624--8629 []@textrm For op-tions avail-able @textit via @textrm the en-vi-ron-ment vari-a ble @texttt ASAN_OPTIONS[] @textrm see Underfull \hbox (badness 10000) in paragraph at lines 8624--8629 [][]@texttt https://code.google.com/p/address-sanitizer/wiki/AddressSanitizerFL ags[][][]@textrm . Underfull \hbox (badness 10000) in paragraph at lines 8640--8644 []@textrm Recent ver-sions$[]$ added the flag `@texttt -fsanitize-address-use-a fter-scope[]@textrm '[]: see [100 [176]] [9 Overfull \hbox (56.55324pt too wide) in paragraph at lines 8688--8688 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8716--8718 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by Underfull \hbox (badness 6542) in paragraph at lines 8754--8759 []@textrm See [][]@texttt https://gcc.gnu.org/onlinedocs/gcc/Instrumentation-Op tions.html[][][] @textrm (or the Underfull \hbox (badness 10000) in paragraph at lines 8777--8781 []@textrm From GCC 8 @texttt signed-integer-overflow[] @textrm is no longer a d e-fault part of Underfull \hbox (badness 10000) in paragraph at lines 8777--8781 @textrm `@texttt -fsanitize=undefined[]@textrm '[], but can be spec-i-fied sep- a-rately. It adds op-tions [101]] Underfull \hbox (badness 5878) in paragraph at lines 8804--8808 []@textrm For more de-tails on the topic see [][]@texttt http://blog.regehr.org /archives/213[][][] @textrm and Underfull \hbox (badness 10000) in paragraph at lines 8818--8825 []@textrm Recent ver-sions of @texttt clang[] @textrm on `@texttt x86_64[]@text rm '[] Linux have `Thread-San-i-tizer' Underfull \hbox (badness 4441) in paragraph at lines 8818--8825 @textrm ([][]@texttt https://code.google.com/p/thread-sanitizer/[][][]@textrm ) , a `data race de-tec-tor for C/C@texttt ++ Overfull \hbox (50.80455pt too wide) in paragraph at lines 8847--8847 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [102] [10 [103 [177]]] [104] [105 [11] Chapter 5 [106]] Chapter 3 [12] Underfull \hbox (badness 4048) in paragraph at lines 12110--12120 []\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me nt into an ex-pres-sion ob-ject. It is Underfull \hbox (badness 3657) in paragraph at lines 12110--12120 \T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d e-fault method calls [178 [107]] [108 [13]] [109] [110 [14] [179]] Chapter 4 [111 [15]] [112] [16 Underfull \hbox (badness 4505) in paragraph at lines 9749--9754 @textrm Without or with reg-is-tra-tion, these will both work. If @texttt R_ini t_mypkg[] @textrm calls @texttt R_ [113 [180]]] Chapter 5 [114 [17]] [115] Overfull \hbox (30.03963pt too wide) in paragraph at lines 9995--9995 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [116] [18 Underfull \hbox (badness 5460) in paragraph at lines 12358--12367 []\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l- Underfull \hbox (badness 2221) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes e op-er-a-tions are those Underfull \hbox (badness 2707) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x, inherits = FALSE)\T1/ptm/m/ n/10 . If no match is found then \T1/pcr/m/n/10 NULL Underfull \hbox (badness 2818) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T 1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again, Underfull \hbox (badness 6978) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th is case are those of [181] [117]] [19] [118] [119 [182 [20]] [120]] Overfull \hbox (61.1125pt too wide) in paragraph at lines 10435--10437 [][][]@smallrm For ex-am-ple, `@smalltt _GLIBCXX_USE_CXX11_ABI[]@smallrm '[] in @smalltt g++[] @smallrm 5.1 and later: [][]@smalltt https://gcc.gnu.org/online docs/libstdc++/manual/using_ [121] [21 [183]] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10574--10574 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [122] [123 [184] [22] [124]] [125] [185 [23] [126]] [127] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12732--12732 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [186 [128]] [24 [129]] Chapter 6 [25] [130] Underfull \hbox (badness 2781) in paragraph at lines 11325--11327 [][][]@smallrm You can as-sign a @smallit copy @smallrm of the ob-ject in the e n-vi-ron-ment frame @smalltt rho[] @smallrm us-ing @smalltt defineVar(symbol, [131 [26] [187]] Underfull \hbox (badness 10000) in paragraph at lines 11407--11409 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [132] [133] [27 [134]] [135 [188] [28 [136]] [137]] Chapter 7 [138 [29]] [139] [140] [189 [30] [141]] [142] [31] [143 Chapter 8 [32]] Underfull \hbox (badness 10000) in paragraph at lines 12415--12420 []@textrm A toy ex-am-ple of the use of weak ref-er-ences can be found at Underfull \hbox (badness 10000) in paragraph at lines 12415--12420 [][]@texttt https://homepage.stat.uiowa.edu/~luke/R/references/weakfinex.html[] [][]@textrm , but Overfull \hbox (22.06111pt too wide) in paragraph at lines 12440--12440 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [144 Underfull \hbox (badness 5119) in paragraph at lines 13017--13020 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [190]] [145] Chapter 6 [33 [146]] (TRUE,FALSE) : ok for A but not B as it exists already[] [202]] Overfull \hbox (30.78088pt too wide) in paragraph at lines 13868--13868 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [203 [164]] Underfull \hbox (badness 10000) in paragraph at lines 14235--14241 []@textrm The graph-ics sys-tems are ex-posed in head-ers `@texttt R_ext/Graphi csEngine.h[]@textrm '[], Underfull \hbox (badness 3240) in paragraph at lines 14235--14241 @textrm `@texttt R_ext/GraphicsDevice.h[]@textrm '[] (which it in-cludes) and ` @texttt R_ext/QuartzDevice.h[]@textrm '[]. Fa-cil-i- Chapter 7 [165] Underfull \hbox (badness 10000) in paragraph at lines 13960--13963 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 13970--13970 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [204 [166]] Chapter 8 [167] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14045--14045 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] [205] [168 Overfull \hbox (0.78088pt too wide) in paragraph at lines 14074--14074 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, Underfull \hbox (badness 7238) in paragraph at lines 14098--14105 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr /m/n/10 vec\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14098--14105 \T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial , equiv-a-lent to Underfull \hbox (badness 2126) in paragraph at lines 14098--14105 \T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter of fact, the in-ter-nal al-go- Underfull \hbox (badness 3965) in paragraph at lines 14106--14110 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [206]] [169] [207] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14647--14647 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [170] [208] Overfull \hbox (33.55849pt too wide) in paragraph at lines 14706--14706 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [171] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14269--14269 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 14270--14270 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [209] [172] Underfull \hbox (badness 10000) in paragraph at lines 14349--14353 []\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a Underfull \hbox (badness 1389) in paragraph at lines 14349--14353 \T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m ay not be equiv-a-lent to [210 [173]]> [211 Underfull \hbox (badness 10000) in paragraph at lines 14949--14956 @texttt internet/nanoftp.c[]@textrm '[], `@texttt src/modules/internet/nanohtt p.c[]@textrm '[] and `@texttt src/modules/ [174 [34]]] ] Underfull \hbox (badness 2418) in paragraph at lines 16029--16033 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 16036--16039 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/ m/n/10 , then the sin-gle Underfull \hbox (badness 2326) in paragraph at lines 16064--16071 [][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 , [234]] [236] Output written on R-exts.pdf (190 pages, 1100694 bytes). Transcript written on R-exts.log. [237] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16310--16310 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, Underfull \hbox (badness 1867) in paragraph at lines 16335--16342 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [238] [239] [240]> [35] [36] [[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] [243] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16683--16683 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 16689--16693 []\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o r fixed pat-tern for Underfull \hbox (badness 1028) in paragraph at lines 16689--16693 \T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec- tor. Co-erced by [244] [245] [246] [247] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17048--17048 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z < - c(2, 1:9))) [248>] [37] [38] Chapter 9 [249 [39]] [40 [250]] Chapter 10 [41] [42] [251] [43] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17302--17302 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [252 [44]] [45] [46 [253]] [47]This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. [48 [254]] [49] Chapter 11 [50]entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, [51 Underfull \hbox (badness 2435) in paragraph at lines 17563--17565 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www . unicode . org / reports / tr35 / [255]] [52] Underfull \hbox (badness 1867) in paragraph at lines 17605--17612 []\T1/ptm/m/n/10 It is op-tional on Win-dows: if \T1/phv/m/n/10 R \T1/ptm/m/n/1 0 has been built against ICU, it will only be used if Underfull \hbox (badness 1490) in paragraph at lines 17605--17612 \T1/ptm/m/n/10 en-vi-ron-ment vari-able \T1/pcr/m/n/10 R_ICU_LOCALE \T1/ptm/m/n /10 is set or once \T1/pcr/m/n/10 icuSetCollate \T1/ptm/m/n/10 is called to se- Underfull \hbox (badness 1490) in paragraph at lines 17605--17612 \T1/ptm/m/n/10 lect the lo-cale (as ICU and Win-dows dif-fer in their idea of l o-cale names). Note that Underfull \hbox (badness 2285) in paragraph at lines 17620--17622 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 http : / / userguide . icu-[]project . org / Overfull \hbox (9.78043pt too wide) in paragraph at lines 17628--17628 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s ettings, we can only reset to the default.[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17638--17638 [] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p rint(sort(x))[] [256 page headings, tables,] conditionals, [53 indexing, sectioning,] toc, environments, defuns, macros, cross references, insertions, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex [54 This is `epsf.tex' v2.7.4 <14 February 2011> ) localization,] formatting, Overfull \hbox (24.78088pt too wide) in paragraph at lines 17658--17658 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [257 and turning on texinfo input format.) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-exts.aux] [55] [258] [56] [57 Overfull \hbox (25.98041pt too wide) in paragraph at lines 17792--17792 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17798--17798 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17801--17801 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share an environment:[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17807--17807 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [259]] [58] [59 [260]] [60]) (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex) Overfull \hbox (4.38043pt too wide) in paragraph at lines 17934--17934 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u se ifelse(),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17942--17942 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] [261]) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi) [1{/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map [61 [262] Chapter 12] [62] [63] [263] [64] Underfull \hbox (badness 10000) in paragraph at lines 18147--18149 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/ pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and [264] [65] [66] Underfull \hbox (badness 4217) in paragraph at lines 18231--18240 [][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 2057) in paragraph at lines 18246--18262 [][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [265] [67] [68 [266]}]] [2] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-exts.toc [267 [69]] [70 [268]] [-1 = 0. Smaller dif-fer-ences are not con-sid-ere d, see [275]] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-exts.toc) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-exts.toc [276] [277]) (Acknowledgements) Chapter 1 [1] [278 [2]> [71]] [279 [289 [72 Underfull \hbox (badness 2376) in paragraph at lines 1009--1016 @textrm this is OK if that con-di-tion-ing is done in ex-am-ples/tests/vignette s, al-though us-ing [11]] [73]] [290] [12 [74 Underfull \hbox (badness 1077) in paragraph at lines 19935--19940 []\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/ n/10 and [291]]] [75 Underfull \hbox (badness 10000) in paragraph at lines 19949--19956 [][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / [292]] [13 Underfull \hbox (badness 10000) in paragraph at lines 6412--6415 @textrm and these can be ac-cessed from R via the pack-age [][]@textbf rggobi[] []@textrm , de-scribed at Chapter 13 [76]] Underfull \hbox (badness 10000) in paragraph at lines 20023--20027 []\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory [293] [14] [77 Underfull \hbox (badness 10000) in paragraph at lines 20153--20157 []\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use Underfull \hbox (badness 1454) in paragraph at lines 20153--20157 [][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self [294] Chapter 14] [78] [15] [295 [79]] Underfull \hbox (badness 10000) in paragraph at lines 1439--1446 @textrm `@texttt RnavGraph/inst/tcl[]@textrm '[], `@texttt RProtoBuf/inst/pytho n[]@textrm '[] and `@texttt emdbook/inst/BUGS[]@textrm '[] and [16 Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as `@texttt \\server\dir1\dir2\file[]@t extrm '[] and Underfull \hbox (badness 5189) in paragraph at lines 6647--6652 @textrm `@texttt \\?\UNC\server\dir1\dir2\file[]@textrm '[]) are not sup-porte d, but they may work in [80 Underfull \hbox (badness 10000) in paragraph at lines 20251--20258 [][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/ m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 , [296]]] Underfull \hbox (badness 10000) in paragraph at lines 6724--6728 []@textrm There is some con-fu-sion be-tween @texttt xz[] @textrm and @texttt l zma[] @textrm com-pres-sion (see Underfull \hbox (badness 10000) in paragraph at lines 6724--6728 [][]@texttt https://en.wikipedia.org/wiki/Xz[][][] @textrm and [][]@texttt http s://en.wikipedia.org/wiki/LZMA[][][]@textrm ): Appendix A [81] Underfull \hbox (badness 5288) in paragraph at lines 1476--1480 @textrm then down-load the sources from [][]@texttt https://sourceforge.net/pro jects/tcllib/files/ [17 [297 [82]]] [18 [83]] Underfull \hbox (badness 10000) in paragraph at lines 20372--20376 []\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10 on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use [298] Appendix B [84] [19 Underfull \hbox (badness 5161) in paragraph at lines 20442--20447 []\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di s-tributed un-der the Underfull \hbox (badness 6592) in paragraph at lines 20442--20447 \T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c opy of Underfull \hbox (badness 5133) in paragraph at lines 20442--20447 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 20442--20447 \T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 3 of the li-cense can be dis-played by [299]] Underfull \hbox (badness 2635) in paragraph at lines 7023--7029 @textrm `@texttt --no-site-file[]@textrm '[] was given. The name of this file is taken from the value Underfull \hbox (badness 2158) in paragraph at lines 7023--7029 @textrm of the @texttt R_PROFILE[] @textrm en-vi-ron-ment vari-able. If that v ari-able is un-set, the de-fault [85 [20] [300]] [86] Underfull \hbox (badness 10000) in paragraph at lines 1871--1876 []@textrm [@texttt libRlapack[] @textrm in-cludes all the double-precision LA- PACK rou-tines which Underfull \hbox (badness 2875) in paragraph at lines 1871--1876 @textrm were cur-rent in 2003: a list of which rou-tines are in-cluded is in f ile [21 [87 Overfull \hbox (6.78088pt too wide) in paragraph at lines 20609--20609 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20613--20613 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [301]]] [22 Underfull \hbox (badness 4752) in paragraph at lines 7295--7307 []@textrm In ad-di-tion, you can use op-tions `@texttt --arch=[]@textrm '[], `@ texttt --no-environ[]@textrm '[], `@texttt --no-init-file[]@textrm '[], [88]] Underfull \hbox (badness 3343) in paragraph at lines 20669--20673 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for many more file han-dling func-tions and [302] Underfull \hbox (badness 10000) in paragraph at lines 2063--2065 [][][][][]@smalltt http://www.openmp.org/[][][]@smallrm , [][]@smalltt https:// en.wikipedia.org/wiki/OpenMP[][][]@smallrm , [][]@smalltt https://computing.lln l.gov/ [23 [89]] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20755--20755 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 20766--20766 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, pr = 0.2))),[] [303 [24] [90]] Appendix C [91 [304] [25]] Overfull \hbox (9.78043pt too wide) in paragraph at lines 20877--20877 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the same names ![] Overfull \hbox (74.58035pt too wide) in paragraph at lines 20880--20880 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w / same name in .GlobalEnv[] [305 [92] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2271--2271 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2273--2273 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [26]] Appendix D [93] [27 Underfull \hbox (badness 6380) in paragraph at lines 20925--20930 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- Underfull \hbox (badness 1337) in paragraph at lines 20983--20990 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t ails of the string are system-specific: it might be Underfull \hbox (badness 1960) in paragraph at lines 20983--20990 \T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by \T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, ma-cOS) or Underfull \hbox (badness 1043) in paragraph at lines 20983--20990 \T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in [306 (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-intro.vrs]] [28 Underfull \hbox (badness 2564) in paragraph at lines 21016--21019 []\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/ ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of Overfull \hbox (4.38043pt too wide) in paragraph at lines 21046--21046 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] [307]] Underfull \hbox (badness 10000) in paragraph at lines 2527--2529 [][][]@smallrm The changes are linked from [][]@smalltt https://isocpp.org/std/ standing-documents/ [29 Underfull \hbox (badness 1205) in paragraph at lines 21069--21074 \T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form [308] [94] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2654--2654 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [30]] [309] Underfull \hbox (badness 10000) in paragraph at lines 2702--2708 [][][]@smallrm See [][]@smalltt https://isocpp.org/std/standing-documents/sd-6- sg10-feature-test-recommendations[][][] @smallrm or [31] Underfull \hbox (badness 1400) in paragraph at lines 21214--21218 [][][]\T1/pcr/m/n/10 raw[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][]\T1/pcr/m/n/10 do uble[][][] \T1/ptm/m/n/10 (class Overfull \hbox (36.83002pt too wide) in paragraph at lines 21234--21241 []\T1/pcr/m/n/10 isTRUE(x) \T1/ptm/m/n/10 is the same as \T1/pcr/m/n/10 { is.lo gical(x) && length(x) == 1 && !is.na(x) && x }\T1/ptm/m/n/10 ; Underfull \hbox (badness 4886) in paragraph at lines 21234--21241 \T1/ptm/m/n/10 In ear-lier \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions, \T1/pcr/m /n/10 isTRUE <- function(x) identical(x, TRUE)\T1/ptm/m/n/10 , had the [310] [32] [95 [311 [33]]] Underfull \hbox (badness 2469) in paragraph at lines 21384--21390 []\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s, Underfull \hbox (badness 1939) in paragraph at lines 21384--21390 \T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la -bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri butes in-clud-ing names. Underfull \hbox (badness 10000) in paragraph at lines 21384--21390 \T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true" ) \T1/ptm/m/n/10 are re-garded as true, [312] [34]) [313] Appendix E [96 [35] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-intro.cps] [314] Underfull \hbox (badness 2809) in paragraph at lines 3204--3210 @textrm (or set the en-vi-ron-ment vari-able @texttt _R_BUILD_KEEP_EMPTY_DIRS_[ ] @textrm to `@texttt TRUE[]@textrm '[], or have a [36 [315]] [97 [37 [316]]]) Appendix F [98] [99] Underfull \hbox (badness 10000) in paragraph at lines 21701--21703 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [317 [38] ) (see the transcript file for additional information)] [320 [321 Overfull \hbox (52.98038pt too wide) in paragraph at lines 22005--22005 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real = r , imaginary = NA ),[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22006--22006 [] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N aN, imaginary = r ))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 22009--22009 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] [322]] [325]] [326] [46 Output written on R-intro.pdf (105 pages, 703651 bytes). Transcript written on R-intro.log. ] Underfull \hbox (badness 2277) in paragraph at lines 22382--22385 []\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][] \T1/pcr/m/n/10 crossprod[][][]() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tcrossprod() \T1/ptm/m/n/10 are typ-i-cally prefer-able. [327] [47] [328 Underfull \hbox (badness 10000) in paragraph at lines 4264--4284 @textrm at [][]@texttt http://pubs.opengroup.org/onlinepubs/9699919799/utiliti es/make.html[][][]@textrm ; [48]] [329 [49]] [50] [330] [51 [331]] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4635--4635 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4637--4637 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4638--4638 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Underfull \hbox (badness 3826) in paragraph at lines 4641--4648 @textrm Java 9 changed the for-mat of this string (which used to be some-thing like [52 [332]] Overfull \hbox (55.2397pt too wide) in paragraph at lines 4653--4653 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [53] [333] [54] [334 [55]] [56 Underfull \hbox (badness 10000) in paragraph at lines 22867--22873 []\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age space can-not ex-ceed Underfull \hbox (badness 6316) in paragraph at lines 22867--22873 \T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er -ror mes-sage be-gins Underfull \hbox (badness 1484) in paragraph at lines 22899--22907 []\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less the OS's de-fault has been Underfull \hbox (badness 2951) in paragraph at lines 22899--22907 \T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http s : / / www . microsoft . com / whdc / Underfull \hbox (badness 3460) in paragraph at lines 22899--22907 \T1/pcr/m/n/10 system / platform / server / PAE / PAEmem . mspx$[][] \T1/ptm/m/ n/10 and [][]$\T1/pcr/m/n/10 https : / / msdn . microsoft . [335]] Underfull \hbox (badness 3826) in paragraph at lines 5081--5084 []@textrm Some (but not all) ex-ten-sions are listed at [][]@texttt https://gc c.gnu.org/onlinedocs/ Underfull \hbox (badness 10000) in paragraph at lines 5081--5084 @texttt gcc/C-Extensions.html[][][] @textrm and [][]@texttt https://gcc.gnu.or g/onlinedocs/gcc/C_002b_ [57] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22976--22976 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [336 [58]] [59] Underfull \hbox (badness 10000) in paragraph at lines 23030--23034 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by. x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng th zero vec- Underfull \hbox (badness 10000) in paragraph at lines 23030--23034 \T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr /m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/ n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i. e., [337 Overfull \hbox (32.24495pt too wide) in paragraph at lines 5284--5284 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [60]] [338] [61] [339 [62]] [340] [63] [341] [64] [342] Chapter 2 [65This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) file:line:error style messages enabled. %&-line parsing enabled. ] Underfull \hbox (badness 10000) in paragraph at lines 23481--23489 \T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T 1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; [343 [66]]entering extended mode (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi [344 (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2008-04-18.10]:] [67 pdf, fonts,] Underfull \hbox (badness 3849) in paragraph at lines 23595--23600 []\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na lly to a char-ac-ter vec-tor (so meth-ods for [345 [68]] Underfull \hbox (badness 7308) in paragraph at lines 23672--23678 []\T1/ptm/m/n/10 For an [][]\T1/pcr/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/pcr/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 5077) in paragraph at lines 23672--23678 \T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23682--23685 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23682--23685 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [346 [69 page headings,]] tables, conditionals, indexing, sectioning, toc, environments, [347 [70 defuns,] macros,] cross references, insertions, (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, [71] formatting, and turning on texinfo input format.) Underfull \hbox (badness 10000) in paragraph at lines 23834--23836 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of [348 (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-intro.aux] [72] [349 Underfull \hbox (badness 2707) in paragraph at lines 6409--6415 []@textrm Packages may have an over-view help page with an @texttt \alias[] @te xtttsl pkg-name@texttt -package[]@textrm , e.g. Underfull \hbox (badness 3635) in paragraph at lines 6416--6422 []@textrm Skeletons of doc-u-men-ta-tion for a pack-age can be gen-er-ated us-i ng the func-tion [73]] [350] [74]) (/tmp/B.61K3e5/BUILD/R-3.5.2/doc/manual/R-defs.texi [351 (/usr/share/texmf-dist/tex/texinfo/txi-en.tex) [75]]) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/version.texi) [1{/usr/share/texmf /fonts/map/pdftex/updmap/pdftex.map Underfull \hbox (badness 6188) in paragraph at lines 24053--24056 []\T1/ptm/m/n/10 optional [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/pcr/m/n/10 print()\T1/ptm/m/n/10 , used by [352 [76]] Underfull \hbox (badness 10000) in paragraph at lines 6806--6813 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and Underfull \hbox (badness 3919) in paragraph at lines 6806--6813 @texttt \figure{@textttsl filename@texttt }{@textttsl alternate text@texttt }[] @textrm . This will in-clude a copy of the fig-ure in [77] [353] [78] [354] Underfull \hbox (badness 10000) in paragraph at lines 6983--6989 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text @textrm part of [79] [355] [80] Underfull \hbox (badness 10000) in paragraph at lines 7125--7129 []@textrm As of R ver-sion 3.2.0, a num-ber of macros are de-fined in the file Underfull \hbox (badness 4686) in paragraph at lines 7125--7129 @textrm `@texttt share/Rd/macros/system.Rd[]@textrm '[] of the R source or home di-rec-tory, and these will [81}] [356] [2]] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-intro.toc [82 [357] [-1 Overfull \hbox (3.59178pt too wide) in paragraph at lines 7295--7298 []@textrm Another is the Eclipse IDE with the Stat-ET plu-gin ([][]@texttt http ://www.walware.de/goto/statet[][][]@textrm ), Underfull \hbox (badness 3029) in paragraph at lines 7302--7304 []@textrm Some R front-ends pro-vide edit-ing sup-port for `@texttt .Rd[]@textr m '[] files, for ex-am-ple RStu-dio Chapter 3 [83]]] [84] [358 [85]] [-2] [86 Underfull \hbox (badness 2197) in paragraph at lines 24535--24539 []\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s tartup mes-sages given by Underfull \hbox (badness 4048) in paragraph at lines 24535--24539 \T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use Underfull \hbox (badness 2846) in paragraph at lines 24549--24553 []\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment \T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the pack- Underfull \hbox (badness 1990) in paragraph at lines 24549--24553 \T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p uted pack-age in-for-ma-tion ob-ject and pass this to [359]] Underfull \hbox (badness 2443) in paragraph at lines 7653--7656 []@textrm Data frames are slower than ma-tri-ces and this is an ex-am-ple of wh y. Us-ing Underfull \hbox (badness 10000) in paragraph at lines 7676--7681 []@textrm Options in-clude us-ing @texttt sprof[] @textrm for a shared ob-ject, and @texttt oprofile[] @textrm (see Underfull \hbox (badness 4927) in paragraph at lines 7676--7681 [][]@texttt http://oprofile.sourceforge.net/[][][]@textrm ) and @texttt perf[] @textrm (see [][]@texttt https://perf.wiki.kernel.org/ [87 [-3] [88 Underfull \hbox (badness 10000) in paragraph at lines 24642--24648 []\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i t loads to the search path. Underfull \hbox (badness 1168) in paragraph at lines 24642--24648 \T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co n-tain-ing the ex-ported val-ues of a [360]]]) [-4 [89] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-intro.toc] [90) (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-intro.toc] Overfull \hbox (213.15503pt too wide) in paragraph at lines 7896--7901 [][]@texttt https://developer.apple.com/library/content/documentation/Developer Tools/Conceptual/InstrumentsUserGuide/index.html[][][]@textrm ). Chapter 4 [91] Underfull \hbox (badness 10000) in paragraph at lines 24655--24657 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than Overfull \hbox (4.38043pt too wide) in paragraph at lines 24706--24706 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/ n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] [361] [92]) (Preface) [93 Chapter 1 [1]] [94 [362]] [2 [95]] Underfull \hbox (badness 10000) in paragraph at lines 8278--8287 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [96 [3] [363]] [97 [4]] Underfull \hbox (badness 10000) in paragraph at lines 8502--8508 []@texttt valgrind[] @textrm is good at spot-ting the use of unini-tial-ized va l-ues: use op-tion [98 Underfull \hbox (badness 10000) in paragraph at lines 24899--24905 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of Underfull \hbox (badness 10000) in paragraph at lines 24899--24905 [][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type [][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\ T1/ptm/m/n/10 ) and not a fac-tor, Underfull \hbox (badness 10000) in paragraph at lines 24899--24905 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T 1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or [364] [5]] Chapter 2 [6] Underfull \hbox (badness 10000) in paragraph at lines 8541--8551 @textrm See [][]@texttt https://clang.llvm.org/docs/UsersManual.html#controllin g-code-generation[][][]@textrm , Underfull \hbox (badness 2478) in paragraph at lines 8541--8551 [][]@texttt https://clang.llvm.org/docs/AddressSanitizer.html[][][] @textrm and [][]@texttt https://code.google.com/ Overfull \hbox (39.30319pt too wide) in paragraph at lines 8555--8556 [][][]@smallrm see [][]@smalltt http://llvm.org/devmtg/2014-04/PDFs/LightningTa lks/EuroLLVM%202014%20--%20container%20overflow.pdf[][][]@smallrm .| Underfull \hbox (badness 4913) in paragraph at lines 8584--8587 [][][]@smallrm installed on some Linux sys-tems as @smalltt asan_symbolize[]@sm allrm , and ob-tain-able from [][]@smalltt https://llvm.org/ Underfull \hbox (badness 10000) in paragraph at lines 8584--8587 @smalltt svn/llvm-project/compiler-rt/trunk/lib/asan/scripts/asan_symbolize.py[ ][][]@smallrm : it makes use of [99] Underfull \hbox (badness 10000) in paragraph at lines 8624--8629 []@textrm For op-tions avail-able @textit via @textrm the en-vi-ron-ment vari-a ble @texttt ASAN_OPTIONS[] @textrm see Underfull \hbox (badness 10000) in paragraph at lines 8624--8629 [][]@texttt https://code.google.com/p/address-sanitizer/wiki/AddressSanitizerFL ags[][][]@textrm . Underfull \hbox (badness 10000) in paragraph at lines 8640--8644 []@textrm Recent ver-sions$[]$ added the flag `@texttt -fsanitize-address-use-a fter-scope[]@textrm '[]: see [100 Underfull \hbox (badness 4120) in paragraph at lines 24985--24992 []\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/ n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from [365 [7]]] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8688--8688 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8716--8718 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by Underfull \hbox (badness 6542) in paragraph at lines 8754--8759 []@textrm See [][]@texttt https://gcc.gnu.org/onlinedocs/gcc/Instrumentation-Op tions.html[][][] @textrm (or the Underfull \hbox (badness 10000) in paragraph at lines 8777--8781 []@textrm From GCC 8 @texttt signed-integer-overflow[] @textrm is no longer a d e-fault part of Underfull \hbox (badness 10000) in paragraph at lines 8777--8781 @textrm `@texttt -fsanitize=undefined[]@textrm '[], but can be spec-i-fied sep- a-rately. It adds op-tions [101 [8 [366]]] Underfull \hbox (badness 5878) in paragraph at lines 8804--8808 []@textrm For more de-tails on the topic see [][]@texttt http://blog.regehr.org /archives/213[][][] @textrm and Underfull \hbox (badness 10000) in paragraph at lines 8818--8825 []@textrm Recent ver-sions of @texttt clang[] @textrm on `@texttt x86_64[]@text rm '[] Linux have `Thread-San-i-tizer' Underfull \hbox (badness 4441) in paragraph at lines 8818--8825 @textrm ([][]@texttt https://code.google.com/p/thread-sanitizer/[][][]@textrm ) , a `data race de-tec-tor for C/C@texttt ++ Overfull \hbox (50.80455pt too wide) in paragraph at lines 8847--8847 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [102] [9 [103]] Underfull \hbox (badness 1694) in paragraph at lines 25121--25124 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [367 [10 [104]]] [105] Chapter 5 [106 [11] [368]] Chapter 3 [12] [107 [13] [369]] [108] [14] [109 Chapter 4 [15] [370]] [110 [16]] Chapter 5 [17 Underfull \hbox (badness 1603) in paragraph at lines 25368--25370 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [371 [111]]] [112 Overfull \hbox (73.28088pt too wide) in paragraph at lines 25491--25499 \T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats", "methods")\T1/ptm/m/n/10 . [372 [18]]] Underfull \hbox (badness 4505) in paragraph at lines 9749--9754 @textrm Without or with reg-is-tra-tion, these will both work. If @texttt R_ini t_mypkg[] @textrm calls @texttt R_ [113 [19]] [373] [114 [20]] Underfull \hbox (badness 5475) in paragraph at lines 25628--25638 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 3271) in paragraph at lines 25670--25673 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able Underfull \hbox (badness 10000) in paragraph at lines 25685--25687 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [374 [115]] [21 Overfull \hbox (30.03963pt too wide) in paragraph at lines 9995--9995 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [116]] [375] [117] [376] [22] [118 Underfull \hbox (badness 3138) in paragraph at lines 25948--25954 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 2088) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by [377]] [23 [119]] [120] Underfull \hbox (badness 1194) in paragraph at lines 25961--25964 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 1389) in paragraph at lines 25987--25989 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 10000) in paragraph at lines 25999--26003 []\T1/ptm/m/n/10 string used as the user agent in HTTP(S) re-quests. If Underfull \hbox (badness 6592) in paragraph at lines 25999--26003 \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , re-quests will be made with-out a user agen t header. The de-fault is Underfull \hbox (badness 10000) in paragraph at lines 26004--26010 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 26019--26024 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Overfull \hbox (49.4607pt too wide) in paragraph at lines 26025--26036 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][](type = "both ") Underfull \hbox (badness 1009) in paragraph at lines 26037--26040 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 26047--26059 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see Underfull \hbox (badness 1072) in paragraph at lines 26047--26059 [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 . Pos-si-ble val-ues ar e \T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a [378 [24]] Chapter 6 [25] Overfull \hbox (61.1125pt too wide) in paragraph at lines 10435--10437 [][][]@smallrm For ex-am-ple, `@smalltt _GLIBCXX_USE_CXX11_ABI[]@smallrm '[] in @smalltt g++[] @smallrm 5.1 and later: [][]@smalltt https://gcc.gnu.org/online docs/libstdc++/manual/using_ [121 Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 \T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 26061--26068 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Overfull \hbox (34.78088pt too wide) in paragraph at lines 26061--26068 \T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [379]] [26 [380]] [381 Overfull \hbox (16.31242pt too wide) in paragraph at lines 10574--10574 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [122 [27]]] [382 [28]] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26392--26392 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec, 300X faster[] Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n /10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 \T1/pcr/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A[c(arrayindex.x, arrayindex.y)] [383] Chapter 7 [29 [123]] [384 [30]] [124] [385] [31 [125] Chapter 8 [32]] [386] [126 [33] [387]] [34 [413]] [169 ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T 1/ptm/m/n/10 '. [443]] (Function and variable index) [179] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-exts.vrs [444] [445] Underfull \hbox (badness 7558) in paragraph at lines 30664--30668 []\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1968) in paragraph at lines 30674--30676 []\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P OSIX stan-dard, and the Underfull \hbox (badness 5417) in paragraph at lines 30679--30682 [][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/ ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 ls[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 30683--30685 []\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la urikari . net / tre / documentation / Underfull \hbox (badness 10000) in paragraph at lines 30686--30688 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / [446] [180 [447]] [448] [449] [450] [181 [451]]> Underfull \hbox (badness 10000) in paragraph at lines 31091--31095 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [452 [35]] [36] [462] 1e7))[] [463>]>] [466]] Chapter 10 [41] Output written on R-exts.pdf (190 pages, 1100689 bytes). Transcript written on R-exts.log. [467 [42]] [43] Underfull \hbox (badness 2302) in paragraph at lines 32188--32195 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3815) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [468] [44] [45] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32240--32240 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [469 [46]] [47] [48 Underfull \hbox (badness 1158) in paragraph at lines 32344--32349 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if [470]] [49] Chapter 11 [50] Underfull \hbox (badness 10000) in paragraph at lines 32371--32377 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1953) in paragraph at lines 32371--32377 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o c-tal and hex-adec-i-mal rep-re- [471 [51]] [52] Underfull \hbox (badness 10000) in paragraph at lines 32447--32452 []\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by Underfull \hbox (badness 6725) in paragraph at lines 32447--32452 \T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10 will give an empty [472] [53] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32529--32529 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [473] [54] [474 [55]] [475] [56] [57] Underfull \hbox (badness 2809) in paragraph at lines 32793--32799 []\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2, ..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment Underfull \hbox (badness 7759) in paragraph at lines 32800--32803 []\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/ n/10 1, 2, ..., length.out \T1/ptm/m/n/10 un-less [476] [58] [59] [477 [60]] [478 [61]] Chapter 12 [62] [479] [63] [64 [480]] [65 [481]] [66] [482] [67] [483] [68] [484] [69] [70 [485]] [71] Overfull \hbox (66.78088pt too wide) in paragraph at lines 33939--33939 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [493] [72] [73 [505]] [506] [74] [507] [75 [508]] Underfull \hbox (badness 10000) in paragraph at lines 6412--6415 @textrm and these can be ac-cessed from R via the pack-age [][]@textbf rggobi[] []@textrm , de-scribed at Chapter 13 [76] [509] Overfull \hbox (12.78088pt too wide) in paragraph at lines 35129--35129 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 35130--35130 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [510] [77] Chapter 14 [78] [511] [79] [512] Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as `@texttt \\server\dir1\dir2\file[]@t extrm '[] and Underfull \hbox (badness 5189) in paragraph at lines 6647--6652 @textrm `@texttt \\?\UNC\server\dir1\dir2\file[]@textrm '[]) are not sup-porte d, but they may work in [80] Underfull \hbox (badness 10000) in paragraph at lines 6724--6728 []@textrm There is some con-fu-sion be-tween @texttt xz[] @textrm and @texttt l zma[] @textrm com-pres-sion (see Underfull \hbox (badness 10000) in paragraph at lines 6724--6728 [][]@texttt https://en.wikipedia.org/wiki/Xz[][][] @textrm and [][]@texttt http s://en.wikipedia.org/wiki/LZMA[][][]@textrm ): Appendix A [81 [513]] [82 Overfull \hbox (63.78036pt too wide) in paragraph at lines 35394--35394 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [514]] [83] Underfull \hbox (badness 10000) in paragraph at lines 35478--35488 []\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/ pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want Underfull \hbox (badness 8113) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s tart, in-sert a call Underfull \hbox (badness 10000) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n /10 ' file. For ex-am-ple, Underfull \hbox (badness 6542) in paragraph at lines 35478--35488 \T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta ch no ex-tra pack-ages on Underfull \hbox (badness 5189) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) ( or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi- Underfull \hbox (badness 4193) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/ 10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or [515 Appendix B [84]] Underfull \hbox (badness 2635) in paragraph at lines 7023--7029 @textrm `@texttt --no-site-file[]@textrm '[] was given. The name of this file is taken from the value Underfull \hbox (badness 2158) in paragraph at lines 7023--7029 @textrm of the @texttt R_PROFILE[] @textrm en-vi-ron-ment vari-able. If that v ari-able is un-set, the de-fault [85 Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1496) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be Underfull \hbox (badness 1728) in paragraph at lines 35534--35541 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm /m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment [516]] [517 [86]] [87 [518]] Underfull \hbox (badness 4752) in paragraph at lines 7295--7307 []@textrm In ad-di-tion, you can use op-tions `@texttt --arch=[]@textrm '[], `@ texttt --no-environ[]@textrm '[], `@texttt --no-init-file[]@textrm '[], [88] [519] [89] [520] [90] Appendix C [91] Underfull \hbox (badness 10000) in paragraph at lines 35875--35881 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form at \T1/ptm/m/n/10 meth-ods is [521] [92] [522 Appendix D [93]] (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-intro.vrs [523] Underfull \hbox (badness 1163) in paragraph at lines 36064--36071 []\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10 %OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr /m/n/10 0 <= n <= 6 Underfull \hbox (badness 8132) in paragraph at lines 36064--36071 \T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no t fol-lowed by a digit, it uses the set-ting of [524] [94 [525]] [526] [95 [527]] Underfull \hbox (badness 1142) in paragraph at lines 36346--36352 []\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1 /ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or Overfull \hbox (0.78088pt too wide) in paragraph at lines 36361--36361 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [528] [529)] Appendix E [96] [530 (/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual/R-intro.cps] [97 [531]] Overfull \hbox (6.78088pt too wide) in paragraph at lines 36609--36609 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36653--36653 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [532) Appendix F] [98] [99] [533] ) (see the transcript file for additional information)]] [536]] summary.data.frame(...), defau lt precision [540>] [542] Output written on R-intro.pdf (105 pages, 703654 bytes). Transcript written on R-intro.log. [543] Underfull \hbox (badness 2762) in paragraph at lines 37431--37440 \T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there is a match then that el-e-ment is eval-u-ated un-less Underfull \hbox (badness 1466) in paragraph at lines 37431--37440 \T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is eval-u-ated, so for ex-am-ple [544] Overfull \hbox (31.3804pt too wide) in paragraph at lines 37493--37493 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [545] [546] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37658--37658 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS 1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. [547] Overfull \hbox (20.58041pt too wide) in paragraph at lines 37696--37696 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] [548] Underfull \hbox (badness 3219) in paragraph at lines 37745--37750 []\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple Underfull \hbox (badness 1107) in paragraph at lines 37745--37750 \T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr /m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match [549] Underfull \hbox (badness 2452) in paragraph at lines 37835--37838 \T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/ ptm/m/n/10 sys-tem call. The lo-gin name comes Underfull \hbox (badness 10000) in paragraph at lines 37835--37838 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and [550] [551] [552] Underfull \hbox (badness 10000) in paragraph at lines 38022--38026 []\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents \T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n /10 and Underfull \hbox (badness 1584) in paragraph at lines 38037--38040 []\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \ T1/ptm/m/n/10 and [553] [554] Overfull \hbox (25.98041pt too wide) in paragraph at lines 38169--38169 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [555] Overfull \hbox (20.58041pt too wide) in paragraph at lines 38239--38239 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/pcr/ m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used [556] [557] [558] Underfull \hbox (badness 1082) in paragraph at lines 38377--38380 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [559] [560] Underfull \hbox (badness 1038) in paragraph at lines 38564--38567 []\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or [561] [562] [563] [564] [565] [566] Underfull \hbox (badness 1515) in paragraph at lines 38928--38931 []\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc r/m/n/10 stderr = TRUE \T1/ptm/m/n/10 im-plies [567] [568] [569] Underfull \hbox (badness 4096) in paragraph at lines 39169--39172 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[ ][][]\T1/ptm/m/n/10 , [570] [571] Underfull \hbox (badness 10000) in paragraph at lines 39283--39287 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., [572] [573] Overfull \hbox (63.78036pt too wide) in paragraph at lines 39436--39436 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 39438--39438 [] \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr /m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 39440--39440 [] \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n /9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 = NULL ), dim=4, dimnames=list(as.character(2:5)))))[] [574] Underfull \hbox (badness 10000) in paragraph at lines 39453--39455 []\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha t was reg-is-tered ear-lier via [575] Underfull \hbox (badness 10000) in paragraph at lines 39533--39536 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [576] [577] Underfull \hbox (badness 1867) in paragraph at lines 39651--39655 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 5475) in paragraph at lines 39713--39717 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / [578] [579] [580] [581] [582] [583] [584] Underfull \hbox (badness 10000) in paragraph at lines 40131--40138 \T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/ n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', ` \T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ', Underfull \hbox (badness 4467) in paragraph at lines 40187--40196 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn s the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 40187--40196 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, Underfull \hbox (badness 10000) in paragraph at lines 40197--40205 []\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op -tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de- Underfull \hbox (badness 10000) in paragraph at lines 40197--40205 \T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da tabase at Underfull \hbox (badness 1303) in paragraph at lines 40197--40205 \T1/pcr/m/n/10 file.path(R.home("share"), "zoneinfo") \T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 ' [585] Underfull \hbox (badness 1337) in paragraph at lines 40263--40271 \T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 / usr/local/etc\T1/ptm/m/n/10 ' or Underfull \hbox (badness 10000) in paragraph at lines 40272--40275 []\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym -link tar-get name of [586] Underfull \hbox (badness 4429) in paragraph at lines 40329--40331 [][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol- Overfull \hbox (31.3804pt too wide) in paragraph at lines 40338--40338 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [587] [588] [589] Underfull \hbox (badness 10000) in paragraph at lines 40555--40557 []\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal l-ing [590] [591] Overfull \hbox (15.18042pt too wide) in paragraph at lines 40677--40677 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15 g)\n", ncp))),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 40679--40679 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] Underfull \vbox (badness 10000) has occurred while \output is active [592] [593] [594] [595] [596] Underfull \hbox (badness 6542) in paragraph at lines 41041--41043 []\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x )\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and [597] [598] [599] Underfull \hbox (badness 3460) in paragraph at lines 41207--41210 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1708) in paragraph at lines 41214--41222 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e r-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 3713) in paragraph at lines 41214--41222 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less Underfull \hbox (badness 10000) in paragraph at lines 41223--41227 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10 tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in- Underfull \hbox (badness 10000) in paragraph at lines 41223--41227 \T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 , some-thing like Underfull \hbox (badness 3281) in paragraph at lines 41223--41227 \T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s im-ple er-ror han-dler func- Underfull \hbox (badness 4859) in paragraph at lines 41244--41249 [][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers and sup-press-ing the print-ing of er-ror mes-sages; [600] Underfull \hbox (badness 3895) in paragraph at lines 41306--41318 []\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in Underfull \hbox (badness 1303) in paragraph at lines 41306--41318 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , [601] [602] [603] Underfull \hbox (badness 10000) in paragraph at lines 41491--41494 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [604] [605] Overfull \hbox (9.78043pt too wide) in paragraph at lines 41628--41628 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [606] [607] [608] [609] [610] [611] Overfull \hbox (4.38043pt too wide) in paragraph at lines 42095--42095 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] [612] Overfull \hbox (20.58041pt too wide) in paragraph at lines 42104--42104 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little- endian platform[] [613] Underfull \hbox (badness 1803) in paragraph at lines 42221--42224 []\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1 0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ), Underfull \hbox (badness 2334) in paragraph at lines 42225--42232 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and [614] Underfull \hbox (badness 4726) in paragraph at lines 42251--42255 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec tor(x, mode = "numeric") \T1/ptm/m/n/10 can be Underfull \hbox (badness 1122) in paragraph at lines 42251--42255 \T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/ 10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x , mode = [615] [616] Underfull \hbox (badness 3668) in paragraph at lines 42440--42442 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [617] [618] Overfull \hbox (36.78088pt too wide) in paragraph at lines 42544--42544 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [619] Overfull \hbox (4.38043pt too wide) in paragraph at lines 42619--42619 []\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n /9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 42627--42627 []\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) # There were 105 warnings ...[] [620] [621] Underfull \hbox (badness 6220) in paragraph at lines 42757--42762 []\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][] (.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true, Underfull \hbox (badness 3098) in paragraph at lines 42757--42762 \T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array Ind() \T1/ptm/m/n/10 (and hence, Underfull \hbox (badness 1533) in paragraph at lines 42757--42762 \T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty, Underfull \hbox (badness 6592) in paragraph at lines 42773--42778 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [622] Underfull \hbox (badness 1603) in paragraph at lines 42792--42796 [][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[] [][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the [623] Underfull \hbox (badness 10000) in paragraph at lines 42857--42860 []\T1/ptm/m/n/10 If this ex-tremum is unique (or empty), the re-sults are the s ame as Underfull \hbox (badness 10000) in paragraph at lines 42857--42860 \T1/ptm/m/n/10 (but more ef-fi-cient than) \T1/pcr/m/n/10 which(x == min(x, na. rm = TRUE)) \T1/ptm/m/n/10 or Underfull \hbox (badness 2818) in paragraph at lines 42863--42869 []\T1/ptm/m/n/10 For a [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with both \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 a nd \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 val-ues, \T1/pcr/m/n/10 which.min(x) \T1/ ptm/m/n/10 and Overfull \hbox (15.18042pt too wide) in paragraph at lines 42898--42898 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [624] [625] Underfull \hbox (badness 1622) in paragraph at lines 42992--42994 []\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer . [626] [627] [628] [629] Underfull \hbox (badness 10000) in paragraph at lines 43260--43265 []\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu nc-tion than [][]\T1/pcr/m/n/10 rank[][][] Underfull \hbox (badness 10000) in paragraph at lines 43260--43265 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to Underfull \hbox (badness 10000) in paragraph at lines 43260--43265 \T1/pcr/m/n/10 rank(x, ties.method = "min", na.last = "keep")\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are [630] Underfull \hbox (badness 2846) in paragraph at lines 43354--43358 []\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [631] Overfull \hbox (4.38043pt too wide) in paragraph at lines 43394--43394 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 43415--43419 []\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard ' reg-exps, in-clud-ing el-e-ments named [632]) (./compiler-pkg.tex Chapter 2. [633] Underfull \hbox (badness 2884) in paragraph at lines 101--115 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 options \T1/ptm/m/n/10 ar-gu-ment can be us ed to con-trol com-piler op-er-a-tion. There are cur- Underfull \hbox (badness 10000) in paragraph at lines 101--115 \T1/ptm/m/n/10 rently four op-tions: \T1/pcr/m/n/10 optimize\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 suppressAll\T1/ptm/m/n/10 , \T1/pcr/m/n/10 suppressUndefined\T1/pt m/m/n/10 , and [634] [635] [636]) (./datasets-pkg.tex Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple te list, use [637] [638] [639] [640] [641] Overfull \hbox (15.18042pt too wide) in paragraph at lines 301--301 [] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang e", cex = 1.2,[] [642] Overfull \hbox (4.38043pt too wide) in paragraph at lines 379--379 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi ven = FALSE)[] Underfull \vbox (badness 1033) has occurred while \output is active [643] [644] [645] [646] [647] Overfull \hbox (66.81013pt too wide) in paragraph at lines 702--705 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [648] [649] Overfull \hbox (66.81013pt too wide) in paragraph at lines 835--838 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [650] [651] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [652] [653] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1146--1149 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [654] [655] [656] [657] [658] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1456--1456 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption time (sec)")[] [659] [660] Underfull \hbox (badness 10000) in paragraph at lines 1541--1544 []\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r evenue\T1/ptm/m/n/10 , Underfull \hbox (badness 2903) in paragraph at lines 1541--1544 \T1/pcr/m/n/10 price.index\T1/ptm/m/n/10 , \T1/pcr/m/n/10 income.level\T1/ptm/m /n/10 , and \T1/pcr/m/n/10 market.potential \T1/ptm/m/n/10 ob-tained from the a bove [661] [662] [663] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1730--1733 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [664] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1824--1824 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil y = binomial())[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1832--1832 [] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum), data = infert)[] [665] [666] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1948--1948 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1949--1949 [] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d ni3[[3]]))))[] [667] [668] [669] [670] Overfull \hbox (66.81013pt too wide) in paragraph at lines 2152--2155 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [671] [672] [673] [674] [675] [676] [677] [678] Overfull \hbox (66.81013pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [679] Overfull \vbox (13.87083pt too high) has occurred while \output is active [680] Underfull \vbox (badness 1789) has occurred while \output is active [681] [682] Overfull \vbox (12.25539pt too high) has occurred while \output is active [683] [684] Overfull \vbox (17.12102pt too high) has occurred while \output is active [685] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3137--3137 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [686] [687] [688] [689] [690] [691] [692] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3594--3594 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [693] [694] Overfull \hbox (66.81013pt too wide) in paragraph at lines 3742--3745 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [695] Overfull \vbox (10.49593pt too high) has occurred while \output is active [696] Underfull \hbox (badness 1173) in paragraph at lines 3876--3880 \T1/ptm/m/it/10 Ed-u-ca-tion\T1/ptm/m/n/10 , \T1/ptm/b/n/10 3\T1/ptm/m/n/10 . [ ][]$\T1/pcr/m/n/10 https : / / www . amstat . org / publications / jse / v3n3 / datasets . Overfull \vbox (27.49593pt too high) has occurred while \output is active [697] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3951--3951 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 3980--3983 []\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www -[]personal . buseco . monash . edu . au / Underfull \hbox (badness 10000) in paragraph at lines 3989--3991 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h ttps : / / web . archive . org / web / Underfull \hbox (badness 10000) in paragraph at lines 3989--3991 \T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma n / sitephotos / [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711]) (./grDevices-pkg.tex [712] Chapter 4. [713] [714] [715] [716] [717] [718] Underfull \hbox (badness 10000) in paragraph at lines 374--382 []\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til e, i.e., close to Underfull \hbox (badness 10000) in paragraph at lines 374--382 [][]\T1/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where [719] Overfull \hbox (6.78088pt too wide) in paragraph at lines 479--479 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [720] [721] [722] [723] [724] [725] [726] [727] [728] Underfull \hbox (badness 5175) in paragraph at lines 1082--1084 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [729] Underfull \hbox (badness 1325) in paragraph at lines 1144--1150 \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 , [730] Underfull \hbox (badness 10000) in paragraph at lines 1185--1187 []\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2 . com / Lab / Graphics / Colors / [731] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1237--1237 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] [732] Underfull \hbox (badness 1173) in paragraph at lines 1279--1282 []\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col- ors that will be used in plot-ting, call-ing [733] [734] [735] Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 []\T1/ptm/m/n/10 character: Which events can be gen-er-ated on Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 \T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 \T1/pcr/m/n/10 c("MouseDown", "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10 , Underfull \hbox (badness 2221) in paragraph at lines 1539--1542 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture, oth-er-wise a ma-trix of color names (for [736] Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 []\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 [][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is [737] [738] [739] Underfull \hbox (badness 1565) in paragraph at lines 1767--1772 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to pro-duce and print a postscript copy. This will not Underfull \hbox (badness 1354) in paragraph at lines 1767--1772 \T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10 for how to set this up. Win-dows users may pre-fer to use [740] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1850--1850 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] [741] Underfull \hbox (badness 1184) in paragraph at lines 1891--1901 []\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m /n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in- Underfull \hbox (badness 2057) in paragraph at lines 1891--1901 \T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p tm/m/n/10 , [742] Underfull \hbox (badness 10000) in paragraph at lines 1996--1998 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [743] [744] Underfull \hbox (badness 6758) in paragraph at lines 2157--2160 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [745] [746] Underfull \hbox (badness 2326) in paragraph at lines 2267--2277 \T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra phicsEventHandlers \T1/ptm/m/n/10 to re-place Underfull \hbox (badness 2318) in paragraph at lines 2267--2277 \T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co m-pat-i-bil-ity with pre-2.12.0 Underfull \hbox (badness 2460) in paragraph at lines 2267--2277 \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e vent han-dlers is to set them us-ing Underfull \hbox (badness 1221) in paragraph at lines 2267--2277 \T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics [747] [748] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2370--2370 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r" , yaxs = "r") {[] Underfull \vbox (badness 10000) has occurred while \output is active [749] [750] [751] [752] [753] [754] Underfull \hbox (badness 10000) in paragraph at lines 2750--2751 Underfull \vbox (badness 10000) has occurred while \output is active [755] [756] [757] [758] [759] [760] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3156--3156 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", scale.in = 255))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3157--3157 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] Underfull \hbox (badness 1210) in paragraph at lines 3188--3190 []\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m /n/10 giv-ing the num-ber of rows and columns, ful-fill-ing [761] Underfull \hbox (badness 10000) in paragraph at lines 3248--3253 []\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [762] [763] [764] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3407--3407 []\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al pha = 1) [765] Underfull \hbox (badness 3525) in paragraph at lines 3514--3517 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as [766] Underfull \hbox (badness 1968) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [767] [768] [769] [770] Underfull \hbox (badness 5939) in paragraph at lines 3822--3827 []\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\ T1/ptm/m/n/10 , [771] [772] [773] [774] [775] Underfull \hbox (badness 7576) in paragraph at lines 4199--4206 \T1/pcr/m/n/10 / / www . adobe . com / products / postscript / pdfs / PLRM . pd f$[][] \T1/ptm/m/n/10 or PDF [][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 3701) in paragraph at lines 4199--4206 \T1/pcr/m/n/10 www . adobe . com / devnet / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i- [776] Underfull \vbox (badness 10000) has occurred while \output is active [777] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4316--4316 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [778] Underfull \hbox (badness 1502) in paragraph at lines 4363--4368 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the type of anti-aliasing (if any) to be [779] [780] Underfull \hbox (badness 1348) in paragraph at lines 4515--4518 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also Underfull \hbox (badness 4765) in paragraph at lines 4525--4527 [][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if Overfull \hbox (9.78043pt too wide) in paragraph at lines 4539--4539 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, height = 768)[] [781] Underfull \hbox (badness 5077) in paragraph at lines 4579--4585 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as Underfull \hbox (badness 1342) in paragraph at lines 4595--4597 []\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [782] Underfull \hbox (badness 1874) in paragraph at lines 4672--4680 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as [783] Underfull \hbox (badness 1755) in paragraph at lines 4739--4741 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [784] [785] Underfull \hbox (badness 7344) in paragraph at lines 4910--4912 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso Underfull \hbox (badness 7397) in paragraph at lines 4921--4925 [][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm /m/n/10 which is called from both [786] [787] Underfull \hbox (badness 1552) in paragraph at lines 5034--5043 \T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG othic"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m /n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW Helvetica"\T1/ptm/m/n/10 ), Underfull \hbox (badness 2221) in paragraph at lines 5044--5046 []\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and [788] Underfull \hbox (badness 4686) in paragraph at lines 5076--5082 \T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap an1Ryumin" \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 5102--5109 []\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / [789] [790] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5203--5203 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [791] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5315--5315 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] Underfull \hbox (badness 1648) in paragraph at lines 5321--5325 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [792] [793] Underfull \hbox (badness 10000) in paragraph at lines 5401--5403 []\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10 for on-screen de-vices and to Underfull \hbox (badness 1072) in paragraph at lines 5437--5443 []\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots due to cor-rupted or du-pli- [794] [795] [796] [797] [798] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5759--5759 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15, sep = "."))[] Underfull \hbox (badness 10000) in paragraph at lines 5772--5775 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [799] [800] [801] [802] [803] [804] [805] Underfull \hbox (badness 1189) in paragraph at lines 6169--6171 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [806] Underfull \hbox (badness 10000) in paragraph at lines 6267--6269 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and Underfull \hbox (badness 10000) in paragraph at lines 6306--6313 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T 1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and Underfull \hbox (badness 2469) in paragraph at lines 6306--6313 \T1/pcr/m/n/10 expression(10^degree)\T1/ptm/m/n/10 ) have been seen on Linux sy s-tems which have the Wine [807] Underfull \hbox (badness 3088) in paragraph at lines 6390--6394 []\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do- Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and [808] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6435--6435 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [809] Underfull \hbox (badness 10000) in paragraph at lines 6467--6470 []\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][ ] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 -- [810] Underfull \hbox (badness 5637) in paragraph at lines 6558--6564 \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n /10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 1721) in paragraph at lines 6591--6594 []\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt p : / / www . schmidt-[]web-[]berlin . de / [811] [812] [813] Underfull \hbox (badness 6157) in paragraph at lines 6748--6751 \T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them via Underfull \hbox (badness 1231) in paragraph at lines 6759--6761 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [814] [815] [816]) (./graphics-pkg.tex Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag es, use [817] [818] [819] [820] Underfull \hbox (badness 1412) in paragraph at lines 287--292 []\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal data. \T1/ptm/m/it/10 SAS User Group In-ter-na- [821] [822] [823] Underfull \hbox (badness 2726) in paragraph at lines 466--472 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark lo-ca-tions are com-puted in-ter-nally (the same way [824] [825] [826] Underfull \hbox (badness 10000) in paragraph at lines 659--663 []\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m /n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or Underfull \hbox (badness 3250) in paragraph at lines 659--663 [][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/ m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1 0 if Underfull \hbox (badness 2735) in paragraph at lines 687--694 []\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [827] Overfull \hbox (4.38043pt too wide) in paragraph at lines 744--744 [] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n intLog = 5))[] [828] [829] Underfull \hbox (badness 1062) in paragraph at lines 853--856 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic h di-vide ad-ja-cent (non-stacked!) bars [830] [831] [832] [833] [834] [835] [836] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1290--1290 [] \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = NULL,[] [837] Underfull \hbox (badness 1024) in paragraph at lines 1335--1343 \T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 cex.lab\T1/ptm/m/n/10 , and Underfull \hbox (badness 1248) in paragraph at lines 1363--1369 \T1/ptm/m/n/10 width, point char-ac-ter, point size ex-pan-sion, color, and bac k-ground Underfull \hbox (badness 6893) in paragraph at lines 1363--1369 \T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su p-presses the point, and Underfull \hbox (badness 3375) in paragraph at lines 1369--1371 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), Overfull \hbox (19.3703pt too wide) in paragraph at lines 1391--1395 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10 xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim = range(at, *) + c(-0.5, 0.5)\T1/ptm/m/n/10 . [838] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1439--1439 []\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi s=..,main=..)")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1440--1440 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi s=..,main=..)")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1446--1446 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill = "grey40",[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1447--1447 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [839] [840] [841] [842] [843] Underfull \hbox (badness 10000) in paragraph at lines 1747--1753 [][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 (and [844] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1784--1784 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1793--1793 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [845] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1876--1876 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [846] [847] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2005--2005 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept h, rows = 1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2010--2010 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [848] [849] [850] [851] [852] Underfull \hbox (badness 1009) in paragraph at lines 2296--2303 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [853] [854] [855] [856] [857] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2624--2624 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [858] [859] Underfull \hbox (badness 5878) in paragraph at lines 2785--2789 \T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T 1/ptm/m/n/10 and in gen-eral sat-isfy Underfull \hbox (badness 10000) in paragraph at lines 2810--2813 []\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1 /ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n /10 or [860] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2838--2838 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2842--2842 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] [861] Underfull \hbox (badness 10000) in paragraph at lines 2894--2897 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as [862] [863] [864] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3091--3091 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL SE, pch = 19, ...)[] Overfull \hbox (79.98035pt too wide) in paragraph at lines 3096--3096 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [865] Underfull \hbox (badness 1755) in paragraph at lines 3161--3165 []\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/ 10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/ n/10 , [866] Underfull \hbox (badness 10000) in paragraph at lines 3236--3241 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3236--3241 [][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3236--3241 [][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/ n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is [867] [868] [869] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3423--3423 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 0, horiz = TRUE)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3442--3442 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3446--3446 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [870] [871] [872] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3623--3623 [] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c ex = 0.8, adj = 0)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3624--3624 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3663--3663 [] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj = c(0, 0.3))[] Underfull \vbox (badness 10000) has occurred while \output is active [873] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3715--3715 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3723--3723 []\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset = .05", inset = .05)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3725--3725 []\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset = .02",inset = .02)[] Underfull \vbox (badness 10000) has occurred while \output is active [874] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3733--3733 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] Underfull \hbox (badness 10000) in paragraph at lines 3796--3800 [][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method ; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for [875] [876] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3907--3907 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [877] Underfull \hbox (badness 1867) in paragraph at lines 3950--3954 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [878] [879] Underfull \hbox (badness 3930) in paragraph at lines 4114--4116 []\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a mul-ti-ple of [880] [881] [882] [883] Underfull \hbox (badness 1924) in paragraph at lines 4400--4405 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [884] Underfull \hbox (badness 1286) in paragraph at lines 4424--4427 \T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 oma \T1/ptm/m/n/10 when chang-ing Underfull \hbox (badness 3229) in paragraph at lines 4432--4437 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [885] [886] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4525--4525 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel = panel.cor,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4530--4530 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4574--4574 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = " blue") # hmm...[] [887] Underfull \hbox (badness 1264) in paragraph at lines 4648--4661 \T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/ m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1 /ptm/m/n/10 , [888] [889] Underfull \hbox (badness 7925) in paragraph at lines 4785--4791 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. [890] [891] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 <"/tmp/B.61K3e5/BUILD/R-3.5.2/build/library/graphics/help/figures/"mai.pdf, id= 15566, 289.08pt x 289.08pt> [892 ] Underfull \hbox (badness 10000) in paragraph at lines 4977--4979 <"/tmp/B.61K3e5/BUILD/R-3.5.2/build/library/graphics/help/figures/"oma.pdf, id= 15580, 259.97125pt x 332.24126pt> [893 ] [894] Underfull \hbox (badness 10000) in paragraph at lines 5167--5169 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [895] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5223--5223 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5224--5224 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] Underfull \vbox (badness 10000) has occurred while \output is active [896] [897] Underfull \hbox (badness 3954) in paragraph at lines 5325--5328 []\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm /m/n/10 co-or-di-nates. Of-ten used with Underfull \hbox (badness 10000) in paragraph at lines 5381--5385 \T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and [898] [899] [900] [901] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5589--5589 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5590--5590 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 5641--5645 []\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing or an er-ror; us-ing, e.g., Underfull \hbox (badness 1024) in paragraph at lines 5641--5645 \T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/ n/10 type = "p" \T1/ptm/m/n/10 for S com- [902] [903] [904] [905] [906] [907] [908] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6068--6068 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6074--6074 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [909] [910] [911] [912] [913] [914] Underfull \hbox (badness 10000) in paragraph at lines 6501--6503 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [915] [916] Underfull \hbox (badness 1028) in paragraph at lines 6595--6597 []\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th is works as a mul-ti-ple of <"/tmp/B.61K3e5/BUILD/R-3.5.2/build/library/graphics/help/figures/"pch.pdf, id= 16018, 361.35pt x 50.1875pt> Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639 [][] [917 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6732--6732 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [918] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6763--6763 [] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab = "", main = main)[] Underfull \vbox (badness 10000) has occurred while \output is active [919] [920] Underfull \hbox (badness 10000) in paragraph at lines 6885--6887 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr Overfull \hbox (15.18042pt too wide) in paragraph at lines 6912--6912 [] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b order = "red")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6918--6918 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [921] Underfull \hbox (badness 2600) in paragraph at lines 6978--6980 []\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/ pcr/m/n/10 "winding" \T1/ptm/m/n/10 or [922] [923] [924] Underfull \hbox (badness 1881) in paragraph at lines 7167--7172 []\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m /n/10 par("fg")\T1/ptm/m/n/10 . Use [925] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7210--7210 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [926] [927] [928] [929] [930] [931] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7597--7597 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7601--7601 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [932] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7613--7613 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [933] [934] [935] [936] [937] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7962--7962 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7965--7965 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] [938] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7969--7969 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [939] [940] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8140--8140 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...) Overfull \hbox (36.78088pt too wide) in paragraph at lines 8141--8141 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [941] [942] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8245--8245 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8256--8261 []\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1 /pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for [943] [944] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8364--8364 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035 , seg.lwd = .8)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8379--8379 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [945] [946] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8510--8510 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [947] [948] [949] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8695--8695 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] Underfull \hbox (badness 10000) in paragraph at lines 8723--8725 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8725--8727 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8757--8763 []\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr /m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m /n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing [950]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8805 \HeaderA{units}{Graphical Units}{units} [951] Underfull \hbox (badness 1205) in paragraph at lines 8870--8872 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [952] [953] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8989--8989 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 2, length = 0.1)[] [954]) (./grid-pkg.tex Chapter 6. [955] [956] [957] [958] [959] [960] Underfull \hbox (badness 10000) in paragraph at lines 385--391 \T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo r ex-am-ple, Underfull \hbox (badness 1024) in paragraph at lines 385--391 \T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f ault be-haviour for grobs is to [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1025--1025 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1027--1027 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1029--1029 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] Underfull \vbox (badness 10000) has occurred while \output is active [971] Underfull \hbox (badness 1430) in paragraph at lines 1074--1079 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [972] [973] [974] Underfull \hbox (badness 3219) in paragraph at lines 1288--1291 []\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject de-scrib-ing a cir-cle), but only [975] [976] [977] [978] [979] [980] [981] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1675--1675 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [982] [983] [984] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1889--1889 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla ck"), name="r1")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1890--1890 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey" ), name="r2")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1891--1891 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [985] Underfull \hbox (badness 2961) in paragraph at lines 1926--1931 []\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 , [986] Underfull \hbox (badness 1430) in paragraph at lines 1985--1990 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- Underfull \hbox (badness 4479) in paragraph at lines 2014--2017 []\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10 to al-low a grob to per-form cus-tom ac-tions and [987] [988] [989] Underfull \hbox (badness 2894) in paragraph at lines 2221--2228 []\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de -scrib-ing a frame), but only [990] [991] [992] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2377--2377 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] Underfull \hbox (badness 1430) in paragraph at lines 2389--2394 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [993] [994] [995] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2590--2590 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2622--2622 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [996] [997] [998] [999] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2864--2864 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [1000] [1001] [1002] [1003] [1004] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3179--3179 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1005] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3275--3275 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] [1006] Underfull \hbox (badness 2799) in paragraph at lines 3309--3315 []\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage " \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see [1007] [1008] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3401--3401 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3408--3408 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1009] [1010] [1011] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3602--3602 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3617--3617 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] Underfull \hbox (badness 1067) in paragraph at lines 4355--4358 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1025] Underfull \hbox (badness 1430) in paragraph at lines 4401--4406 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1026] [1027] [1028] Underfull \hbox (badness 7256) in paragraph at lines 4600--4602 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] Underfull \hbox (badness 10000) in paragraph at lines 5189--5191 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu -ments above are passed to [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] Underfull \hbox (badness 3449) in paragraph at lines 5877--5883 \T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1, "npc") - unit(1, "inches")\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 5877--5883 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1048] [1049] [1050] [1051] [1052] Underfull \hbox (badness 1867) in paragraph at lines 6187--6189 []\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or [1053] Underfull \hbox (badness 10000) in paragraph at lines 6224--6230 [][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV iewport[][][]\T1/ptm/m/n/10 , [1054] [1055] Underfull \hbox (badness 7649) in paragraph at lines 6356--6359 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like [1056] [1057] [1058] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6560--6560 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1059]) (./methods-pkg.tex [1060] Chapter 7. [1061] [1062] Underfull \hbox (badness 1688) in paragraph at lines 166--171 \T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c o-erce meth-ods work. Use [1063] [1064] [1065] Underfull \hbox (badness 1348) in paragraph at lines 392--395 [][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo r-ma-tion about group generic func-tions; [][]Meth- [1066] [1067] Overfull \hbox (15.18042pt too wide) in paragraph at lines 558--558 []\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall y a primitive.[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w ith no arguments[] [1068] Overfull \hbox (4.38043pt too wide) in paragraph at lines 619--619 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho ut arguments[] Underfull \vbox (badness 10000) has occurred while \output is active [1069] Overfull \hbox (25.98041pt too wide) in paragraph at lines 637--637 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th e default method[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 640--640 []\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b y callNextMethod[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the "B0" method[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 672--672 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[ ] Underfull \vbox (badness 10000) has occurred while \output is active [1070] [1071] Underfull \hbox (badness 1546) in paragraph at lines 791--797 []\T1/ptm/m/n/10 A ma-trix (or ma-trix like ob-ject) com-bin-ing the columns (o r rows) of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 . Note Underfull \hbox (badness 3780) in paragraph at lines 791--797 \T1/ptm/m/n/10 that meth-ods must con-struct [][]\T1/pcr/m/n/10 colnames[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 rownames[][][] \T1/ptm/m/n/10 from the co r-re-spond-ing col- Underfull \hbox (badness 1789) in paragraph at lines 791--797 \T1/ptm/m/n/10 umn and row names of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr /m/n/10 y \T1/ptm/m/n/10 (but not from de-pars-ing ar-gu-ment names such as in [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1794--1794 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N umber" method[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1796--1796 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE)) ) # the default[] Underfull \hbox (badness 10000) in paragraph at lines 1838--1840 []\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca lls [1085] [1086] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class [1087] [1088] [1089] Underfull \hbox (badness 1132) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/pcr/m/n/10 where = [1090] [1091] Underfull \hbox (badness 10000) in paragraph at lines 2328--2332 []\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od s dis-patch, call Overfull \hbox (6.78088pt too wide) in paragraph at lines 2360--2360 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F ALSE}:[] [1092] [1093] [1094] Underfull \hbox (badness 3792) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class Underfull \hbox (badness 1194) in paragraph at lines 2605--2609 []\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10 (a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and [1095] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2661--2661 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1096] [1097] [1098] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2880--2880 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1099] [1100] [1101] [1102] [1103] [1104] [1105] Underfull \hbox (badness 10000) in paragraph at lines 3403--3408 []\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu rns the im-plicit generic ver-sion, Underfull \hbox (badness 6268) in paragraph at lines 3403--3408 \T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \ T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents [1106] [1107] Underfull \hbox (badness 10000) in paragraph at lines 3531--3535 []\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class [1108] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Overfull \hbox (28.78088pt too wide) in paragraph at lines 3642--3651 [] [1109] [1110] Overfull \hbox (276.78088pt too wide) in paragraph at lines 3762--3763 [] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 Underfull \hbox (badness 10000) in paragraph at lines 3809--3810 []\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) { [1111] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3828--3829 []\T1/pcr/m/n/10 GPS <- setClass("GPS", slots = c(time = "POSIXt"), contains = "Pos") Overfull \hbox (120.78088pt too wide) in paragraph at lines 3846--3847 []\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") Underfull \hbox (badness 6157) in paragraph at lines 3908--3912 []\T1/ptm/m/n/10 A call to [][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) \T1/ ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to [1112] [1113] [1114] Underfull \hbox (badness 10000) in paragraph at lines 4135--4137 []\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method ex-ists for [1115] [1116] Underfull \hbox (badness 1629) in paragraph at lines 4247--4256 \T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is to mod-ify a field ex-plic-itly by [1117] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4308--4308 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4309--4309 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1118] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4366--4366 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here) [1119] [1120] Underfull \hbox (badness 1033) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T 1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si g-na-ture [1121] Underfull \hbox (badness 2126) in paragraph at lines 4574--4582 []\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the im-por-tant steps: ([][]\T1/pcr/m/n/10 setMethod[][][]()\T1/ptm/m/n/10 , [1122] [1123] [1124] Underfull \hbox (badness 10000) in paragraph at lines 4811--4820 []\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha t eval-u-ates a call to [1125] [1126] [1127] [1128] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5195--5195 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] [1129] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5223--5223 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli er fails here)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5237--5237 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho d for classB[] Underfull \vbox (badness 10000) has occurred while \output is active [1130] [1131] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1132] Underfull \hbox (badness 10000) in paragraph at lines 5463--5465 []\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t er-nally by [1133] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1134] [1135] [1136] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1137] Underfull \hbox (badness 10000) in paragraph at lines 5757--5761 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 5757--5761 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1138] Underfull \hbox (badness 10000) in paragraph at lines 5848--5852 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 5848--5852 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1139] [1140] [1141] [1142] Underfull \hbox (badness 10000) in paragraph at lines 6210--6226 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m /n/10 is equiv-a-lent to in-vok-ing the method [1143] [1144] Underfull \hbox (badness 1248) in paragraph at lines 6343--6347 []\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt m/m/n/10 method car-ries out its own com-pu-ta-tions, Underfull \hbox (badness 1960) in paragraph at lines 6343--6347 \T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per -form stan-dard ini-tial-iza-tion, as shown in the [1145] Underfull \hbox (badness 4647) in paragraph at lines 6498--6500 []\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func- tion re-turned by [1146] Underfull \hbox (badness 1072) in paragraph at lines 6575--6582 []\T1/ptm/m/n/10 Establish a traced ver-sion of method [1147] Underfull \hbox (badness 2875) in paragraph at lines 6647--6656 []\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen se as any S4 class (see Underfull \hbox (badness 1436) in paragraph at lines 6647--6656 [][]\T1/pcr/m/n/10 setValidity[][][]\T1/ptm/m/n/10 ). Such meth-ods are of-ten a good idea; they will be called by call-ing [1148] Underfull \vbox (badness 10000) has occurred while \output is active [1149] [1150] [1151]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1152] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7009--7009 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement version of as().[] Underfull \hbox (badness 2042) in paragraph at lines 7065--7072 \T1/ptm/m/n/10 i-nat-ing all the for-mally de-fined slots and turn-ing off the S4 bit of the ob-ject. With [1153] [1154] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7200--7200 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data = datasets::iris)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7204--7204 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con tains = "mlm")[] [1155]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com plex}) has been already used, duplicate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1156] Underfull \hbox (badness 6708) in paragraph at lines 7309--7321 []\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "cummax"\T1/ptm/m/n/10 , Underfull \hbox (badness 2012) in paragraph at lines 7309--7321 \T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr /m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 , Underfull \hbox (badness 3209) in paragraph at lines 7309--7321 \T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m /n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 , [1157] [1158] Underfull \hbox (badness 1694) in paragraph at lines 7472--7474 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see Underfull \hbox (badness 10000) in paragraph at lines 7496--7499 []\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup erClasses() \T1/ptm/m/n/10 which calls [1159] [1160] Underfull \hbox (badness 10000) in paragraph at lines 7663--7670 []\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method, \T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her- Underfull \hbox (badness 7704) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \ T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the Underfull \hbox (badness 10000) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about it, you'll prob-a-bly agree that you wouldn't Underfull \hbox (badness 5817) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/ n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus, Overfull \hbox (0.78088pt too wide) in paragraph at lines 7663--7670 \T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE )) [1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] Underfull \hbox (badness 1052) in paragraph at lines 8489--8496 []\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it [1172] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8622--8622 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(), [1173] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8697--8697 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1174] [1175] [1176] [1177] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8959--8959 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] [1178] [1179] [1180] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9167--9167 [] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns), "setCount")[] [1181] [1182] Underfull \vbox (badness 2277) has occurred while \output is active [1183] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9429--9429 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo rmal arguments[] [1184] [1185] [1186] [1187] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9737--9737 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre es of freedom[] [1188] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9847--9847 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1189] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9858--9858 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] Underfull \hbox (badness 10000) in paragraph at lines 10556--10558 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function " \T1/ptm/m/n/10 for class Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., Underfull \hbox (badness 1681) in paragraph at lines 10564--10568 \T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends [1199] [1200] [1201] [1202]) (./parallel-pkg.tex Chapter 8. Underfull \hbox (badness 2418) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr /m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1203] Underfull \hbox (badness 4242) in paragraph at lines 96--98 []\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \ T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for [1204] [1205] Underfull \hbox (badness 1024) in paragraph at lines 213--216 []\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10 for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and [1206] Underfull \hbox (badness 10000) in paragraph at lines 318--326 []\T1/ptm/m/n/10 On Sparc So-laris \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/1 0 re-turns the num-ber of phys-i-cal cores and [1207] [1208] Underfull \hbox (badness 10000) in paragraph at lines 443--445 []\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/ 10 Rscript \T1/ptm/m/n/10 such as [1209] [1210] [1211] [1212] Underfull \hbox (badness 1917) in paragraph at lines 742--751 []\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr /m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class Underfull \hbox (badness 1178) in paragraph at lines 742--751 \T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in -herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If [1213] [1214] Overfull \hbox (60.78088pt too wide) in paragraph at lines 824--824 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1215] Underfull \hbox (badness 10000) in paragraph at lines 884--887 []\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T 1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1 \T1/ptm/m/n/10 : for [1216] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1005--1005 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit y.list = affL)[] [1217] Overfull \hbox (63.78036pt too wide) in paragraph at lines 1009--1009 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1218] Underfull \hbox (badness 5388) in paragraph at lines 1119--1124 []\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1 /pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from Underfull \hbox (badness 10000) in paragraph at lines 1143--1151 []\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/ m/n/10 is dif-fer-ent only if [1219] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1180--1180 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] [1220] [1221] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1296--1296 [] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif (N, 1, 28)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1310--1310 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] Underfull \hbox (badness 1577) in paragraph at lines 1339--1342 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1222] Underfull \hbox (badness 3375) in paragraph at lines 1385--1387 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/ n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to [1223] [1224]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1225] [1226] [1227] [1228] [1229] [1230] [1231] Overfull \hbox (4.38043pt too wide) in paragraph at lines 492--492 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl ine = TRUE))[] [1232] [1233] [1234] [1235] Overfull \hbox (25.98041pt too wide) in paragraph at lines 706--706 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, sparse = TRUE)))[] [1236] [1237] [1238]) (./stats-pkg.tex Chapter 10. [1239] Underfull \hbox (badness 2781) in paragraph at lines 65--68 []\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 , [1240] [1241] [1242] [1243] [1244] Overfull \hbox (20.58041pt too wide) in paragraph at lines 417--417 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea rson Chi-square[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 438--438 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE) [1245] [1246] [1247] [1248] [1249] [1250] [1251] Underfull \hbox (badness 1024) in paragraph at lines 847--849 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm \T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] Underfull \hbox (badness 10000) in paragraph at lines 1391--1393 []\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu- ment [1260] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 \T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e r-ror strata of class Underfull \hbox (badness 1490) in paragraph at lines 1508--1512 \T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\ T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \ T1/ptm/m/n/10 meth-ods avail-able for [1261] [1262] [1263] [1264] Underfull \hbox (badness 10000) in paragraph at lines 1773--1777 []\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently, via Underfull \hbox (badness 2197) in paragraph at lines 1773--1777 \T1/pcr/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can han-dle miss- [1265] [1266] Underfull \hbox (badness 4303) in paragraph at lines 1874--1876 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 x \T1/ptm/m/n/10 con-tains miss-ing val-ues, see [][]\T1/pcr/m/n/10 NA[][][]\T1/ptm/m/n/10 , also con-sider us-ing [][]\T1/ pcr/m/n/10 arima[][][]()\T1/ptm/m/n/10 , pos-si-bly with [1267] [1268] [1269] Underfull \hbox (badness 10000) in paragraph at lines 2096--2101 []\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en- sure Underfull \hbox (badness 10000) in paragraph at lines 2096--2101 \T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo r Underfull \hbox (badness 1371) in paragraph at lines 2096--2101 \T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\ T1/ptm/m/n/10 , it has been ad-van-ta-geous Underfull \hbox (badness 1221) in paragraph at lines 2102--2108 []\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num -ber of pa- Underfull \hbox (badness 4608) in paragraph at lines 2102--2108 \T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied. [1270] [1271] Underfull \hbox (badness 3965) in paragraph at lines 2183--2185 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1272] [1273] [1274] Underfull \hbox (badness 1221) in paragraph at lines 2457--2462 []\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num -ber of pa- Underfull \hbox (badness 4608) in paragraph at lines 2457--2462 \T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied. [1275] Underfull \hbox (badness 3965) in paragraph at lines 2534--2536 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1276] [1277] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2679--2679 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1278] [1279] [1280] [1281] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2919--2919 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1282] [1283] [1284] Overfull \hbox (19.88992pt too wide) in paragraph at lines 3128--3130 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of variances"\T1/ptm/m/n/10 . [1285] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3176--3176 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3177--3177 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1286] Underfull \hbox (badness 2726) in paragraph at lines 3260--3276 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1287] [1288] [1289] [1290] [1291] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3568--3568 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1292] [1293] [1294] [1295] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3846--3846 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1296] [1297] [1298] [1299] [1300] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4135--4135 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4136--4136 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1301] [1302] [1303] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4374--4374 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1304] [1305] [1306] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4542--4542 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1307] Underfull \hbox (badness 3989) in paragraph at lines 4634--4641 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1308] [1309] Underfull \hbox (badness 2080) in paragraph at lines 4754--4756 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por t aliased co-ef-fi-cients (see [][]\T1/pcr/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b y de-fault where Underfull \hbox (badness 2050) in paragraph at lines 4757--4763 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 complete \T1/ptm/m/n/10 ar-gu-ment also ex- ists for com-pat-i-bil-ity with [][]\T1/pcr/m/n/10 vcov[][][] \T1/ptm/m/n/10 me th-ods, and \T1/pcr/m/n/10 coef Underfull \hbox (badness 4954) in paragraph at lines 4757--4763 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aov \T1/ptm/m/n/10 meth-ods for other classes should typ-i-cally also keep the \T1/pcr/m/n/10 complete = * Underfull \hbox (badness 4726) in paragraph at lines 4757--4763 \T1/ptm/m/n/10 be-hav-ior in sync. By that, with \T1/pcr/m/n/10 p <- length(coe f(obj, complete = TF))\T1/ptm/m/n/10 , [1310] [1311] [1312] [1313] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5019--5019 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1)) , ci = c(-1,-1))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5021--5021 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci = c(-0.9,0.1))[] [1314] Underfull \hbox (badness 7397) in paragraph at lines 5108--5112 []\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an ar-gu-ment to all these con-trast func-tions, how-ever Underfull \hbox (badness 7326) in paragraph at lines 5108--5112 \T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for [1315] [1316] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5242--5242 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5260--5260 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) Underfull \hbox (badness 2680) in paragraph at lines 5287--5289 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is given by [1317] Underfull \hbox (badness 10000) in paragraph at lines 5292--5294 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m /n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 , [1318] [1319] Underfull \hbox (badness 1436) in paragraph at lines 5470--5475 []\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i ng co-vari-ances Underfull \hbox (badness 1377) in paragraph at lines 5470--5475 \T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi -a-tion of) Underfull \hbox (badness 1448) in paragraph at lines 5470--5475 \T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \ T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/ n/10 , [1320] [1321] [1322] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5668--5668 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1323] Underfull \hbox (badness 1168) in paragraph at lines 5740--5745 []\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and [1324] [1325] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5835--5835 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1326] [1327] [1328] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6020--6020 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1329] [1330] Underfull \hbox (badness 10000) in paragraph at lines 6183--6188 []\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When [1331] [1332] [1333] Underfull \hbox (badness 5954) in paragraph at lines 6379--6381 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1334] Underfull \hbox (badness 2503) in paragraph at lines 6461--6464 []\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 5563) in paragraph at lines 6465--6467 []\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also Underfull \hbox (badness 1655) in paragraph at lines 6468--6473 \T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm /m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1 /phv/m/n/10 R \T1/ptm/m/n/10 3.1.2, [1335] Underfull \hbox (badness 7238) in paragraph at lines 6504--6507 [][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr am[][][] \T1/ptm/m/n/10 and [1336] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6539--6539 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, type = "tr")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6554--6554 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6569--6569 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1337] [1338] [1339] [1340] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6813--6813 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1341] [1342] Underfull \vbox (badness 10000) has occurred while \output is active [1343] [1344] [1345] [1346] Underfull \hbox (badness 10000) in paragraph at lines 7211--7215 \T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/ m/n/10 or [1347] Underfull \hbox (badness 6493) in paragraph at lines 7310--7313 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1348] [1349] Underfull \hbox (badness 10000) in paragraph at lines 7447--7450 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht tps : / / CRAN . R-[]project . org / view = [1350] [1351] [1352] [1353] [1354] [1355] Underfull \hbox (badness 10000) in paragraph at lines 7857--7862 []\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T 1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ..., [1356] [1357] Overfull \hbox (33.6622pt too wide) in paragraph at lines 7995--7997 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log = TRUE)\T1/ptm/m/n/10 . [1358] [1359] [1360] Underfull \hbox (badness 1210) in paragraph at lines 8212--8214 []\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b e sup-plied as named ar-gu-ments to [1361] [1362] [1363] [1364] [1365] [1366] [1367] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8687--8687 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link = "log")) # fails[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8690--8690 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1368] [1369] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8828--8828 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2), .90) # ~= 7e-9[] [1370] Underfull \hbox (badness 1859) in paragraph at lines 8867--8872 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\ T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned, i.e., if [1371] [1372] [1373] Underfull \hbox (badness 2865) in paragraph at lines 9113--9122 []\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/pcr/m/n/10 hybrid = TRUE\T1/ptm/m/n /10 , asymp-totic chi-squared prob-a-bil-i- Underfull \hbox (badness 1331) in paragraph at lines 9113--9122 \T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied ver-sion thereof) spec-i-fied by [1374] [1375] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9255--9255 [] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4 0k", "> 40k"),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 9256--9256 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1376] [1377] [1378] Overfull \hbox (61.88992pt too wide) in paragraph at lines 9435--9437 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1379] [1380] [1381] [1382] [1383] [1384] [1385] Underfull \hbox (badness 2443) in paragraph at lines 9888--9894 [][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment); [1386] [1387] [1388] Underfull \hbox (badness 3758) in paragraph at lines 10101--10104 []\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or [1389] [1390] [1391] [1392] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10337--10337 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10363--10368 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1393] Underfull \hbox (badness 4132) in paragraph at lines 10402--10406 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od [1394] Underfull \hbox (badness 10000) in paragraph at lines 10507--10510 []\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fitted.values \T1/ptm/m/n/10 and [1395] [1396] [1397] Underfull \hbox (badness 2142) in paragraph at lines 10711--10714 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ [1398] Underfull \hbox (badness 1708) in paragraph at lines 10792--10796 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1399] Underfull \hbox (badness 10000) in paragraph at lines 10834--10840 [][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, Underfull \hbox (badness 1418) in paragraph at lines 10872--10877 \T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \ T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (= [1400] [1401] Underfull \hbox (badness 2635) in paragraph at lines 11005--11008 \T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1 /pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1 0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th e [1402] [1403] [1404] Underfull \hbox (badness 1694) in paragraph at lines 11190--11193 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1337) in paragraph at lines 11209--11218 []\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate den-dro-gram is re-ordered ac-cord- Underfull \hbox (badness 3049) in paragraph at lines 11209--11218 \T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos ed by the den-dro-gram, by [1405] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11291--11291 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1406] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11324--11324 [] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 0.1),[] Underfull \hbox (badness 10000) in paragraph at lines 11337--11341 []\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p tm/m/n/10 (the de-fault) or [1407] [1408] [1409] Underfull \hbox (badness 7379) in paragraph at lines 11517--11520 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1410] [1411] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11656--11656 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11671 \aliasA{hat}{influence.measures}{hat} [1412] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11724--11724 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11736--11736 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] [1413] Underfull \hbox (badness 1062) in paragraph at lines 11785--11790 []\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther e to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1414] [1415] Underfull \hbox (badness 3623) in paragraph at lines 11956--11958 []\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max (50*.Machine$double.eps, 0.5e-28) \T1/ptm/m/n/10 if [1416] [1417] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12052--12052 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] [1418] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12145--12145 [] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label = "tobacco",[] [1419] Underfull \hbox (badness 10000) in paragraph at lines 12193--12196 []\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1 /ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is [1420] [1421] [1422] Underfull \hbox (badness 4441) in paragraph at lines 12388--12390 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12395--12397 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1423] Underfull \hbox (badness 4739) in paragraph at lines 12418--12420 []\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^ @ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by [1424] Underfull \hbox (badness 2753) in paragraph at lines 12487--12489 []\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https : / / bugs . r-[]project . org / bugzilla3 / [1425] [1426] Underfull \hbox (badness 1292) in paragraph at lines 12612--12616 \T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion \T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for [1427] Underfull \hbox (badness 10000) in paragraph at lines 12725--12727 []\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/ n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm /m/n/10 of Underfull \hbox (badness 2894) in paragraph at lines 12731--12735 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method Underfull \hbox (badness 1038) in paragraph at lines 12731--12735 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive ( or true), trac-ing in-for-ma-tion on the [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13438--13438 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1439] Underfull \hbox (badness 4518) in paragraph at lines 13481--13486 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1440] [1441] Underfull \hbox (badness 10000) in paragraph at lines 13680--13684 []\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/ 10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10 , [1442] [1443] [1444] Underfull \hbox (badness 6995) in paragraph at lines 13865--13867 [][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had [1445] [1446] Underfull \hbox (badness 1163) in paragraph at lines 14013--14021 \T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual s[][][]\T1/ptm/m/n/10 , [1447] [1448] Underfull \hbox (badness 4518) in paragraph at lines 14133--14138 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1449] [1450] Underfull \hbox (badness 10000) in paragraph at lines 14271--14275 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/pcr/m/n/10 (surface = Underfull \hbox (badness 7133) in paragraph at lines 14271--14275 \T1/pcr/m/n/10 "interpolate", statistics = "approximate")\T1/ptm/m/n/10 : shoul d the [1451] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14319--14319 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14320--14320 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1452] Underfull \hbox (badness 10000) in paragraph at lines 14375--14378 []\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g ent, Underfull \hbox (badness 1715) in paragraph at lines 14375--14378 \T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts [1453] [1454] [1455] [1456] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14663--14663 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14664--14664 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1457] Overfull \hbox (45.6622pt too wide) in paragraph at lines 14714--14716 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l og = TRUE)\T1/ptm/m/n/10 . Overfull \hbox (18.78088pt too wide) in paragraph at lines 14757--14757 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 2726) in paragraph at lines 15164--15167 []\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 , [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] Overfull \hbox (31.3804pt too wide) in paragraph at lines 15879--15879 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1476] [1477] Underfull \hbox (badness 1014) in paragraph at lines 16017--16022 \T1/ptm/m/n/10 those spec-i-fied in \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 which are re-cy-cled to the num-ber of data frame rows. Un-like [1478] Underfull \hbox (badness 1648) in paragraph at lines 16083--16085 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 2591) in paragraph at lines 16097--16106 \T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must sup-ply vari-ables with the same names as would Underfull \hbox (badness 3930) in paragraph at lines 16097--16106 \T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/ ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing [1479] Overfull \hbox (25.98041pt too wide) in paragraph at lines 16165--16165 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b = "contr.poly"))[] [1480] [1481] [1482] [1483] [1484] [1485] [1486] [1487] [1488] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16719--16719 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] [1489] [1490] [1491] Overfull \hbox (25.98041pt too wide) in paragraph at lines 16947--16947 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] Underfull \hbox (badness 2359) in paragraph at lines 17533--17535 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1501] Underfull \vbox (badness 10000) has occurred while \output is active [1502] Underfull \vbox (badness 10000) has occurred while \output is active [1503] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17705--17705 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1504] Underfull \hbox (badness 10000) in paragraph at lines 17785--17789 []\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m /n/10 b0 + [1505] [1506] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17865--17865 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17912--17912 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1507] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17959--17959 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1508] [1509] [1510] [1511] [1512] [1513] [1514] [1515] Underfull \hbox (badness 1248) in paragraph at lines 18450--18453 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1127) in paragraph at lines 18463--18467 \T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 1478) in paragraph at lines 18471--18475 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De -faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and [1516] Underfull \hbox (badness 2042) in paragraph at lines 18529--18531 []\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm /m/n/10 method; see com-po-nent [1517] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18635--18635 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] [1518] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18677--18677 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 18695--18695 []\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 18698--18698 []\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 18718--18718 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), [1519] Overfull \hbox (36.78088pt too wide) in paragraph at lines 18721--18721 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] Underfull \hbox (badness 2564) in paragraph at lines 18756--18767 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u- ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1 0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 , Underfull \hbox (badness 1082) in paragraph at lines 18756--18767 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately \T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm /m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa [1520] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18819--18819 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1521] [1522] [1523] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19044--19044 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1524] Underfull \hbox (badness 1337) in paragraph at lines 19120--19123 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1525] [1526] [1527] [1528] [1529] [1530] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19439--19439 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1531] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19527--19527 [] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist vs Leverage " * h[ii] / (1 - h[ii]))),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 19530--19530 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1532] Underfull \hbox (badness 3049) in paragraph at lines 19609--19613 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1533] [1534] [1535] [1536] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19857--19857 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 4779) in paragraph at lines 19864--19866 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19867--19870 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1537] Underfull \hbox (badness 1107) in paragraph at lines 19925--19927 []\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to [1538] Overfull \hbox (20.58041pt too wide) in paragraph at lines 19980--19980 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] [1539] Overfull \hbox (31.3804pt too wide) in paragraph at lines 19987--19987 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 1, y.intersp = 1)[] Underfull \hbox (badness 10000) in paragraph at lines 20037--20040 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/ m/n/10 which gives Underfull \hbox (badness 10000) in paragraph at lines 20037--20040 \T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for [1540] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20081--20081 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1541] [1542] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20206--20206 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1543] Underfull \hbox (badness 10000) in paragraph at lines 20269--20271 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1544] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20317--20317 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) Underfull \hbox (badness 10000) in paragraph at lines 20372--20374 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 poly(*, simple=TRUE)\T1/ptm/m/n/10 , \T1/pc r/m/n/10 polym(*, coefs=)\T1/ptm/m/n/10 , and [1545] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20409--20409 [] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or just poly():[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 20414--20414 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] Overfull \hbox (25.98041pt too wide) in paragraph at lines 21264--21264 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly equal typically[] [1559] Underfull \hbox (badness 6859) in paragraph at lines 21331--21338 [][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre dict.poly[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 21342--21348 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22080--22080 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1572] [1573] [1574] [1575] [1576] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22364--22364 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 22365--22365 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1577] [1578] [1579] [1580] [1581] Underfull \hbox (badness 1337) in paragraph at lines 22689--22695 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] Overfull \hbox (133.98029pt too wide) in paragraph at lines 23251--23251 [] \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1590] [1591] Underfull \hbox (badness 1028) in paragraph at lines 23392--23395 []\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/ pcr/m/n/10 write() \T1/ptm/m/n/10 and [1592] [1593] Underfull \hbox (badness 10000) in paragraph at lines 23502--23505 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 5091) in paragraph at lines 23502--23505 \T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for ef-fi-ciency if [1594] Underfull \hbox (badness 10000) in paragraph at lines 23557--23559 []\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 reorder[][][]()\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing Underfull \hbox (badness 10000) in paragraph at lines 23619--23621 []\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 relevel[][][]()\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [1595] [1596] Overfull \hbox (9.78043pt too wide) in paragraph at lines 23721--23721 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1597] [1598] [1599] Overfull \hbox (31.3804pt too wide) in paragraph at lines 23941--23941 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1600] [1601] [1602] Underfull \hbox (badness 10000) in paragraph at lines 24087--24090 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has Underfull \hbox (badness 2134) in paragraph at lines 24139--24143 [][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's end point rule and is called by de-fault from [1603] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24152--24152 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1604] [1605] [1606] [1607] [1608] [1609] [1610] Underfull \hbox (badness 6268) in paragraph at lines 24616--24621 [][]\T1/pcr/m/n/10 SSasympOrig[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSbiexp [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 SSfpl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSgompertz[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSmicmen[][][]\T1/ptm/m/n/10 , [1611] Overfull \hbox (58.38037pt too wide) in paragraph at lines 24644--24644 [] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As ym", "xmid", "scal")])[] [1612] [1613] Underfull \hbox (badness 1867) in paragraph at lines 24821--24823 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/pcr/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was [1614] Overfull \hbox (20.58041pt too wide) in paragraph at lines 24870--24870 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] [1615] [1616] [1617] Underfull \hbox (badness 2495) in paragraph at lines 25060--25069 []\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/ m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1 /ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en . [1618] Overfull \hbox (24.78088pt too wide) in paragraph at lines 25142--25142 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] Underfull \hbox (badness 1412) in paragraph at lines 25149--25151 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1619] Overfull \hbox (25.98041pt too wide) in paragraph at lines 25236--25236 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] [1620] Overfull \hbox (84.78088pt too wide) in paragraph at lines 25261--25261 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 25264--25264 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1621] Underfull \hbox (badness 10000) in paragraph at lines 25306--25311 []\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when Underfull \hbox (badness 2435) in paragraph at lines 25306--25311 \T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault ), the num-ber of [1622] Underfull \hbox (badness 2980) in paragraph at lines 25451--25453 []\T1/ptm/m/n/10 the value of \T1/pcr/m/n/10 spar \T1/ptm/m/n/10 com-puted or g iven, un-less it has been given as [1623] Overfull \hbox (18.78088pt too wide) in paragraph at lines 25487--25487 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / tol) ))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25536--25536 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] [1624] Overfull \hbox (47.58038pt too wide) in paragraph at lines 25557--25557 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] Underfull \vbox (badness 10000) has occurred while \output is active [1625] [1626] Overfull \hbox (15.18042pt too wide) in paragraph at lines 25661--25661 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"), sep = " = "),[] [1627] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25728--25728 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1628] [1629] [1630] [1631] [1632] [1633] Overfull \hbox (36.78088pt too wide) in paragraph at lines 26107--26107 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] Underfull \hbox (badness 6477) in paragraph at lines 26161--26164 []\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of an [1634] [1635] Overfull \hbox (31.3804pt too wide) in paragraph at lines 26292--26292 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c ol = 3, n = 1001)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 26293--26293 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] Underfull \vbox (badness 10000) has occurred while \output is active [1636] Underfull \hbox (badness 2922) in paragraph at lines 26362--26367 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1637] Overfull \hbox (9.78043pt too wide) in paragraph at lines 26399--26399 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim = c(-.3, 5),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 26402--26402 [] \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^ {-e^{phi[3]}*~x}}))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 26411--26411 [] \T1/pcr/m/n/9 c(0 , 1 ), 1, length = 0.08, angle = 25); text(0. 5, 1, quote(1))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26412--26412 [] \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3 # (Asym + R0)/2[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 26416--26416 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] [1638] Underfull \hbox (badness 2922) in paragraph at lines 26458--26463 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Underfull \hbox (badness 3240) in paragraph at lines 26470--26473 [][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][] []\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap h show-ing the \T1/pcr/m/n/10 SSasympOff Overfull \hbox (36.7804pt too wide) in paragraph at lines 26491--26491 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log( 0.4), c0 = 3/4)) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26494--26494 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1639] Underfull \hbox (badness 2922) in paragraph at lines 26544--26549 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1640] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26577--26577 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log (log(2)))) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26581--26581 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim = c(-1/4, 5),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 26591--26591 [] \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2), phi[1]), pos=0, las=1)[] Overfull \hbox (106.98032pt too wide) in paragraph at lines 26596--26596 [] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1641] Underfull \hbox (badness 2922) in paragraph at lines 26632--26638 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 26654--26654 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26670--26670 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] [1642] [1643] Overfull \hbox (30.78088pt too wide) in paragraph at lines 26784--26784 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1644] Underfull \hbox (badness 2922) in paragraph at lines 26846--26851 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1645] Overfull \hbox (69.18036pt too wide) in paragraph at lines 26884--26884 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] [1646] Underfull \hbox (badness 2922) in paragraph at lines 26933--26938 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 26964--26964 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = " red", lwd=2)[] [1647] Underfull \hbox (badness 2922) in paragraph at lines 26998--27003 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (25.98041pt too wide) in paragraph at lines 27023--27023 []\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number of iter...: 0" :[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 27027--27027 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR UE), trace = TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27047--27047 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] [1648] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27057--27057 [] \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0, 2.5,3.5), # NB. SSlogis(x = xmid = 2) = 2.5[] Underfull \hbox (badness 2922) in paragraph at lines 27092--27097 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1649] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27114--27114 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 27132--27132 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] [1650] Underfull \hbox (badness 6493) in paragraph at lines 27184--27189 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27211--27211 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27213--27213 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 27216--27216 []\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul l() fit to Chick.6")[] Overfull \hbox (69.18036pt too wide) in paragraph at lines 27219--27219 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1659] [1660] [1661] [1662] [1663] [1664] [1665] Underfull \hbox (badness 3396) in paragraph at lines 28143--28145 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10 , usu-ally, a re-sult of a call to [1666] [1667] [1668] Underfull \hbox (badness 2237) in paragraph at lines 28320--28322 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1669] [1670] Underfull \hbox (badness 2591) in paragraph at lines 28484--28486 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10 , usu-ally the re-sult of a call to [1671] Underfull \hbox (badness 2237) in paragraph at lines 28530--28533 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1672] Overfull \hbox (48.78088pt too wide) in paragraph at lines 28603--28603 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1673] [1674] Underfull \hbox (badness 3407) in paragraph at lines 28711--28715 []\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low) [1675] [1676] Underfull \hbox (badness 1337) in paragraph at lines 28844--28848 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1677] [1678] Underfull \hbox (badness 10000) in paragraph at lines 28961--28964 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for [1679] [1680] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29090--29090 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29118--29118 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1681] Underfull \hbox (badness 1616) in paragraph at lines 29144--29147 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1682] Overfull \hbox (20.58041pt too wide) in paragraph at lines 29223--29223 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1683] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29300--29300 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1684] Underfull \hbox (badness 5050) in paragraph at lines 29336--29341 []\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject is re-turned. The ob-ject it-self is the re-ordered (un-less [1685] Underfull \hbox (badness 2205) in paragraph at lines 29389--29394 []\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a [1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29984--29984 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE) [1694] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29985--29985 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1695] [1696] [1697] [1698] Underfull \hbox (badness 10000) in paragraph at lines 30274--30278 []\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect Underfull \hbox (badness 1596) in paragraph at lines 30274--30278 \T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign( f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at Overfull \hbox (30.78088pt too wide) in paragraph at lines 30285--30285 [] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con v = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30286--30286 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1699] [1700] Overfull \hbox (31.3804pt too wide) in paragraph at lines 30412--30412 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30421--30421 []\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[] [1701] [1702] [1703] [1704] Underfull \hbox (badness 1337) in paragraph at lines 30638--30642 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] Underfull \hbox (badness 1337) in paragraph at lines 31165--31169 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1713] Underfull \hbox (badness 1946) in paragraph at lines 31242--31247 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 (and \T1/pcr/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the Underfull \hbox (badness 5161) in paragraph at lines 31264--31266 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1714] [1715] [1716] [1717] [1718] Overfull \hbox (0.78088pt too wide) in paragraph at lines 31590--31590 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1719] Underfull \hbox (badness 6775) in paragraph at lines 31647--31652 []\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or [1720] Overfull \hbox (47.58038pt too wide) in paragraph at lines 31710--31710 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] [1721]) (./stats4-pkg.tex [1722] Chapter 11. [1723] [1724] [1725] Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192 [] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf)) , log = TRUE))[] [1726] [1727] [1728]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1729] Underfull \hbox (badness 10000) in paragraph at lines 440--443 []\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class [1730] [1731]) (./tcltk-pkg.tex [1732] Chapter 12. [1733] [1734] [1735] [1736] Overfull \hbox (4.38043pt too wide) in paragraph at lines 349--349 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback ref in here[] [1737] [1738] [1739] Underfull \vbox (badness 10000) has occurred while \output is active [1740] Underfull \hbox (badness 1292) in paragraph at lines 664--671 []\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing any Tk or Tcl com-mand by sim-ply run-ning [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] Underfull \hbox (badness 1189) in paragraph at lines 1407--1410 [][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1752]) (./tools-pkg.tex Chapter 13. [1753] Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for new methods.[] [1754] Underfull \hbox (badness 10000) in paragraph at lines 138--140 []\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion which will be eval-u-ated via Underfull \hbox (badness 1253) in paragraph at lines 164--167 []\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1755] Overfull \hbox (4.38043pt too wide) in paragraph at lines 215--215 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch ing warning)[] [1756] Underfull \hbox (badness 5147) in paragraph at lines 285--298 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 Underfull \hbox (badness 4792) in paragraph at lines 285--298 \T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1 0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou- Underfull \hbox (badness 2237) in paragraph at lines 285--298 \T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1 0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 , [1757] Overfull \hbox (42.78088pt too wide) in paragraph at lines 370--370 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta ngle = TRUE, Underfull \hbox (badness 2460) in paragraph at lines 389--391 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1758] [1759] [1760] [1761] [1762] [1763] [1764] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1765] [1766] Overfull \hbox (0.78088pt too wide) in paragraph at lines 901--901 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 956--956 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1767] [1768] Underfull \hbox (badness 1635) in paragraph at lines 1056--1058 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1769] Underfull \hbox (badness 5431) in paragraph at lines 1131--1134 []\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa ssed to Underfull \hbox (badness 4441) in paragraph at lines 1134--1144 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- [1770] Underfull \hbox (badness 1014) in paragraph at lines 1156--1158 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1162--1164 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1199--1202 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us- Underfull \hbox (badness 10000) in paragraph at lines 1199--1202 \T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p tm/m/n/10 and [1771] Underfull \hbox (badness 10000) in paragraph at lines 1207--1210 []\T1/pcr/m/n/10 check_packages_in_dir \T1/ptm/m/n/10 re-turns an ob-ject in-he r-it-ing from class [1772] [1773] Underfull \hbox (badness 10000) in paragraph at lines 1356--1359 []\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1 0 and Underfull \hbox (badness 10000) in paragraph at lines 1377--1379 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1774] [1775] [1776] [1777] [1778] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1679--1679 [] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking To"),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1682--1682 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1689--1694 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 1689--1694 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . [1779] [1780] [1781]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1782] [1783] [1784] [1785] Underfull \hbox (badness 1142) in paragraph at lines 2161--2167 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgRdMacros \T1/ptm/m/n/10 func-tion fi rst looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-ag e Overfull \hbox (101.58032pt too wide) in paragraph at lines 2195--2195 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1786] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2196--2196 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2223--2230 []\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user and site spe-cific com-pi-la- Underfull \hbox (badness 1102) in paragraph at lines 2223--2230 \T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1 0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com- Underfull \hbox (badness 4168) in paragraph at lines 2223--2230 \T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/ m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m /n/10 with [1787] Underfull \hbox (badness 1342) in paragraph at lines 2275--2281 \T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in [1788] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2351--2351 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb ose"))[] Underfull \hbox (badness 7981) in paragraph at lines 2364--2370 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 2364--2370 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . [1789] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2397--2397 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2406--2406 [] \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo ", "Suggests"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2423--2423 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1790] [1791] [1792] [1793] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2688--2688 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1794] Underfull \hbox (badness 2486) in paragraph at lines 2733--2741 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d efined macros may be given in a sep-a-rate file us-ing [1795] [1796] [1797] [1798] [1799] Underfull \hbox (badness 1072) in paragraph at lines 3111--3113 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to r of links, as re-turned by [1800] [1801] [1802] [1803] [1804] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3447--3447 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1805] [1806] [1807] [1808] Underfull \hbox (badness 4108) in paragraph at lines 3691--3698 []\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o n the loop-back in-ter-face [1809] [1810] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3791--3791 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3794--3794 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3811--3813 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , Underfull \hbox (badness 2932) in paragraph at lines 3828--3834 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1811] [1812] Underfull \hbox (badness 7832) in paragraph at lines 3950--3953 []\T1/ptm/m/n/10 Where sup-ported (\T1/pcr/m/n/10 texi2dvi \T1/ptm/m/n/10 5.0 a nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1813] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4025--4025 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] [1814] Underfull \hbox (badness 1137) in paragraph at lines 4048--4050 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1815] [1816] [1817] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4222--4222 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) Underfull \hbox (badness 10000) in paragraph at lines 4233--4236 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and Underfull \hbox (badness 6859) in paragraph at lines 4249--4254 []\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/ m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p tm/m/n/10 ' are up-dated from Underfull \hbox (badness 1184) in paragraph at lines 4257--4263 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po /\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T he Underfull \hbox (badness 2941) in paragraph at lines 4257--4263 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t he pack-age are ex-am-ined to cre-ate a file [1818] Underfull \hbox (badness 10000) in paragraph at lines 4337--4342 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De pendsList Underfull \hbox (badness 10000) in paragraph at lines 4337--4342 \T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i- fied (for in-stance if Underfull \hbox (badness 10000) in paragraph at lines 4337--4342 \T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1 /ptm/m/n/10 ', it would only re-turn [1819] [1820] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4469--4469 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4470--4470 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz")[] Underfull \hbox (badness 3240) in paragraph at lines 4482--4485 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ', [1821] Underfull \hbox (badness 1742) in paragraph at lines 4486--4496 \T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 , Underfull \hbox (badness 1127) in paragraph at lines 4521--4527 []\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4521--4527 \T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file , and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1 0 ', Underfull \hbox (badness 1571) in paragraph at lines 4549--4553 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1822] [1823] [1824]) (./utils-pkg.tex Chapter 14. Underfull \hbox (badness 1072) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [1825] [1826] [1827] Underfull \hbox (badness 6316) in paragraph at lines 212--216 []\T1/pcr/m/n/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for a si m-i-lar task to \T1/pcr/m/n/10 apropos\T1/ptm/m/n/10 . By de-fault [1828] Overfull \hbox (4.38043pt too wide) in paragraph at lines 256--256 []\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with these names[] [1829] Overfull \hbox (60.78088pt too wide) in paragraph at lines 370--370 [] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No ", "Cancel"))),[] [1830] [1831] [1832] Underfull \hbox (badness 1946) in paragraph at lines 527--531 \T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org / archive / 2011-[]2 / RJournal _ 2011-[]2 _ Overfull \hbox (0.78088pt too wide) in paragraph at lines 577--577 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc es"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 583--583 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 584--584 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 585--585 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] [1833] Overfull \hbox (0.78088pt too wide) in paragraph at lines 586--586 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Underfull \hbox (badness 10000) in paragraph at lines 620--626 []\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10 , \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 4416) in paragraph at lines 620--626 \T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_ package_C_files \T1/ptm/m/n/10 per-form spell check- [1834] Overfull \hbox (0.78088pt too wide) in paragraph at lines 689--689 [] \T1/pcr/m/n/10 ignore_repo_cache = FALSE, max_repo_cache _age,[] [1835] Underfull \hbox (badness 4505) in paragraph at lines 753--759 \T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][](" available_packages_filters") \T1/ptm/m/n/10 and to [1836] Underfull \hbox (badness 1603) in paragraph at lines 870--876 \T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/ pcr/m/n/10 infile \T1/ptm/m/n/10 starts Underfull \hbox (badness 3029) in paragraph at lines 870--876 \T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 -- \T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are [1837] Overfull \hbox (6.78088pt too wide) in paragraph at lines 927--927 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1838] Underfull \hbox (badness 1817) in paragraph at lines 992--999 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1003--1005 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1839] [1840] Underfull \hbox (badness 10000) in paragraph at lines 1111--1114 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1841] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1194--1194 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1842] [1843] [1844] [1845] [1846] Underfull \hbox (badness 1859) in paragraph at lines 1565--1574 []\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b e quite large the com- [1847] [1848] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1666--1666 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] [1849] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1701--1701 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1850] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1847--1847 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1851] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1867--1867 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, Overfull \hbox (6.78088pt too wide) in paragraph at lines 1919--1919 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1852] Underfull \hbox (badness 2213) in paragraph at lines 1953--1956 []\T1/pcr/m/n/10 ind \T1/ptm/m/n/10 chooses a row in the list of cur-rent mir-r ors, by num-ber. It is best used with [1853] [1854] Underfull \hbox (badness 10000) in paragraph at lines 2054--2056 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via Overfull \hbox (36.7804pt too wide) in paragraph at lines 2088--2088 [] \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] [1855] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2111--2111 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] Underfull \hbox (badness 5189) in paragraph at lines 2156--2158 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1856] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2231--2231 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1857] Underfull \hbox (badness 1082) in paragraph at lines 2305--2309 [][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files; [1858] Underfull \hbox (badness 10000) in paragraph at lines 2342--2344 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see Underfull \hbox (badness 1057) in paragraph at lines 2374--2381 \T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w hen [1859] [1860] [1861] Underfull \hbox (badness 10000) in paragraph at lines 2563--2565 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1862] [1863] [1864] [1865] Underfull \hbox (badness 10000) in paragraph at lines 2800--2804 []\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m /n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us- ing Underfull \hbox (badness 5203) in paragraph at lines 2800--2804 [][]\T1/pcr/m/n/10 read.table[][][](..., header = TRUE, as.is=FALSE)\T1/ptm/m/n /10 , and hence re-sult in a Overfull \hbox (133.10922pt too wide) in paragraph at lines 2805--2808 []\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr /m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][ ](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2854--2857 []\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re c-tory of the cur-rent work-ing di-rec-tory, set [1866] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2926--2926 []\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m /n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] [1867] Underfull \hbox (badness 2452) in paragraph at lines 3002--3005 []\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1 /pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources [1868] [1869] [1870] [1871] [1872] [1873] [1874] Underfull \hbox (badness 1072) in paragraph at lines 3484--3492 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [1875] Underfull \hbox (badness 1231) in paragraph at lines 3533--3539 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 3540--3545 []\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method = "libcurl"\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 7595) in paragraph at lines 3540--3545 \T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1 0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents of Underfull \hbox (badness 1331) in paragraph at lines 3540--3545 \T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in brack-ets are op-tional. See [1876] [1877] Underfull \hbox (badness 4660) in paragraph at lines 3662--3665 \T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/ 10 which makes an in-ter-nal call to Underfull \hbox (badness 10000) in paragraph at lines 3686--3688 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down load.file[][][] \T1/ptm/m/n/10 and [1878] [1879] [1880] Underfull \hbox (badness 1565) in paragraph at lines 3871--3875 []\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of Underfull \hbox (badness 10000) in paragraph at lines 3892--3898 []\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i- nal ob-ject if [1881] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3954--3954 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] Overfull \hbox (2.55087pt too wide) in paragraph at lines 3982--3989 \T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n /10 . [1882] [1883] [1884] [1885] [1886] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4309--4309 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1887]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4380 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4380 ...mat Unordered and Ordered Lists}{format} [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901] [1902] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5333--5333 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [1903] Underfull \hbox (badness 10000) in paragraph at lines 5417--5419 []\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[] project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also [1904] Underfull \hbox (badness 1502) in paragraph at lines 5466--5471 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 5466--5471 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1905] [1906] [1907] Underfull \hbox (badness 10000) in paragraph at lines 5639--5648 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, Underfull \hbox (badness 10000) in paragraph at lines 5639--5648 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 ', which can be re-made by [1908] Underfull \hbox (badness 2150) in paragraph at lines 5702--5705 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See Underfull \hbox (badness 5175) in paragraph at lines 5718--5721 []\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search database for sub-se-quent use by [1909] [1910] Underfull \hbox (badness 3118) in paragraph at lines 5839--5841 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for Underfull \hbox (badness 2409) in paragraph at lines 5872--5876 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1911] Underfull \hbox (badness 5091) in paragraph at lines 5976--5978 []\T1/ptm/m/n/10 download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1 /ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL [1912] Overfull \hbox (44.55087pt too wide) in paragraph at lines 5992--5997 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . Overfull \hbox (48.30977pt too wide) in paragraph at lines 6005--6012 []\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", " Imports", "LinkingTo", "Suggests") [1913] Underfull \hbox (badness 10000) in paragraph at lines 6063--6066 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 6063--6066 \T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack -age in-stall. E.g., Underfull \hbox (badness 10000) in paragraph at lines 6122--6126 []\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T 1/ptm/m/n/10 , [1914] Underfull \hbox (badness 2376) in paragraph at lines 6136--6143 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1 0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6136--6143 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 6136--6143 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1314) in paragraph at lines 6195--6202 []\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from [1915] Underfull \hbox (badness 10000) in paragraph at lines 6236--6241 [][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][ ][]\T1/ptm/m/n/10 , Overfull \hbox (25.98041pt too wide) in paragraph at lines 6259--6259 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] [1916] Underfull \hbox (badness 5133) in paragraph at lines 6295--6299 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each pack-age's Underfull \hbox (badness 1983) in paragraph at lines 6309--6312 []\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along Overfull \hbox (9.78043pt too wide) in paragraph at lines 6356--6356 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [1917] [1918] Underfull \hbox (badness 4132) in paragraph at lines 6475--6477 []\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at [1919] [1920] [1921] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6633--6633 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [1922] [1923] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6776--6776 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [1924] Underfull \hbox (badness 10000) in paragraph at lines 6816--6818 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1925] [1926] Underfull \hbox (badness 10000) in paragraph at lines 6957--6959 []\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if Underfull \hbox (badness 10000) in paragraph at lines 6962--6964 []\T1/ptm/m/n/10 typically the re-sult of \T1/pcr/m/n/10 methods(..)\T1/ptm/m/n /10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class [1927] [1928] [1929] Underfull \hbox (badness 1859) in paragraph at lines 7185--7188 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by [1930] Underfull \hbox (badness 1655) in paragraph at lines 7267--7270 []\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db" \T1/ptm/m/n/10 , with [][]\T1/pcr/m/n/10 attributes[][][] "package" \T1/ptm/m/n /10 (and [1931] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7278--7278 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre pl("PR#", Text),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7282--7282 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 7290--7290 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [1932] Underfull \hbox (badness 10000) in paragraph at lines 7375--7379 []\T1/ptm/m/n/10 For all stan-dards, \T1/pcr/m/n/10 unit = "auto" \T1/ptm/m/n/1 0 is also al-lowed. If [1933] [1934] [1935] [1936] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7639--7639 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 7640--7640 [] \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/ %d/%y"),[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 7641--7641 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] [1937] Underfull \hbox (badness 10000) in paragraph at lines 7669--7671 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/pcr /m/n/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 7683--7685 []\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 1259) in paragraph at lines 7691--7696 []\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [1938] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7737--7737 [] \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an d "stats" are[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7738--7738 [] \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[] [1939] [1940] Underfull \hbox (badness 10000) in paragraph at lines 7867--7872 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 7867--7872 [][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els Underfull \hbox (badness 10000) in paragraph at lines 7874--7877 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 7874--7877 [][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els [1941] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7990--7990 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7991--7991 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [1942] [1943] [1944] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8162--8162 [] \T1/pcr/m/n/9 "S original, "),[] [1945] Underfull \hbox (badness 1789) in paragraph at lines 8285--8287 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [1946] Underfull \hbox (badness 10000) in paragraph at lines 8343--8347 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8343--8347 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1947] [1948] Underfull \hbox (badness 10000) in paragraph at lines 8458--8462 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8458--8462 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1949] Underfull \hbox (badness 10000) in paragraph at lines 8523--8527 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8523--8527 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1950] [1951] [1952] [1953] Underfull \hbox (badness 5203) in paragraph at lines 8854--8857 []\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 ex-trac-tor are de-ter-mined by the generic func-tion [1954] [1955] [1956] Underfull \hbox (badness 1776) in paragraph at lines 9080--9087 []\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o f pieces of code, you should set [1957] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9104--9104 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [1958] [1959] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9265--9265 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [1960] [1961] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9446--9446 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 456 98 76 54[] [1962] [1963] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9532--9532 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9535--9535 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 9540--9540 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [1964] Underfull \hbox (badness 1077) in paragraph at lines 9612--9615 []\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL [1965] [1966] [1967] [1968] [1969] [1970] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10052--10052 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [1971] Underfull \hbox (badness 10000) in paragraph at lines 10139--10141 []\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/ m/n/10 in-stead of the de-fault one, use [1972] [1973] Underfull \hbox (badness 2181) in paragraph at lines 10262--10266 []\T1/pcr/m/n/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/pcr/m/n /10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10262--10266 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 10000) in paragraph at lines 10274--10278 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s&oldid = 78252134$[][]\T1/ptm/m/n/10 . [1974] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10292--10292 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10296--10296 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [1975] [1976] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10428--10428 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [1977] Underfull \hbox (badness 1917) in paragraph at lines 10551--10554 []\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari- Underfull \hbox (badness 4328) in paragraph at lines 10551--10554 \T1/ptm/m/n/10 able \T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES\T1/ptm/m/n/10 . If this is set, then it takes prece-dence over [1978] Overfull \hbox (106.98032pt too wide) in paragraph at lines 10574--10574 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] [1979] Underfull \hbox (badness 8075) in paragraph at lines 10637--10639 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\ T1/ptm/m/n/10 s are nicely viewed via [1980] Underfull \hbox (badness 6725) in paragraph at lines 10687--10696 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \ T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first, Underfull \hbox (badness 6428) in paragraph at lines 10687--10696 \T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i- Underfull \hbox (badness 10000) in paragraph at lines 10687--10696 \T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for re-verse al-pha-bet-i-cal or-der, Underfull \hbox (badness 1997) in paragraph at lines 10687--10696 \T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/ n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or [1981] Underfull \hbox (badness 3646) in paragraph at lines 10813--10815 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software / [1982] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10851--10851 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [1983] [1984] [1985] Underfull \hbox (badness 10000) in paragraph at lines 11032--11036 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no w taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 11063--11069 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [1986] Underfull \hbox (badness 2012) in paragraph at lines 11158--11164 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments for fig-ures should be auto-generated. Use [1987] Underfull \hbox (badness 2096) in paragraph at lines 11171--11173 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether EPS fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 2698) in paragraph at lines 11174--11176 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh ether PDF fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 11181--11184 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1067) in paragraph at lines 11185--11188 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether JPEG fig-ures should be gen-er-ated. Ig-nored if Overfull \hbox (6.78088pt too wide) in paragraph at lines 11239--11239 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] [1988] Underfull \hbox (badness 1009) in paragraph at lines 11257--11268 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [1989] Underfull \hbox (badness 2846) in paragraph at lines 11344--11354 \T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault [1990] [1991] Underfull \hbox (badness 10000) in paragraph at lines 11483--11486 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10 R \T1/ptm/m/n/10 was built un- Underfull \hbox (badness 10000) in paragraph at lines 11483--11486 \T1/ptm/m/n/10 der. Where sub-architectures are in use this is of the form Underfull \hbox (badness 10000) in paragraph at lines 11500--11503 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [1992] Underfull \hbox (badness 2158) in paragraph at lines 11579--11582 []\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe -cially: the value is taken from the cur-rent set-ting of [1993] [1994] [1995] Underfull \hbox (badness 3333) in paragraph at lines 11759--11761 []\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file- [1996] [1997] Overfull \hbox (42.78088pt too wide) in paragraph at lines 11924--11924 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] [1998] Underfull \hbox (badness 5970) in paragraph at lines 11957--11960 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive Underfull \hbox (badness 2600) in paragraph at lines 11957--11960 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less Underfull \hbox (badness 1052) in paragraph at lines 11968--11977 \T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][][]\T1/ptm/m/n/10 ) which de-f aults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons ; [1999] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12012--12012 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12043--12043 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo ng" non-ASCII:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12050--12050 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se e 1 (in UTF-8!):[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 12052--12052 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [2000] [2001] [2002] Underfull \hbox (badness 10000) in paragraph at lines 12220--12222 []\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/ 10 ap-ply only to files pro-duced by [2003] [2004] Underfull \hbox (badness 4492) in paragraph at lines 12377--12384 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in Underfull \hbox (badness 6252) in paragraph at lines 12377--12384 \T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/ n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 2452) in paragraph at lines 12377--12384 \T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 ( with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and [2005] [2006] [2007] Underfull \hbox (badness 2020) in paragraph at lines 12539--12555 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl at-forms), Underfull \hbox (badness 1194) in paragraph at lines 12539--12555 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s im-i-lar) and on Win-dows [2008] Underfull \hbox (badness 2809) in paragraph at lines 12659--12663 []\T1/ptm/m/n/10 NetBSD prior to 8.0 used flag `\T1/pcr/m/n/10 --xz\T1/ptm/m/n/ 10 ' rather than `\T1/pcr/m/n/10 -J\T1/ptm/m/n/10 ', so this should be used \T1 /ptm/m/it/10 via Underfull \hbox (badness 1596) in paragraph at lines 12659--12663 \T1/pcr/m/n/10 extra_flags = "--xz" \T1/ptm/m/n/10 rather than \T1/pcr/m/n/10 c ompression = "xz"\T1/ptm/m/n/10 . The com-mands from Underfull \hbox (badness 5022) in paragraph at lines 12674--12678 []\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl e Underfull \hbox (badness 10000) in paragraph at lines 12681--12684 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs . Underfull \hbox (badness 10000) in paragraph at lines 12681--12684 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml#tag _ 20 _ [2009] [2010] [2011] Overfull \hbox (18.78088pt too wide) in paragraph at lines 12846--12846 [] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss "), ...)[] [2012] [2013] [2014] [2015] [2016] [2017] Overfull \hbox (6.78088pt too wide) in paragraph at lines 13230--13230 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 13236--13236 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Underfull \hbox (badness 4467) in paragraph at lines 13257--13259 []\T1/ptm/m/n/10 Download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1 /ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL Underfull \hbox (badness 4660) in paragraph at lines 13270--13274 \T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/ 10 which makes an in-ter-nal call to Overfull \hbox (36.87935pt too wide) in paragraph at lines 13284--13288 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 13290--13295 []\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T 1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be Underfull \hbox (badness 10000) in paragraph at lines 13290--13295 \T1/ptm/m/n/10 passed to [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 and \T1/pcr/m/n/10 ignore_repo_cache\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13290--13295 \T1/pcr/m/n/10 max_repo_cache_age \T1/ptm/m/n/10 and \T1/pcr/m/n/10 noCache \T1 /ptm/m/n/10 to [][]\T1/pcr/m/n/10 available.packages[][][] [2018] Underfull \hbox (badness 1052) in paragraph at lines 13296--13298 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 13326--13331 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined see Underfull \hbox (badness 10000) in paragraph at lines 13326--13331 [][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai lable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 10000) in paragraph at lines 13326--13331 \T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1 /ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 13347--13352 []\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/ 10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with Underfull \hbox (badness 10000) in paragraph at lines 13355--13358 [][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[] [][]\T1/ptm/m/n/10 , [2019] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13409--13409 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c sb/ch3a.txt") [2020] [2021] [2022] Underfull \hbox (badness 10000) in paragraph at lines 13597--13600 [][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi- gnette browser; Overfull \hbox (42.18039pt too wide) in paragraph at lines 13613--13613 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[] [2023] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13680--13680 [] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d ata = DAT)))[] [2024] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13702--13702 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 13721--13721 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2025] Underfull \hbox (badness 1454) in paragraph at lines 13748--13752 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, Underfull \hbox (badness 1715) in paragraph at lines 13773--13776 []\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 13818--13820 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion [2026] Underfull \hbox (badness 3271) in paragraph at lines 13830--13834 \T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1 /ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if [2027] [2028]) [2029] [2030] (./KernSmooth-pkg.tex Chapter 15. [2031] Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat e = TRUE) [2032] [2033] [2034] [2035] [2036] Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun = 0.05, [2037] [2038] [2039] [2040]) (./MASS-pkg.tex Chapter 16. [2041] [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] Overfull \hbox (20.58041pt too wide) in paragraph at lines 774--774 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b eav2$hours/24))[] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] Underfull \hbox (badness 7256) in paragraph at lines 1604--1606 []\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo r [2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2412--2412 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2416--2416 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] [2075] [2076] [2077] [2078] Underfull \hbox (badness 6559) in paragraph at lines 2694--2697 []\T1/ptm/m/n/10 further ar-gu-ments for \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 and graph-i-cal pa-ram-e-ters. Note that [2079] [2080] [2081] Underfull \hbox (badness 10000) in paragraph at lines 2864--2869 \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "geometric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/pt m/m/n/10 , Underfull \hbox (badness 8189) in paragraph at lines 2864--2869 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "negative binomial"\T1 /ptm/m/n/10 , \T1/pcr/m/n/10 "normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Poisson"\ T1/ptm/m/n/10 , Underfull \hbox (badness 3557) in paragraph at lines 2900--2908 []\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start -ing val-ues will be com-puted if Underfull \hbox (badness 3118) in paragraph at lines 2900--2908 \T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied: \T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , [2082] [2083] Underfull \hbox (badness 4686) in paragraph at lines 3032--3034 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds Underfull \hbox (badness 1515) in paragraph at lines 3046--3050 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n /10 cycles \T1/ptm/m/n/10 terms or when a [2084] [2085] [2086] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3227--3227 [] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL SE, ...)[] Underfull \hbox (badness 5817) in paragraph at lines 3234--3236 []\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1 0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with [2087] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3357--3357 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist = "exponential")[] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097] [2098] [2099] Underfull \hbox (badness 1845) in paragraph at lines 4143--4145 []\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm /m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and [2100] [2101] [2102] [2103] [2104] [2105] [2106] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4639--4639 [] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n", ...)[] [2107] [2108] Underfull \hbox (badness 10000) in paragraph at lines 4791--4794 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2109] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4861--4861 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, Underfull \hbox (badness 10000) in paragraph at lines 4869--4872 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2110] [2111] [2112] [2113] [2114] Underfull \hbox (badness 5681) in paragraph at lines 5269--5271 []\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/ n/10 . This is over-ridden if Underfull \hbox (badness 5022) in paragraph at lines 5273--5276 []\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_ \OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10 \OT1/cmr/m/n/10 ()$ \ T1/ptm/m/n/10 func-tions when [2115] Underfull \hbox (badness 1975) in paragraph at lines 5322--5324 []\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in the case of [2116] [2117] [2118] [2119] [2120] [2121] [2122] [2123] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5908--5908 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP ACK = FALSE) [2124] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5969--5969 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/ 10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") [2125] [2126]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.npk}) has been already used, duplicate ignored \relax l.6111 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica te ignored \relax l.6111 ...sical N, P, K Factorial Experiment}{npk} [2127] Underfull \hbox (badness 1783) in paragraph at lines 6229--6233 []\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space. That is [2128] [2129] [2130] [2131] Underfull \vbox (badness 10000) has occurred while \output is active [2132] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6527--6527 [] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb ose = TRUE)))[] [2133] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6615--6615 [] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr ellis"))[] [2134] [2135] [2136] [2137] [2138] [2139] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7054--7054 []\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100 , A=10, B=1))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7071--7071 [] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c auchit"))[] Underfull \hbox (badness 10000) in paragraph at lines 7078--7085 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2140] Underfull \hbox (badness 10000) in paragraph at lines 7094--7096 []\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat Underfull \hbox (badness 3138) in paragraph at lines 7149--7155 []\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c mr/m/n/10 ) = [2141] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7219--7219 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2142] [2143] Underfull \hbox (badness 5091) in paragraph at lines 7328--7331 \T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na nt com-po-nents are used (ex-cept for [2144] [2145] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7458--7458 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam p = "exact")[] [2146] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7523--7523 [] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC V"), ...)[] [2147] [2148] [2149] [2150] [2151] [2152] Underfull \hbox (badness 4686) in paragraph at lines 7961--7963 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds Underfull \hbox (badness 1515) in paragraph at lines 7977--7981 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n /10 cycles \T1/ptm/m/n/10 terms or when a [2153] [2154] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8080--8080 [] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control = NULL)[] Underfull \hbox (badness 1590) in paragraph at lines 8104--8108 []\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n /10 NA\T1/ptm/m/n/10 s are found. The [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9483--9483 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS E, ...)[] [2175] Underfull \hbox (badness 1158) in paragraph at lines 9610--9613 []\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10 "Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly), [2176] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9692--9692 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub le.eps^0.25) Overfull \hbox (30.78088pt too wide) in paragraph at lines 9694--9694 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double .eps^0.25,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9697--9697 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub le.eps^0.25)[] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189]) (./Matrix-pkg.tex [2190] Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 41--44 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 41--44 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2191] Underfull \hbox (badness 1769) in paragraph at lines 95--98 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2192] Underfull \hbox (badness 2229) in paragraph at lines 159--162 []\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm /m/n/10 ob-jects; here, when the first is Underfull \hbox (badness 1147) in paragraph at lines 159--162 \T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th ese ar-gu-ments will be con-cate-nated to a new [2193] Underfull \hbox (badness 10000) in paragraph at lines 257--260 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 263--265 []\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][ ]sparseVector[][][]"\T1/ptm/m/n/10 's, see [2194] [2195] Overfull \hbox (42.78088pt too wide) in paragraph at lines 488--488 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp arse = TRUE) Underfull \hbox (badness 5147) in paragraph at lines 495--498 []\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal mean-ing as in [2196] Underfull \hbox (badness 5119) in paragraph at lines 508--512 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class Underfull \hbox (badness 4621) in paragraph at lines 512--516 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m /n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a Overfull \hbox (4.38043pt too wide) in paragraph at lines 535--535 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 537--537 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 546--546 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c( 1:3,2:3,3:2)],[] [2197] [2198] Overfull \hbox (52.98038pt too wide) in paragraph at lines 660--660 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd iag() -- for the case of *many* (k x k) matrices:[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(, , ....., ) where each mat_j is a k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 matrix\TS1/pcr/m/n/9 '[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 662--662 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k) matrix of class \code{"\linkS4class{dgCMatrix}"}.[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 675--675 [] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \ T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri x indexing), but elegant?[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 676--676 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 681--681 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim plify=FALSE)[] [2199] Underfull \hbox (badness 3189) in paragraph at lines 732--736 []\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib . [2200] [2201] [2202] Overfull \hbox (72.78088pt too wide) in paragraph at lines 947--947 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2203] Underfull \hbox (badness 10000) in paragraph at lines 1022--1024 []\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n /10 (or equiv-a- Underfull \hbox (badness 10000) in paragraph at lines 1045--1050 []\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of the lower tri- Underfull \hbox (badness 10000) in paragraph at lines 1045--1050 \T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the de-com-po-si-tion. This method is equiv-a-lent to Underfull \hbox (badness 1092) in paragraph at lines 1045--1050 \T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in the above de-scrip-tion of Underfull \hbox (badness 10000) in paragraph at lines 1068--1075 []\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm = "logical") [2204]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho l}) has been already used, duplicate ignored \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic ate ignored \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} [2205pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha s been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' pdfTeX warning (ext4): destina tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' pdfTeX warning (ext4): destina tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' ] [2206] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1266--1266 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2207] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1360--1360 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) Underfull \hbox (badness 2277) in paragraph at lines 1388--1391 []\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer -ent types of ma-tri-ces. Use [2208] Underfull \hbox (badness 1609) in paragraph at lines 1435--1439 []\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion [] []\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra [2209] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so me GOTOblas:[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1476--1476 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 , sep="") ## dQuote() gives bad plots[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1484--1484 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE) , super = c(FALSE,TRUE)))[] [2210] Underfull \hbox (badness 6445) in paragraph at lines 1531--1538 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("Cholesky", ...) \T1/ptm/m/n/10 or Underfull \hbox (badness 3861) in paragraph at lines 1531--1538 \T1/pcr/m/n/10 new("BunchKaufman", ...)\T1/ptm/m/n/10 , etc, or rather by calls of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or Underfull \hbox (badness 1783) in paragraph at lines 1566--1570 []\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1 /ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend Underfull \hbox (badness 1221) in paragraph at lines 1582--1588 \T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and [2211]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col Sums}) has been already used, duplicate ignored \relax l.1623 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup licate ignored \relax l.1623 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl icate ignored \relax l.1624 \aliasA{colMeans}{colSums}{colMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i gnored \relax l.1645 \aliasA{rowMeans}{colSums}{rowMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig nored \relax l.1656 \aliasA{rowSums}{colSums}{rowSums} [2212] Underfull \hbox (badness 2922) in paragraph at lines 1710--1714 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i n-her-it-ing from Underfull \hbox (badness 1728) in paragraph at lines 1710--1714 \T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a Underfull \hbox (badness 1237) in paragraph at lines 1721--1724 [][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1 /pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10 v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since [2213] Underfull \hbox (badness 10000) in paragraph at lines 1801--1805 []\T1/pcr/m/n/10 signature(x = "compMatrix", value = "list")\T1/ptm/m/n/10 : se t the [2214] Underfull \hbox (badness 3547) in paragraph at lines 1875--1878 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2215] [2216] [2217] Underfull \hbox (badness 10000) in paragraph at lines 2112--2114 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix ", where = [2218] [2219] Underfull \hbox (badness 10000) in paragraph at lines 2234--2236 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix" , where = Underfull \hbox (badness 3068) in paragraph at lines 2295--2299 \T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10 or sim-i-lar. Of-ten how-ever, more eas-ily via [2220] Underfull \hbox (badness 4713) in paragraph at lines 2330--2332 []\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de -com-po-si-tion of a square [2221] Underfull \hbox (badness 10000) in paragraph at lines 2447--2450 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10 or [2222] Underfull \hbox (badness 10000) in paragraph at lines 2549--2553 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dgTMatrix", ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2549--2553 \T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or [2223] Underfull \hbox (badness 2707) in paragraph at lines 2605--2609 []\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T 1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d gTMatrix" \T1/ptm/m/n/10 (and other Underfull \hbox (badness 2368) in paragraph at lines 2610--2614 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i n more than one pos-si-ble Underfull \hbox (badness 10000) in paragraph at lines 2617--2620 []\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\ T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ; [2224] Underfull \hbox (badness 2689) in paragraph at lines 2673--2675 []\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix. If miss-ing, Underfull \hbox (badness 10000) in paragraph at lines 2677--2682 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 .symDiagonal \T1/ptm/m/n/10 (\T1/pcr/m/n/10 .trDiagonal\T1/ptm/m/n/10 ), the re-sult-ing sparse Underfull \hbox (badness 3482) in paragraph at lines 2677--2682 [][]\T1/pcr/m/n/10 symmetricMatrix[][][] \T1/ptm/m/n/10 (or [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 ) will have slot \T1/pcr/m/n/10 uplo [2225] Underfull \hbox (badness 1097) in paragraph at lines 2700--2703 []\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1 /pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][ ] \T1/ptm/m/n/10 (with ``su-per-class'' Underfull \hbox (badness 1142) in paragraph at lines 2713--2718 [][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de -pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm /m/n/10 ) rep-re-sen-ta-tion of [2226] Underfull \hbox (badness 3646) in paragraph at lines 2951--2954 []\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T 1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][] \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally Underfull \hbox (badness 10000) in paragraph at lines 2973--2974 []\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1 /ptm/m/n/10 : Underfull \hbox (badness 1810) in paragraph at lines 2980--2982 []\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri v-ially im-ple-mented, of Underfull \hbox (badness 10000) in paragraph at lines 2983--2985 []\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv -a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion Underfull \hbox (badness 3803) in paragraph at lines 2986--2990 []\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou p meth-ods re-turn a [2227] Underfull \hbox (badness 1371) in paragraph at lines 2995--3001 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 : the re-sult is from class Underfull \hbox (badness 10000) in paragraph at lines 3002--3006 []\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec t of S3 class Underfull \hbox (badness 2318) in paragraph at lines 3012--3016 [][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr /m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and [2228] [2229] Underfull \hbox (badness 1859) in paragraph at lines 3196--3198 []\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t his group con-tains Underfull \hbox (badness 10000) in paragraph at lines 3243--3245 [][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre fer-able to (and more ef-fi-cient than) [2230] Underfull \hbox (badness 1168) in paragraph at lines 3363--3366 []\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T 1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , via [2231] [2232] Underfull \hbox (badness 4967) in paragraph at lines 3528--3532 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsCMatrix", ...) \T1/ptm/m/n/10 or [2233] Overfull \hbox (2.39853pt too wide) in paragraph at lines 3533--3535 []\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][] \T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 . Underfull \hbox (badness 6364) in paragraph at lines 3575--3578 []\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr /m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves [2234] [2235] Underfull \hbox (badness 10000) in paragraph at lines 3725--3730 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1 /ptm/m/n/10 , by Underfull \hbox (badness 6961) in paragraph at lines 3725--3730 \T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m /n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm /m/n/10 by class Underfull \hbox (badness 10000) in paragraph at lines 3735--3737 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a triv-ial Underfull \hbox (badness 10000) in paragraph at lines 3737--3740 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 : if [2236] Underfull \hbox (badness 4967) in paragraph at lines 3813--3815 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsyMatrix", ...) \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 3852--3855 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 , or Underfull \hbox (badness 1735) in paragraph at lines 3852--3855 \T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing "\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the [2237] Underfull \hbox (badness 10000) in paragraph at lines 3855--3858 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 , or Underfull \hbox (badness 2318) in paragraph at lines 3855--3858 \T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing "\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion Underfull \hbox (badness 6364) in paragraph at lines 3859--3862 []\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr /m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves [2238] Underfull \hbox (badness 4060) in paragraph at lines 3983--3986 []\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse tri-an-gu-lar solve (aka [2239] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4023--4023 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] [2240] Underfull \hbox (badness 3635) in paragraph at lines 4091--4095 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class Underfull \hbox (badness 10000) in paragraph at lines 4100--4103 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma - Underfull \hbox (badness 10000) in paragraph at lines 4100--4103 \T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co m-bi-na-tions, see Underfull \hbox (badness 10000) in paragraph at lines 4105--4109 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1 0 : the [2241] [2242] [2243] [2244] Underfull \hbox (badness 10000) in paragraph at lines 4393--4398 []\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite Tay-lor se-ries [2245] [2246] Overfull \hbox (85.38034pt too wide) in paragraph at lines 4527--4527 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/ Boeing/msc00726.tar.gz"))))[] Overfull \hbox (139.38028pt too wide) in paragraph at lines 4530--4530 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe ll-Boeing/counterx/jgl009.mtx.gz"))))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4534--4534 []\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary dir./folder:[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4537--4537 []\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 4547--4547 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2247] [2248] Underfull \hbox (badness 10000) in paragraph at lines 4702--4704 [][][]\T1/pcr/m/n/10 symmpart[][][] \T1/ptm/m/n/10 for the sym-met-ric part of a ma-trix, or the co-er-cions [2249] [2250] Underfull \hbox (badness 10000) in paragraph at lines 4849--4854 []\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1 /ptm/m/n/10 , [2251] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4930--4930 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che cking reasons" Overfull \hbox (20.58041pt too wide) in paragraph at lines 4932--4932 [] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2, dimnames=dns))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4936--4936 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] [2252] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4943--4943 [] \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] [2253] Underfull \hbox (badness 10000) in paragraph at lines 5068--5073 []\T1/ptm/m/n/10 color for the bor-der of each rect-an-gle. \T1/pcr/m/n/10 NA \ T1/ptm/m/n/10 means Underfull \hbox (badness 10000) in paragraph at lines 5068--5073 \T1/ptm/m/n/10 no bor-der is drawn. When \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 as by de-fault, Underfull \hbox (badness 2644) in paragraph at lines 5068--5073 \T1/pcr/m/n/10 border.col <- if(lwd < .01) NA else NULL \T1/ptm/m/n/10 is used. Con- Underfull \hbox (badness 4108) in paragraph at lines 5068--5073 \T1/ptm/m/n/10 sider us-ing an opaque color in-stead of \T1/pcr/m/n/10 NULL \T1 /ptm/m/n/10 which cor-re-sponds to [2254] Underfull \hbox (badness 4120) in paragraph at lines 5087--5090 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use Overfull \hbox (15.18042pt too wide) in paragraph at lines 5124--5124 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col /row) indices:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5130--5130 [] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, border.col=NA)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5131--5131 [] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd =2, border.col=NA)[] Overfull \hbox (144.78027pt too wide) in paragraph at lines 5134--5134 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5136--5136 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH ECK_EXTRA")) ||[] [2255] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5143--5143 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a nti-aliasing[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5146--5146 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2256] Underfull \hbox (badness 1817) in paragraph at lines 5235--5244 []\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within the Underfull \hbox (badness 5637) in paragraph at lines 5277--5279 []\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use [2257] Underfull \hbox (badness 3138) in paragraph at lines 5303--5305 []\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the [2258] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5370--5370 [] \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1 , I2)) else TRUE,[] Underfull \hbox (badness 1603) in paragraph at lines 5391--5393 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault, Underfull \hbox (badness 10000) in paragraph at lines 5399--5404 []\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault, Underfull \hbox (badness 10000) in paragraph at lines 5399--5404 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 ) , \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as Underfull \hbox (badness 10000) in paragraph at lines 5399--5404 [][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to [2259] [2260] [2261] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5628--5628 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/ pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] [2262] Underfull \hbox (badness 10000) in paragraph at lines 5709--5712 [][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and Overfull \hbox (9.78043pt too wide) in paragraph at lines 5720--5720 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n ot "formally"[] [2263] Underfull \hbox (badness 1622) in paragraph at lines 5757--5762 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \ T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy /m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ), Underfull \hbox (badness 1418) in paragraph at lines 5757--5762 \T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy /m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m /it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/ m/n/10 is the kro-necker prod-uct [2264] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5818--5818 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1) , c(12L, 4L)),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5819--5819 [] \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2) , c(12L, 4L)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5826--5826 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2265] Underfull \hbox (badness 1062) in paragraph at lines 5955--5958 []\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both [2266] Underfull \hbox (badness 2809) in paragraph at lines 5984--5987 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2267] Underfull \hbox (badness 2635) in paragraph at lines 6096--6101 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 6096--6101 \T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/ pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/ m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 6104--6107 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us e, e.g., [2268] Underfull \hbox (badness 10000) in paragraph at lines 6214--6224 \T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/ n/10 ) or in com-pressed column-oriented form (class Underfull \hbox (badness 1242) in paragraph at lines 6214--6224 [][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/ 10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 -- in [2269] Underfull \hbox (badness 1184) in paragraph at lines 6296--6299 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2270] Underfull \hbox (badness 10000) in paragraph at lines 6394--6397 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2271] Underfull \hbox (badness 10000) in paragraph at lines 6469--6472 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., Overfull \hbox (25.98041pt too wide) in paragraph at lines 6485--6485 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] [2272] Underfull \hbox (badness 2443) in paragraph at lines 6524--6530 []\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][ ]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see Underfull \hbox (badness 1776) in paragraph at lines 6524--6530 [][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr /m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar, Underfull \hbox (badness 1675) in paragraph at lines 6545--6548 []\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth- ods for dif-fer-ent types of ma-tri-ces. Use [2273] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6615--6615 [] \T1/pcr/m/n/9 # q is a 0-based permutation o f the columns[] [2274] [2275] Underfull \hbox (badness 6268) in paragraph at lines 6751--6754 []\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math- e-mat-i-cally''), [2276] Underfull \hbox (badness 5036) in paragraph at lines 6775--6779 []\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1 /ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . How-ever, Underfull \hbox (badness 10000) in paragraph at lines 6775--6779 \T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e mpty'' [][]sparse-Ma-trix[][][], as does [2277]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.6868 \aliasA{det}{Matrix-class}{det} Underfull \hbox (badness 1348) in paragraph at lines 6948--6951 []\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10 diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing Underfull \hbox (badness 10000) in paragraph at lines 6953--6956 []\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \ T1/pcr/m/n/10 value \T1/ptm/m/n/10 is Underfull \hbox (badness 10000) in paragraph at lines 6953--6956 \T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p tm/m/n/10 Ma-trix ob-jects, but only when Underfull \hbox (badness 10000) in paragraph at lines 6971--6974 Underfull \hbox (badness 7326) in paragraph at lines 6981--6983 []\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")\T1/ptm/m/n/10 : This re -lies on a cor-rect [2278]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \relax l.7044 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.crossprod}) has been already used, dup licate ignored \relax l.7152 ...A{crossprod}{matrix-products}{crossprod} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du plicate ignored \relax l.7252 ...tcrossprod}{matrix-products}{tcrossprod} [2279] Underfull \hbox (badness 1881) in paragraph at lines 7350--7356 \T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn [2280pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros sprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7412 \end{Details} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrossprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7412 \end{Details} ] Underfull \hbox (badness 10000) in paragraph at lines 7423--7426 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma - Underfull \hbox (badness 10000) in paragraph at lines 7423--7426 \T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co m-bi-na-tions, see Underfull \hbox (badness 5637) in paragraph at lines 7426--7431 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use Underfull \hbox (badness 10000) in paragraph at lines 7435--7437 []\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r e-turns Underfull \hbox (badness 10000) in paragraph at lines 7437--7439 []\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r e-turns Underfull \hbox (badness 10000) in paragraph at lines 7441--7442 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and [2281] [2282] Underfull \hbox (badness 1062) in paragraph at lines 7622--7625 []\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both [2283] Underfull \hbox (badness 2809) in paragraph at lines 7656--7659 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2284] Underfull \hbox (badness 10000) in paragraph at lines 7708--7710 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <- (X + t(X))/2 \T1/ ptm/m/n/10 should be done, af-ter [2285] Underfull \hbox (badness 1406) in paragraph at lines 7748--7752 []\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b y Jens Oehlschlaegel did not Underfull \hbox (badness 1019) in paragraph at lines 7748--7752 \T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t his sim-pli-fi-ca-tion, now only via [2286] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7846--7846 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a ll in this example[] Underfull \vbox (badness 10000) has occurred while \output is active [2287] Underfull \hbox (badness 2635) in paragraph at lines 7911--7916 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 7911--7916 \T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/ pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/ m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 7919--7922 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us e, e.g., [2288] [2289] Underfull \hbox (badness 10000) in paragraph at lines 8113--8115 []\T1/ptm/m/n/10 fast [2290]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8153 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.8153 \HeaderA{norm}{Matrix Norms}{norm} [2291] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8240--8240 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8241--8241 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8242--8242 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Underfull \hbox (badness 2401) in paragraph at lines 8355--8365 []\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1 0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p tm/m/n/10 , [2292] Underfull \hbox (badness 1184) in paragraph at lines 8426--8429 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2293] Underfull \hbox (badness 10000) in paragraph at lines 8516--8519 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2294] Underfull \hbox (badness 10000) in paragraph at lines 8592--8595 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2295] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8608--8608 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] Overfull \vbox (41.60564pt too high) has occurred while \output is active [2296] Underfull \hbox (badness 10000) in paragraph at lines 8718--8720 []\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe r sig-na-tures (use Underfull \hbox (badness 1596) in paragraph at lines 8734--8736 []\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 : co-er-cion to sparse Underfull \hbox (badness 1721) in paragraph at lines 8740--8744 \T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S ee [2297] [2298] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8819--8819 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8824--8824 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8829--8829 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 8852--8862 []\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T 1/pcr/m/n/10 x \T1/ptm/m/n/10 should Underfull \hbox (badness 10000) in paragraph at lines 8852--8862 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2299] [2300]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.qr}) has been already used, duplicate ignored \relax l.8953 \aliasA{qr}{qr-methods}{qr} Underfull \hbox (badness 5119) in paragraph at lines 8999--9002 []\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma- trix with Overfull \hbox (9.78043pt too wide) in paragraph at lines 9026--9026 []\T1/pcr/m/n/9 stopifnot(identical(dimnames(X), dnX))# some versions changed X\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s dimnames![] [2301] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9037--9037 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n ot supported[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9041--9041 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9058--9058 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9066--9066 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor rect colnames[] [2302] Underfull \hbox (badness 10000) in paragraph at lines 9119--9125 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of Underfull \hbox (badness 10000) in paragraph at lines 9136--9139 []\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p tm/m/n/10 , it cor-re-sponds to [2303] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9208--9208 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/ n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale free"[] [2304] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9229--9229 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war ning+ ~1.5 sec (2013)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 9230--9230 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con siderably faster![] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h as been already used, duplicate ignored \relax l.9249 ... the Reciprocal Condition Number}{rcond} [2305] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9362--9362 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2306] [2307] [2308] Underfull \hbox (badness 10000) in paragraph at lines 9547--9549 []\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably Underfull \hbox (badness 1325) in paragraph at lines 9553--9561 \T1/ptm/m/n/10 gets \T1/pcr/m/n/10 x <- rand.x(nnz) \T1/ptm/m/n/10 and calls [] []\T1/pcr/m/n/10 sparseMatrix[][][](i=i, j=j, x=x, ..)\T1/ptm/m/n/10 . When [2309] [2310] Underfull \hbox (badness 1558) in paragraph at lines 9698--9701 []\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1 0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional [2311] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9760--9760 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9764--9764 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2312]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol ve}) has been already used, duplicate ignored \relax l.9826 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (54.78088pt too wide) in paragraph at lines 9923--9923 [] \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P ", "Pt"), ...)[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9928--9928 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2313] Underfull \hbox (badness 6047) in paragraph at lines 9963--9975 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods Underfull \hbox (badness 10000) in paragraph at lines 9980--9983 []\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via Underfull \hbox (badness 7203) in paragraph at lines 9985--9986 []\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar Underfull \hbox (badness 7851) in paragraph at lines 9989--9996 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 10000) in paragraph at lines 9989--9996 \T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U ses the sparse Underfull \hbox (badness 10000) in paragraph at lines 10002--10012 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 2165) in paragraph at lines 10002--10012 \T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym- [2314] Underfull \hbox (badness 1194) in paragraph at lines 10036--10038 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines Underfull \hbox (badness 10000) in paragraph at lines 10050--10053 []\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 10000) in paragraph at lines 10059--10060 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 10065--10067 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10069--10070 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 10077--10080 [][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1 /ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10095--10095 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i s singular!][] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10099--10099 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2315] Underfull \hbox (badness 10000) in paragraph at lines 10120--10123 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu la and data frame Underfull \hbox (badness 1648) in paragraph at lines 10148--10150 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 10000) in paragraph at lines 10156--10159 []\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co- er-ca-ble to) Underfull \hbox (badness 2591) in paragraph at lines 10156--10159 \T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t rasts to be ap-plied to the [2316] Underfull \hbox (badness 10000) in paragraph at lines 10167--10171 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for Underfull \hbox (badness 2828) in paragraph at lines 10167--10171 \T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m /n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for Underfull \hbox (badness 6592) in paragraph at lines 10178--10180 []\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in -di-cat-ing if the re-sult must be a [2317] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10255--10255 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M) == c(0, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10256--10256 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M) == c(3, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10257--10257 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2318] [2319] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10441--10441 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10442--10442 [] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = FALSE)[] [2320] Underfull \hbox (badness 4621) in paragraph at lines 10482--10486 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m /n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a [2321] Underfull \hbox (badness 10000) in paragraph at lines 10558--10561 []\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][]( *, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10570--10570 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10574--10574 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10575--10575 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10580--10580 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims = c(10,20)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10583--10583 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2322] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10606--10606 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 10607--10607 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10633--10633 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep resentations.[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 10635--10635 [] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack age = "SparseM"))) {[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10637--10637 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] [2323] Underfull \hbox (badness 10000) in paragraph at lines 10730--10738 []\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject of S3 class Underfull \hbox (badness 1325) in paragraph at lines 10751--10755 []\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a [2324] Underfull \hbox (badness 10000) in paragraph at lines 10781--10785 [][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s uch as [][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)\T1/ptm/m/n/10 , or pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha s been already used, duplicate ignored \relax l.10821 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2325] [2326] Underfull \hbox (badness 1430) in paragraph at lines 10951--10953 []\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses Overfull \hbox (58.38037pt too wide) in paragraph at lines 10979--10979 [] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai led in Matrix <= 1.1-0[] Underfull \hbox (badness 5036) in paragraph at lines 11007--11009 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2327] Underfull \hbox (badness 2970) in paragraph at lines 11140--11146 []\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/ 10 "sparseVector" \T1/ptm/m/n/10 has the five ac- Underfull \hbox (badness 3679) in paragraph at lines 11140--11146 \T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec tor"\T1/ptm/m/n/10 , [2328] Underfull \hbox (badness 10000) in paragraph at lines 11191--11194 []\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/ 10 co-erces Underfull \hbox (badness 10000) in paragraph at lines 11213--11216 []\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m /n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list [2329] Underfull \hbox (badness 10000) in paragraph at lines 11231--11236 []\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/ 10 logical[][][] \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 11246--11248 [][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc -tion of sparse vec-tors (apart from [2330] [2331] Underfull \hbox (badness 3525) in paragraph at lines 11364--11368 []\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/ pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/ ptm/m/n/10 , where Underfull \hbox (badness 1831) in paragraph at lines 11371--11377 [][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more u sual con-struc-tor of such ma-tri-ces. Then, [2332] Underfull \hbox (badness 10000) in paragraph at lines 11466--11470 []\T1/pcr/m/n/10 signature(object = "symmetricMatrix")\T1/ptm/m/n/10 : re-turns \T1/ptm/m/it/10 sym-met-ric Underfull \hbox (badness 1043) in paragraph at lines 11466--11470 [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , even when the \T1/pcr/m/n/10 Dimnames \T1/ptm/m/n/10 slot only has row or col-umn names. This Underfull \hbox (badness 10000) in paragraph at lines 11482--11487 []\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/ n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be Underfull \hbox (badness 1259) in paragraph at lines 11482--11487 \T1/pcr/m/n/10 list(NULL, )\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. How-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other Underfull \hbox (badness 2591) in paragraph at lines 11490--11495 \T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 , and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1 /ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or [2333] Underfull \hbox (badness 2057) in paragraph at lines 11562--11564 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., [2334] [2335] Underfull \hbox (badness 6641) in paragraph at lines 11648--11651 []\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm /m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit h Underfull \hbox (badness 5133) in paragraph at lines 11688--11692 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the vir-tual class of all sparse ma-tri-ces coded in Underfull \hbox (badness 2818) in paragraph at lines 11688--11692 \T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c re-ated from it. See [2336] Underfull \hbox (badness 7649) in paragraph at lines 11795--11797 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2337] [2338] [2339] Underfull \hbox (badness 7362) in paragraph at lines 11996--11998 []\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a sparse ma-trix (i.e., of sub-class of [2340] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12034--12034 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 12035--12035 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] [2341] [2342] Underfull \hbox (badness 6910) in paragraph at lines 12285--12287 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2343] [2344] [2345]) (./boot-pkg.tex [2346] Chapter 18. [2347] [2348] [2349] [2350] [2351] [2352] [2353] Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f" , "w"), [2354] Underfull \hbox (badness 1325) in paragraph at lines 568--575 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r e-quired. Pos-si-ble Underfull \hbox (badness 1275) in paragraph at lines 583--588 []\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m ulti-sample prob- Underfull \hbox (badness 1264) in paragraph at lines 583--588 \T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n ored when [2355] Overfull \hbox (43.25928pt too wide) in paragraph at lines 643--649 []\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1 0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0 [2356] Underfull \hbox (badness 6268) in paragraph at lines 797--807 \T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de -fault clus-ter, a sec-ond ap-proach is used if [2357] Underfull \hbox (badness 1881) in paragraph at lines 824--826 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 6493) in paragraph at lines 851--855 [][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 , [2358] Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, data = nuke)[] Underfull \vbox (badness 10000) has occurred while \output is active [2359] [2360] Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 []\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i n-ter- Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 \T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues [2361] Underfull \hbox (badness 1496) in paragraph at lines 1082--1091 []\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari- ance of the Underfull \hbox (badness 2005) in paragraph at lines 1082--1091 \T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i n-ter-vals. If it Underfull \hbox (badness 2343) in paragraph at lines 1082--1091 \T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10 is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to Underfull \hbox (badness 2150) in paragraph at lines 1103--1109 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2362] [2363] [2364] [2365] [2366] Underfull \hbox (badness 1571) in paragraph at lines 1443--1445 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2367] [2368] [2369] [2370] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix( 1,n,2), [2371] [2372] [2373] [2374] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4) + strata(ulcer),[] Underfull \vbox (badness 10000) has occurred while \output is active [2375] Underfull \hbox (badness 6268) in paragraph at lines 2081--2083 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2376] [2377] [2378] [2379] Underfull \hbox (badness 1565) in paragraph at lines 2335--2340 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set Underfull \hbox (badness 4595) in paragraph at lines 2360--2365 \T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis tic \T1/ptm/m/n/10 is called. [2380] Underfull \hbox (badness 1881) in paragraph at lines 2429--2431 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 2057) in paragraph at lines 2437--2438 [][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 , [2381] Underfull \hbox (badness 1077) in paragraph at lines 2533--2537 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n /10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the sam-ple Underfull \hbox (badness 1112) in paragraph at lines 2533--2537 \T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1 0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10 is used. This is mul-ti-plied by [2382] [2383] [2384] [2385] [2386] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25, Overfull \hbox (18.78088pt too wide) in paragraph at lines 2894--2894 []\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25,[] [2387] [2388] [2389] Underfull \hbox (badness 3861) in paragraph at lines 3102--3105 [][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [2390] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1 :ncol(mat)) [2391] [2392] [2393] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling [2394] [2395] [2396] [2397] [2398] [2399] [2400] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835 [] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q = NULL)[] [2401] [2402] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])[] [2403] [2404] [2405] Underfull \hbox (badness 10000) in paragraph at lines 4187--4189 []\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault is [2406] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256 []\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz e data as in [2407] [2408] Underfull \hbox (badness 10000) in paragraph at lines 4359--4361 []\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o f Underfull \hbox (badness 1430) in paragraph at lines 4368--4372 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T 1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to Underfull \hbox (badness 2269) in paragraph at lines 4386--4389 []\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by [2409] [2410] [2411] [2412] [2413] [2414] [2415] [2416] [2417] Underfull \hbox (badness 3000) in paragraph at lines 4956--4959 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2418] [2419] [2420] [2421] Underfull \hbox (badness 2293) in paragraph at lines 5235--5238 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5235--5238 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2422] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat a = grav1[, 2])[] [2423] [2424] [2425] [2426] [2427] [2428] [2429] [2430] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c ity.sp1$spa[1][] [2431] Underfull \hbox (badness 1127) in paragraph at lines 5985--6003 \T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then [2432] Underfull \hbox (badness 2837) in paragraph at lines 6018--6021 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad dle.distn"\T1/ptm/m/n/10 . See the help file for [2433] [2434] [2435] [2436] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and Wright (1991). [2437] [2438] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling Overfull \hbox (20.58041pt too wide) in paragraph at lines 6494--6494 []\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t ilting was used[] [2439] [2440] [2441] Underfull \hbox (badness 1596) in paragraph at lines 6739--6743 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2442] [2443] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899 [] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha = c(0.05, 0.95),[] [2444] [2445] [2446] [2447] [2448] [2449] [2450] [2451]) (./class-pkg.tex [2452] Chapter 19. [2453] [2454] [2455] [2456] [2457] [2458] [2459] [2460] Underfull \hbox (badness 10000) in paragraph at lines 608--610 []\T1/ptm/m/n/10 the size of the code-book. De-faults to [2461] [2462] [2463] [2464] [2465] [2466] [2467] [2468]) (./cluster-pkg.tex Chapter 20. [2469] Underfull \hbox (badness 3098) in paragraph at lines 133--142 []\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u- Underfull \hbox (badness 2253) in paragraph at lines 133--142 \T1/ptm/m/n/10 larly for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is spec-i-fied of longer length than one. Since Underfull \hbox (badness 3323) in paragraph at lines 133--142 \T1/ptm/b/n/10 clus-ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-val id \T1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror Underfull \hbox (badness 10000) in paragraph at lines 133--142 \T1/ptm/m/n/10 as \T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n /10 . Fur-ther, \T1/pcr/m/n/10 method= "single" Underfull \hbox (badness 10000) in paragraph at lines 133--142 \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method = c(.5,.5,0,-.5)\T1/ptm/m/n/10 , and Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--142 \T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/ 10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 . [2470] Underfull \hbox (badness 10000) in paragraph at lines 167--169 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \ T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method = [2471] Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252 [] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met hod = 0.5)[iC]) ,[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 253--253 [] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, -.5))[iC]),[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254 [] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, +.5))[iC]))[] [2472] [2473] Underfull \vbox (badness 10000) has occurred while \output is active [2474] [2475] Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518 [] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot = axes,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 522--522 [] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5, ...)[] [2476] Underfull \hbox (badness 5374) in paragraph at lines 539--541 []\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use d when [2477] Overfull \hbox (66.78088pt too wide) in paragraph at lines 637--637 [] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c orrect.d = TRUE)[] [2478] Underfull \hbox (badness 3078) in paragraph at lines 688--691 []\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem- ory (and hence time), but dis-ables [2479] [2480] Underfull \hbox (badness 2941) in paragraph at lines 778--781 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 816--816 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo r this seed):[] [2481] Underfull \hbox (badness 10000) in paragraph at lines 863--865 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2482] Overfull \hbox (24.78088pt too wide) in paragraph at lines 928--928 [] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code =3), ...)[] [2483] Underfull \hbox (badness 4872) in paragraph at lines 974--976 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 988--992 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2484] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1095--1095 [] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE. factor = SEf)))[] [2485] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1112--1112 []\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras < - TRUE # or FALSE[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1150--1150 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] [2486] Underfull \hbox (badness 4144) in paragraph at lines 1182--1186 []\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m /n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent, e.g., for [2487] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1258--1258 [] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1, cex.txt = cex,[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1264--1264 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2488] [2489] Underfull \hbox (badness 10000) in paragraph at lines 1403--1408 []\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1 0 princomp[][][](*, cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 1451--1454 [2490] Underfull \hbox (badness 10000) in paragraph at lines 1468--1472 [][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 , Overfull \hbox (31.3804pt too wide) in paragraph at lines 1492--1492 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a nd label ellipses[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1502--1502 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2491] Underfull \hbox (badness 5741) in paragraph at lines 1542--1545 []\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der -ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only [2492] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1608--1608 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2493] Underfull \hbox (badness 5008) in paragraph at lines 1725--1733 \T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1 0 w[]^^N[]$\T1/ptm/m/n/10 , where [2494] [2495] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1816--1816 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord ratio = 7)))[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 1835--1835 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2496] [2497] [2498] [2499] Underfull \hbox (badness 10000) in paragraph at lines 2143--2145 []\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as Underfull \hbox (badness 10000) in paragraph at lines 2154--2157 Underfull \hbox (badness 3179) in paragraph at lines 2168--2174 [][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [ ][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips oid \T1/ptm/m/n/10 ob-jects. [2500] [2501] [2502] Underfull \hbox (badness 10000) in paragraph at lines 2326--2329 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par tition.object[][][]\T1/ptm/m/n/10 , [2503] Underfull \hbox (badness 1292) in paragraph at lines 2394--2397 []\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t he num-ber of it-er-a-tions needed and Underfull \hbox (badness 6675) in paragraph at lines 2403--2405 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see Underfull \hbox (badness 10000) in paragraph at lines 2426--2429 [][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n /10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [2504] [2505] [2506] [2507] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2642--2642 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] [2508] [2509] Underfull \hbox (badness 1067) in paragraph at lines 2829--2834 []\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger \T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g o-rithm, whereas [2510] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2888--2888 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2511] [2512] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2991--2991 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2513] [2514] [2515] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3187--3187 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3188--3188 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2516] Underfull \hbox (badness 10000) in paragraph at lines 3255--3258 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n /10 pltree() \T1/ptm/m/n/10 is pro-vided by [2517] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3305--3305 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3306--3306 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2518] [2519] [2520] Underfull \hbox (badness 10000) in paragraph at lines 3491--3494 []\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m /n/10 diss \T1/ptm/m/n/10 com-po-nent as for Underfull \hbox (badness 3471) in paragraph at lines 3491--3494 [][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a [2521] Underfull \hbox (badness 10000) in paragraph at lines 3554--3559 [][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [2522] Underfull \hbox (badness 4621) in paragraph at lines 3616--3621 []\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 1990) in paragraph at lines 3616--3621 \T1/ptm/m/n/10 which dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1 /ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider Underfull \hbox (badness 6268) in paragraph at lines 3628--3631 [][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.agnes[][][]\T1/ptm/m/n/10 , [2523] [2524] [2525] Underfull \hbox (badness 10000) in paragraph at lines 3813--3816 [][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3844--3847 [][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [2526] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3897--3897 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] Underfull \hbox (badness 2035) in paragraph at lines 3908--3910 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1 /pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for [2527] [2528] [2529] [2530] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4101--4101 [] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w idth "* s[i]),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 4103--4103 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] Underfull \hbox (badness 1946) in paragraph at lines 4132--4137 []\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n /10 ; note that the de-fault used to be \T1/pcr/m/n/10 col [2531] Underfull \hbox (badness 10000) in paragraph at lines 4199--4207 \T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by [2532] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4241--4241 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus ter-wise coloring[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4250--4250 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4252--4252 [] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma in")); frame()[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 4255--4255 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol denrod4", "gray20")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4257--4257 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4264--4264 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro wnames == indices[] [2533] [2534] [2535] [2536] [2537] [2538] Underfull \hbox (badness 10000) in paragraph at lines 4622--4628 []\T1/ptm/m/n/10 Our ver-sion of the \T1/pcr/m/n/10 xclara \T1/ptm/m/n/10 is sl ightly more rounded than the one from Underfull \hbox (badness 10000) in paragraph at lines 4638--4640 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side Overfull \hbox (52.98038pt too wide) in paragraph at lines 4651--4651 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10 01:2000}, {2001:3000} Overfull \hbox (9.78043pt too wide) in paragraph at lines 4653--4653 []\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s medoid indices == pam(xclara, 3)$id.med[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4663--4663 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o bservations:[] [2539] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4667--4667 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? - - Robust range:[] [2540]) (./codetools-pkg.tex Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17 [] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = !all,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18 [] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress Undefined,[] [2541] Underfull \hbox (badness 10000) in paragraph at lines 65--70 []\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2542] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2543] [2544] [2545]) (./foreign-pkg.tex [2546] Chapter 22. [2547] Underfull \hbox (badness 1231) in paragraph at lines 67--70 []\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr om, or a Underfull \hbox (badness 6708) in paragraph at lines 78--81 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2548] [2549] Underfull \hbox (badness 3601) in paragraph at lines 235--243 []\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n /10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 , [2550] Overfull \hbox (12.78088pt too wide) in paragraph at lines 296--296 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates = FALSE, [2551] [2552] [2553] Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t o.data.frame,[] [2554] Overfull \hbox (30.78088pt too wide) in paragraph at lines 463--463 [] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen d", "no"),[] Underfull \hbox (badness 10000) in paragraph at lines 506--515 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer- Underfull \hbox (badness 6001) in paragraph at lines 506--515 \T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de- fault), the first orig-i-nal value Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named to Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/pcr/m/n/10 paste0(label, duplicated.value.labels.infix, level)\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 516--519 []\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with du- Underfull \hbox (badness 10000) in paragraph at lines 516--519 \T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault \T1/pcr/m/n/10 "_dupli cated_"\T1/ptm/m/n/10 ) if [2555] Underfull \hbox (badness 10000) in paragraph at lines 551--559 []\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en -[]us / library / ms776446(VS . 85 ) .aspx$[][] Underfull \hbox (badness 7613) in paragraph at lines 569--575 []\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/ m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute [2556] Overfull \hbox (20.58041pt too wide) in paragraph at lines 624--624 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg ument settings.[] Overfull \hbox (112.38031pt too wide) in paragraph at lines 625--625 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2557] Overfull \hbox (9.78043pt too wide) in paragraph at lines 658--658 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ ate variables[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 662--662 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt h=w), "\n"))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 669--669 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, collapse="")[] [2558] [2559] Underfull \hbox (badness 10000) in paragraph at lines 813--814 Overfull \hbox (4.38043pt too wide) in paragraph at lines 823--823 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f oreign")[1])[] [2560] [2561] Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899 [] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G lobalEnv) [2562] Overfull \hbox (0.78088pt too wide) in paragraph at lines 963--963 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute (x))) Underfull \hbox (badness 6708) in paragraph at lines 989--992 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2563] [2564] Underfull \hbox (badness 10000) in paragraph at lines 1073--1074 [][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase / format / data _ types . Overfull \hbox (24.78088pt too wide) in paragraph at lines 1109--1109 [] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", "codes"))[] [2565] Underfull \hbox (badness 1286) in paragraph at lines 1194--1198 []\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates = FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec ts [2566] Underfull \hbox (badness 10000) in paragraph at lines 1267--1273 []\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign: ::writeForeignStata\T1/ptm/m/n/10 , [2567] Underfull \hbox (badness 6725) in paragraph at lines 1293--1296 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef -fect, the dec-i-mal in-di-ca-tor is al-ways set by [2568]) (./lattice-pkg.tex Chapter 23. [2569] [2570] [2571] Overfull \hbox (12.78088pt too wide) in paragraph at lines 286--286 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 290--290 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .xyplot"),[] [2572] Overfull \hbox (42.78088pt too wide) in paragraph at lines 298--298 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul t.dotplot"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 305--305 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.barchart"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 313--313 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.stripplot"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 334--334 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 338--338 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .bwplot"),[] [2573] Underfull \hbox (badness 4060) in paragraph at lines 357--369 []\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a lly of the Underfull \hbox (badness 10000) in paragraph at lines 357--369 \T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ iv-a-lently, \T1/pcr/m/n/10 y ~ x | Underfull \hbox (badness 1028) in paragraph at lines 397--412 \T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot both Underfull \hbox (badness 10000) in paragraph at lines 413--415 []\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum, one can ei-ther set [2574] Underfull \hbox (badness 7631) in paragraph at lines 479--484 []\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \ T1/ptm/m/n/10 in this case may be [2575] [2576] Underfull \hbox (badness 1221) in paragraph at lines 650--658 []\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as ar-gu-ments to [2577] [2578] [2579] [2580] Underfull \hbox (badness 2005) in paragraph at lines 986--998 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of fac-tors will be Underfull \hbox (badness 1199) in paragraph at lines 986--998 \T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a use-ful lay-out. [2581] Underfull \hbox (badness 1661) in paragraph at lines 1099--1105 []\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be num-bers be-tween 0 and 1, giv-ing co-or-di-nates [2582] [2583] Underfull \hbox (badness 1097) in paragraph at lines 1225--1227 []\T1/ptm/m/n/10 Logical flag, whether leg-end should have a Underfull \hbox (badness 1917) in paragraph at lines 1239--1240 []\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to [2584] [2585] [2586] Underfull \hbox (badness 1540) in paragraph at lines 1479--1485 []\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/ 10 plot.trellis[][][]\T1/ptm/m/n/10 , [2587] Underfull \hbox (badness 10000) in paragraph at lines 1566--1583 [][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel .stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 , [2588] Underfull \vbox (badness 10000) has occurred while \output is active [2589] Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671 [] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar dSprays$rowpos))),[] Underfull \hbox (badness 2012) in paragraph at lines 1725--1727 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][] []\T1/ptm/m/n/10 , which may pass them on to [2590] Underfull \hbox (badness 6808) in paragraph at lines 1755--1759 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to Underfull \hbox (badness 10000) in paragraph at lines 1772--1775 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 , etc; see [2591] Underfull \hbox (badness 10000) in paragraph at lines 1825--1827 []\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix An-drews [2592] [2593] [2594] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] Underfull \hbox (badness 10000) in paragraph at lines 2086--2093 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/ m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form Underfull \hbox (badness 1997) in paragraph at lines 2086--2093 \T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra ms or ker-nel den-sity [2595] Underfull \hbox (badness 10000) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t he value of Underfull \hbox (badness 1320) in paragraph at lines 2141--2144 \T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch ecked. If [2596] [2597] [2598] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2349--2349 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .qqmath"),[] Underfull \hbox (badness 4441) in paragraph at lines 2362--2366 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2599] [2600] [2601] Underfull \hbox (badness 4441) in paragraph at lines 2547--2554 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2602] [2603] Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689 [] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev elplot.raster")[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2721--2721 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl ot"),[] [2604] Underfull \hbox (badness 10000) in paragraph at lines 2761--2766 []\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu la of the form \T1/pcr/m/n/10 z ~ x * y [2605] Underfull \hbox (badness 2913) in paragraph at lines 2791--2796 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 2791--2796 \T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p tm/m/n/10 must have the same lengths as Underfull \hbox (badness 6758) in paragraph at lines 2877--2881 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be Underfull \hbox (badness 7576) in paragraph at lines 2877--2881 \T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast er[][][]\T1/ptm/m/n/10 . See also Underfull \hbox (badness 10000) in paragraph at lines 2883--2885 []\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T 1/ptm/m/n/10 when [2606] Underfull \hbox (badness 1609) in paragraph at lines 2935--2941 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti ons should be used, Underfull \hbox (badness 2772) in paragraph at lines 2935--2941 \T1/ptm/m/n/10 both for the false color im-age and the color key (if present). Ef- Underfull \hbox (badness 1400) in paragraph at lines 2935--2941 \T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 changes the de-fault panel func-tion from Underfull \hbox (badness 2486) in paragraph at lines 2959--2963 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2607] [2608] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3060--3060 [] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3061--3061 [] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062 [] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite = TRUE),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3073--3073 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. cloud"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 3085--3085 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.wireframe"),[] [2609] Underfull \hbox (badness 10000) in paragraph at lines 3110--3118 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo r-mula of the form \T1/pcr/m/n/10 z ~ x Underfull \hbox (badness 2913) in paragraph at lines 3143--3150 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 3143--3150 \T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p tm/m/n/10 must have the same lengths as [2610] [2611] [2612] [2613]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.parallel}) has been already used, duplicate ignored \relax l.3431 \aliasA{parallel}{B\_08\_splom}{parallel} Overfull \hbox (18.78088pt too wide) in paragraph at lines 3473--3473 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. splom"),[] [2614] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3496--3496 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.parallel"),[] [2615] [2616] [2617] [2618] [2619] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3832--3832 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt( var(x))) [2620] Underfull \hbox (badness 10000) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white bg")\T1/ptm/m/n/10 . Underfull \hbox (badness 2435) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2621] [2622] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4052--4052 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict = FALSE) Underfull \hbox (badness 1173) in paragraph at lines 4061--4065 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4088--4090 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when Underfull \hbox (badness 1728) in paragraph at lines 4105--4109 \T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se t-tings (ob-tained by [2623] Underfull \hbox (badness 5161) in paragraph at lines 4170--4174 []\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis .settings \T1/ptm/m/n/10 has not been fi-nal-ized, Underfull \hbox (badness 4913) in paragraph at lines 4170--4174 \T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca n be ob-tained by [2624] [2625] Underfull \hbox (badness 1067) in paragraph at lines 4284--4294 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm /m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 1735) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points Underfull \hbox (badness 10000) in paragraph at lines 4284--4294 \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and Underfull \hbox (badness 5231) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for Underfull \hbox (badness 1701) in paragraph at lines 4309--4312 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot .symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4312--4314 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl ot.polygon \T1/ptm/m/n/10 and [2626] [2627] [2628] [2629] [2630] [2631] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4716--4716 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab = "Height")[] [2632] [2633] Underfull \hbox (badness 10000) in paragraph at lines 4903--4906 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 . [2634] [2635] Underfull \hbox (badness 1442) in paragraph at lines 5035--5038 []\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and [2636] [2637] [2638] [2639] [2640] [2641] Underfull \hbox (badness 3646) in paragraph at lines 5367--5370 [][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f or Overfull \hbox (36.78088pt too wide) in paragraph at lines 5397--5397 [] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh ich.given],[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5398--5398 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which .given],[] [2642] Underfull \hbox (badness 10000) in paragraph at lines 5486--5489 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 2103) in paragraph at lines 5486--5489 \T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef t of pan-els us-ing Underfull \hbox (badness 6412) in paragraph at lines 5503--5509 []\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl y be-cause of the \T1/pcr/m/n/10 style Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive , es-pe-cially when Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm /m/n/10 are small. Tra-di-tional use is as Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 , though this can be [2643] Underfull \hbox (badness 1635) in paragraph at lines 5512--5517 []\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh ich is to draw a strip ap-pro-pri-ate for [2644] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5661--5661 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la bels,[] [2645] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5675--5675 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose "), ...)[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5676--5676 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos e"), ...)[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5679--5679 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location" , "toplevel",[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5682--5682 [] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig ht", "page"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 5684--5684 [] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in side"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5690--5690 [] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi ch.given",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5691--5691 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692 [] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi ch.panel",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5694--5694 [] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co lumn",[] Underfull \hbox (badness 10000) in paragraph at lines 5710--5712 []\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of [2646] Underfull \hbox (badness 2376) in paragraph at lines 5721--5723 []\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point. De-faults to [2647] Underfull \hbox (badness 2538) in paragraph at lines 5846--5850 \T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and Underfull \hbox (badness 4205) in paragraph at lines 5857--5864 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr a pa-ram-e-ters are passed on to Underfull \hbox (badness 4792) in paragraph at lines 5857--5864 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are used (in com-bi-na-tion with [2648] [2649] Underfull \hbox (badness 10000) in paragraph at lines 6010--6014 [][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , [] []\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 , [2650] [2651] Underfull \hbox (badness 4242) in paragraph at lines 6157--6162 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- [2652] [2653] Underfull \hbox (badness 3601) in paragraph at lines 6273--6278 []\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1 0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round Underfull \hbox (badness 2486) in paragraph at lines 6273--6278 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault, the ac-tual box-plot statis-tics are cal-cu-lated us-ing [2654] [2655] Overfull \hbox (60.78088pt too wide) in paragraph at lines 6360--6360 [] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co lors")$palette,[] [2656] Underfull \hbox (badness 1888) in paragraph at lines 6492--6499 \T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col. regions \T1/ptm/m/n/10 a vec-tor of col-ors, and [2657] Underfull \hbox (badness 10000) in paragraph at lines 6549--6552 []\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The Underfull \hbox (badness 1558) in paragraph at lines 6549--6552 \T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v alid color. The [2658] Underfull \hbox (badness 1005) in paragraph at lines 6599--6607 \T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/ 10 z \T1/ptm/m/n/10 are all passed to Underfull \hbox (badness 1571) in paragraph at lines 6599--6607 \T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/ 10 y \T1/ptm/m/n/10 are in- [2659] [2660] [2661] [2662] [2663] Underfull \hbox (badness 1320) in paragraph at lines 6955--6962 []\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan el func-tion that uses the raster draw- Underfull \hbox (badness 1715) in paragraph at lines 6955--6962 \T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more ef-fi-cient. When us-ing [2664] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7025--7025 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] [2665] Underfull \hbox (badness 10000) in paragraph at lines 7055--7059 []\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments to Underfull \hbox (badness 1584) in paragraph at lines 7055--7059 \T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu nc-tion is passed [2666] Underfull \hbox (badness 10000) in paragraph at lines 7160--7163 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by [2667] [2668] Underfull \hbox (badness 2012) in paragraph at lines 7326--7329 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2669] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7372--7372 [] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta ils.n = 50))[] [2670] [2671] Underfull \hbox (badness 2644) in paragraph at lines 7513--7517 \T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on to Underfull \hbox (badness 2772) in paragraph at lines 7526--7529 []\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a list of ar-gu-ments to be sup-plied to Underfull \hbox (badness 4242) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos -si-bly Underfull \hbox (badness 1147) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is co-erced to a list. This al-lows ar- Underfull \hbox (badness 2351) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline = c(0, 1)\T1/ptm/ m/n/10 , which adds the di- Underfull \hbox (badness 1675) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v = 0)\T1 /ptm/m/n/10 , which adds the Underfull \hbox (badness 1769) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol; e.g., [2672] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7596--7596 [] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y = c(1/6, 4/6)),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7606--7606 [] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d raw = FALSE),[] [2673] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7667--7667 [] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam e.type)[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7672--7672 [] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident ifier, name.type)[] [2674] [2675] [2676] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7857--7857 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden tifier = "grid")[] [2677] Underfull \hbox (badness 1436) in paragraph at lines 7912--7918 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for Underfull \hbox (badness 1231) in paragraph at lines 7912--7918 \T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti ngs. The [2678] [2679] [2680] [2681] [2682] [2683] [2684] [2685] Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo se Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1 /pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from [2686] [2687] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8645--8645 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st ack, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8646--8646 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin t, ...)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8658--8658 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr ipts, ...)[] [2688] Underfull \hbox (badness 3118) in paragraph at lines 8677--8680 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1 /ptm/m/n/10 has a dif-fer-ent mean-ing in [2689] Underfull \hbox (badness 1515) in paragraph at lines 8753--8757 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2690] Underfull \hbox (badness 6316) in paragraph at lines 8859--8864 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2691] [2692] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8966--8966 [] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b ottom$labels$labels)[] [2693] [2694] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9105--9105 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su nspot.year)),[] [2695] Overfull \hbox (84.94879pt too wide) in paragraph at lines 9164--9168 []\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr /m/n/10 left, right, left.name, right.name, condition Overfull \hbox (104.63074pt too wide) in paragraph at lines 9164--9168 \T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left, right.x, right.y, left.name , right.x.name, right.y.name, condition [2696] [2697] [2698] [2699] [2700] [2701] [2702] Underfull \hbox (badness 4205) in paragraph at lines 9622--9626 []\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 , Underfull \hbox (badness 4518) in paragraph at lines 9622--9626 \T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 , Underfull \hbox (badness 6300) in paragraph at lines 9627--9630 []\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm" \T1/ptm/m/n/10 , [2703] [2704] [2705]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma} [2706] [2707] [2708] Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 []\T1/ptm/m/n/10 Cause of death. A fac-tor with lev-els \T1/pcr/m/n/10 Alzheime rs\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Cancer\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 Cerebrovascular diseases\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Diabetes \T1/ptm/m/n/10 , \T1/pcr/m/n/10 Flu and pneumonia\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 Heart disease\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower respiratory\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 Nephritis\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Suicide\ T1/ptm/m/n/10 , and [2709] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10088--10088 [] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list( columns = 2),[] [2710]) (./mgcv-pkg.tex Chapter 24. [2711] [2712] Overfull \hbox (6.78088pt too wide) in paragraph at lines 147--147 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL, Overfull \hbox (18.78088pt too wide) in paragraph at lines 150--150 [] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret e=FALSE,[] [2713] Overfull \hbox (72.78088pt too wide) in paragraph at lines 152--152 [] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in tercept=NULL,...)[] Underfull \hbox (badness 1142) in paragraph at lines 171--175 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 196--201 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2714] [2715] [2716] [2717] Underfull \hbox (badness 10000) in paragraph at lines 361--368 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo th.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 361--368 [][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 361--368 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2718] Overfull \hbox (4.38043pt too wide) in paragraph at lines 404--404 []\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2 ,bs=bs,k=k)+[] [2719] [2720] [2721] Underfull \hbox (badness 2922) in paragraph at lines 603--604 []\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/ n/10 and [2722] [2723] [2724] Underfull \hbox (badness 1158) in paragraph at lines 727--729 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2725] Underfull \hbox (badness 1259) in paragraph at lines 790--791 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [2726] [2727] [2728] [2729] [2730] [2731] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1138--1138 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1139--1139 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1145--1145 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct+adhere,[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1152--1152 []\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for this stratum...[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1154--1154 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in d]),type="l",ylim=c(0,1),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1156--1156 [] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind]) ,lwd=2,col=i)[] Underfull \vbox (badness 10000) has occurred while \output is active [2732] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1187--1187 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights= d,data=surv)[] [2733] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1248--1248 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] [2734] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1293--1293 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] [2735] [2736] [2737] [2738] [2739] [2740] [2741] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1750--1750 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2742] [2743] [2744] [2745] [2746] [2747] Underfull \hbox (badness 1052) in paragraph at lines 2125--2133 \T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo oths. Lin-ear func-tion-als of [2748] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2142--2142 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2154--2157 []\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1 0 formula.gam[][][] \T1/ptm/m/n/10 and also Underfull \hbox (badness 1142) in paragraph at lines 2167--2171 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 2193--2198 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2749] [2750] [2751] Underfull \hbox (badness 1043) in paragraph at lines 2356--2362 \T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v en-tion mech-a-nism de-scribed in [2752] [2753] Underfull \hbox (badness 10000) in paragraph at lines 2492--2498 [][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2492--2498 [][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2492--2498 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2754] Underfull \vbox (badness 10000) has occurred while \output is active [2755] Underfull \vbox (badness 10000) has occurred while \output is active [2756] Underfull \vbox (badness 10000) has occurred while \output is active [2757] [2758] [2759] [2760] [2761] [2762] [2763] [2764] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3148--3148 [] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco l(x)),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3151--3151 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] [2765] [2766] [2767] [2768] [2769] [2770] Underfull \hbox (badness 5189) in paragraph at lines 3512--3516 []\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n /10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see [2771] [2772] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3629--3629 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \vbox (badness 10000) has occurred while \output is active [2773] [2774] [2775] Underfull \hbox (badness 1184) in paragraph at lines 3798--3802 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2776] [2777] [2778] [2779] [2780] [2781] [2782] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4244--4244 [] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i d=1)+s(x1,id=1)+[] [2783] [2784] [2785] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4394--4394 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2786] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4488--4488 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR UE,...)[] [2787] Underfull \hbox (badness 1142) in paragraph at lines 4519--4523 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2788] Underfull \hbox (badness 10000) in paragraph at lines 4588--4597 []\T1/ptm/m/n/10 In the event of \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 con-ver-genc e fail-ures, con-sider mod-i-fy-ing [2789] [2790] Underfull \hbox (badness 5970) in paragraph at lines 4705--4711 [][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 1418) in paragraph at lines 4705--4711 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p cr/m/n/10 pdTens[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 gamm4 \T1/ptm/m/n/10 ( [] []$\T1/pcr/m/n/10 https : / / cran . r-[]project . [2791] Underfull \vbox (badness 10000) has occurred while \output is active [2792] [2793] [2794] Underfull \hbox (badness 1577) in paragraph at lines 4985--4988 []\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see [] []\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment Underfull \hbox (badness 2181) in paragraph at lines 4992--4993 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2795] [2796] [2797] [2798] [2799] [2800] [2801] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5396--5396 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2802] [2803] [2804] [2805] [2806] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5720--5720 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, [2807] Overfull \hbox (36.78088pt too wide) in paragraph at lines 5722--5722 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 5743--5747 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2808] [2809] [2810] Underfull \vbox (badness 10000) has occurred while \output is active [2811] [2812] [2813] Overfull \hbox (72.78088pt too wide) in paragraph at lines 6058--6058 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999, all.derivs=FALSE) [2814] [2815] [2816] [2817] Underfull \vbox (badness 10000) has occurred while \output is active [2818] Underfull \vbox (badness 10000) has occurred while \output is active [2819] [2820] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6487--6487 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] [2821] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6514--6514 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2822] [2823] [2824] [2825] [2826] [2827] [2828] [2829] [2830] Underfull \hbox (badness 1242) in paragraph at lines 7057--7058 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2831] [2832] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7144--7144 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [2833] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7207--7207 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate d covariates[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7226--7226 [] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]] ,na.rm=TRUE)[] [2834] [2835] [2836] [2837] [2838] [2839] [2840] [2841] [2842] [2843] [2844] [2845] [2846] [2847] [2848] [2849] [2850] [2851] Underfull \vbox (badness 10000) has occurred while \output is active [2852] [2853] Underfull \hbox (badness 10000) in paragraph at lines 8446--8449 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8446--8449 \T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\ T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 3118) in paragraph at lines 8446--8449 \T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot \T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su mmary.pdIdnot\T1/ptm/m/n/10 . [2854] Underfull \hbox (badness 10000) in paragraph at lines 8502--8505 []\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p tm/m/n/10 , Underfull \hbox (badness 3108) in paragraph at lines 8502--8505 \T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally be [2855] [2856] [2857] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8722--8722 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s cale=-1,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8723--8723 [] \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS E,xlab=NULL,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8726--8726 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [2858] [2859] [2860] Underfull \hbox (badness 1629) in paragraph at lines 8883--8888 \T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is some-times to clone the [2861] [2862] [2863] [2864] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9094--9094 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,...)[] [2865] [2866] Overfull \hbox (6.78088pt too wide) in paragraph at lines 9258--9258 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [2867] [2868] [2869] [2870] Underfull \vbox (badness 10000) has occurred while \output is active [2871] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9526--9526 [] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s mooth deriv i[] [2872] Underfull \hbox (badness 1205) in paragraph at lines 9564--9566 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9564--9566 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 9570--9575 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2873] Underfull \hbox (badness 1205) in paragraph at lines 9654--9656 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9654--9656 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2874] Underfull \hbox (badness 10000) in paragraph at lines 9723--9726 []\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from Underfull \hbox (badness 2057) in paragraph at lines 9723--9726 [][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n /10 are not needed, [2875] [2876] Underfull \hbox (badness 1253) in paragraph at lines 9853--9855 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [2877] [2878] [2879] [2880] Underfull \hbox (badness 1946) in paragraph at lines 10031--10038 []\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef- fects in a GAM in the same Underfull \hbox (badness 2221) in paragraph at lines 10031--10038 \T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre s-sion terms. This method Underfull \hbox (badness 2042) in paragraph at lines 10031--10038 \T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s ee Underfull \hbox (badness 2846) in paragraph at lines 10039--10042 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1 0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n /10 can be used: Underfull \hbox (badness 5862) in paragraph at lines 10039--10042 \T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [2881] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10105--10105 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \hbox (badness 10000) in paragraph at lines 10134--10137 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 , [2882] [2883] [2884] [2885] [2886] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10421--10421 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU LL,pc=NULL) [2887] [2888] [2889] [2890] [2891] [2892] Underfull \hbox (badness 3861) in paragraph at lines 10762--10765 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if Overfull \hbox (36.78088pt too wide) in paragraph at lines 10769--10769 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE, Underfull \hbox (badness 10000) in paragraph at lines 10782--10786 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [2893] Underfull \hbox (badness 10000) in paragraph at lines 10822--10826 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [2894] [2895] [2896] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10963--10963 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$ vectors[,ind]))[] Underfull \hbox (badness 1975) in paragraph at lines 10974--10979 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2897] Underfull \hbox (badness 1803) in paragraph at lines 11051--11055 \T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T 1/ptm/m/n/10 . Underfull \hbox (badness 1502) in paragraph at lines 11063--11075 \T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec Underfull \hbox (badness 2401) in paragraph at lines 11080--11084 \T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able. Plot meth-ods can be Underfull \hbox (badness 2970) in paragraph at lines 11080--11084 \T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/ m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 , [2898] [2899] [2900] Underfull \vbox (badness 10000) has occurred while \output is active [2901] Underfull \hbox (badness 6876) in paragraph at lines 11275--11281 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one or two vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 11316--11317 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2902] [2903] Underfull \hbox (badness 10000) in paragraph at lines 11433--11434 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2904] [2905] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11487--11487 [] \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs, m=c(4,3,0))+[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11499--11499 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11510--11510 [] \T1/pcr/m/n/9 "1st order penalties: red tps; blue bs over (0,1); black bs over (-.5,1.5)")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11511--11511 [] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions and intervals[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11516--11516 [] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i ntervals away[] [2906] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11522--11522 [] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w ild and wide[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11523--11523 [] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/pcr/m/n/9 `\T1/ pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] [2907] Underfull \hbox (badness 10000) in paragraph at lines 11592--11594 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term Underfull \hbox (badness 10000) in paragraph at lines 11592--11594 \T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 s(...,bs="cs", ...) \T1/ptm/m/n/10 or [2908] [2909] Underfull \hbox (badness 10000) in paragraph at lines 11720--11721 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2910] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11801--11801 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first deriv penalty[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11802--11802 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi ed 2nd deriv[] [2911] [2912] [2913] Underfull \hbox (badness 10000) in paragraph at lines 11952--11953 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2914] [2915] [2916] [2917] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12191--12191 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [2918] Underfull \hbox (badness 10000) in paragraph at lines 12252--12254 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2919] [2920] Underfull \vbox (badness 10000) has occurred while \output is active [2921] Underfull \hbox (badness 10000) in paragraph at lines 12411--12414 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method a smooth spec-i-fi-ca-tion ob- Underfull \hbox (badness 3312) in paragraph at lines 12411--12414 \T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs=" re",)\T1/ptm/m/n/10 . For the Underfull \hbox (badness 7099) in paragraph at lines 12411--12414 \T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr /m/n/10 "random.effect" [2922] [2923] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12493--12493 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] Underfull \hbox (badness 10000) in paragraph at lines 12538--12544 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 2698) in paragraph at lines 12538--12544 \T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1 /pcr/m/n/10 gam \T1/ptm/m/n/10 for- [2924] [2925] [2926] Underfull \vbox (badness 10000) has occurred while \output is active [2927] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12752--12752 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] Underfull \vbox (badness 10000) has occurred while \output is active [2928] [2929] Underfull \hbox (badness 10000) in paragraph at lines 12855--12863 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the sphere, via terms like Underfull \hbox (badness 10000) in paragraph at lines 12881--12882 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2930] [2931] [2932] [2933] Underfull \hbox (badness 3396) in paragraph at lines 13142--13145 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any num-ber of vari-ables, spec-i-fied via terms like [2934] Underfull \hbox (badness 10000) in paragraph at lines 13187--13189 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2935] [2936] [2937] [2938] Underfull \hbox (badness 10000) in paragraph at lines 13411--13414 []\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t en pro- Underfull \hbox (badness 3068) in paragraph at lines 13411--13414 \T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see [] []\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas s (see [2939] Underfull \hbox (badness 10000) in paragraph at lines 13444--13448 [][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr /m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression .spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13444--13448 [][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13444--13448 [][]\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 , [2940] [2941] [2942] [2943] [2944] Underfull \hbox (badness 2158) in paragraph at lines 13734--13734 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [2945] Overfull \hbox (48.78088pt too wide) in paragraph at lines 13809--13809 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [2946] [2947] Overfull \hbox (12.78088pt too wide) in paragraph at lines 13943--13943 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [2948] [2949] Underfull \hbox (badness 4846) in paragraph at lines 14074--14077 []\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or es-ti-ma-tors if [2950] [2951] [2952] [2953] [2954] [2955] [2956] [2957] [2958] [2959] [2960] [2961] [2962] [2963] Underfull \hbox (badness 10000) in paragraph at lines 14899--14907 []\T1/ptm/m/n/10 Suppose that \T1/pcr/m/n/10 m=1 \T1/ptm/m/n/10 and you fill an ar-ray us-ing code like Underfull \hbox (badness 10000) in paragraph at lines 14899--14907 \T1/pcr/m/n/10 for(i in 1:K) for(j in i:K) for(k in j:K) for(l in k:K) [2964] [2965] [2966] [2967] Overfull \hbox (24.78088pt too wide) in paragraph at lines 15171--15171 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA LSE, ...)[] [2968] [2969] [2970] [2971] [2972] [2973] Overfull \hbox (20.58041pt too wide) in paragraph at lines 15465--15465 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li near predictor,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15466--15466 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun ded in regions[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15478--15478 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [2974] [2975] [2976]) (./nlme-pkg.tex Chapter 25. [2977] Underfull \hbox (badness 1009) in paragraph at lines 84--93 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [2978] Underfull \hbox (badness 1009) in paragraph at lines 174--183 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [2979] [2980] [2981] [2982] [2983] Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454 [] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [2984] [2985] Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 --------------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n on-sensical!)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 --------------------------- ---------------[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 --------------------------- ---------------[] [2986] [2987] [2988] [2989] [2990] [2991] [2992] [2993] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil lary fissure"),[] [2994] Underfull \hbox (badness 5446) in paragraph at lines 1147--1149 []\T1/ptm/m/n/10 `\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel.h tm\T1/ptm/m/n/10 ', the first edi-tion of [2995] [2996] [2997] [2998] [2999] [3000] [3001] Underfull \hbox (badness 10000) in paragraph at lines 1630--1633 [][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 , [3002] Underfull \hbox (badness 3780) in paragraph at lines 1647--1649 []\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a ted with each com-po-nent of the [3003] [3004] [3005] [3006] [3007] Underfull \hbox (badness 2042) in paragraph at lines 1994--2000 \T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3008] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla pse = "Dog")[] [3009] Underfull \hbox (badness 1132) in paragraph at lines 2144--2146 []\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac ted us-ing the [3010] [3011] Underfull \hbox (badness 4168) in paragraph at lines 2255--2261 [][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize .corStruct[][][]\T1/ptm/m/n/10 , [3012] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2280--2280 [] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3013] [3014] [3015] [3016] [3017] [3018] [3019] [3020] Underfull \hbox (badness 10000) in paragraph at lines 2843--2847 [][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1 /ptm/m/n/10 , [3021] [3022] [3023] [3024] [3025] [3026] [3027] [3028] [3029] [3030] [3031] [3032] Underfull \hbox (badness 6493) in paragraph at lines 3579--3587 [][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [3033] [3034] [3035] [3036] [3037] [3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] Underfull \hbox (badness 10000) in paragraph at lines 5159--5163 [][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [3057] [3058] [3059] [3060] [3061] Underfull \hbox (badness 10000) in paragraph at lines 5476--5480 []\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit- ted in the fit if Underfull \hbox (badness 2671) in paragraph at lines 5476--5480 \T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if \T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 . [3062] [3063] Underfull \hbox (badness 10000) in paragraph at lines 5591--5594 [][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][] []\T1/ptm/m/n/10 , [3064] [3065] [3066] [3067] [3068] [3069] [3070] [3071] [3072] Underfull \hbox (badness 2799) in paragraph at lines 6097--6103 \T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/ ptm/m/n/10 for the random-effects [3073] Underfull \hbox (badness 7133) in paragraph at lines 6158--6162 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \ T1/pcr/m/n/10 model\T1/ptm/m/n/10 , [3074] Underfull \hbox (badness 2057) in paragraph at lines 6242--6253 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 , [3075] Underfull \hbox (badness 10000) in paragraph at lines 6306--6308 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 6338--6338 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3076] [3077] [3078] [3079] Underfull \hbox (badness 7133) in paragraph at lines 6556--6560 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \ T1/pcr/m/n/10 model\T1/ptm/m/n/10 , [3080] Underfull \hbox (badness 10000) in paragraph at lines 6655--6661 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict .gnls[][][]\T1/ptm/m/n/10 , Overfull \hbox (54.78088pt too wide) in paragraph at lines 6682--6682 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min Scale = 0.001, [3081] Underfull \hbox (badness 10000) in paragraph at lines 6720--6722 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3082] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6750--6750 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3083] [3084] [3085] Underfull \hbox (badness 10000) in paragraph at lines 6993--7000 [][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][ ]\T1/ptm/m/n/10 , [3086] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7010--7010 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7018--7018 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7040--7042 []\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou pedData \T1/ptm/m/n/10 ob-ject or a [3087] [3088] [3089] Underfull \hbox (badness 10000) in paragraph at lines 7255--7260 [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl sStruct[][][]\T1/ptm/m/n/10 , [3090] [3091] [3092] Underfull \hbox (badness 10000) in paragraph at lines 7407--7415 []\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial -iza- Underfull \hbox (badness 10000) in paragraph at lines 7407--7415 \T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 1817) in paragraph at lines 7407--7415 \T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 20 EM it-er-a- Underfull \hbox (badness 3118) in paragraph at lines 7430--7433 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 , [3093] [3094] [3095] Underfull \hbox (badness 3354) in paragraph at lines 7645--7647 []\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10 which \T1/ptm/m/n/10 is not equal to [3096] [3097] [3098] [3099] [3100] [3101] Underfull \hbox (badness 1642) in paragraph at lines 8037--8059 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3102] [3103] Underfull \hbox (badness 10000) in paragraph at lines 8157--8174 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme Object[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8157--8174 [][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 , Overfull \hbox (12.78088pt too wide) in paragraph at lines 8200--8200 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] Underfull \hbox (badness 1642) in paragraph at lines 8209--8231 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3104] [3105] [3106] [3107] [3108] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8474--8474 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, Underfull \hbox (badness 10000) in paragraph at lines 8520--8522 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3109] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8558--8558 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h as been already used, duplicate ignored \relax l.8565 \aliasA{sigma}{lmeObject}{sigma} [3110] [3111] [3112] Underfull \hbox (badness 10000) in paragraph at lines 8726--8738 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo r-mula ob-ject of the form [3113] [3114] [3115] [3116] [3117] [3118] [3119] [3120] [3121] Underfull \hbox (badness 10000) in paragraph at lines 9317--9324 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS truct[][][]\T1/ptm/m/n/10 , Overfull \hbox (4.38043pt too wide) in paragraph at lines 9328--9328 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3122] Underfull \hbox (badness 6300) in paragraph at lines 9410--9413 []\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr /m/n/10 lm \T1/ptm/m/n/10 com-po-nents of [3123] [3124] [3125] [3126]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3127] Underfull \hbox (badness 10000) in paragraph at lines 9699--9702 []\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a s Underfull \hbox (badness 3108) in paragraph at lines 9743--9746 []\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive -definite Underfull \hbox (badness 2521) in paragraph at lines 9743--9746 \T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M ust have the same di-men-sions as [3128] [3129] [3130] Underfull \hbox (badness 2435) in paragraph at lines 9917--9922 []\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/ 10 , [3131] [3132] [3133] [3134] [3135] Underfull \hbox (badness 7291) in paragraph at lines 10207--10209 []\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to [3136] [3137] [3138] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10423--10423 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3139] Underfull \hbox (badness 1596) in paragraph at lines 10452--10478 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3140] [3141] [3142] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10628--10628 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3143] [3144] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10779--10779 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] Underfull \hbox (badness 2213) in paragraph at lines 10790--10795 []\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][]\T1/pcr/m/n/10 nlminb [][][] \T1/ptm/m/n/10 (\T1/pcr/m/n/10 iter.max\T1/ptm/m/n/10 ) or the [][]\T1/p cr/m/n/10 nlm[][][] [3145] Underfull \hbox (badness 10000) in paragraph at lines 10812--10816 []\T1/ptm/m/n/10 a log-i-cal value passed as the \T1/pcr/m/n/10 trace \T1/ptm/m /n/10 to Underfull \hbox (badness 10000) in paragraph at lines 10831--10833 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 10867--10867 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3146] [3147] [3148] [3149] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11123--11123 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* message instead of one *each*[] [3150] [3151] [3152] [3153] [3154] [3155] [3156] [3157] [3158] [3159] [3160] [3161] Underfull \hbox (badness 6268) in paragraph at lines 11902--11912 [][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 pdMatrix[][][]\T1/ptm/m/n/10 , [3162] [3163] [3164] [3165] Underfull \hbox (badness 10000) in paragraph at lines 12163--12169 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon struct[][][]\T1/ptm/m/n/10 , [3166] [3167] [3168] [3169] [3170] Underfull \hbox (badness 6876) in paragraph at lines 12485--12487 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i ni-tial-ized \T1/pcr/m/n/10 pdMat \T1/ptm/m/n/10 ob-ject, \T1/pcr/m/n/10 object \T1/ptm/m/n/10 will be con-structed from [3171] [3172] Underfull \hbox (badness 2452) in paragraph at lines 12641--12648 [][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 reStruct[][][]\T1/ptm/m/n/10 , [3173] Underfull \hbox (badness 10000) in paragraph at lines 12706--12712 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re Struct[][][]\T1/ptm/m/n/10 , [3174] [3175] [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] [3187] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13658--13658 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3188] Underfull \hbox (badness 10000) in paragraph at lines 13685--13688 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 6016) in paragraph at lines 13713--13716 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i- zon-tal axis. Underfull \hbox (badness 2653) in paragraph at lines 13713--13716 \T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T 1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and Underfull \hbox (badness 1975) in paragraph at lines 13720--13723 []\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/ ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot Underfull \hbox (badness 1838) in paragraph at lines 13728--13735 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/ 10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner Underfull \hbox (badness 3713) in paragraph at lines 13728--13735 \T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n /10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner [3189] Overfull \hbox (12.78088pt too wide) in paragraph at lines 13785--13785 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] Underfull \hbox (badness 10000) in paragraph at lines 13792--13795 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 2469) in paragraph at lines 13792--13795 \T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v ari-ate and a sin-gle [3190] Underfull \hbox (badness 4582) in paragraph at lines 13820--13823 []\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De -fault is Underfull \hbox (badness 2418) in paragraph at lines 13820--13823 \T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and Underfull \hbox (badness 2990) in paragraph at lines 13824--13827 []\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/ ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot [3191] Underfull \hbox (badness 10000) in paragraph at lines 13900--13903 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa ta\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 1472) in paragraph at lines 13925--13932 \T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3192] Underfull \hbox (badness 10000) in paragraph at lines 13994--13996 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][ ][]\T1/ptm/m/n/10 , [3193] [3194] [3195] [3196] Underfull \hbox (badness 1540) in paragraph at lines 14209--14214 \T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1 /ptm/m/n/10 in-cludes an Underfull \hbox (badness 1215) in paragraph at lines 14256--14258 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [3197] [3198] [3199] [3200] [3201] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14500--14500 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3202] [3203] [3204] [3205] [3206] [3207] [3208] [3209] [3210]pdfTeX warning (e xt4): destination with the same identifier (name{Rfn.random.effects}) has been already used, duplicate ignored \relax l.15153 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15153 ...Extract Random Effects}{random.effects} [3211] [3212] [3213] [3214] [3215] [3216] [3217] [3218] [3219] [3220] Underfull \hbox (badness 1009) in paragraph at lines 15810--15819 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3221] [3222] [3223] Overfull \hbox (66.78088pt too wide) in paragraph at lines 15957--15957 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3224] [3225] [3226] [3227] Underfull \hbox (badness 10000) in paragraph at lines 16235--16253 []\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form Underfull \hbox (badness 1708) in paragraph at lines 16235--16253 \T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+.. .+xn \T1/ptm/m/n/10 spec-i-fy-ing the model [3228] Underfull \hbox (badness 10000) in paragraph at lines 16292--16298 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc t[][][]\T1/ptm/m/n/10 , [3229] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16323--16323 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3230] [3231] [3232] [3233] [3234] [3235] [3236] Underfull \hbox (badness 1728) in paragraph at lines 16812--16815 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3237] [3238] [3239] [3240] [3241] Underfull \hbox (badness 1867) in paragraph at lines 17147--17156 \T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17147--17156 \T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm \T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" Underfull \hbox (badness 10000) in paragraph at lines 17147--17156 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17147--17156 \T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization" [3242] Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu nc-tion: Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m /n/10 varComb\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/ n/10 varConstPower\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m /n/10 varExp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 , [3243] [3244] [3245] [3246] Underfull \hbox (badness 10000) in paragraph at lines 17458--17465 [][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 , [3247] [3248] [3249] [3250] [3251] [3252] [3253] [3254] Underfull \hbox (badness 10000) in paragraph at lines 17993--18003 [][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][] []\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17993--18003 [][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe r[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 3579) in paragraph at lines 18031--18036 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3255] Underfull \hbox (badness 3579) in paragraph at lines 18095--18100 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3256] Underfull \hbox (badness 3579) in paragraph at lines 18158--18163 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3257] Underfull \hbox (badness 1577) in paragraph at lines 18219--18221 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal Underfull \hbox (badness 3579) in paragraph at lines 18221--18226 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3258] Underfull \hbox (badness 3579) in paragraph at lines 18284--18289 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3259] Underfull \hbox (badness 10000) in paragraph at lines 18317--18326 [][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n /10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18317--18326 [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][] []\T1/ptm/m/n/10 , Underfull \hbox (badness 3579) in paragraph at lines 18356--18361 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3260] [3261] [3262] Underfull \hbox (badness 1009) in paragraph at lines 18505--18514 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3263] [3264] Underfull \hbox (badness 1009) in paragraph at lines 18639--18648 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3265] [3266] [3267] [3268] [3269] [3270] [3271] [3272]) (./nnet-pkg.tex Chapter 26. pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.multinom.1}) has been already used, du plicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} [3273] Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70 [] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored = FALSE,[] Underfull \hbox (badness 10000) in paragraph at lines 78--87 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [3274] [3275] [3276] Overfull \hbox (15.18042pt too wide) in paragraph at lines 369--369 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3277] Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c( 0,0,1),50)),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 429--429 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay =5e-4, maxit=200)[] [3278] Underfull \hbox (badness 4013) in paragraph at lines 474--477 \T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if the net was gen-er-ated by [3279] Overfull \hbox (15.18042pt too wide) in paragraph at lines 509--509 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3280]) (./rpart-pkg.tex Chapter 27. [3281] [3282] [3283] [3284] Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse = TRUE, ...)[] [3285] Underfull \hbox (badness 10000) in paragraph at lines 373--377 []\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm /m/n/10 ) or ma-trix of left and right splits [3286] [3287] [3288] Underfull \hbox (badness 1442) in paragraph at lines 591--597 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be at the hor-i-zon-tal plot co-or-di-nates of [3289] [3290] Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] [3291] Underfull \hbox (badness 2941) in paragraph at lines 785--787 []\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice if [3292] Overfull \hbox (25.98041pt too wide) in paragraph at lines 902--902 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] [3293] Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"), ...)[] [3294] [3295] [3296] Underfull \hbox (badness 2310) in paragraph at lines 1113--1116 []\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees all three resid-ual def-i-ni-tions re-duce to Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m ethod, Overfull \hbox (12.78088pt too wide) in paragraph at lines 1164--1164 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] Underfull \hbox (badness 2837) in paragraph at lines 1187--1196 []\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 " poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1 0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method Underfull \hbox (badness 2088) in paragraph at lines 1187--1196 \T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu ess. If \T1/pcr/m/n/10 y Underfull \hbox (badness 1817) in paragraph at lines 1187--1196 \T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2 [3297] Underfull \hbox (badness 2846) in paragraph at lines 1226--1228 []\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1 0 rpart \T1/ptm/m/n/10 al-go-rithm. See [3298] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1286--1286 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c p = 0.01, Overfull \hbox (60.78088pt too wide) in paragraph at lines 1287--1287 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3299] [3300] [3301] [3302] [3303] [3304] Underfull \hbox (badness 1565) in paragraph at lines 1739--1742 []\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val- ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ', [3305] [3306] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3307] [3308] [3309]) (./spatial-pkg.tex [3310] Chapter 28. [3311] [3312] [3313] [3314] [3315] [3316] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3317] [3318] [3319] [3320] [3321] [3322] [3323] [3324] [3325] [3326] [3327] [3328] [3329]) (./survival-pkg.tex [3330] Chapter 29. [3331] [3332] Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data = lung, nmin = 1[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t he last point[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 193--193 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a nd Grambsch.[] [3333] [3334]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.aml}) has been already used, duplicate ignored \relax l.326 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica te ignored \relax l.326 ... Myelogenous Leukemia survival data}{aml} [3335] [3336] Overfull \hbox (9.78043pt too wide) in paragraph at lines 423--423 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da ta = ovarian) Overfull \hbox (4.38043pt too wide) in paragraph at lines 425--425 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d ata=ovarian)[] [3337] Overfull \hbox (6.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog), lung)[] [3338] [3339] Underfull \vbox (badness 10000) has occurred while \output is active [3340] Overfull \hbox (36.78088pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c ohort.size, Overfull \hbox (48.78088pt too wide) in paragraph at lines 662--662 [] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan", "II.Borgan"),[] [3341] [3342] Overfull \hbox (9.78043pt too wide) in paragraph at lines 805--805 [] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz e=stratsizes,[] [3343] [3344] [3345] Underfull \hbox (badness 1097) in paragraph at lines 975--977 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. Overfull \hbox (4.38043pt too wide) in paragraph at lines 995--995 []\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit h large rate[] [3346] [3347] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1110--1110 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat um), data=infert) [3348]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col on}) has been already used, duplicate ignored \relax l.1178 ...erapy for Stage B/C colon cancer}{colon} Underfull \vbox (badness 2698) has occurred while \output is active [3349] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1271--1271 [] \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G 2", "I"),[] [3350] [3351] [3352] [3353] [3354] [3355] Underfull \hbox (badness 1337) in paragraph at lines 1753--1757 [][][]\T1/pcr/m/n/10 coxph.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 coxp h.control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cluster[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 strata[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Surv[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 pspline[][][]\T1/ptm/m/n/10 , [3356] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1808--1808 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3357] [3358] [3359] [3360] [3361] [3362] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2246--2246 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] [3363] [3364] [3365] [3366] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2495--2495 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3367] [3368] [3369] [3370] [3371] Underfull \vbox (badness 2012) has occurred while \output is active [3372] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2812--2812 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) Overfull \hbox (36.7804pt too wide) in paragraph at lines 2848--2848 [] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre ssion", "death")))[] Underfull \hbox (badness 1389) in paragraph at lines 2862--2864 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with [3373] Underfull \hbox (badness 1048) in paragraph at lines 2917--2919 []\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se e the note in [3374] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2995--2995 [] \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3375] [3376] [3377] [3378] [3379] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3241--3241 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3380] [3381] [3382] [3383] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3507--3507 [] \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5" , sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3384] Underfull \vbox (badness 10000) has occurred while \output is active [3385] [3386] [3387] [3388] [3389] [3390] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3924--3924 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3391] [3392] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4119--4119 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3393] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4245--4245 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] [3394] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4253--4253 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3395] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4339--4339 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3396] [3397] Underfull \hbox (badness 1852) in paragraph at lines 4487--4489 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/ n/10 , which is the re-sult of the [3398] [3399] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4622--4622 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me thod, Overfull \hbox (36.78088pt too wide) in paragraph at lines 4623--4623 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3400] [3401] [3402] Overfull \hbox (30.78088pt too wide) in paragraph at lines 4787--4787 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] Underfull \hbox (badness 1540) in paragraph at lines 4842--4845 []\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per -son years if [3403] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4889--4889 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4910--4910 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50 ,60,70,100)) +[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4912--4912 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3404] [3405] [3406] [3407] [3408] Underfull \vbox (badness 2126) has occurred while \output is active [3409] [3410] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5387--5387 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 1043) in paragraph at lines 5399--5402 \T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and [3411] [3412] [3413] [3414] [3415] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5699--5699 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the ta=5), cancer)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 5700--5700 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), cancer)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.5705 ...ata from a soldering experiment}{solder} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.solder.1}) has been already used, dupl icate ignored \relax l.5705 ...ata from a soldering experiment}{solder} [3416] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5811--5811 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3417] [3418] [3419] [3420] [3421] [3422] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6166--6166 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r r =expected,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6167--6167 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3423] [3424] [3425] [3426] Overfull \hbox (54.78088pt too wide) in paragraph at lines 6459--6459 [] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/ 10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/ n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] [3427] [3428] Underfull \vbox (badness 10000) has occurred while \output is active [3429] Underfull \hbox (badness 10000) in paragraph at lines 6722--6729 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 length \T1/ptm/m/n/10 of a \T1/pcr/m/n/10 S urv \T1/ptm/m/n/10 ob-ject is the num-ber of sur-vival times Underfull \hbox (badness 10000) in paragraph at lines 6722--6729 \T1/ptm/m/n/10 it con-tains, not the num-ber of items re-quired to en-code it, e.g., Underfull \hbox (badness 1412) in paragraph at lines 6722--6729 \T1/pcr/m/n/10 x <- Surv(1:4, 5:9, c(1,0,1,0)); length(x) \T1/ptm/m/n/10 has a value of 4. Like- Underfull \hbox (badness 1253) in paragraph at lines 6733--6736 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 median\T1/ptm/m/n/10 , \T1/pcr/m/n/10 quant ile \T1/ptm/m/n/10 and \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 meth-ods first con-st ruct a sur-vival curve us-ing [3430] [3431] Underfull \hbox (badness 10000) in paragraph at lines 6876--6885 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form [3432] Overfull \hbox (36.7804pt too wide) in paragraph at lines 6972--6972 [] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1 , year=accept.dt),[] [3433] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6990--6990 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] Underfull \hbox (badness 1038) in paragraph at lines 7032--7038 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival [3434] Underfull \hbox (badness 3000) in paragraph at lines 7054--7056 []\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab le \T1/ptm/m/n/10 is in units/day, Overfull \hbox (48.78088pt too wide) in paragraph at lines 7084--7084 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3435] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7170--7170 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3436] [3437] [3438] Underfull \hbox (badness 10000) in paragraph at lines 7395--7400 [][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 , [3439] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7416--7416 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3440] [3441] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7633--7633 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3442] [3443] Underfull \hbox (badness 6332) in paragraph at lines 7740--7745 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val- ues are [3444] [3445] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7933--7933 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3446] [3447] [3448] [3449] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8223--8223 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3450] Underfull \hbox (badness 1354) in paragraph at lines 8264--8268 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3451] [3452] Underfull \hbox (badness 2035) in paragraph at lines 8439--8446 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv reg.distributions[][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 8439--8446 \T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/ m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 , Underfull \hbox (badness 1297) in paragraph at lines 8439--8446 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n /10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is [3453] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8515--8515 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3454] Overfull \vbox (31.11076pt too high) has occurred while \output is active [3455] [3456] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8672--8672 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3457] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8804--8804 [] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x ^2*temp -1))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8807--8807 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3458] [3459] [3460] [3461] [3462] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9109--9109 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic al trial plus[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9110--9110 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9116--9116 [] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day , alk.phos))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9118--9118 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3463] [3464] [3465] [3466] [3467] [3468]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.xtfrm.Surv}) has been already used, duplicate i gnored \relax l.9488 ...ting order for Surv objects}{xtfrm.Surv} [3469] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9556--9556 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3470] [3471] [3472]) No file fullrefman.ind. (./fullrefman.aux) ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.tree} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.viewports} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.xyplot.zoo} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ellipsePoints} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ellipse} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.cluster.stats} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.chorizon} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.as.Rul.dsTMatrix.Rul.listw} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.similar.listw} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.nb2listw} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.read.gal} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.matrix.csr} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.SparseM.ontology} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.modelMatrix} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.model.Matrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.nearcor} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.posdefify} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.get.adjacency} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.graph.adjacency} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.graph} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.sqrtm} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.logm} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.showClass} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.loglm1} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.lmrob} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.wilcox.Rul.test} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.spearman.test} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.pSpearman} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.pKendall} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.Kendall} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.cor.fk} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dMatrix} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgCMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ansari.Rul.test} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.showDefault} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getGroupMembers} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.resetGeneric} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.linearizeMlist} has been referenced but does no t exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getGeneric} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getMethodsForDispatch} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.setDataPart} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getDataPart} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.possibleExtends} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.mosaic} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.assoc} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getNamespace} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.asNamespace} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.formalArgs} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.isRematched} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, replaced by a fixed one {/usr/share/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on fullrefman.pdf (3475 pages, 8795435 bytes). Transcript written on fullrefman.log. make[2]: fullrefman: Command not found make[2]: [Makefile:274: fullrefman.pdf] Error 127 (ignored) This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) %&-line parsing enabled. entering extended mode (./fullrefman.tex LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, german-x-2008-06-18, ngerman-x-2008-06-18, ancientgreek, ibycus, ar abic, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danish, dutc h, esperanto, estonian, farsi, finnish, french, galician, german, ngerman, mono greek, greek, hungarian, icelandic, indonesian, interlingua, irish, italian, la tin, mongolian, mongolian2a, bokmal, nynorsk, polish, portuguese, romanian, rus sian, sanskrit, serbian, slovak, slovenian, spanish, swedish, turkish, ukenglis h, ukrainian, uppersorbian, welsh, loaded. (/usr/share/texmf-dist/tex/latex/base/book.cls Document Class: book 2005/09/16 v1.4f Standard LaTeX document class (/usr/share/texmf-dist/tex/latex/base/bk10.clo)) (../../.././share/texmf/tex/latex/Rd.sty (/usr/share/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texmf/tex/latex/latex2html/url.sty) (/usr/share/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texmf-dist/tex/latex/base/ts1enc.def)) (/usr/share/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texmf-dist/tex/latex/base/t1enc.def)) (/usr/share/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texmf/tex/latex/config/color.cfg) (/usr/share/texmf-dist/tex/latex/pdftex-def/pdftex.def)) (/usr/share/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texmf-dist/tex/latex/oberdiek/hycolor.sty (/usr/share/texmf-dist/tex/latex/oberdiek/xcolor-patch.sty)) (/usr/share/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texmf-dist/tex/generic/oberdiek/infwarerr.sty)) (/usr/share/texmf/tex/latex/config/hyperref.cfg) (/usr/share/texmf-dist/tex/latex/oberdiek/kvoptions.sty) Implicit mode ON; LaTeX internals redefined (/usr/share/texmf-dist/tex/generic/oberdiek/bitset.sty (/usr/share/texmf-dist/tex/generic/oberdiek/intcalc.sty) (/usr/share/texmf-dist/tex/generic/oberdiek/bigintcalc.sty (/usr/share/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty))) (/usr/share/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty) (/usr/share/texmf-dist/tex/generic/oberdiek/atbegshi.sty)) *hyperref using default driver hpdftex* (/usr/share/texmf-dist/tex/latex/hyperref/hpdftex.def) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 366. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 366. ) (/usr/share/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texmf-dist/tex/latex/base/utf8.def (/usr/share/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texmf-dist/tex/latex/base/omsenc.dfu) (/usr/share/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texmf/tex/latex/config/graphics.cfg))) (/usr/share/texmf-dist/tex/latex/base/makeidx.sty) Writing index file fullrefman.idx (./fullrefman.aux) (/usr/share/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texmf-dist/tex/context/base/supp-pdf.tex [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texmf-dist/tex/latex/oberdiek/refcount.sty)) (./fullrefman.out) (./fullrefman.out) (/usr/share/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex) (/usr/share/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/usr/shar e/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./fullrefman.toc (/usr/share/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48]) [49] [50] [1] [2] (./base-pkg.tex Chapter 1. Underfull \hbox (badness 4595) in paragraph at lines 40--43 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [3] Underfull \hbox (badness 4168) in paragraph at lines 94--99 []\T1/pcr/m/n/10 .Devices \T1/ptm/m/n/10 is a [][]pairlist[][][] of length-one char-ac-ter vec-tors. The first en-try is al-ways [4] Underfull \hbox (badness 10000) in paragraph at lines 135--141 []\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1/ptm/m/n/10 such that Underfull \hbox (badness 10000) in paragraph at lines 135--141 \T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . It equals \T1/pcr/m/n/10 double.base ^ ulp.digits \T1/ptm/m/n/10 if ei- Underfull \hbox (badness 6236) in paragraph at lines 135--141 \T1/ptm/m/n/10 ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m /n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er-wise, Underfull \hbox (badness 10000) in paragraph at lines 135--141 \T1/ptm/m/n/10 it is \T1/pcr/m/n/10 (double.base ^ double.ulp.digits) / 2\T1/pt m/m/n/10 . Nor-mally Underfull \hbox (badness 10000) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1 /ptm/m/n/10 such that \T1/pcr/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 4328) in paragraph at lines 141--149 \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/pcr/m/n/10 (double.base ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-ma lly Underfull \hbox (badness 10000) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ- Underfull \hbox (badness 10000) in paragraph at lines 152--159 \T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) * [5] [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 339--342 [][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys. info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar, [8] Underfull \hbox (badness 2359) in paragraph at lines 386--389 []\T1/ptm/m/n/10 logical: should \T1/pcr/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [9] [10] Underfull \hbox (badness 1072) in paragraph at lines 534--540 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [11] [12] (/usr/share/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [13] [14] [15] Overfull \hbox (0.78088pt too wide) in paragraph at lines 860--860 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [16] [17] [18] [19] Underfull \hbox (badness 1838) in paragraph at lines 1147--1150 []\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [20] [21] [22] [23] Underfull \hbox (badness 5862) in paragraph at lines 1381--1387 []\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m /n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I t is guar-an-teed that [24] [25] [26] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1639--1639 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] Underfull \hbox (badness 3168) in paragraph at lines 1656--1663 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , set-ting row n ames and con-vert-ing col-umn names Underfull \hbox (badness 3128) in paragraph at lines 1656--1663 \T1/ptm/m/n/10 (to syn-tac-tic names: see [][]\T1/pcr/m/n/10 make.names[][][]\T 1/ptm/m/n/10 ) is op-tional. Note that all Underfull \hbox (badness 6094) in paragraph at lines 1656--1663 \T1/ptm/m/n/10 of \T1/phv/m/n/10 R\T1/ptm/m/n/10 's \T1/ptm/b/n/10 base \T1/ptm /m/n/10 pack-age \T1/pcr/m/n/10 as.data.frame() \T1/ptm/m/n/10 meth-ods use \T1 /pcr/m/n/10 optional Underfull \hbox (badness 10000) in paragraph at lines 1656--1663 \T1/ptm/m/n/10 only for col-umn names treat-ment, ba-si-cally with the mean-ing of Underfull \hbox (badness 10000) in paragraph at lines 1656--1663 [][]\T1/pcr/m/n/10 data.frame[][][](*, check.names = !optional)\T1/ptm/m/n/10 . See also the [27] Underfull \hbox (badness 1303) in paragraph at lines 1667--1670 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [28] Underfull \hbox (badness 10000) in paragraph at lines 1785--1787 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 Date \T1/ptm/m/n/10 ob-ject, or some-thing wh ich can be co-erced by [29] [30] Overfull \hbox (112.38031pt too wide) in paragraph at lines 1922--1922 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] Overfull \hbox (19.13934pt too wide) in paragraph at lines 1957--1959 []\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e nv[][][](x, parent = emptyenv()) Underfull \hbox (badness 10000) in paragraph at lines 1960--1962 []\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2120--2122 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2233--2233 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [36] [37] Underfull \hbox (badness 1107) in paragraph at lines 2366--2368 []\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1 0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see [38] [39] Overfull \hbox (36.78088pt too wide) in paragraph at lines 2533--2533 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse(substitute(what), backt ick=FALSE), [40] [41] [42] Underfull \hbox (badness 5878) in paragraph at lines 2698--2703 []\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to \T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at- Underfull \hbox (badness 10000) in paragraph at lines 2698--2703 \T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3656--3658 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] Overfull \hbox (102.78088pt too wide) in paragraph at lines 3897--3897 [] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [60] [61] [62] [63] Underfull \hbox (badness 4927) in paragraph at lines 4136--4140 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an ob-ject Underfull \hbox (badness 2012) in paragraph at lines 4136--4140 \T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or [64] [65] Underfull \hbox (badness 4595) in paragraph at lines 4280--4283 []\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par -i-son[][][] and [66] [67] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4435--4435 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] [68] Underfull \hbox (badness 1199) in paragraph at lines 4465--4471 []\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na med ar-gu- Underfull \hbox (badness 2573) in paragraph at lines 4476--4479 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [69] Underfull \hbox (badness 10000) in paragraph at lines 4556--4561 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j ust a wrap-per for Underfull \hbox (badness 10000) in paragraph at lines 4556--4561 [][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T his means that it will split ma- Underfull \hbox (badness 2181) in paragraph at lines 4556--4561 \T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter columns to fac-tors un-less [70] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4635--4635 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [71] [72] [73] [74] Underfull \hbox (badness 2521) in paragraph at lines 4888--4890 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [75] [76] [77] [78] [79] [80] Underfull \hbox (badness 10000) in paragraph at lines 5285--5293 []\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [81] [82] [83] [84] [85] [86] [87] [88] Underfull \hbox (badness 1796) in paragraph at lines 5845--5853 []\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / / [89] [90] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6039--6039 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile r, math-library:[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 6041--6041 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6042--6042 []\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows \TS1/pcr/m/n/9 '\T1/pcr /m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[] [91] [92] [93] Underfull \hbox (badness 1635) in paragraph at lines 6208--6211 []\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1 0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class Underfull \hbox (badness 3009) in paragraph at lines 6212--6215 []\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. They can be es-tab-lished us-ing Underfull \hbox (badness 1102) in paragraph at lines 6229--6242 []\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in Underfull \hbox (badness 1308) in paragraph at lines 6243--6251 []\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should [94] [95] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6396--6396 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [96] Overfull \hbox (107.35893pt too wide) in paragraph at lines 6438--6440 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [97] [98] Underfull \hbox (badness 10000) in paragraph at lines 6580--6583 []\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is Underfull \hbox (badness 2057) in paragraph at lines 6580--6583 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T 1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/ 10 host [99] [100] Underfull \hbox (badness 1248) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it Underfull \hbox (badness 10000) in paragraph at lines 6782--6784 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from [101] Underfull \hbox (badness 1067) in paragraph at lines 6824--6831 \T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar ds . freedesktop . org / clipboards-[]spec / [102] [103] Underfull \vbox (badness 10000) has occurred while \output is active [104] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7016--7016 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [105] Underfull \hbox (badness 1231) in paragraph at lines 7141--7147 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [106] [107] [108] [109] Underfull \hbox (badness 10000) in paragraph at lines 7352--7354 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [110] [111] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7497--7497 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] Underfull \hbox (badness 4595) in paragraph at lines 7539--7542 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [112] [113] [114] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7735--7735 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [115] [116] Underfull \hbox (badness 8132) in paragraph at lines 7836--7840 []\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors ? The Underfull \hbox (badness 4543) in paragraph at lines 7836--7840 \T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , but this can be changed by set-ting Underfull \hbox (badness 10000) in paragraph at lines 7855--7865 []\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing Underfull \hbox (badness 1062) in paragraph at lines 7855--7865 [][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that is a generic func-tion, meth-ods can be [117] Overfull \hbox (4.63962pt too wide) in paragraph at lines 7887--7891 []\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors") Underfull \hbox (badness 7451) in paragraph at lines 7926--7936 [][][]\T1/pcr/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col- Underfull \hbox (badness 3449) in paragraph at lines 7926--7936 \T1/ptm/m/n/10 umn names), [][]\T1/pcr/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods and \T1/pcr/m/n/10 I(matrix(..)) \T1/ptm/m/n/10 ex-a m- [118] [119] [120] [121] [122] [123] Underfull \hbox (badness 10000) in paragraph at lines 8358--8370 \T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n /10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8358--8370 \T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59", tz = "UTC") \T1/ptm/m/n/10 will give [124] [125] [126] Underfull \hbox (badness 5802) in paragraph at lines 8585--8589 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10 reads the file byte-by-byte. This al-lows a Underfull \hbox (badness 10000) in paragraph at lines 8620--8621 [][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy / index . [127] [128] [129] Underfull \hbox (badness 10000) in paragraph at lines 8805--8809 []\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu nc-tions should be listed in [130] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8893--8893 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8895--8895 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] [131] Overfull \hbox (60.78088pt too wide) in paragraph at lines 8920--8920 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 8921--8921 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [132] [133] Underfull \hbox (badness 5403) in paragraph at lines 9039--9041 []\T1/pcr/m/n/10 ..deparseOpts \T1/ptm/m/n/10 is the [][]\T1/pcr/m/n/10 charact er[][][] \T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used by Underfull \hbox (badness 6063) in paragraph at lines 9058--9060 []\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][]\T1/pcr/m/n /10 formula[][][]\T1/ptm/m/n/10 s, with [134] Underfull \hbox (badness 1132) in paragraph at lines 9130--9137 \T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to make the re-sult parseable. [135] Underfull \hbox (badness 1603) in paragraph at lines 9266--9269 []\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t er-mi-nant if [136] [137] [138] [139] [140] [141] [142] [143] [144] Underfull \hbox (badness 1917) in paragraph at lines 9872--9877 []\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has [145] Overfull \hbox (36.7804pt too wide) in paragraph at lines 9927--9927 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE RS)))) # recycling[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9928--9928 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [146] [147] Underfull \hbox (badness 1168) in paragraph at lines 10030--10035 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by Underfull \hbox (badness 10000) in paragraph at lines 10069--10075 []\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m /n/10 .. \T1/ptm/m/n/10 and ba-si-cally the same as Underfull \hbox (badness 5403) in paragraph at lines 10076--10079 []\T1/pcr/m/n/10 ...length() \T1/ptm/m/n/10 re-turns the num-ber of ex-pres-sio ns in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . This is the same as [148] [149] [150] Underfull \hbox (badness 2828) in paragraph at lines 10235--10239 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 10235--10239 \T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr /m/n/10 https : / / en . wikipedia . org / wiki / Double _ Overfull \hbox (42.78088pt too wide) in paragraph at lines 10268--10268 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [151] [152] [153] [154] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10483--10483 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [155] Underfull \hbox (badness 1629) in paragraph at lines 10557--10561 []\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re -sult of lazy-loading (when [156] Underfull \hbox (badness 2150) in paragraph at lines 10658--10661 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [157] Underfull \hbox (badness 3690) in paragraph at lines 10672--10680 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10 anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for Underfull \hbox (badness 10000) in paragraph at lines 10681--10683 []\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent to but faster than Underfull \hbox (badness 3735) in paragraph at lines 10701--10708 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [158] [159] [160] Underfull \hbox (badness 10000) in paragraph at lines 10897--10900 []\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use [161] [162] [163] [164] [165] [166] [167] [168] [169] Underfull \hbox (badness 5288) in paragraph at lines 11594--11596 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of Underfull \hbox (badness 3039) in paragraph at lines 11604--11609 []\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10 dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10 and [170] Underfull \hbox (badness 10000) in paragraph at lines 11664--11666 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [171] [172] Underfull \hbox (badness 4569) in paragraph at lines 11781--11785 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11781--11785 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [173] [174] Underfull \hbox (badness 10000) in paragraph at lines 11896--11898 []\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/ m/n/10 where \T1/ptm/m/n/10 as Underfull \hbox (badness 2790) in paragraph at lines 11939--11941 []\T1/pcr/m/n/10 get0(): \T1/ptm/m/n/10 The object---as from [][]\T1/pcr/m/n/10 get[][][](x, *)\T1/ptm/m/n/10 --- if \T1/pcr/m/n/10 exists(x, *) \T1/ptm/m/n/1 0 is true, oth-er-wise [175] [176] [177] Underfull \hbox (badness 4048) in paragraph at lines 12110--12120 []\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me nt into an ex-pres-sion ob-ject. It is Underfull \hbox (badness 3657) in paragraph at lines 12110--12120 \T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d e-fault method calls [178] [179] [180] Underfull \hbox (badness 5460) in paragraph at lines 12358--12367 []\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l- Underfull \hbox (badness 2221) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes e op-er-a-tions are those Underfull \hbox (badness 2707) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x, inherits = FALSE)\T1/ptm/m/ n/10 . If no match is found then \T1/pcr/m/n/10 NULL Underfull \hbox (badness 2818) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T 1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again, Underfull \hbox (badness 6978) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th is case are those of [181] [182] [183] [184] [185] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12732--12732 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [186] [187] [188] [189] Underfull \hbox (badness 5119) in paragraph at lines 13017--13020 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [190] [191] Underfull \hbox (badness 2221) in paragraph at lines 13178--13187 \T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas s [192] [193] [194] [195] Underfull \hbox (badness 2253) in paragraph at lines 13439--13441 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [196] [197] Underfull \hbox (badness 10000) in paragraph at lines 13554--13556 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m /n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with [198] [199] Underfull \hbox (badness 10000) in paragraph at lines 13704--13706 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [200] [201] Underfull \hbox (badness 10000) in paragraph at lines 13813--13817 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13824--13827 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Overfull \hbox (47.58038pt too wide) in paragraph at lines 13845--13845 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] [202] Overfull \hbox (30.78088pt too wide) in paragraph at lines 13868--13868 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [203] Underfull \hbox (badness 10000) in paragraph at lines 13960--13963 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 13970--13970 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [204] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14045--14045 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] [205] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14074--14074 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, Underfull \hbox (badness 7238) in paragraph at lines 14098--14105 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr /m/n/10 vec\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14098--14105 \T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial , equiv-a-lent to Underfull \hbox (badness 2126) in paragraph at lines 14098--14105 \T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter of fact, the in-ter-nal al-go- Underfull \hbox (badness 3965) in paragraph at lines 14106--14110 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [206] [207] [208] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14269--14269 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 14270--14270 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [209] Underfull \hbox (badness 10000) in paragraph at lines 14349--14353 []\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a Underfull \hbox (badness 1389) in paragraph at lines 14349--14353 \T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m ay not be equiv-a-lent to [210] [211] Overfull \hbox (63.78036pt too wide) in paragraph at lines 14497--14497 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have type symbol (aka name).[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 14500--14500 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [212] Underfull \hbox (badness 1168) in paragraph at lines 14584--14588 []\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real or com-plex vec- Underfull \hbox (badness 2012) in paragraph at lines 14584--14588 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [213] Underfull \hbox (badness 6944) in paragraph at lines 14679--14682 [][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 toString[][][]\T1/ptm/m/n/10 , [214] Overfull \hbox (4.38043pt too wide) in paragraph at lines 14704--14704 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [215] [216] Underfull \hbox (badness 10000) in paragraph at lines 14838--14840 []\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos -si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 14857--14857 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14859--14859 [] \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx = NA,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14862--14862 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)))[] Underfull \hbox (badness 2790) in paragraph at lines 14868--14871 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [217] Underfull \hbox (badness 4254) in paragraph at lines 14884--14892 []\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/ m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied, Underfull \hbox (badness 1024) in paragraph at lines 14899--14903 []\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10 xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m /n/10 "E" \T1/ptm/m/n/10 give [218] Underfull \hbox (badness 10000) in paragraph at lines 14968--14970 []\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 []\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 \T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f g") \T1/ptm/m/n/10 gives Underfull \hbox (badness 10000) in paragraph at lines 14979--14987 []\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti -fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be com-plex (or Underfull \hbox (badness 3601) in paragraph at lines 15013--15017 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 3302) in paragraph at lines 15013--15017 \T1/ptm/m/n/10 within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [219] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15080--15080 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big .mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] [220] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15102--15102 []\T1/pcr/m/n/9 doLC <- FALSE # R warns, so change to TRUE manually if you wan t see the effect[] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] [232] Overfull \hbox (20.58041pt too wide) in paragraph at lines 15920--15920 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [233] Underfull \hbox (badness 2418) in paragraph at lines 16029--16033 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 16036--16039 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/ m/n/10 , then the sin-gle Underfull \hbox (badness 2326) in paragraph at lines 16064--16071 [][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 , [234] [235] [236] [237] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16310--16310 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, Underfull \hbox (badness 1867) in paragraph at lines 16335--16342 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [238] [239] [240] [241] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16603--16603 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Underfull \vbox (badness 10000) has occurred while \output is active [242] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16632--16632 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] [243] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16683--16683 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 16689--16693 []\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o r fixed pat-tern for Underfull \hbox (badness 1028) in paragraph at lines 16689--16693 \T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec- tor. Co-erced by [244] [245] [246] [247] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17048--17048 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z < - c(2, 1:9))) [248] [249] [250] [251] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17302--17302 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [252] [253] [254] Underfull \hbox (badness 2435) in paragraph at lines 17563--17565 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www . unicode . org / reports / tr35 / [255] Underfull \hbox (badness 1867) in paragraph at lines 17605--17612 []\T1/ptm/m/n/10 It is op-tional on Win-dows: if \T1/phv/m/n/10 R \T1/ptm/m/n/1 0 has been built against ICU, it will only be used if Underfull \hbox (badness 1490) in paragraph at lines 17605--17612 \T1/ptm/m/n/10 en-vi-ron-ment vari-able \T1/pcr/m/n/10 R_ICU_LOCALE \T1/ptm/m/n /10 is set or once \T1/pcr/m/n/10 icuSetCollate \T1/ptm/m/n/10 is called to se- Underfull \hbox (badness 1490) in paragraph at lines 17605--17612 \T1/ptm/m/n/10 lect the lo-cale (as ICU and Win-dows dif-fer in their idea of l o-cale names). Note that Underfull \hbox (badness 2285) in paragraph at lines 17620--17622 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 http : / / userguide . icu-[]project . org / Overfull \hbox (9.78043pt too wide) in paragraph at lines 17628--17628 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s ettings, we can only reset to the default.[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17638--17638 [] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p rint(sort(x))[] [256] Overfull \hbox (24.78088pt too wide) in paragraph at lines 17658--17658 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [257] [258] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17792--17792 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17798--17798 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17801--17801 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share an environment:[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17807--17807 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [259] [260] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17934--17934 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u se ifelse(),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17942--17942 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] [261] [262] [263] Underfull \hbox (badness 10000) in paragraph at lines 18147--18149 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/ pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and [264] Underfull \hbox (badness 4217) in paragraph at lines 18231--18240 [][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 2057) in paragraph at lines 18246--18262 [][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [265] [266] [267] [268] [269] [270] Underfull \hbox (badness 4699) in paragraph at lines 18660--18663 []\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , [271] [272] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18783--18783 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [273] [274] Underfull \hbox (badness 4739) in paragraph at lines 18918--18920 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [275] [276] [277] [278] [279] [280] [281] Underfull \hbox (badness 1430) in paragraph at lines 19331--19336 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 19331--19336 \T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 is the same as [282] Underfull \hbox (badness 10000) in paragraph at lines 19392--19397 []\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/ 10 will pro-duce a (``higher Underfull \hbox (badness 10000) in paragraph at lines 19392--19397 \T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe r = FALSE \T1/ptm/m/n/10 would Underfull \hbox (badness 5008) in paragraph at lines 19392--19397 \T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon d to Underfull \hbox (badness 10000) in paragraph at lines 19392--19397 \T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s implify = TRUE\T1/ptm/m/n/10 , re- [283] Underfull \hbox (badness 10000) in paragraph at lines 19452--19459 []\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If Underfull \hbox (badness 6364) in paragraph at lines 19452--19459 \T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth- Underfull \hbox (badness 5064) in paragraph at lines 19452--19459 \T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix with Underfull \hbox (badness 5908) in paragraph at lines 19452--19459 \T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length( X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1 0 with Underfull \hbox (badness 10000) in paragraph at lines 19468--19470 []\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 is equiv-a-lent to [284] Underfull \hbox (badness 1975) in paragraph at lines 19540--19543 []\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to [285] [286] [287] [288] [289] [290] Underfull \hbox (badness 1077) in paragraph at lines 19935--19940 []\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/ n/10 and [291] Underfull \hbox (badness 10000) in paragraph at lines 19949--19956 [][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / [292] Underfull \hbox (badness 10000) in paragraph at lines 20023--20027 []\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory [293] Underfull \hbox (badness 10000) in paragraph at lines 20153--20157 []\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use Underfull \hbox (badness 1454) in paragraph at lines 20153--20157 [][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self [294] [295] Underfull \hbox (badness 10000) in paragraph at lines 20251--20258 [][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/ m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 , [296] [297] Underfull \hbox (badness 10000) in paragraph at lines 20372--20376 []\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10 on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use [298] Underfull \hbox (badness 5161) in paragraph at lines 20442--20447 []\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di s-tributed un-der the Underfull \hbox (badness 6592) in paragraph at lines 20442--20447 \T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c opy of Underfull \hbox (badness 5133) in paragraph at lines 20442--20447 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 20442--20447 \T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 3 of the li-cense can be dis-played by [299] [300] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20609--20609 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20613--20613 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [301] Underfull \hbox (badness 3343) in paragraph at lines 20669--20673 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for many more file han-dling func-tions and [302] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20755--20755 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 20766--20766 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, pr = 0.2))),[] [303] [304] Overfull \hbox (9.78043pt too wide) in paragraph at lines 20877--20877 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the same names ![] Overfull \hbox (74.58035pt too wide) in paragraph at lines 20880--20880 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w / same name in .GlobalEnv[] [305] Underfull \hbox (badness 6380) in paragraph at lines 20925--20930 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- Underfull \hbox (badness 1337) in paragraph at lines 20983--20990 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t ails of the string are system-specific: it might be Underfull \hbox (badness 1960) in paragraph at lines 20983--20990 \T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by \T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, ma-cOS) or Underfull \hbox (badness 1043) in paragraph at lines 20983--20990 \T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in [306] Underfull \hbox (badness 2564) in paragraph at lines 21016--21019 []\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/ ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of Overfull \hbox (4.38043pt too wide) in paragraph at lines 21046--21046 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] [307] Underfull \hbox (badness 1205) in paragraph at lines 21069--21074 \T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form [308] [309] Underfull \hbox (badness 1400) in paragraph at lines 21214--21218 [][][]\T1/pcr/m/n/10 raw[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][]\T1/pcr/m/n/10 do uble[][][] \T1/ptm/m/n/10 (class Overfull \hbox (36.83002pt too wide) in paragraph at lines 21234--21241 []\T1/pcr/m/n/10 isTRUE(x) \T1/ptm/m/n/10 is the same as \T1/pcr/m/n/10 { is.lo gical(x) && length(x) == 1 && !is.na(x) && x }\T1/ptm/m/n/10 ; Underfull \hbox (badness 4886) in paragraph at lines 21234--21241 \T1/ptm/m/n/10 In ear-lier \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions, \T1/pcr/m /n/10 isTRUE <- function(x) identical(x, TRUE)\T1/ptm/m/n/10 , had the [310] [311] Underfull \hbox (badness 2469) in paragraph at lines 21384--21390 []\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s, Underfull \hbox (badness 1939) in paragraph at lines 21384--21390 \T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la -bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri butes in-clud-ing names. Underfull \hbox (badness 10000) in paragraph at lines 21384--21390 \T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true" ) \T1/ptm/m/n/10 are re-garded as true, [312] [313] [314] [315] [316] Underfull \hbox (badness 10000) in paragraph at lines 21701--21703 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [317] [318] [319] [320] [321] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22005--22005 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real = r , imaginary = NA ),[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22006--22006 [] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N aN, imaginary = r ))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 22009--22009 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] [322] [323] Underfull \hbox (badness 1655) in paragraph at lines 22133--22137 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [324] [325] [326] Underfull \hbox (badness 2277) in paragraph at lines 22382--22385 []\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][] \T1/pcr/m/n/10 crossprod[][][]() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tcrossprod() \T1/ptm/m/n/10 are typ-i-cally prefer-able. [327] [328] [329] [330] [331] [332] [333] [334] Underfull \hbox (badness 10000) in paragraph at lines 22867--22873 []\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age space can-not ex-ceed Underfull \hbox (badness 6316) in paragraph at lines 22867--22873 \T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er -ror mes-sage be-gins Underfull \hbox (badness 1484) in paragraph at lines 22899--22907 []\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less the OS's de-fault has been Underfull \hbox (badness 2951) in paragraph at lines 22899--22907 \T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http s : / / www . microsoft . com / whdc / Underfull \hbox (badness 3460) in paragraph at lines 22899--22907 \T1/pcr/m/n/10 system / platform / server / PAE / PAEmem . mspx$[][] \T1/ptm/m/ n/10 and [][]$\T1/pcr/m/n/10 https : / / msdn . microsoft . [335] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22976--22976 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [336] Underfull \hbox (badness 10000) in paragraph at lines 23030--23034 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by. x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng th zero vec- Underfull \hbox (badness 10000) in paragraph at lines 23030--23034 \T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr /m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/ n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i. e., [337] [338] [339] [340] [341] [342] Underfull \hbox (badness 10000) in paragraph at lines 23481--23489 \T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T 1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; [343] [344] Underfull \hbox (badness 3849) in paragraph at lines 23595--23600 []\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na lly to a char-ac-ter vec-tor (so meth-ods for [345] Underfull \hbox (badness 7308) in paragraph at lines 23672--23678 []\T1/ptm/m/n/10 For an [][]\T1/pcr/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/pcr/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 5077) in paragraph at lines 23672--23678 \T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23682--23685 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23682--23685 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [346] [347] Underfull \hbox (badness 10000) in paragraph at lines 23834--23836 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of [348] [349] [350] [351] Underfull \hbox (badness 6188) in paragraph at lines 24053--24056 []\T1/ptm/m/n/10 optional [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/pcr/m/n/10 print()\T1/ptm/m/n/10 , used by [352] [353] [354] [355] [356] [357] [358] Underfull \hbox (badness 2197) in paragraph at lines 24535--24539 []\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s tartup mes-sages given by Underfull \hbox (badness 4048) in paragraph at lines 24535--24539 \T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use Underfull \hbox (badness 2846) in paragraph at lines 24549--24553 []\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment \T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the pack- Underfull \hbox (badness 1990) in paragraph at lines 24549--24553 \T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p uted pack-age in-for-ma-tion ob-ject and pass this to [359] Underfull \hbox (badness 10000) in paragraph at lines 24642--24648 []\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i t loads to the search path. Underfull \hbox (badness 1168) in paragraph at lines 24642--24648 \T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co n-tain-ing the ex-ported val-ues of a [360] Underfull \hbox (badness 10000) in paragraph at lines 24655--24657 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than Overfull \hbox (4.38043pt too wide) in paragraph at lines 24706--24706 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/ n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] [361] [362] [363] Underfull \hbox (badness 10000) in paragraph at lines 24899--24905 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of Underfull \hbox (badness 10000) in paragraph at lines 24899--24905 [][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type [][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\ T1/ptm/m/n/10 ) and not a fac-tor, Underfull \hbox (badness 10000) in paragraph at lines 24899--24905 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T 1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or [364] Underfull \hbox (badness 4120) in paragraph at lines 24985--24992 []\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/ n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from [365] [366] Underfull \hbox (badness 1694) in paragraph at lines 25121--25124 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [367] [368] [369] [370] Underfull \hbox (badness 1603) in paragraph at lines 25368--25370 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [371] Overfull \hbox (73.28088pt too wide) in paragraph at lines 25491--25499 \T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats", "methods")\T1/ptm/m/n/10 . [372] [373] Underfull \hbox (badness 5475) in paragraph at lines 25628--25638 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 3271) in paragraph at lines 25670--25673 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able Underfull \hbox (badness 10000) in paragraph at lines 25685--25687 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [374] [375] [376] Underfull \hbox (badness 3138) in paragraph at lines 25948--25954 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 2088) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by [377] Underfull \hbox (badness 1194) in paragraph at lines 25961--25964 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 1389) in paragraph at lines 25987--25989 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 10000) in paragraph at lines 25999--26003 []\T1/ptm/m/n/10 string used as the user agent in HTTP(S) re-quests. If Underfull \hbox (badness 6592) in paragraph at lines 25999--26003 \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , re-quests will be made with-out a user agen t header. The de-fault is Underfull \hbox (badness 10000) in paragraph at lines 26004--26010 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 26019--26024 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Overfull \hbox (49.4607pt too wide) in paragraph at lines 26025--26036 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][](type = "both ") Underfull \hbox (badness 1009) in paragraph at lines 26037--26040 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 26047--26059 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see Underfull \hbox (badness 1072) in paragraph at lines 26047--26059 [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 . Pos-si-ble val-ues ar e \T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a [378] Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 \T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 26061--26068 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Overfull \hbox (34.78088pt too wide) in paragraph at lines 26061--26068 \T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [379] [380] [381] [382] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26392--26392 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec, 300X faster[] Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n /10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 \T1/pcr/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A[c(arrayindex.x, arrayindex.y)] [383] [384] [385] [386] [387] Underfull \hbox (badness 4341) in paragraph at lines 26729--26731 []\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 , Underfull \hbox (badness 4518) in paragraph at lines 26765--26771 [][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/ n/10 paste(*, collapse=", ")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with [388] Overfull \hbox (42.18039pt too wide) in paragraph at lines 26787--26787 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as the longest input.[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26799--26799 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] [389] [390] [391] [392] [393] [394] [395] Underfull \hbox (badness 10000) in paragraph at lines 27233--27237 []\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr /m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [396] Underfull \hbox (badness 1796) in paragraph at lines 27299--27302 []\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 27499--27502 []\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print -ing of vec-tors, ma-tri-ces and ar-rays, and op-tion [400] [401] [402] [403] [404] [405] [406] [407] [408] Underfull \hbox (badness 1226) in paragraph at lines 28131--28136 \T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T 1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/ n/10 ncol \T1/ptm/m/n/10 is greater than [409] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28176--28176 [] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = rep(c(0,0,1),2))[] [410] [411] [412] [413] Overfull \hbox (15.18042pt too wide) in paragraph at lines 28442--28442 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3 \u147b\u203c")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28453--28453 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\ U147b\U203c"[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 28459--28459 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm l#Literal-constants[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 28460--28460 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug .cgi?id=16098[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 28463--28463 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] [414] Underfull \hbox (badness 7415) in paragraph at lines 28538--28542 []\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use [415] Overfull \hbox (42.18039pt too wide) in paragraph at lines 28559--28559 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] [416] [417] Underfull \hbox (badness 2418) in paragraph at lines 28718--28729 []\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n ot [418] Underfull \hbox (badness 1248) in paragraph at lines 28852--28859 \T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM Trans-ac-tions on Mod-el-ing and Com-puter Underfull \hbox (badness 10000) in paragraph at lines 28852--28859 \T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS / [419] [420] Underfull \hbox (badness 1533) in paragraph at lines 28968--28971 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [421] Underfull \hbox (badness 1337) in paragraph at lines 29065--29068 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute d, i.e., [422] Overfull \hbox (42.78088pt too wide) in paragraph at lines 29113--29113 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] Underfull \hbox (badness 1038) in paragraph at lines 29131--29142 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [423] Underfull \hbox (badness 10000) in paragraph at lines 29143--29146 []\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal: for \T1/pcr/m/n/10 na.last = TRUE \T1/ptm/m/n/10 and [424] Underfull \hbox (badness 1117) in paragraph at lines 29238--29244 \T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \ T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing [425] [426] [427] [428] [429] [430] Underfull \hbox (badness 4048) in paragraph at lines 29616--29621 []\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor to Underfull \hbox (badness 4582) in paragraph at lines 29616--29621 \T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the mode: Underfull \hbox (badness 1824) in paragraph at lines 29616--29621 \T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 " double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , [431] [432] [433] [434] [435] [436] [437] [438] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30162--30162 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [439] [440] [441] [442] Overfull \hbox (13.9408pt too wide) in paragraph at lines 30448--30450 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( ) * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T 1/ptm/m/n/10 '. [443] [444] [445] Underfull \hbox (badness 7558) in paragraph at lines 30664--30668 []\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1968) in paragraph at lines 30674--30676 []\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P OSIX stan-dard, and the Underfull \hbox (badness 5417) in paragraph at lines 30679--30682 [][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/ ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 ls[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 30683--30685 []\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la urikari . net / tre / documentation / Underfull \hbox (badness 10000) in paragraph at lines 30686--30688 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / [446] [447] [448] [449] [450] [451] Underfull \hbox (badness 10000) in paragraph at lines 31091--31095 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [452] [453] [454] [455] [456] Overfull \hbox (12.78088pt too wide) in paragraph at lines 31422--31422 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 31425--31425 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [457] [458] [459] Underfull \hbox (badness 3375) in paragraph at lines 31653--31660 \T1/ptm/m/n/10 pen if the spec-i-fied row names, i.e., \T1/pcr/m/n/10 value\T1/ ptm/m/n/10 , are in-valid, e.g., du- Underfull \hbox (badness 2359) in paragraph at lines 31653--31660 \T1/ptm/m/n/10 pli-cated or \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 . The de-fault (is back com-pat-i-ble), \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , will sig-nal Underfull \hbox (badness 2582) in paragraph at lines 31653--31660 \T1/ptm/m/n/10 an er-ror, where \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 will ``au-to-m atic'' row names and \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 will call [460] [461] [462] Overfull \hbox (54.78088pt too wide) in paragraph at lines 31806--31806 [] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/ 2 && n > 1e7))[] [463] [464] Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 []\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 \T1/ptm/m/n/10 workspace', i.e., \T1/pcr/m/n/10 save(list = ls(all.names = TRUE ), file = [465] [466] [467] Underfull \hbox (badness 2302) in paragraph at lines 32188--32195 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3815) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [468] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32240--32240 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [469] Underfull \hbox (badness 1158) in paragraph at lines 32344--32349 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if [470] Underfull \hbox (badness 10000) in paragraph at lines 32371--32377 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1953) in paragraph at lines 32371--32377 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o c-tal and hex-adec-i-mal rep-re- [471] Underfull \hbox (badness 10000) in paragraph at lines 32447--32452 []\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by Underfull \hbox (badness 6725) in paragraph at lines 32447--32452 \T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10 will give an empty [472] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32529--32529 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [473] [474] [475] Underfull \hbox (badness 2809) in paragraph at lines 32793--32799 []\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2, ..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment Underfull \hbox (badness 7759) in paragraph at lines 32800--32803 []\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/ n/10 1, 2, ..., length.out \T1/ptm/m/n/10 un-less [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] [487] Underfull \hbox (badness 1735) in paragraph at lines 33605--33611 \T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co n-sole. Mes-sages sent [488] Underfull \hbox (badness 4303) in paragraph at lines 33621--33624 []\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault out-put from [489] [490] [491] [492] Overfull \hbox (66.78088pt too wide) in paragraph at lines 33939--33939 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [493] [494] [495] [496] Overfull \hbox (6.78088pt too wide) in paragraph at lines 34191--34191 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 34193--34193 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] [497] Underfull \hbox (badness 10000) in paragraph at lines 34236--34242 [][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 vec-tor, passed as \T1/pcr/ m/n/10 control \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 deparse[][][]()\T1/ptm/m/n/ 10 , see Underfull \hbox (badness 10000) in paragraph at lines 34236--34242 \T1/ptm/m/n/10 also [][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T 1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard- Underfull \hbox (badness 10000) in paragraph at lines 34236--34242 \T1/ptm/m/n/10 coded to \T1/pcr/m/n/10 "showAttributes"\T1/ptm/m/n/10 , which i s the de-fault cur-rently; Underfull \hbox (badness 2512) in paragraph at lines 34251--34253 []\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s kip if [498] Overfull \hbox (20.58041pt too wide) in paragraph at lines 34347--34347 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [499] [500] [501] Underfull \vbox (badness 10000) has occurred while \output is active [502] [503] Overfull \hbox (4.38043pt too wide) in paragraph at lines 34675--34675 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m /n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 34690--34690 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [504] [505] [506] [507] [508] [509] Overfull \hbox (12.78088pt too wide) in paragraph at lines 35129--35129 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 35130--35130 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [510] [511] [512] [513] Overfull \hbox (63.78036pt too wide) in paragraph at lines 35394--35394 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [514] Underfull \hbox (badness 10000) in paragraph at lines 35478--35488 []\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/ pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want Underfull \hbox (badness 8113) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s tart, in-sert a call Underfull \hbox (badness 10000) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n /10 ' file. For ex-am-ple, Underfull \hbox (badness 6542) in paragraph at lines 35478--35488 \T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta ch no ex-tra pack-ages on Underfull \hbox (badness 5189) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) ( or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi- Underfull \hbox (badness 4193) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/ 10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or [515] Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1496) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be Underfull \hbox (badness 1728) in paragraph at lines 35534--35541 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm /m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment [516] [517] [518] [519] [520] Underfull \hbox (badness 10000) in paragraph at lines 35875--35881 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form at \T1/ptm/m/n/10 meth-ods is [521] [522] [523] Underfull \hbox (badness 1163) in paragraph at lines 36064--36071 []\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10 %OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr /m/n/10 0 <= n <= 6 Underfull \hbox (badness 8132) in paragraph at lines 36064--36071 \T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no t fol-lowed by a digit, it uses the set-ting of [524] [525] [526] [527] Underfull \hbox (badness 1142) in paragraph at lines 36346--36352 []\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1 /ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or Overfull \hbox (0.78088pt too wide) in paragraph at lines 36361--36361 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [528] [529] [530] [531] Overfull \hbox (6.78088pt too wide) in paragraph at lines 36609--36609 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36653--36653 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [532] [533] [534] [535] [536] [537] [538] Overfull \hbox (52.98038pt too wide) in paragraph at lines 37087--37087 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e verything gets added.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 37090--37090 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [539] Underfull \hbox (badness 10000) in paragraph at lines 37141--37148 []\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10 signif[][][]() \T1/ptm/m/n/10 (for Underfull \hbox (badness 10000) in paragraph at lines 37141--37148 \T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][] []() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ). Overfull \hbox (4.38043pt too wide) in paragraph at lines 37192--37192 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [540] [541] [542] [543] Underfull \hbox (badness 2762) in paragraph at lines 37431--37440 \T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there is a match then that el-e-ment is eval-u-ated un-less Underfull \hbox (badness 1466) in paragraph at lines 37431--37440 \T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is eval-u-ated, so for ex-am-ple [544] Overfull \hbox (31.3804pt too wide) in paragraph at lines 37493--37493 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [545] [546] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37658--37658 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS 1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. [547] Overfull \hbox (20.58041pt too wide) in paragraph at lines 37696--37696 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] [548] Underfull \hbox (badness 3219) in paragraph at lines 37745--37750 []\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple Underfull \hbox (badness 1107) in paragraph at lines 37745--37750 \T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr /m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match [549] Underfull \hbox (badness 2452) in paragraph at lines 37835--37838 \T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/ ptm/m/n/10 sys-tem call. The lo-gin name comes Underfull \hbox (badness 10000) in paragraph at lines 37835--37838 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and [550] [551] [552] Underfull \hbox (badness 10000) in paragraph at lines 38022--38026 []\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents \T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n /10 and Underfull \hbox (badness 1584) in paragraph at lines 38037--38040 []\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \ T1/ptm/m/n/10 and [553] [554] Overfull \hbox (25.98041pt too wide) in paragraph at lines 38169--38169 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [555] Overfull \hbox (20.58041pt too wide) in paragraph at lines 38239--38239 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/pcr/ m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used [556] [557] [558] Underfull \hbox (badness 1082) in paragraph at lines 38377--38380 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [559] [560] Underfull \hbox (badness 1038) in paragraph at lines 38564--38567 []\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or [561] [562] [563] [564] [565] [566] Underfull \hbox (badness 1515) in paragraph at lines 38928--38931 []\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc r/m/n/10 stderr = TRUE \T1/ptm/m/n/10 im-plies [567] [568] [569] Underfull \hbox (badness 4096) in paragraph at lines 39169--39172 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[ ][][]\T1/ptm/m/n/10 , [570] [571] Underfull \hbox (badness 10000) in paragraph at lines 39283--39287 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., [572] [573] Overfull \hbox (63.78036pt too wide) in paragraph at lines 39436--39436 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 39438--39438 [] \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr /m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 39440--39440 [] \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n /9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 = NULL ), dim=4, dimnames=list(as.character(2:5)))))[] [574] Underfull \hbox (badness 10000) in paragraph at lines 39453--39455 []\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha t was reg-is-tered ear-lier via [575] Underfull \hbox (badness 10000) in paragraph at lines 39533--39536 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [576] [577] Underfull \hbox (badness 1867) in paragraph at lines 39651--39655 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 5475) in paragraph at lines 39713--39717 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / [578] [579] [580] [581] [582] [583] [584] Underfull \hbox (badness 10000) in paragraph at lines 40131--40138 \T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/ n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', ` \T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ', Underfull \hbox (badness 4467) in paragraph at lines 40187--40196 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn s the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 40187--40196 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, Underfull \hbox (badness 10000) in paragraph at lines 40197--40205 []\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op -tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de- Underfull \hbox (badness 10000) in paragraph at lines 40197--40205 \T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da tabase at Underfull \hbox (badness 1303) in paragraph at lines 40197--40205 \T1/pcr/m/n/10 file.path(R.home("share"), "zoneinfo") \T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 ' [585] Underfull \hbox (badness 1337) in paragraph at lines 40263--40271 \T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 / usr/local/etc\T1/ptm/m/n/10 ' or Underfull \hbox (badness 10000) in paragraph at lines 40272--40275 []\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym -link tar-get name of [586] Underfull \hbox (badness 4429) in paragraph at lines 40329--40331 [][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol- Overfull \hbox (31.3804pt too wide) in paragraph at lines 40338--40338 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [587] [588] [589] Underfull \hbox (badness 10000) in paragraph at lines 40555--40557 []\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal l-ing [590] [591] Overfull \hbox (15.18042pt too wide) in paragraph at lines 40677--40677 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15 g)\n", ncp))),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 40679--40679 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] Underfull \vbox (badness 10000) has occurred while \output is active [592] [593] [594] [595] [596] Underfull \hbox (badness 6542) in paragraph at lines 41041--41043 []\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x )\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and [597] [598] [599] Underfull \hbox (badness 3460) in paragraph at lines 41207--41210 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1708) in paragraph at lines 41214--41222 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e r-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 3713) in paragraph at lines 41214--41222 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less Underfull \hbox (badness 10000) in paragraph at lines 41223--41227 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10 tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in- Underfull \hbox (badness 10000) in paragraph at lines 41223--41227 \T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 , some-thing like Underfull \hbox (badness 3281) in paragraph at lines 41223--41227 \T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s im-ple er-ror han-dler func- Underfull \hbox (badness 4859) in paragraph at lines 41244--41249 [][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers and sup-press-ing the print-ing of er-ror mes-sages; [600] Underfull \hbox (badness 3895) in paragraph at lines 41306--41318 []\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in Underfull \hbox (badness 1303) in paragraph at lines 41306--41318 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , [601] [602] [603] Underfull \hbox (badness 10000) in paragraph at lines 41491--41494 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [604] [605] Overfull \hbox (9.78043pt too wide) in paragraph at lines 41628--41628 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [606] [607] [608] [609] [610] [611] Overfull \hbox (4.38043pt too wide) in paragraph at lines 42095--42095 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] [612] Overfull \hbox (20.58041pt too wide) in paragraph at lines 42104--42104 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little- endian platform[] [613] Underfull \hbox (badness 1803) in paragraph at lines 42221--42224 []\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1 0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ), Underfull \hbox (badness 2334) in paragraph at lines 42225--42232 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and [614] Underfull \hbox (badness 4726) in paragraph at lines 42251--42255 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec tor(x, mode = "numeric") \T1/ptm/m/n/10 can be Underfull \hbox (badness 1122) in paragraph at lines 42251--42255 \T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/ 10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x , mode = [615] [616] Underfull \hbox (badness 3668) in paragraph at lines 42440--42442 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [617] [618] Overfull \hbox (36.78088pt too wide) in paragraph at lines 42544--42544 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [619] Overfull \hbox (4.38043pt too wide) in paragraph at lines 42619--42619 []\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n /9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 42627--42627 []\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) # There were 105 warnings ...[] [620] [621] Underfull \hbox (badness 6220) in paragraph at lines 42757--42762 []\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][] (.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true, Underfull \hbox (badness 3098) in paragraph at lines 42757--42762 \T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array Ind() \T1/ptm/m/n/10 (and hence, Underfull \hbox (badness 1533) in paragraph at lines 42757--42762 \T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty, Underfull \hbox (badness 6592) in paragraph at lines 42773--42778 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [622] Underfull \hbox (badness 1603) in paragraph at lines 42792--42796 [][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[] [][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the [623] Underfull \hbox (badness 10000) in paragraph at lines 42857--42860 []\T1/ptm/m/n/10 If this ex-tremum is unique (or empty), the re-sults are the s ame as Underfull \hbox (badness 10000) in paragraph at lines 42857--42860 \T1/ptm/m/n/10 (but more ef-fi-cient than) \T1/pcr/m/n/10 which(x == min(x, na. rm = TRUE)) \T1/ptm/m/n/10 or Underfull \hbox (badness 2818) in paragraph at lines 42863--42869 []\T1/ptm/m/n/10 For a [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with both \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 a nd \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 val-ues, \T1/pcr/m/n/10 which.min(x) \T1/ ptm/m/n/10 and Overfull \hbox (15.18042pt too wide) in paragraph at lines 42898--42898 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [624] [625] Underfull \hbox (badness 1622) in paragraph at lines 42992--42994 []\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer . [626] [627] [628] [629] Underfull \hbox (badness 10000) in paragraph at lines 43260--43265 []\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu nc-tion than [][]\T1/pcr/m/n/10 rank[][][] Underfull \hbox (badness 10000) in paragraph at lines 43260--43265 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to Underfull \hbox (badness 10000) in paragraph at lines 43260--43265 \T1/pcr/m/n/10 rank(x, ties.method = "min", na.last = "keep")\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are [630] Underfull \hbox (badness 2846) in paragraph at lines 43354--43358 []\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [631] Overfull \hbox (4.38043pt too wide) in paragraph at lines 43394--43394 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 43415--43419 []\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard ' reg-exps, in-clud-ing el-e-ments named [632]) (./compiler-pkg.tex Chapter 2. [633] Underfull \hbox (badness 2884) in paragraph at lines 101--115 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 options \T1/ptm/m/n/10 ar-gu-ment can be us ed to con-trol com-piler op-er-a-tion. There are cur- Underfull \hbox (badness 10000) in paragraph at lines 101--115 \T1/ptm/m/n/10 rently four op-tions: \T1/pcr/m/n/10 optimize\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 suppressAll\T1/ptm/m/n/10 , \T1/pcr/m/n/10 suppressUndefined\T1/pt m/m/n/10 , and [634] [635] [636]) (./datasets-pkg.tex Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple te list, use [637] [638] [639] [640] [641] Overfull \hbox (15.18042pt too wide) in paragraph at lines 301--301 [] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang e", cex = 1.2,[] [642] Overfull \hbox (4.38043pt too wide) in paragraph at lines 379--379 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi ven = FALSE)[] Underfull \vbox (badness 1033) has occurred while \output is active [643] [644] [645] [646] [647] Overfull \hbox (66.81013pt too wide) in paragraph at lines 702--705 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [648] [649] Overfull \hbox (66.81013pt too wide) in paragraph at lines 835--838 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [650] [651] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [652] [653] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1146--1149 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [654] [655] [656] [657] [658] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1456--1456 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption time (sec)")[] [659] [660] Underfull \hbox (badness 10000) in paragraph at lines 1541--1544 []\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r evenue\T1/ptm/m/n/10 , Underfull \hbox (badness 2903) in paragraph at lines 1541--1544 \T1/pcr/m/n/10 price.index\T1/ptm/m/n/10 , \T1/pcr/m/n/10 income.level\T1/ptm/m /n/10 , and \T1/pcr/m/n/10 market.potential \T1/ptm/m/n/10 ob-tained from the a bove [661] [662] [663] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1730--1733 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [664] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1824--1824 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil y = binomial())[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1832--1832 [] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum), data = infert)[] [665] [666] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1948--1948 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1949--1949 [] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d ni3[[3]]))))[] [667] [668] [669] [670] Overfull \hbox (66.81013pt too wide) in paragraph at lines 2152--2155 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [671] [672] [673] [674] [675] [676] [677] [678] Overfull \hbox (66.81013pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [679] Overfull \vbox (13.87083pt too high) has occurred while \output is active [680] Underfull \vbox (badness 1789) has occurred while \output is active [681] [682] Overfull \vbox (12.25539pt too high) has occurred while \output is active [683] [684] Overfull \vbox (17.12102pt too high) has occurred while \output is active [685] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3137--3137 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [686] [687] [688] [689] [690] [691] [692] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3594--3594 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [693] [694] Overfull \hbox (66.81013pt too wide) in paragraph at lines 3742--3745 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [695] Overfull \vbox (10.49593pt too high) has occurred while \output is active [696] Underfull \hbox (badness 1173) in paragraph at lines 3876--3880 \T1/ptm/m/it/10 Ed-u-ca-tion\T1/ptm/m/n/10 , \T1/ptm/b/n/10 3\T1/ptm/m/n/10 . [ ][]$\T1/pcr/m/n/10 https : / / www . amstat . org / publications / jse / v3n3 / datasets . Overfull \vbox (27.49593pt too high) has occurred while \output is active [697] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3951--3951 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 3980--3983 []\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www -[]personal . buseco . monash . edu . au / Underfull \hbox (badness 10000) in paragraph at lines 3989--3991 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h ttps : / / web . archive . org / web / Underfull \hbox (badness 10000) in paragraph at lines 3989--3991 \T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma n / sitephotos / [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711]) (./grDevices-pkg.tex [712] Chapter 4. [713] [714] [715] [716] [717] [718] Underfull \hbox (badness 10000) in paragraph at lines 374--382 []\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til e, i.e., close to Underfull \hbox (badness 10000) in paragraph at lines 374--382 [][]\T1/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where [719] Overfull \hbox (6.78088pt too wide) in paragraph at lines 479--479 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [720] [721] [722] [723] [724] [725] [726] [727] [728] Underfull \hbox (badness 5175) in paragraph at lines 1082--1084 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [729] Underfull \hbox (badness 1325) in paragraph at lines 1144--1150 \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 , [730] Underfull \hbox (badness 10000) in paragraph at lines 1185--1187 []\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2 . com / Lab / Graphics / Colors / [731] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1237--1237 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] [732] Underfull \hbox (badness 1173) in paragraph at lines 1279--1282 []\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col- ors that will be used in plot-ting, call-ing [733] [734] [735] Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 []\T1/ptm/m/n/10 character: Which events can be gen-er-ated on Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 \T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 \T1/pcr/m/n/10 c("MouseDown", "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10 , Underfull \hbox (badness 2221) in paragraph at lines 1539--1542 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture, oth-er-wise a ma-trix of color names (for [736] Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 []\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 [][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is [737] [738] [739] Underfull \hbox (badness 1565) in paragraph at lines 1767--1772 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to pro-duce and print a postscript copy. This will not Underfull \hbox (badness 1354) in paragraph at lines 1767--1772 \T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10 for how to set this up. Win-dows users may pre-fer to use [740] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1850--1850 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] [741] Underfull \hbox (badness 1184) in paragraph at lines 1891--1901 []\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m /n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in- Underfull \hbox (badness 2057) in paragraph at lines 1891--1901 \T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p tm/m/n/10 , [742] Underfull \hbox (badness 10000) in paragraph at lines 1996--1998 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [743] [744] Underfull \hbox (badness 6758) in paragraph at lines 2157--2160 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [745] [746] Underfull \hbox (badness 2326) in paragraph at lines 2267--2277 \T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra phicsEventHandlers \T1/ptm/m/n/10 to re-place Underfull \hbox (badness 2318) in paragraph at lines 2267--2277 \T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co m-pat-i-bil-ity with pre-2.12.0 Underfull \hbox (badness 2460) in paragraph at lines 2267--2277 \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e vent han-dlers is to set them us-ing Underfull \hbox (badness 1221) in paragraph at lines 2267--2277 \T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics [747] [748] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2370--2370 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r" , yaxs = "r") {[] Underfull \vbox (badness 10000) has occurred while \output is active [749] [750] [751] [752] [753] [754] Underfull \hbox (badness 10000) in paragraph at lines 2750--2751 Underfull \vbox (badness 10000) has occurred while \output is active [755] [756] [757] [758] [759] [760] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3156--3156 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", scale.in = 255))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3157--3157 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] Underfull \hbox (badness 1210) in paragraph at lines 3188--3190 []\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m /n/10 giv-ing the num-ber of rows and columns, ful-fill-ing [761] Underfull \hbox (badness 10000) in paragraph at lines 3248--3253 []\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [762] [763] [764] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3407--3407 []\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al pha = 1) [765] Underfull \hbox (badness 3525) in paragraph at lines 3514--3517 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as [766] Underfull \hbox (badness 1968) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [767] [768] [769] [770] Underfull \hbox (badness 5939) in paragraph at lines 3822--3827 []\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\ T1/ptm/m/n/10 , [771] [772] [773] [774] [775] Underfull \hbox (badness 7576) in paragraph at lines 4199--4206 \T1/pcr/m/n/10 / / www . adobe . com / products / postscript / pdfs / PLRM . pd f$[][] \T1/ptm/m/n/10 or PDF [][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 3701) in paragraph at lines 4199--4206 \T1/pcr/m/n/10 www . adobe . com / devnet / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i- [776] Underfull \vbox (badness 10000) has occurred while \output is active [777] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4316--4316 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [778] Underfull \hbox (badness 1502) in paragraph at lines 4363--4368 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the type of anti-aliasing (if any) to be [779] [780] Underfull \hbox (badness 1348) in paragraph at lines 4515--4518 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also Underfull \hbox (badness 4765) in paragraph at lines 4525--4527 [][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if Overfull \hbox (9.78043pt too wide) in paragraph at lines 4539--4539 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, height = 768)[] [781] Underfull \hbox (badness 5077) in paragraph at lines 4579--4585 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as Underfull \hbox (badness 1342) in paragraph at lines 4595--4597 []\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [782] Underfull \hbox (badness 1874) in paragraph at lines 4672--4680 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as [783] Underfull \hbox (badness 1755) in paragraph at lines 4739--4741 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [784] [785] Underfull \hbox (badness 7344) in paragraph at lines 4910--4912 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso Underfull \hbox (badness 7397) in paragraph at lines 4921--4925 [][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm /m/n/10 which is called from both [786] [787] Underfull \hbox (badness 1552) in paragraph at lines 5034--5043 \T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG othic"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m /n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW Helvetica"\T1/ptm/m/n/10 ), Underfull \hbox (badness 2221) in paragraph at lines 5044--5046 []\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and [788] Underfull \hbox (badness 4686) in paragraph at lines 5076--5082 \T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap an1Ryumin" \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 5102--5109 []\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / [789] [790] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5203--5203 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [791] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5315--5315 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] Underfull \hbox (badness 1648) in paragraph at lines 5321--5325 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [792] [793] Underfull \hbox (badness 10000) in paragraph at lines 5401--5403 []\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10 for on-screen de-vices and to Underfull \hbox (badness 1072) in paragraph at lines 5437--5443 []\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots due to cor-rupted or du-pli- [794] [795] [796] [797] [798] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5759--5759 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15, sep = "."))[] Underfull \hbox (badness 10000) in paragraph at lines 5772--5775 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [799] [800] [801] [802] [803] [804] [805] Underfull \hbox (badness 1189) in paragraph at lines 6169--6171 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [806] Underfull \hbox (badness 10000) in paragraph at lines 6267--6269 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and Underfull \hbox (badness 10000) in paragraph at lines 6306--6313 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T 1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and Underfull \hbox (badness 2469) in paragraph at lines 6306--6313 \T1/pcr/m/n/10 expression(10^degree)\T1/ptm/m/n/10 ) have been seen on Linux sy s-tems which have the Wine [807] Underfull \hbox (badness 3088) in paragraph at lines 6390--6394 []\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do- Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and [808] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6435--6435 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [809] Underfull \hbox (badness 10000) in paragraph at lines 6467--6470 []\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][ ] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 -- [810] Underfull \hbox (badness 5637) in paragraph at lines 6558--6564 \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n /10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 1721) in paragraph at lines 6591--6594 []\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt p : / / www . schmidt-[]web-[]berlin . de / [811] [812] [813] Underfull \hbox (badness 6157) in paragraph at lines 6748--6751 \T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them via Underfull \hbox (badness 1231) in paragraph at lines 6759--6761 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [814] [815] [816]) (./graphics-pkg.tex Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag es, use [817] [818] [819] [820] Underfull \hbox (badness 1412) in paragraph at lines 287--292 []\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal data. \T1/ptm/m/it/10 SAS User Group In-ter-na- [821] [822] [823] Underfull \hbox (badness 2726) in paragraph at lines 466--472 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark lo-ca-tions are com-puted in-ter-nally (the same way [824] [825] [826] Underfull \hbox (badness 10000) in paragraph at lines 659--663 []\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m /n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or Underfull \hbox (badness 3250) in paragraph at lines 659--663 [][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/ m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1 0 if Underfull \hbox (badness 2735) in paragraph at lines 687--694 []\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [827] Overfull \hbox (4.38043pt too wide) in paragraph at lines 744--744 [] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n intLog = 5))[] [828] [829] Underfull \hbox (badness 1062) in paragraph at lines 853--856 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic h di-vide ad-ja-cent (non-stacked!) bars [830] [831] [832] [833] [834] [835] [836] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1290--1290 [] \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = NULL,[] [837] Underfull \hbox (badness 1024) in paragraph at lines 1335--1343 \T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 cex.lab\T1/ptm/m/n/10 , and Underfull \hbox (badness 1248) in paragraph at lines 1363--1369 \T1/ptm/m/n/10 width, point char-ac-ter, point size ex-pan-sion, color, and bac k-ground Underfull \hbox (badness 6893) in paragraph at lines 1363--1369 \T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su p-presses the point, and Underfull \hbox (badness 3375) in paragraph at lines 1369--1371 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), Overfull \hbox (19.3703pt too wide) in paragraph at lines 1391--1395 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10 xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim = range(at, *) + c(-0.5, 0.5)\T1/ptm/m/n/10 . [838] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1439--1439 []\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi s=..,main=..)")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1440--1440 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi s=..,main=..)")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1446--1446 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill = "grey40",[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1447--1447 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [839] [840] [841] [842] [843] Underfull \hbox (badness 10000) in paragraph at lines 1747--1753 [][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 (and [844] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1784--1784 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1793--1793 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [845] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1876--1876 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [846] [847] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2005--2005 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept h, rows = 1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2010--2010 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [848] [849] [850] [851] [852] Underfull \hbox (badness 1009) in paragraph at lines 2296--2303 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [853] [854] [855] [856] [857] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2624--2624 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [858] [859] Underfull \hbox (badness 5878) in paragraph at lines 2785--2789 \T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T 1/ptm/m/n/10 and in gen-eral sat-isfy Underfull \hbox (badness 10000) in paragraph at lines 2810--2813 []\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1 /ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n /10 or [860] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2838--2838 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2842--2842 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] [861] Underfull \hbox (badness 10000) in paragraph at lines 2894--2897 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as [862] [863] [864] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3091--3091 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL SE, pch = 19, ...)[] Overfull \hbox (79.98035pt too wide) in paragraph at lines 3096--3096 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [865] Underfull \hbox (badness 1755) in paragraph at lines 3161--3165 []\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/ 10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/ n/10 , [866] Underfull \hbox (badness 10000) in paragraph at lines 3236--3241 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3236--3241 [][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3236--3241 [][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/ n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is [867] [868] [869] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3423--3423 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 0, horiz = TRUE)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3442--3442 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3446--3446 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [870] [871] [872] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3623--3623 [] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c ex = 0.8, adj = 0)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3624--3624 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3663--3663 [] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj = c(0, 0.3))[] Underfull \vbox (badness 10000) has occurred while \output is active [873] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3715--3715 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3723--3723 []\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset = .05", inset = .05)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3725--3725 []\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset = .02",inset = .02)[] Underfull \vbox (badness 10000) has occurred while \output is active [874] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3733--3733 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] Underfull \hbox (badness 10000) in paragraph at lines 3796--3800 [][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method ; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for [875] [876] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3907--3907 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [877] Underfull \hbox (badness 1867) in paragraph at lines 3950--3954 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [878] [879] Underfull \hbox (badness 3930) in paragraph at lines 4114--4116 []\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a mul-ti-ple of [880] [881] [882] [883] Underfull \hbox (badness 1924) in paragraph at lines 4400--4405 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [884] Underfull \hbox (badness 1286) in paragraph at lines 4424--4427 \T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 oma \T1/ptm/m/n/10 when chang-ing Underfull \hbox (badness 3229) in paragraph at lines 4432--4437 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [885] [886] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4525--4525 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel = panel.cor,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4530--4530 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4574--4574 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = " blue") # hmm...[] [887] Underfull \hbox (badness 1264) in paragraph at lines 4648--4661 \T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/ m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1 /ptm/m/n/10 , [888] [889] Underfull \hbox (badness 7925) in paragraph at lines 4785--4791 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. [890] [891] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 <"/tmp/B.61K3e5/BUILD/R-3.5.2/build/library/graphics/help/figures/"mai.pdf, id= 29409, 289.08pt x 289.08pt> [892 ] Underfull \hbox (badness 10000) in paragraph at lines 4977--4979 <"/tmp/B.61K3e5/BUILD/R-3.5.2/build/library/graphics/help/figures/"oma.pdf, id= 29423, 259.97125pt x 332.24126pt> [893 ] [894] Underfull \hbox (badness 10000) in paragraph at lines 5167--5169 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [895] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5223--5223 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5224--5224 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] Underfull \vbox (badness 10000) has occurred while \output is active [896] [897] Underfull \hbox (badness 3954) in paragraph at lines 5325--5328 []\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm /m/n/10 co-or-di-nates. Of-ten used with Underfull \hbox (badness 10000) in paragraph at lines 5381--5385 \T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and [898] [899] [900] [901] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5589--5589 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5590--5590 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 5641--5645 []\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing or an er-ror; us-ing, e.g., Underfull \hbox (badness 1024) in paragraph at lines 5641--5645 \T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/ n/10 type = "p" \T1/ptm/m/n/10 for S com- [902] [903] [904] [905] [906] [907] [908] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6068--6068 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6074--6074 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [909] [910] [911] [912] [913] [914] Underfull \hbox (badness 10000) in paragraph at lines 6501--6503 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [915] [916] Underfull \hbox (badness 1028) in paragraph at lines 6595--6597 []\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th is works as a mul-ti-ple of <"/tmp/B.61K3e5/BUILD/R-3.5.2/build/library/graphics/help/figures/"pch.pdf, id= 29833, 361.35pt x 50.1875pt> Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639 [][] [917 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6732--6732 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [918] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6763--6763 [] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab = "", main = main)[] Underfull \vbox (badness 10000) has occurred while \output is active [919] [920] Underfull \hbox (badness 10000) in paragraph at lines 6885--6887 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr Overfull \hbox (15.18042pt too wide) in paragraph at lines 6912--6912 [] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b order = "red")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6918--6918 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [921] Underfull \hbox (badness 2600) in paragraph at lines 6978--6980 []\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/ pcr/m/n/10 "winding" \T1/ptm/m/n/10 or [922] [923] [924] Underfull \hbox (badness 1881) in paragraph at lines 7167--7172 []\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m /n/10 par("fg")\T1/ptm/m/n/10 . Use [925] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7210--7210 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [926] [927] [928] [929] [930] [931] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7597--7597 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7601--7601 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [932] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7613--7613 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [933] [934] [935] [936] [937] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7962--7962 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7965--7965 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] [938] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7969--7969 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [939] [940] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8140--8140 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...) Overfull \hbox (36.78088pt too wide) in paragraph at lines 8141--8141 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [941] [942] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8245--8245 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8256--8261 []\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1 /pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for [943] [944] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8364--8364 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035 , seg.lwd = .8)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8379--8379 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [945] [946] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8510--8510 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [947] [948] [949] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8695--8695 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] Underfull \hbox (badness 10000) in paragraph at lines 8723--8725 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8725--8727 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8757--8763 []\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr /m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m /n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing [950]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8805 \HeaderA{units}{Graphical Units}{units} [951] Underfull \hbox (badness 1205) in paragraph at lines 8870--8872 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [952] [953] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8989--8989 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 2, length = 0.1)[] [954]) (./grid-pkg.tex Chapter 6. [955] [956] [957] [958] [959] [960] Underfull \hbox (badness 10000) in paragraph at lines 385--391 \T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo r ex-am-ple, Underfull \hbox (badness 1024) in paragraph at lines 385--391 \T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f ault be-haviour for grobs is to [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1025--1025 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1027--1027 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1029--1029 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] Underfull \vbox (badness 10000) has occurred while \output is active [971] Underfull \hbox (badness 1430) in paragraph at lines 1074--1079 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [972] [973] [974] Underfull \hbox (badness 3219) in paragraph at lines 1288--1291 []\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject de-scrib-ing a cir-cle), but only [975] [976] [977] [978] [979] [980] [981] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1675--1675 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [982] [983] [984] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1889--1889 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla ck"), name="r1")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1890--1890 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey" ), name="r2")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1891--1891 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [985] Underfull \hbox (badness 2961) in paragraph at lines 1926--1931 []\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 , [986] Underfull \hbox (badness 1430) in paragraph at lines 1985--1990 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- Underfull \hbox (badness 4479) in paragraph at lines 2014--2017 []\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10 to al-low a grob to per-form cus-tom ac-tions and [987] [988] [989] Underfull \hbox (badness 2894) in paragraph at lines 2221--2228 []\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de -scrib-ing a frame), but only [990] [991] [992] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2377--2377 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] Underfull \hbox (badness 1430) in paragraph at lines 2389--2394 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [993] [994] [995] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2590--2590 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2622--2622 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [996] [997] [998] [999] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2864--2864 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [1000] [1001] [1002] [1003] [1004] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3179--3179 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1005] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3275--3275 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] [1006] Underfull \hbox (badness 2799) in paragraph at lines 3309--3315 []\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage " \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see [1007] [1008] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3401--3401 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3408--3408 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1009] [1010] [1011] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3602--3602 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3617--3617 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] Underfull \hbox (badness 1067) in paragraph at lines 4355--4358 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1025] Underfull \hbox (badness 1430) in paragraph at lines 4401--4406 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1026] [1027] [1028] Underfull \hbox (badness 7256) in paragraph at lines 4600--4602 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] Underfull \hbox (badness 10000) in paragraph at lines 5189--5191 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu -ments above are passed to [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] Underfull \hbox (badness 3449) in paragraph at lines 5877--5883 \T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1, "npc") - unit(1, "inches")\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 5877--5883 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1048] [1049] [1050] [1051] [1052] Underfull \hbox (badness 1867) in paragraph at lines 6187--6189 []\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or [1053] Underfull \hbox (badness 10000) in paragraph at lines 6224--6230 [][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV iewport[][][]\T1/ptm/m/n/10 , [1054] [1055] Underfull \hbox (badness 7649) in paragraph at lines 6356--6359 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like [1056] [1057] [1058] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6560--6560 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1059]) (./methods-pkg.tex [1060] Chapter 7. [1061] [1062] Underfull \hbox (badness 1688) in paragraph at lines 166--171 \T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c o-erce meth-ods work. Use [1063] [1064] [1065] Underfull \hbox (badness 1348) in paragraph at lines 392--395 [][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo r-ma-tion about group generic func-tions; [][]Meth- [1066] [1067] Overfull \hbox (15.18042pt too wide) in paragraph at lines 558--558 []\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall y a primitive.[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w ith no arguments[] [1068] Overfull \hbox (4.38043pt too wide) in paragraph at lines 619--619 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho ut arguments[] Underfull \vbox (badness 10000) has occurred while \output is active [1069] Overfull \hbox (25.98041pt too wide) in paragraph at lines 637--637 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th e default method[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 640--640 []\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b y callNextMethod[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the "B0" method[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 672--672 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[ ] Underfull \vbox (badness 10000) has occurred while \output is active [1070] [1071] Underfull \hbox (badness 1546) in paragraph at lines 791--797 []\T1/ptm/m/n/10 A ma-trix (or ma-trix like ob-ject) com-bin-ing the columns (o r rows) of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 . Note Underfull \hbox (badness 3780) in paragraph at lines 791--797 \T1/ptm/m/n/10 that meth-ods must con-struct [][]\T1/pcr/m/n/10 colnames[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 rownames[][][] \T1/ptm/m/n/10 from the co r-re-spond-ing col- Underfull \hbox (badness 1789) in paragraph at lines 791--797 \T1/ptm/m/n/10 umn and row names of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr /m/n/10 y \T1/ptm/m/n/10 (but not from de-pars-ing ar-gu-ment names such as in [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1794--1794 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N umber" method[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1796--1796 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE)) ) # the default[] Underfull \hbox (badness 10000) in paragraph at lines 1838--1840 []\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca lls [1085] [1086] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class [1087] [1088] [1089] Underfull \hbox (badness 1132) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/pcr/m/n/10 where = [1090] [1091] Underfull \hbox (badness 10000) in paragraph at lines 2328--2332 []\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od s dis-patch, call Overfull \hbox (6.78088pt too wide) in paragraph at lines 2360--2360 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F ALSE}:[] [1092] [1093] [1094] Underfull \hbox (badness 3792) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class Underfull \hbox (badness 1194) in paragraph at lines 2605--2609 []\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10 (a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and [1095] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2661--2661 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1096] [1097] [1098] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2880--2880 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1099] [1100] [1101] [1102] [1103] [1104] [1105] Underfull \hbox (badness 10000) in paragraph at lines 3403--3408 []\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu rns the im-plicit generic ver-sion, Underfull \hbox (badness 6268) in paragraph at lines 3403--3408 \T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \ T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents [1106] [1107] Underfull \hbox (badness 10000) in paragraph at lines 3531--3535 []\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class [1108] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Overfull \hbox (28.78088pt too wide) in paragraph at lines 3642--3651 [] [1109] [1110] Overfull \hbox (276.78088pt too wide) in paragraph at lines 3762--3763 [] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 Underfull \hbox (badness 10000) in paragraph at lines 3809--3810 []\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) { [1111] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3828--3829 []\T1/pcr/m/n/10 GPS <- setClass("GPS", slots = c(time = "POSIXt"), contains = "Pos") Overfull \hbox (120.78088pt too wide) in paragraph at lines 3846--3847 []\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") Underfull \hbox (badness 6157) in paragraph at lines 3908--3912 []\T1/ptm/m/n/10 A call to [][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) \T1/ ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to [1112] [1113] [1114] Underfull \hbox (badness 10000) in paragraph at lines 4135--4137 []\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method ex-ists for [1115] [1116] Underfull \hbox (badness 1629) in paragraph at lines 4247--4256 \T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is to mod-ify a field ex-plic-itly by [1117] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4308--4308 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4309--4309 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1118] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4366--4366 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here) [1119] [1120] Underfull \hbox (badness 1033) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T 1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si g-na-ture [1121] Underfull \hbox (badness 2126) in paragraph at lines 4574--4582 []\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the im-por-tant steps: ([][]\T1/pcr/m/n/10 setMethod[][][]()\T1/ptm/m/n/10 , [1122] [1123] [1124] Underfull \hbox (badness 10000) in paragraph at lines 4811--4820 []\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha t eval-u-ates a call to [1125] [1126] [1127] [1128] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5195--5195 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] [1129] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5223--5223 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli er fails here)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5237--5237 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho d for classB[] Underfull \vbox (badness 10000) has occurred while \output is active [1130] [1131] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1132] Underfull \hbox (badness 10000) in paragraph at lines 5463--5465 []\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t er-nally by [1133] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1134] [1135] [1136] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1137] Underfull \hbox (badness 10000) in paragraph at lines 5757--5761 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 5757--5761 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1138] Underfull \hbox (badness 10000) in paragraph at lines 5848--5852 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 5848--5852 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1139] [1140] [1141] [1142] Underfull \hbox (badness 10000) in paragraph at lines 6210--6226 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m /n/10 is equiv-a-lent to in-vok-ing the method [1143] [1144] Underfull \hbox (badness 1248) in paragraph at lines 6343--6347 []\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt m/m/n/10 method car-ries out its own com-pu-ta-tions, Underfull \hbox (badness 1960) in paragraph at lines 6343--6347 \T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per -form stan-dard ini-tial-iza-tion, as shown in the [1145] Underfull \hbox (badness 4647) in paragraph at lines 6498--6500 []\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func- tion re-turned by [1146] Underfull \hbox (badness 1072) in paragraph at lines 6575--6582 []\T1/ptm/m/n/10 Establish a traced ver-sion of method [1147] Underfull \hbox (badness 2875) in paragraph at lines 6647--6656 []\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen se as any S4 class (see Underfull \hbox (badness 1436) in paragraph at lines 6647--6656 [][]\T1/pcr/m/n/10 setValidity[][][]\T1/ptm/m/n/10 ). Such meth-ods are of-ten a good idea; they will be called by call-ing [1148] Underfull \vbox (badness 10000) has occurred while \output is active [1149] [1150] [1151]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1152] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7009--7009 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement version of as().[] Underfull \hbox (badness 2042) in paragraph at lines 7065--7072 \T1/ptm/m/n/10 i-nat-ing all the for-mally de-fined slots and turn-ing off the S4 bit of the ob-ject. With [1153] [1154] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7200--7200 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data = datasets::iris)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7204--7204 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con tains = "mlm")[] [1155]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com plex}) has been already used, duplicate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1156] Underfull \hbox (badness 6708) in paragraph at lines 7309--7321 []\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "cummax"\T1/ptm/m/n/10 , Underfull \hbox (badness 2012) in paragraph at lines 7309--7321 \T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr /m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 , Underfull \hbox (badness 3209) in paragraph at lines 7309--7321 \T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m /n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 , [1157] [1158] Underfull \hbox (badness 1694) in paragraph at lines 7472--7474 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see Underfull \hbox (badness 10000) in paragraph at lines 7496--7499 []\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup erClasses() \T1/ptm/m/n/10 which calls [1159] [1160] Underfull \hbox (badness 10000) in paragraph at lines 7663--7670 []\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method, \T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her- Underfull \hbox (badness 7704) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \ T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the Underfull \hbox (badness 10000) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about it, you'll prob-a-bly agree that you wouldn't Underfull \hbox (badness 5817) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/ n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus, Overfull \hbox (0.78088pt too wide) in paragraph at lines 7663--7670 \T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE )) [1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] Underfull \hbox (badness 1052) in paragraph at lines 8489--8496 []\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it [1172] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8622--8622 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(), [1173] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8697--8697 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1174] [1175] [1176] [1177] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8959--8959 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] [1178] [1179] [1180] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9167--9167 [] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns), "setCount")[] [1181] [1182] Underfull \vbox (badness 2277) has occurred while \output is active [1183] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9429--9429 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo rmal arguments[] [1184] [1185] [1186] [1187] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9737--9737 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre es of freedom[] [1188] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9847--9847 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1189] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9858--9858 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] Underfull \hbox (badness 10000) in paragraph at lines 10556--10558 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function " \T1/ptm/m/n/10 for class Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., Underfull \hbox (badness 1681) in paragraph at lines 10564--10568 \T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends [1199] [1200] [1201] [1202]) (./parallel-pkg.tex Chapter 8. Underfull \hbox (badness 2418) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr /m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1203] Underfull \hbox (badness 4242) in paragraph at lines 96--98 []\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \ T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for [1204] [1205] Underfull \hbox (badness 1024) in paragraph at lines 213--216 []\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10 for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and [1206] Underfull \hbox (badness 10000) in paragraph at lines 318--326 []\T1/ptm/m/n/10 On Sparc So-laris \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/1 0 re-turns the num-ber of phys-i-cal cores and [1207] [1208] Underfull \hbox (badness 10000) in paragraph at lines 443--445 []\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/ 10 Rscript \T1/ptm/m/n/10 such as [1209] [1210] [1211] [1212] Underfull \hbox (badness 1917) in paragraph at lines 742--751 []\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr /m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class Underfull \hbox (badness 1178) in paragraph at lines 742--751 \T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in -herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If [1213] [1214] Overfull \hbox (60.78088pt too wide) in paragraph at lines 824--824 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1215] Underfull \hbox (badness 10000) in paragraph at lines 884--887 []\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T 1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1 \T1/ptm/m/n/10 : for [1216] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1005--1005 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit y.list = affL)[] [1217] Overfull \hbox (63.78036pt too wide) in paragraph at lines 1009--1009 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1218] Underfull \hbox (badness 5388) in paragraph at lines 1119--1124 []\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1 /pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from Underfull \hbox (badness 10000) in paragraph at lines 1143--1151 []\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/ m/n/10 is dif-fer-ent only if [1219] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1180--1180 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] [1220] [1221] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1296--1296 [] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif (N, 1, 28)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1310--1310 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] Underfull \hbox (badness 1577) in paragraph at lines 1339--1342 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1222] Underfull \hbox (badness 3375) in paragraph at lines 1385--1387 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/ n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to [1223] [1224]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1225] [1226] [1227] [1228] [1229] [1230] [1231] Overfull \hbox (4.38043pt too wide) in paragraph at lines 492--492 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl ine = TRUE))[] [1232] [1233] [1234] [1235] Overfull \hbox (25.98041pt too wide) in paragraph at lines 706--706 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, sparse = TRUE)))[] [1236] [1237] [1238]) (./stats-pkg.tex Chapter 10. [1239] Underfull \hbox (badness 2781) in paragraph at lines 65--68 []\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 , [1240] [1241] [1242] [1243] [1244] Overfull \hbox (20.58041pt too wide) in paragraph at lines 417--417 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea rson Chi-square[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 438--438 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE) [1245] [1246] [1247] [1248] [1249] [1250] [1251] Underfull \hbox (badness 1024) in paragraph at lines 847--849 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm \T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] Underfull \hbox (badness 10000) in paragraph at lines 1391--1393 []\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu- ment [1260] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 \T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e r-ror strata of class Underfull \hbox (badness 1490) in paragraph at lines 1508--1512 \T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\ T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \ T1/ptm/m/n/10 meth-ods avail-able for [1261] [1262] [1263] [1264] Underfull \hbox (badness 10000) in paragraph at lines 1773--1777 []\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently, via Underfull \hbox (badness 2197) in paragraph at lines 1773--1777 \T1/pcr/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can han-dle miss- [1265] [1266] Underfull \hbox (badness 4303) in paragraph at lines 1874--1876 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 x \T1/ptm/m/n/10 con-tains miss-ing val-ues, see [][]\T1/pcr/m/n/10 NA[][][]\T1/ptm/m/n/10 , also con-sider us-ing [][]\T1/ pcr/m/n/10 arima[][][]()\T1/ptm/m/n/10 , pos-si-bly with [1267] [1268] [1269] Underfull \hbox (badness 10000) in paragraph at lines 2096--2101 []\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en- sure Underfull \hbox (badness 10000) in paragraph at lines 2096--2101 \T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo r Underfull \hbox (badness 1371) in paragraph at lines 2096--2101 \T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\ T1/ptm/m/n/10 , it has been ad-van-ta-geous Underfull \hbox (badness 1221) in paragraph at lines 2102--2108 []\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num -ber of pa- Underfull \hbox (badness 4608) in paragraph at lines 2102--2108 \T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied. [1270] [1271] Underfull \hbox (badness 3965) in paragraph at lines 2183--2185 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1272] [1273] [1274] Underfull \hbox (badness 1221) in paragraph at lines 2457--2462 []\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num -ber of pa- Underfull \hbox (badness 4608) in paragraph at lines 2457--2462 \T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied. [1275] Underfull \hbox (badness 3965) in paragraph at lines 2534--2536 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1276] [1277] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2679--2679 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1278] [1279] [1280] [1281] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2919--2919 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1282] [1283] [1284] Overfull \hbox (19.88992pt too wide) in paragraph at lines 3128--3130 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of variances"\T1/ptm/m/n/10 . [1285] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3176--3176 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3177--3177 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1286] Underfull \hbox (badness 2726) in paragraph at lines 3260--3276 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1287] [1288] [1289] [1290] [1291] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3568--3568 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1292] [1293] [1294] [1295] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3846--3846 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1296] [1297] [1298] [1299] [1300] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4135--4135 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4136--4136 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1301] [1302] [1303] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4374--4374 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1304] [1305] [1306] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4542--4542 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1307] Underfull \hbox (badness 3989) in paragraph at lines 4634--4641 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1308] [1309] Underfull \hbox (badness 2080) in paragraph at lines 4754--4756 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por t aliased co-ef-fi-cients (see [][]\T1/pcr/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b y de-fault where Underfull \hbox (badness 2050) in paragraph at lines 4757--4763 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 complete \T1/ptm/m/n/10 ar-gu-ment also ex- ists for com-pat-i-bil-ity with [][]\T1/pcr/m/n/10 vcov[][][] \T1/ptm/m/n/10 me th-ods, and \T1/pcr/m/n/10 coef Underfull \hbox (badness 4954) in paragraph at lines 4757--4763 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aov \T1/ptm/m/n/10 meth-ods for other classes should typ-i-cally also keep the \T1/pcr/m/n/10 complete = * Underfull \hbox (badness 4726) in paragraph at lines 4757--4763 \T1/ptm/m/n/10 be-hav-ior in sync. By that, with \T1/pcr/m/n/10 p <- length(coe f(obj, complete = TF))\T1/ptm/m/n/10 , [1310] [1311] [1312] [1313] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5019--5019 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1)) , ci = c(-1,-1))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5021--5021 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci = c(-0.9,0.1))[] [1314] Underfull \hbox (badness 7397) in paragraph at lines 5108--5112 []\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an ar-gu-ment to all these con-trast func-tions, how-ever Underfull \hbox (badness 7326) in paragraph at lines 5108--5112 \T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for [1315] [1316] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5242--5242 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5260--5260 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) Underfull \hbox (badness 2680) in paragraph at lines 5287--5289 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is given by [1317] Underfull \hbox (badness 10000) in paragraph at lines 5292--5294 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m /n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 , [1318] [1319] Underfull \hbox (badness 1436) in paragraph at lines 5470--5475 []\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i ng co-vari-ances Underfull \hbox (badness 1377) in paragraph at lines 5470--5475 \T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi -a-tion of) Underfull \hbox (badness 1448) in paragraph at lines 5470--5475 \T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \ T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/ n/10 , [1320] [1321] [1322] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5668--5668 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1323] Underfull \hbox (badness 1168) in paragraph at lines 5740--5745 []\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and [1324] [1325] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5835--5835 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1326] [1327] [1328] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6020--6020 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1329] [1330] Underfull \hbox (badness 10000) in paragraph at lines 6183--6188 []\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When [1331] [1332] [1333] Underfull \hbox (badness 5954) in paragraph at lines 6379--6381 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1334] Underfull \hbox (badness 2503) in paragraph at lines 6461--6464 []\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 5563) in paragraph at lines 6465--6467 []\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also Underfull \hbox (badness 1655) in paragraph at lines 6468--6473 \T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm /m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1 /phv/m/n/10 R \T1/ptm/m/n/10 3.1.2, [1335] Underfull \hbox (badness 7238) in paragraph at lines 6504--6507 [][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr am[][][] \T1/ptm/m/n/10 and [1336] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6539--6539 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, type = "tr")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6554--6554 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6569--6569 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1337] [1338] [1339] [1340] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6813--6813 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1341] [1342] Underfull \vbox (badness 10000) has occurred while \output is active [1343] [1344] [1345] [1346] Underfull \hbox (badness 10000) in paragraph at lines 7211--7215 \T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/ m/n/10 or [1347] Underfull \hbox (badness 6493) in paragraph at lines 7310--7313 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1348] [1349] Underfull \hbox (badness 10000) in paragraph at lines 7447--7450 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht tps : / / CRAN . R-[]project . org / view = [1350] [1351] [1352] [1353] [1354] [1355] Underfull \hbox (badness 10000) in paragraph at lines 7857--7862 []\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T 1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ..., [1356] [1357] Overfull \hbox (33.6622pt too wide) in paragraph at lines 7995--7997 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log = TRUE)\T1/ptm/m/n/10 . [1358] [1359] [1360] Underfull \hbox (badness 1210) in paragraph at lines 8212--8214 []\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b e sup-plied as named ar-gu-ments to [1361] [1362] [1363] [1364] [1365] [1366] [1367] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8687--8687 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link = "log")) # fails[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8690--8690 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1368] [1369] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8828--8828 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2), .90) # ~= 7e-9[] [1370] Underfull \hbox (badness 1859) in paragraph at lines 8867--8872 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\ T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned, i.e., if [1371] [1372] [1373] Underfull \hbox (badness 2865) in paragraph at lines 9113--9122 []\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/pcr/m/n/10 hybrid = TRUE\T1/ptm/m/n /10 , asymp-totic chi-squared prob-a-bil-i- Underfull \hbox (badness 1331) in paragraph at lines 9113--9122 \T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied ver-sion thereof) spec-i-fied by [1374] [1375] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9255--9255 [] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4 0k", "> 40k"),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 9256--9256 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1376] [1377] [1378] Overfull \hbox (61.88992pt too wide) in paragraph at lines 9435--9437 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1379] [1380] [1381] [1382] [1383] [1384] [1385] Underfull \hbox (badness 2443) in paragraph at lines 9888--9894 [][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment); [1386] [1387] [1388] Underfull \hbox (badness 3758) in paragraph at lines 10101--10104 []\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or [1389] [1390] [1391] [1392] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10337--10337 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10363--10368 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1393] Underfull \hbox (badness 4132) in paragraph at lines 10402--10406 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od [1394] Underfull \hbox (badness 10000) in paragraph at lines 10507--10510 []\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fitted.values \T1/ptm/m/n/10 and [1395] [1396] [1397] Underfull \hbox (badness 2142) in paragraph at lines 10711--10714 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ [1398] Underfull \hbox (badness 1708) in paragraph at lines 10792--10796 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1399] Underfull \hbox (badness 10000) in paragraph at lines 10834--10840 [][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, Underfull \hbox (badness 1418) in paragraph at lines 10872--10877 \T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \ T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (= [1400] [1401] Underfull \hbox (badness 2635) in paragraph at lines 11005--11008 \T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1 /pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1 0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th e [1402] [1403] [1404] Underfull \hbox (badness 1694) in paragraph at lines 11190--11193 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1337) in paragraph at lines 11209--11218 []\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate den-dro-gram is re-ordered ac-cord- Underfull \hbox (badness 3049) in paragraph at lines 11209--11218 \T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos ed by the den-dro-gram, by [1405] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11291--11291 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1406] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11324--11324 [] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 0.1),[] Underfull \hbox (badness 10000) in paragraph at lines 11337--11341 []\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p tm/m/n/10 (the de-fault) or [1407] [1408] [1409] Underfull \hbox (badness 7379) in paragraph at lines 11517--11520 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1410] [1411] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11656--11656 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11671 \aliasA{hat}{influence.measures}{hat} [1412] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11724--11724 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11736--11736 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] [1413] Underfull \hbox (badness 1062) in paragraph at lines 11785--11790 []\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther e to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1414] [1415] Underfull \hbox (badness 3623) in paragraph at lines 11956--11958 []\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max (50*.Machine$double.eps, 0.5e-28) \T1/ptm/m/n/10 if [1416] [1417] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12052--12052 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] [1418] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12145--12145 [] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label = "tobacco",[] [1419] Underfull \hbox (badness 10000) in paragraph at lines 12193--12196 []\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1 /ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is [1420] [1421] [1422] Underfull \hbox (badness 4441) in paragraph at lines 12388--12390 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12395--12397 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1423] Underfull \hbox (badness 4739) in paragraph at lines 12418--12420 []\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^ @ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by [1424] Underfull \hbox (badness 2753) in paragraph at lines 12487--12489 []\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https : / / bugs . r-[]project . org / bugzilla3 / [1425] [1426] Underfull \hbox (badness 1292) in paragraph at lines 12612--12616 \T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion \T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for [1427] Underfull \hbox (badness 10000) in paragraph at lines 12725--12727 []\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/ n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm /m/n/10 of Underfull \hbox (badness 2894) in paragraph at lines 12731--12735 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method Underfull \hbox (badness 1038) in paragraph at lines 12731--12735 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive ( or true), trac-ing in-for-ma-tion on the [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13438--13438 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1439] Underfull \hbox (badness 4518) in paragraph at lines 13481--13486 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1440] [1441] Underfull \hbox (badness 10000) in paragraph at lines 13680--13684 []\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/ 10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10 , [1442] [1443] [1444] Underfull \hbox (badness 6995) in paragraph at lines 13865--13867 [][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had [1445] [1446] Underfull \hbox (badness 1163) in paragraph at lines 14013--14021 \T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual s[][][]\T1/ptm/m/n/10 , [1447] [1448] Underfull \hbox (badness 4518) in paragraph at lines 14133--14138 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1449] [1450] Underfull \hbox (badness 10000) in paragraph at lines 14271--14275 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/pcr/m/n/10 (surface = Underfull \hbox (badness 7133) in paragraph at lines 14271--14275 \T1/pcr/m/n/10 "interpolate", statistics = "approximate")\T1/ptm/m/n/10 : shoul d the [1451] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14319--14319 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14320--14320 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1452] Underfull \hbox (badness 10000) in paragraph at lines 14375--14378 []\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g ent, Underfull \hbox (badness 1715) in paragraph at lines 14375--14378 \T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts [1453] [1454] [1455] [1456] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14663--14663 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14664--14664 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1457] Overfull \hbox (45.6622pt too wide) in paragraph at lines 14714--14716 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l og = TRUE)\T1/ptm/m/n/10 . Overfull \hbox (18.78088pt too wide) in paragraph at lines 14757--14757 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 2726) in paragraph at lines 15164--15167 []\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 , [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] Overfull \hbox (31.3804pt too wide) in paragraph at lines 15879--15879 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1476] [1477] Underfull \hbox (badness 1014) in paragraph at lines 16017--16022 \T1/ptm/m/n/10 those spec-i-fied in \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 which are re-cy-cled to the num-ber of data frame rows. Un-like [1478] Underfull \hbox (badness 1648) in paragraph at lines 16083--16085 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 2591) in paragraph at lines 16097--16106 \T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must sup-ply vari-ables with the same names as would Underfull \hbox (badness 3930) in paragraph at lines 16097--16106 \T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/ ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing [1479] Overfull \hbox (25.98041pt too wide) in paragraph at lines 16165--16165 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b = "contr.poly"))[] [1480] [1481] [1482] [1483] [1484] [1485] [1486] [1487] [1488] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16719--16719 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] [1489] [1490] [1491] Overfull \hbox (25.98041pt too wide) in paragraph at lines 16947--16947 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] Underfull \hbox (badness 2359) in paragraph at lines 17533--17535 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1501] Underfull \vbox (badness 10000) has occurred while \output is active [1502] Underfull \vbox (badness 10000) has occurred while \output is active [1503] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17705--17705 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1504] Underfull \hbox (badness 10000) in paragraph at lines 17785--17789 []\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m /n/10 b0 + [1505] [1506] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17865--17865 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17912--17912 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1507] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17959--17959 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1508] [1509] [1510] [1511] [1512] [1513] [1514] [1515] Underfull \hbox (badness 1248) in paragraph at lines 18450--18453 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1127) in paragraph at lines 18463--18467 \T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 1478) in paragraph at lines 18471--18475 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De -faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and [1516] Underfull \hbox (badness 2042) in paragraph at lines 18529--18531 []\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm /m/n/10 method; see com-po-nent [1517] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18635--18635 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] [1518] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18677--18677 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 18695--18695 []\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 18698--18698 []\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 18718--18718 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), [1519] Overfull \hbox (36.78088pt too wide) in paragraph at lines 18721--18721 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] Underfull \hbox (badness 2564) in paragraph at lines 18756--18767 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u- ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1 0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 , Underfull \hbox (badness 1082) in paragraph at lines 18756--18767 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately \T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm /m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa [1520] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18819--18819 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1521] [1522] [1523] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19044--19044 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1524] Underfull \hbox (badness 1337) in paragraph at lines 19120--19123 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1525] [1526] [1527] [1528] [1529] [1530] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19439--19439 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1531] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19527--19527 [] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist vs Leverage " * h[ii] / (1 - h[ii]))),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 19530--19530 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1532] Underfull \hbox (badness 3049) in paragraph at lines 19609--19613 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1533] [1534] [1535] [1536] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19857--19857 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 4779) in paragraph at lines 19864--19866 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19867--19870 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1537] Underfull \hbox (badness 1107) in paragraph at lines 19925--19927 []\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to [1538] Overfull \hbox (20.58041pt too wide) in paragraph at lines 19980--19980 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] [1539] Overfull \hbox (31.3804pt too wide) in paragraph at lines 19987--19987 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 1, y.intersp = 1)[] Underfull \hbox (badness 10000) in paragraph at lines 20037--20040 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/ m/n/10 which gives Underfull \hbox (badness 10000) in paragraph at lines 20037--20040 \T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for [1540] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20081--20081 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1541] [1542] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20206--20206 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1543] Underfull \hbox (badness 10000) in paragraph at lines 20269--20271 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1544] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20317--20317 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) Underfull \hbox (badness 10000) in paragraph at lines 20372--20374 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 poly(*, simple=TRUE)\T1/ptm/m/n/10 , \T1/pc r/m/n/10 polym(*, coefs=)\T1/ptm/m/n/10 , and [1545] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20409--20409 [] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or just poly():[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 20414--20414 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] Overfull \hbox (25.98041pt too wide) in paragraph at lines 21264--21264 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly equal typically[] [1559] Underfull \hbox (badness 6859) in paragraph at lines 21331--21338 [][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre dict.poly[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 21342--21348 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22080--22080 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1572] [1573] [1574] [1575] [1576] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22364--22364 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 22365--22365 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1577] [1578] [1579] [1580] [1581] Underfull \hbox (badness 1337) in paragraph at lines 22689--22695 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] Overfull \hbox (133.98029pt too wide) in paragraph at lines 23251--23251 [] \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1590] [1591] Underfull \hbox (badness 1028) in paragraph at lines 23392--23395 []\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/ pcr/m/n/10 write() \T1/ptm/m/n/10 and [1592] [1593] Underfull \hbox (badness 10000) in paragraph at lines 23502--23505 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 5091) in paragraph at lines 23502--23505 \T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for ef-fi-ciency if [1594] Underfull \hbox (badness 10000) in paragraph at lines 23557--23559 []\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 reorder[][][]()\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing Underfull \hbox (badness 10000) in paragraph at lines 23619--23621 []\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 relevel[][][]()\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [1595] [1596] Overfull \hbox (9.78043pt too wide) in paragraph at lines 23721--23721 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1597] [1598] [1599] Overfull \hbox (31.3804pt too wide) in paragraph at lines 23941--23941 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1600] [1601] [1602] Underfull \hbox (badness 10000) in paragraph at lines 24087--24090 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has Underfull \hbox (badness 2134) in paragraph at lines 24139--24143 [][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's end point rule and is called by de-fault from [1603] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24152--24152 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1604] [1605] [1606] [1607] [1608] [1609] [1610] Underfull \hbox (badness 6268) in paragraph at lines 24616--24621 [][]\T1/pcr/m/n/10 SSasympOrig[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSbiexp [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 SSfpl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSgompertz[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSmicmen[][][]\T1/ptm/m/n/10 , [1611] Overfull \hbox (58.38037pt too wide) in paragraph at lines 24644--24644 [] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As ym", "xmid", "scal")])[] [1612] [1613] Underfull \hbox (badness 1867) in paragraph at lines 24821--24823 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/pcr/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was [1614] Overfull \hbox (20.58041pt too wide) in paragraph at lines 24870--24870 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] [1615] [1616] [1617] Underfull \hbox (badness 2495) in paragraph at lines 25060--25069 []\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/ m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1 /ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en . [1618] Overfull \hbox (24.78088pt too wide) in paragraph at lines 25142--25142 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] Underfull \hbox (badness 1412) in paragraph at lines 25149--25151 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1619] Overfull \hbox (25.98041pt too wide) in paragraph at lines 25236--25236 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] [1620] Overfull \hbox (84.78088pt too wide) in paragraph at lines 25261--25261 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 25264--25264 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1621] Underfull \hbox (badness 10000) in paragraph at lines 25306--25311 []\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when Underfull \hbox (badness 2435) in paragraph at lines 25306--25311 \T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault ), the num-ber of [1622] Underfull \hbox (badness 2980) in paragraph at lines 25451--25453 []\T1/ptm/m/n/10 the value of \T1/pcr/m/n/10 spar \T1/ptm/m/n/10 com-puted or g iven, un-less it has been given as [1623] Overfull \hbox (18.78088pt too wide) in paragraph at lines 25487--25487 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / tol) ))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25536--25536 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] [1624] Overfull \hbox (47.58038pt too wide) in paragraph at lines 25557--25557 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] Underfull \vbox (badness 10000) has occurred while \output is active [1625] [1626] Overfull \hbox (15.18042pt too wide) in paragraph at lines 25661--25661 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"), sep = " = "),[] [1627] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25728--25728 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1628] [1629] [1630] [1631] [1632] [1633] Overfull \hbox (36.78088pt too wide) in paragraph at lines 26107--26107 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] Underfull \hbox (badness 6477) in paragraph at lines 26161--26164 []\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of an [1634] [1635] Overfull \hbox (31.3804pt too wide) in paragraph at lines 26292--26292 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c ol = 3, n = 1001)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 26293--26293 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] Underfull \vbox (badness 10000) has occurred while \output is active [1636] Underfull \hbox (badness 2922) in paragraph at lines 26362--26367 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1637] Overfull \hbox (9.78043pt too wide) in paragraph at lines 26399--26399 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim = c(-.3, 5),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 26402--26402 [] \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^ {-e^{phi[3]}*~x}}))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 26411--26411 [] \T1/pcr/m/n/9 c(0 , 1 ), 1, length = 0.08, angle = 25); text(0. 5, 1, quote(1))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26412--26412 [] \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3 # (Asym + R0)/2[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 26416--26416 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] [1638] Underfull \hbox (badness 2922) in paragraph at lines 26458--26463 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Underfull \hbox (badness 3240) in paragraph at lines 26470--26473 [][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][] []\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap h show-ing the \T1/pcr/m/n/10 SSasympOff Overfull \hbox (36.7804pt too wide) in paragraph at lines 26491--26491 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log( 0.4), c0 = 3/4)) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26494--26494 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1639] Underfull \hbox (badness 2922) in paragraph at lines 26544--26549 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1640] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26577--26577 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log (log(2)))) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26581--26581 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim = c(-1/4, 5),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 26591--26591 [] \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2), phi[1]), pos=0, las=1)[] Overfull \hbox (106.98032pt too wide) in paragraph at lines 26596--26596 [] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1641] Underfull \hbox (badness 2922) in paragraph at lines 26632--26638 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 26654--26654 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26670--26670 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] [1642] [1643] Overfull \hbox (30.78088pt too wide) in paragraph at lines 26784--26784 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1644] Underfull \hbox (badness 2922) in paragraph at lines 26846--26851 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1645] Overfull \hbox (69.18036pt too wide) in paragraph at lines 26884--26884 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] [1646] Underfull \hbox (badness 2922) in paragraph at lines 26933--26938 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 26964--26964 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = " red", lwd=2)[] [1647] Underfull \hbox (badness 2922) in paragraph at lines 26998--27003 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (25.98041pt too wide) in paragraph at lines 27023--27023 []\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number of iter...: 0" :[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 27027--27027 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR UE), trace = TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27047--27047 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] [1648] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27057--27057 [] \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0, 2.5,3.5), # NB. SSlogis(x = xmid = 2) = 2.5[] Underfull \hbox (badness 2922) in paragraph at lines 27092--27097 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1649] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27114--27114 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 27132--27132 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] [1650] Underfull \hbox (badness 6493) in paragraph at lines 27184--27189 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27211--27211 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27213--27213 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 27216--27216 []\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul l() fit to Chick.6")[] Overfull \hbox (69.18036pt too wide) in paragraph at lines 27219--27219 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1659] [1660] [1661] [1662] [1663] [1664] [1665] Underfull \hbox (badness 3396) in paragraph at lines 28143--28145 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10 , usu-ally, a re-sult of a call to [1666] [1667] [1668] Underfull \hbox (badness 2237) in paragraph at lines 28320--28322 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1669] [1670] Underfull \hbox (badness 2591) in paragraph at lines 28484--28486 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10 , usu-ally the re-sult of a call to [1671] Underfull \hbox (badness 2237) in paragraph at lines 28530--28533 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1672] Overfull \hbox (48.78088pt too wide) in paragraph at lines 28603--28603 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1673] [1674] Underfull \hbox (badness 3407) in paragraph at lines 28711--28715 []\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low) [1675] [1676] Underfull \hbox (badness 1337) in paragraph at lines 28844--28848 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1677] [1678] Underfull \hbox (badness 10000) in paragraph at lines 28961--28964 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for [1679] [1680] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29090--29090 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29118--29118 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1681] Underfull \hbox (badness 1616) in paragraph at lines 29144--29147 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1682] Overfull \hbox (20.58041pt too wide) in paragraph at lines 29223--29223 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1683] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29300--29300 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1684] Underfull \hbox (badness 5050) in paragraph at lines 29336--29341 []\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject is re-turned. The ob-ject it-self is the re-ordered (un-less [1685] Underfull \hbox (badness 2205) in paragraph at lines 29389--29394 []\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a [1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29984--29984 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE) [1694] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29985--29985 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1695] [1696] [1697] [1698] Underfull \hbox (badness 10000) in paragraph at lines 30274--30278 []\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect Underfull \hbox (badness 1596) in paragraph at lines 30274--30278 \T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign( f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at Overfull \hbox (30.78088pt too wide) in paragraph at lines 30285--30285 [] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con v = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30286--30286 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1699] [1700] Overfull \hbox (31.3804pt too wide) in paragraph at lines 30412--30412 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30421--30421 []\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[] [1701] [1702] [1703] [1704] Underfull \hbox (badness 1337) in paragraph at lines 30638--30642 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] Underfull \hbox (badness 1337) in paragraph at lines 31165--31169 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1713] Underfull \hbox (badness 1946) in paragraph at lines 31242--31247 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 (and \T1/pcr/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the Underfull \hbox (badness 5161) in paragraph at lines 31264--31266 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1714] [1715] [1716] [1717] [1718] Overfull \hbox (0.78088pt too wide) in paragraph at lines 31590--31590 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1719] Underfull \hbox (badness 6775) in paragraph at lines 31647--31652 []\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or [1720] Overfull \hbox (47.58038pt too wide) in paragraph at lines 31710--31710 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] [1721]) (./stats4-pkg.tex [1722] Chapter 11. [1723] [1724] [1725] Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192 [] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf)) , log = TRUE))[] [1726] [1727] [1728]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1729] Underfull \hbox (badness 10000) in paragraph at lines 440--443 []\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class [1730] [1731]) (./tcltk-pkg.tex [1732] Chapter 12. [1733] [1734] [1735] [1736] Overfull \hbox (4.38043pt too wide) in paragraph at lines 349--349 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback ref in here[] [1737] [1738] [1739] Underfull \vbox (badness 10000) has occurred while \output is active [1740] Underfull \hbox (badness 1292) in paragraph at lines 664--671 []\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing any Tk or Tcl com-mand by sim-ply run-ning [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] Underfull \hbox (badness 1189) in paragraph at lines 1407--1410 [][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1752]) (./tools-pkg.tex Chapter 13. [1753] Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for new methods.[] [1754] Underfull \hbox (badness 10000) in paragraph at lines 138--140 []\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion which will be eval-u-ated via Underfull \hbox (badness 1253) in paragraph at lines 164--167 []\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1755] Overfull \hbox (4.38043pt too wide) in paragraph at lines 215--215 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch ing warning)[] [1756] Underfull \hbox (badness 5147) in paragraph at lines 285--298 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 Underfull \hbox (badness 4792) in paragraph at lines 285--298 \T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1 0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou- Underfull \hbox (badness 2237) in paragraph at lines 285--298 \T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1 0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 , [1757] Overfull \hbox (42.78088pt too wide) in paragraph at lines 370--370 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta ngle = TRUE, Underfull \hbox (badness 2460) in paragraph at lines 389--391 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1758] [1759] [1760] [1761] [1762] [1763] [1764] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1765] [1766] Overfull \hbox (0.78088pt too wide) in paragraph at lines 901--901 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 956--956 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1767] [1768] Underfull \hbox (badness 1635) in paragraph at lines 1056--1058 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1769] Underfull \hbox (badness 5431) in paragraph at lines 1131--1134 []\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa ssed to Underfull \hbox (badness 4441) in paragraph at lines 1134--1144 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- [1770] Underfull \hbox (badness 1014) in paragraph at lines 1156--1158 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1162--1164 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1199--1202 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us- Underfull \hbox (badness 10000) in paragraph at lines 1199--1202 \T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p tm/m/n/10 and [1771] Underfull \hbox (badness 10000) in paragraph at lines 1207--1210 []\T1/pcr/m/n/10 check_packages_in_dir \T1/ptm/m/n/10 re-turns an ob-ject in-he r-it-ing from class [1772] [1773] Underfull \hbox (badness 10000) in paragraph at lines 1356--1359 []\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1 0 and Underfull \hbox (badness 10000) in paragraph at lines 1377--1379 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1774] [1775] [1776] [1777] [1778] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1679--1679 [] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking To"),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1682--1682 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1689--1694 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 1689--1694 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . [1779] [1780] [1781]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1782] [1783] [1784] [1785] Underfull \hbox (badness 1142) in paragraph at lines 2161--2167 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgRdMacros \T1/ptm/m/n/10 func-tion fi rst looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-ag e Overfull \hbox (101.58032pt too wide) in paragraph at lines 2195--2195 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1786] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2196--2196 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2223--2230 []\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user and site spe-cific com-pi-la- Underfull \hbox (badness 1102) in paragraph at lines 2223--2230 \T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1 0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com- Underfull \hbox (badness 4168) in paragraph at lines 2223--2230 \T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/ m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m /n/10 with [1787] Underfull \hbox (badness 1342) in paragraph at lines 2275--2281 \T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in [1788] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2351--2351 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb ose"))[] Underfull \hbox (badness 7981) in paragraph at lines 2364--2370 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 2364--2370 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . [1789] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2397--2397 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2406--2406 [] \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo ", "Suggests"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2423--2423 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1790] [1791] [1792] [1793] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2688--2688 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1794] Underfull \hbox (badness 2486) in paragraph at lines 2733--2741 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d efined macros may be given in a sep-a-rate file us-ing [1795] [1796] [1797] [1798] [1799] Underfull \hbox (badness 1072) in paragraph at lines 3111--3113 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to r of links, as re-turned by [1800] [1801] [1802] [1803] [1804] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3447--3447 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1805] [1806] [1807] [1808] Underfull \hbox (badness 4108) in paragraph at lines 3691--3698 []\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o n the loop-back in-ter-face [1809] [1810] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3791--3791 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3794--3794 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3811--3813 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , Underfull \hbox (badness 2932) in paragraph at lines 3828--3834 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1811] [1812] Underfull \hbox (badness 7832) in paragraph at lines 3950--3953 []\T1/ptm/m/n/10 Where sup-ported (\T1/pcr/m/n/10 texi2dvi \T1/ptm/m/n/10 5.0 a nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1813] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4025--4025 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] [1814] Underfull \hbox (badness 1137) in paragraph at lines 4048--4050 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1815] [1816] [1817] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4222--4222 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) Underfull \hbox (badness 10000) in paragraph at lines 4233--4236 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and Underfull \hbox (badness 6859) in paragraph at lines 4249--4254 []\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/ m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p tm/m/n/10 ' are up-dated from Underfull \hbox (badness 1184) in paragraph at lines 4257--4263 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po /\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T he Underfull \hbox (badness 2941) in paragraph at lines 4257--4263 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t he pack-age are ex-am-ined to cre-ate a file [1818] Underfull \hbox (badness 10000) in paragraph at lines 4337--4342 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De pendsList Underfull \hbox (badness 10000) in paragraph at lines 4337--4342 \T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i- fied (for in-stance if Underfull \hbox (badness 10000) in paragraph at lines 4337--4342 \T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1 /ptm/m/n/10 ', it would only re-turn [1819] [1820] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4469--4469 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4470--4470 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz")[] Underfull \hbox (badness 3240) in paragraph at lines 4482--4485 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ', [1821] Underfull \hbox (badness 1742) in paragraph at lines 4486--4496 \T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 , Underfull \hbox (badness 1127) in paragraph at lines 4521--4527 []\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4521--4527 \T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file , and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1 0 ', Underfull \hbox (badness 1571) in paragraph at lines 4549--4553 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1822] [1823] [1824]) (./utils-pkg.tex Chapter 14. Underfull \hbox (badness 1072) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [1825] [1826] [1827] Underfull \hbox (badness 6316) in paragraph at lines 212--216 []\T1/pcr/m/n/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for a si m-i-lar task to \T1/pcr/m/n/10 apropos\T1/ptm/m/n/10 . By de-fault [1828] Overfull \hbox (4.38043pt too wide) in paragraph at lines 256--256 []\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with these names[] [1829] Overfull \hbox (60.78088pt too wide) in paragraph at lines 370--370 [] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No ", "Cancel"))),[] [1830] [1831] [1832] Underfull \hbox (badness 1946) in paragraph at lines 527--531 \T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org / archive / 2011-[]2 / RJournal _ 2011-[]2 _ Overfull \hbox (0.78088pt too wide) in paragraph at lines 577--577 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc es"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 583--583 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 584--584 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 585--585 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] [1833] Overfull \hbox (0.78088pt too wide) in paragraph at lines 586--586 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Underfull \hbox (badness 10000) in paragraph at lines 620--626 []\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10 , \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 4416) in paragraph at lines 620--626 \T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_ package_C_files \T1/ptm/m/n/10 per-form spell check- [1834] Overfull \hbox (0.78088pt too wide) in paragraph at lines 689--689 [] \T1/pcr/m/n/10 ignore_repo_cache = FALSE, max_repo_cache _age,[] [1835] Underfull \hbox (badness 4505) in paragraph at lines 753--759 \T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][](" available_packages_filters") \T1/ptm/m/n/10 and to [1836] Underfull \hbox (badness 1603) in paragraph at lines 870--876 \T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/ pcr/m/n/10 infile \T1/ptm/m/n/10 starts Underfull \hbox (badness 3029) in paragraph at lines 870--876 \T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 -- \T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are [1837] Overfull \hbox (6.78088pt too wide) in paragraph at lines 927--927 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1838] Underfull \hbox (badness 1817) in paragraph at lines 992--999 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1003--1005 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1839] [1840] Underfull \hbox (badness 10000) in paragraph at lines 1111--1114 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1841] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1194--1194 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1842] [1843] [1844] [1845] [1846] Underfull \hbox (badness 1859) in paragraph at lines 1565--1574 []\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b e quite large the com- [1847] [1848] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1666--1666 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] [1849] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1701--1701 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1850] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1847--1847 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1851] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1867--1867 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, Overfull \hbox (6.78088pt too wide) in paragraph at lines 1919--1919 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1852] Underfull \hbox (badness 2213) in paragraph at lines 1953--1956 []\T1/pcr/m/n/10 ind \T1/ptm/m/n/10 chooses a row in the list of cur-rent mir-r ors, by num-ber. It is best used with [1853] [1854] Underfull \hbox (badness 10000) in paragraph at lines 2054--2056 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via Overfull \hbox (36.7804pt too wide) in paragraph at lines 2088--2088 [] \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] [1855] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2111--2111 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] Underfull \hbox (badness 5189) in paragraph at lines 2156--2158 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1856] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2231--2231 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1857] Underfull \hbox (badness 1082) in paragraph at lines 2305--2309 [][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files; [1858] Underfull \hbox (badness 10000) in paragraph at lines 2342--2344 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see Underfull \hbox (badness 1057) in paragraph at lines 2374--2381 \T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w hen [1859] [1860] [1861] Underfull \hbox (badness 10000) in paragraph at lines 2563--2565 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1862] [1863] [1864] [1865] Underfull \hbox (badness 10000) in paragraph at lines 2800--2804 []\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m /n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us- ing Underfull \hbox (badness 5203) in paragraph at lines 2800--2804 [][]\T1/pcr/m/n/10 read.table[][][](..., header = TRUE, as.is=FALSE)\T1/ptm/m/n /10 , and hence re-sult in a Overfull \hbox (133.10922pt too wide) in paragraph at lines 2805--2808 []\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr /m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][ ](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2854--2857 []\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re c-tory of the cur-rent work-ing di-rec-tory, set [1866] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2926--2926 []\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m /n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] [1867] Underfull \hbox (badness 2452) in paragraph at lines 3002--3005 []\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1 /pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources [1868] [1869] [1870] [1871] [1872] [1873] [1874] Underfull \hbox (badness 1072) in paragraph at lines 3484--3492 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [1875] Underfull \hbox (badness 1231) in paragraph at lines 3533--3539 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 3540--3545 []\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method = "libcurl"\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 7595) in paragraph at lines 3540--3545 \T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1 0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents of Underfull \hbox (badness 1331) in paragraph at lines 3540--3545 \T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in brack-ets are op-tional. See [1876] [1877] Underfull \hbox (badness 4660) in paragraph at lines 3662--3665 \T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/ 10 which makes an in-ter-nal call to Underfull \hbox (badness 10000) in paragraph at lines 3686--3688 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down load.file[][][] \T1/ptm/m/n/10 and [1878] [1879] [1880] Underfull \hbox (badness 1565) in paragraph at lines 3871--3875 []\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of Underfull \hbox (badness 10000) in paragraph at lines 3892--3898 []\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i- nal ob-ject if [1881] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3954--3954 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] Overfull \hbox (2.55087pt too wide) in paragraph at lines 3982--3989 \T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n /10 . [1882] [1883] [1884] [1885] [1886] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4309--4309 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1887]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4380 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4380 ...mat Unordered and Ordered Lists}{format} [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901] [1902] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5333--5333 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [1903] Underfull \hbox (badness 10000) in paragraph at lines 5417--5419 []\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[] project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also [1904] Underfull \hbox (badness 1502) in paragraph at lines 5466--5471 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 5466--5471 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1905] [1906] [1907] Underfull \hbox (badness 10000) in paragraph at lines 5639--5648 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, Underfull \hbox (badness 10000) in paragraph at lines 5639--5648 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 ', which can be re-made by [1908] Underfull \hbox (badness 2150) in paragraph at lines 5702--5705 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See Underfull \hbox (badness 5175) in paragraph at lines 5718--5721 []\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search database for sub-se-quent use by [1909] [1910] Underfull \hbox (badness 3118) in paragraph at lines 5839--5841 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for Underfull \hbox (badness 2409) in paragraph at lines 5872--5876 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1911] Underfull \hbox (badness 5091) in paragraph at lines 5976--5978 []\T1/ptm/m/n/10 download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1 /ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL [1912] Overfull \hbox (44.55087pt too wide) in paragraph at lines 5992--5997 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . Overfull \hbox (48.30977pt too wide) in paragraph at lines 6005--6012 []\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", " Imports", "LinkingTo", "Suggests") [1913] Underfull \hbox (badness 10000) in paragraph at lines 6063--6066 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 6063--6066 \T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack -age in-stall. E.g., Underfull \hbox (badness 10000) in paragraph at lines 6122--6126 []\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T 1/ptm/m/n/10 , [1914] Underfull \hbox (badness 2376) in paragraph at lines 6136--6143 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1 0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6136--6143 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 6136--6143 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1314) in paragraph at lines 6195--6202 []\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from [1915] Underfull \hbox (badness 10000) in paragraph at lines 6236--6241 [][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][ ][]\T1/ptm/m/n/10 , Overfull \hbox (25.98041pt too wide) in paragraph at lines 6259--6259 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] [1916] Underfull \hbox (badness 5133) in paragraph at lines 6295--6299 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each pack-age's Underfull \hbox (badness 1983) in paragraph at lines 6309--6312 []\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along Overfull \hbox (9.78043pt too wide) in paragraph at lines 6356--6356 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [1917] [1918] Underfull \hbox (badness 4132) in paragraph at lines 6475--6477 []\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at [1919] [1920] [1921] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6633--6633 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [1922] [1923] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6776--6776 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [1924] Underfull \hbox (badness 10000) in paragraph at lines 6816--6818 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1925] [1926] Underfull \hbox (badness 10000) in paragraph at lines 6957--6959 []\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if Underfull \hbox (badness 10000) in paragraph at lines 6962--6964 []\T1/ptm/m/n/10 typically the re-sult of \T1/pcr/m/n/10 methods(..)\T1/ptm/m/n /10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class [1927] [1928] [1929] Underfull \hbox (badness 1859) in paragraph at lines 7185--7188 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by [1930] Underfull \hbox (badness 1655) in paragraph at lines 7267--7270 []\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db" \T1/ptm/m/n/10 , with [][]\T1/pcr/m/n/10 attributes[][][] "package" \T1/ptm/m/n /10 (and [1931] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7278--7278 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre pl("PR#", Text),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7282--7282 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 7290--7290 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [1932] Underfull \hbox (badness 10000) in paragraph at lines 7375--7379 []\T1/ptm/m/n/10 For all stan-dards, \T1/pcr/m/n/10 unit = "auto" \T1/ptm/m/n/1 0 is also al-lowed. If [1933] [1934] [1935] [1936] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7639--7639 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 7640--7640 [] \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/ %d/%y"),[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 7641--7641 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] [1937] Underfull \hbox (badness 10000) in paragraph at lines 7669--7671 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/pcr /m/n/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 7683--7685 []\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 1259) in paragraph at lines 7691--7696 []\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [1938] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7737--7737 [] \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an d "stats" are[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7738--7738 [] \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[] [1939] [1940] Underfull \hbox (badness 10000) in paragraph at lines 7867--7872 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 7867--7872 [][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els Underfull \hbox (badness 10000) in paragraph at lines 7874--7877 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 7874--7877 [][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els [1941] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7990--7990 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7991--7991 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [1942] [1943] [1944] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8162--8162 [] \T1/pcr/m/n/9 "S original, "),[] [1945] Underfull \hbox (badness 1789) in paragraph at lines 8285--8287 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [1946] Underfull \hbox (badness 10000) in paragraph at lines 8343--8347 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8343--8347 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1947] [1948] Underfull \hbox (badness 10000) in paragraph at lines 8458--8462 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8458--8462 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1949] Underfull \hbox (badness 10000) in paragraph at lines 8523--8527 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8523--8527 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1950] [1951] [1952] [1953] Underfull \hbox (badness 5203) in paragraph at lines 8854--8857 []\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 ex-trac-tor are de-ter-mined by the generic func-tion [1954] [1955] [1956] Underfull \hbox (badness 1776) in paragraph at lines 9080--9087 []\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o f pieces of code, you should set [1957] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9104--9104 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [1958] [1959] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9265--9265 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [1960] [1961] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9446--9446 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 456 98 76 54[] [1962] [1963] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9532--9532 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9535--9535 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 9540--9540 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [1964] Underfull \hbox (badness 1077) in paragraph at lines 9612--9615 []\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL [1965] [1966] [1967] [1968] [1969] [1970] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10052--10052 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [1971] Underfull \hbox (badness 10000) in paragraph at lines 10139--10141 []\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/ m/n/10 in-stead of the de-fault one, use [1972] [1973] Underfull \hbox (badness 2181) in paragraph at lines 10262--10266 []\T1/pcr/m/n/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/pcr/m/n /10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10262--10266 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 10000) in paragraph at lines 10274--10278 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s&oldid = 78252134$[][]\T1/ptm/m/n/10 . [1974] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10292--10292 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10296--10296 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [1975] [1976] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10428--10428 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [1977] Underfull \hbox (badness 1917) in paragraph at lines 10551--10554 []\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari- Underfull \hbox (badness 4328) in paragraph at lines 10551--10554 \T1/ptm/m/n/10 able \T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES\T1/ptm/m/n/10 . If this is set, then it takes prece-dence over [1978] Overfull \hbox (106.98032pt too wide) in paragraph at lines 10574--10574 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] [1979] Underfull \hbox (badness 8075) in paragraph at lines 10637--10639 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\ T1/ptm/m/n/10 s are nicely viewed via [1980] Underfull \hbox (badness 6725) in paragraph at lines 10687--10696 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \ T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first, Underfull \hbox (badness 6428) in paragraph at lines 10687--10696 \T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i- Underfull \hbox (badness 10000) in paragraph at lines 10687--10696 \T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for re-verse al-pha-bet-i-cal or-der, Underfull \hbox (badness 1997) in paragraph at lines 10687--10696 \T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/ n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or [1981] Underfull \hbox (badness 3646) in paragraph at lines 10813--10815 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software / [1982] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10851--10851 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [1983] [1984] [1985] Underfull \hbox (badness 10000) in paragraph at lines 11032--11036 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no w taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 11063--11069 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [1986] Underfull \hbox (badness 2012) in paragraph at lines 11158--11164 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments for fig-ures should be auto-generated. Use [1987] Underfull \hbox (badness 2096) in paragraph at lines 11171--11173 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether EPS fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 2698) in paragraph at lines 11174--11176 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh ether PDF fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 11181--11184 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1067) in paragraph at lines 11185--11188 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether JPEG fig-ures should be gen-er-ated. Ig-nored if Overfull \hbox (6.78088pt too wide) in paragraph at lines 11239--11239 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] [1988] Underfull \hbox (badness 1009) in paragraph at lines 11257--11268 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [1989] Underfull \hbox (badness 2846) in paragraph at lines 11344--11354 \T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault [1990] [1991] Underfull \hbox (badness 10000) in paragraph at lines 11483--11486 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10 R \T1/ptm/m/n/10 was built un- Underfull \hbox (badness 10000) in paragraph at lines 11483--11486 \T1/ptm/m/n/10 der. Where sub-architectures are in use this is of the form Underfull \hbox (badness 10000) in paragraph at lines 11500--11503 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [1992] Underfull \hbox (badness 2158) in paragraph at lines 11579--11582 []\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe -cially: the value is taken from the cur-rent set-ting of [1993] [1994] [1995] Underfull \hbox (badness 3333) in paragraph at lines 11759--11761 []\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file- [1996] [1997] Overfull \hbox (42.78088pt too wide) in paragraph at lines 11924--11924 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] [1998] Underfull \hbox (badness 5970) in paragraph at lines 11957--11960 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive Underfull \hbox (badness 2600) in paragraph at lines 11957--11960 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less Underfull \hbox (badness 1052) in paragraph at lines 11968--11977 \T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][][]\T1/ptm/m/n/10 ) which de-f aults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons ; [1999] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12012--12012 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12043--12043 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo ng" non-ASCII:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12050--12050 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se e 1 (in UTF-8!):[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 12052--12052 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [2000] [2001] [2002] Underfull \hbox (badness 10000) in paragraph at lines 12220--12222 []\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/ 10 ap-ply only to files pro-duced by [2003] [2004] Underfull \hbox (badness 4492) in paragraph at lines 12377--12384 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in Underfull \hbox (badness 6252) in paragraph at lines 12377--12384 \T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/ n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 2452) in paragraph at lines 12377--12384 \T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 ( with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and [2005] [2006] [2007] Underfull \hbox (badness 2020) in paragraph at lines 12539--12555 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl at-forms), Underfull \hbox (badness 1194) in paragraph at lines 12539--12555 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s im-i-lar) and on Win-dows [2008] Underfull \hbox (badness 2809) in paragraph at lines 12659--12663 []\T1/ptm/m/n/10 NetBSD prior to 8.0 used flag `\T1/pcr/m/n/10 --xz\T1/ptm/m/n/ 10 ' rather than `\T1/pcr/m/n/10 -J\T1/ptm/m/n/10 ', so this should be used \T1 /ptm/m/it/10 via Underfull \hbox (badness 1596) in paragraph at lines 12659--12663 \T1/pcr/m/n/10 extra_flags = "--xz" \T1/ptm/m/n/10 rather than \T1/pcr/m/n/10 c ompression = "xz"\T1/ptm/m/n/10 . The com-mands from Underfull \hbox (badness 5022) in paragraph at lines 12674--12678 []\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl e Underfull \hbox (badness 10000) in paragraph at lines 12681--12684 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs . Underfull \hbox (badness 10000) in paragraph at lines 12681--12684 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml#tag _ 20 _ [2009] [2010] [2011] Overfull \hbox (18.78088pt too wide) in paragraph at lines 12846--12846 [] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss "), ...)[] [2012] [2013] [2014] [2015] [2016] [2017] Overfull \hbox (6.78088pt too wide) in paragraph at lines 13230--13230 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 13236--13236 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Underfull \hbox (badness 4467) in paragraph at lines 13257--13259 []\T1/ptm/m/n/10 Download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1 /ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL Underfull \hbox (badness 4660) in paragraph at lines 13270--13274 \T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/ 10 which makes an in-ter-nal call to Overfull \hbox (36.87935pt too wide) in paragraph at lines 13284--13288 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 13290--13295 []\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T 1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be Underfull \hbox (badness 10000) in paragraph at lines 13290--13295 \T1/ptm/m/n/10 passed to [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 and \T1/pcr/m/n/10 ignore_repo_cache\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13290--13295 \T1/pcr/m/n/10 max_repo_cache_age \T1/ptm/m/n/10 and \T1/pcr/m/n/10 noCache \T1 /ptm/m/n/10 to [][]\T1/pcr/m/n/10 available.packages[][][] [2018] Underfull \hbox (badness 1052) in paragraph at lines 13296--13298 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 13326--13331 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined see Underfull \hbox (badness 10000) in paragraph at lines 13326--13331 [][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai lable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 10000) in paragraph at lines 13326--13331 \T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1 /ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 13347--13352 []\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/ 10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with Underfull \hbox (badness 10000) in paragraph at lines 13355--13358 [][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[] [][]\T1/ptm/m/n/10 , [2019] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13409--13409 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c sb/ch3a.txt") [2020] [2021] [2022] Underfull \hbox (badness 10000) in paragraph at lines 13597--13600 [][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi- gnette browser; Overfull \hbox (42.18039pt too wide) in paragraph at lines 13613--13613 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[] [2023] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13680--13680 [] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d ata = DAT)))[] [2024] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13702--13702 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 13721--13721 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2025] Underfull \hbox (badness 1454) in paragraph at lines 13748--13752 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, Underfull \hbox (badness 1715) in paragraph at lines 13773--13776 []\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 13818--13820 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion [2026] Underfull \hbox (badness 3271) in paragraph at lines 13830--13834 \T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1 /ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if [2027] [2028]) [2029] [2030] (./KernSmooth-pkg.tex Chapter 15. [2031] Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat e = TRUE) [2032] [2033] [2034] [2035] [2036] Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun = 0.05, [2037] [2038] [2039] [2040]) (./MASS-pkg.tex Chapter 16. [2041] [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] Overfull \hbox (20.58041pt too wide) in paragraph at lines 774--774 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b eav2$hours/24))[] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] Underfull \hbox (badness 7256) in paragraph at lines 1604--1606 []\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo r [2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2412--2412 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2416--2416 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] [2075] [2076] [2077] [2078] Underfull \hbox (badness 6559) in paragraph at lines 2694--2697 []\T1/ptm/m/n/10 further ar-gu-ments for \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 and graph-i-cal pa-ram-e-ters. Note that [2079] [2080] [2081] Underfull \hbox (badness 10000) in paragraph at lines 2864--2869 \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "geometric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/pt m/m/n/10 , Underfull \hbox (badness 8189) in paragraph at lines 2864--2869 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "negative binomial"\T1 /ptm/m/n/10 , \T1/pcr/m/n/10 "normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Poisson"\ T1/ptm/m/n/10 , Underfull \hbox (badness 3557) in paragraph at lines 2900--2908 []\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start -ing val-ues will be com-puted if Underfull \hbox (badness 3118) in paragraph at lines 2900--2908 \T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied: \T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , [2082] [2083] Underfull \hbox (badness 4686) in paragraph at lines 3032--3034 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds Underfull \hbox (badness 1515) in paragraph at lines 3046--3050 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n /10 cycles \T1/ptm/m/n/10 terms or when a [2084] [2085] [2086] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3227--3227 [] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL SE, ...)[] Underfull \hbox (badness 5817) in paragraph at lines 3234--3236 []\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1 0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with [2087] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3357--3357 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist = "exponential")[] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097] [2098] [2099] Underfull \hbox (badness 1845) in paragraph at lines 4143--4145 []\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm /m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and [2100] [2101] [2102] [2103] [2104] [2105] [2106] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4639--4639 [] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n", ...)[] [2107] [2108] Underfull \hbox (badness 10000) in paragraph at lines 4791--4794 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2109] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4861--4861 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, Underfull \hbox (badness 10000) in paragraph at lines 4869--4872 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2110] [2111] [2112] [2113] [2114] Underfull \hbox (badness 5681) in paragraph at lines 5269--5271 []\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/ n/10 . This is over-ridden if Underfull \hbox (badness 5022) in paragraph at lines 5273--5276 []\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_ \OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10 \OT1/cmr/m/n/10 ()$ \ T1/ptm/m/n/10 func-tions when [2115] Underfull \hbox (badness 1975) in paragraph at lines 5322--5324 []\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in the case of [2116] [2117] [2118] [2119] [2120] [2121] [2122] [2123] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5908--5908 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP ACK = FALSE) [2124] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5969--5969 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/ 10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") [2125] [2126]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.npk}) has been already used, duplicate ignored \relax l.6111 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica te ignored \relax l.6111 ...sical N, P, K Factorial Experiment}{npk} [2127] Underfull \hbox (badness 1783) in paragraph at lines 6229--6233 []\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space. That is [2128] [2129] [2130] [2131] Underfull \vbox (badness 10000) has occurred while \output is active [2132] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6527--6527 [] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb ose = TRUE)))[] [2133] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6615--6615 [] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr ellis"))[] [2134] [2135] [2136] [2137] [2138] [2139] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7054--7054 []\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100 , A=10, B=1))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7071--7071 [] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c auchit"))[] Underfull \hbox (badness 10000) in paragraph at lines 7078--7085 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2140] Underfull \hbox (badness 10000) in paragraph at lines 7094--7096 []\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat Underfull \hbox (badness 3138) in paragraph at lines 7149--7155 []\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c mr/m/n/10 ) = [2141] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7219--7219 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2142] [2143] Underfull \hbox (badness 5091) in paragraph at lines 7328--7331 \T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na nt com-po-nents are used (ex-cept for [2144] [2145] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7458--7458 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam p = "exact")[] [2146] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7523--7523 [] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC V"), ...)[] [2147] [2148] [2149] [2150] [2151] [2152] Underfull \hbox (badness 4686) in paragraph at lines 7961--7963 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds Underfull \hbox (badness 1515) in paragraph at lines 7977--7981 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n /10 cycles \T1/ptm/m/n/10 terms or when a [2153] [2154] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8080--8080 [] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control = NULL)[] Underfull \hbox (badness 1590) in paragraph at lines 8104--8108 []\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n /10 NA\T1/ptm/m/n/10 s are found. The [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9483--9483 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS E, ...)[] [2175] Underfull \hbox (badness 1158) in paragraph at lines 9610--9613 []\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10 "Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly), [2176] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9692--9692 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub le.eps^0.25) Overfull \hbox (30.78088pt too wide) in paragraph at lines 9694--9694 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double .eps^0.25,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9697--9697 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub le.eps^0.25)[] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189]) (./Matrix-pkg.tex [2190] Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 41--44 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 41--44 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2191] Underfull \hbox (badness 1769) in paragraph at lines 95--98 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2192] Underfull \hbox (badness 2229) in paragraph at lines 159--162 []\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm /m/n/10 ob-jects; here, when the first is Underfull \hbox (badness 1147) in paragraph at lines 159--162 \T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th ese ar-gu-ments will be con-cate-nated to a new [2193] Underfull \hbox (badness 10000) in paragraph at lines 257--260 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 263--265 []\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][ ]sparseVector[][][]"\T1/ptm/m/n/10 's, see [2194] [2195] Overfull \hbox (42.78088pt too wide) in paragraph at lines 488--488 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp arse = TRUE) Underfull \hbox (badness 5147) in paragraph at lines 495--498 []\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal mean-ing as in [2196] Underfull \hbox (badness 5119) in paragraph at lines 508--512 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class Underfull \hbox (badness 4621) in paragraph at lines 512--516 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m /n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a Overfull \hbox (4.38043pt too wide) in paragraph at lines 535--535 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 537--537 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 546--546 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c( 1:3,2:3,3:2)],[] [2197] [2198] Overfull \hbox (52.98038pt too wide) in paragraph at lines 660--660 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd iag() -- for the case of *many* (k x k) matrices:[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(, , ....., ) where each mat_j is a k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 matrix\TS1/pcr/m/n/9 '[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 662--662 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k) matrix of class \code{"\linkS4class{dgCMatrix}"}.[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 675--675 [] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \ T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri x indexing), but elegant?[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 676--676 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 681--681 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim plify=FALSE)[] [2199] Underfull \hbox (badness 3189) in paragraph at lines 732--736 []\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib . [2200] [2201] [2202] Overfull \hbox (72.78088pt too wide) in paragraph at lines 947--947 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2203] Underfull \hbox (badness 10000) in paragraph at lines 1022--1024 []\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n /10 (or equiv-a- Underfull \hbox (badness 10000) in paragraph at lines 1045--1050 []\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of the lower tri- Underfull \hbox (badness 10000) in paragraph at lines 1045--1050 \T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the de-com-po-si-tion. This method is equiv-a-lent to Underfull \hbox (badness 1092) in paragraph at lines 1045--1050 \T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in the above de-scrip-tion of Underfull \hbox (badness 10000) in paragraph at lines 1068--1075 []\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm = "logical") [2204]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho l}) has been already used, duplicate ignored \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic ate ignored \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} [2205pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha s been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' pdfTeX warning (ext4): destina tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' pdfTeX warning (ext4): destina tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' ] [2206] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1266--1266 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2207] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1360--1360 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) Underfull \hbox (badness 2277) in paragraph at lines 1388--1391 []\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer -ent types of ma-tri-ces. Use [2208] Underfull \hbox (badness 1609) in paragraph at lines 1435--1439 []\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion [] []\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra [2209] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so me GOTOblas:[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1476--1476 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 , sep="") ## dQuote() gives bad plots[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1484--1484 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE) , super = c(FALSE,TRUE)))[] [2210] Underfull \hbox (badness 6445) in paragraph at lines 1531--1538 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("Cholesky", ...) \T1/ptm/m/n/10 or Underfull \hbox (badness 3861) in paragraph at lines 1531--1538 \T1/pcr/m/n/10 new("BunchKaufman", ...)\T1/ptm/m/n/10 , etc, or rather by calls of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or Underfull \hbox (badness 1783) in paragraph at lines 1566--1570 []\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1 /ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend Underfull \hbox (badness 1221) in paragraph at lines 1582--1588 \T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and [2211]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col Sums}) has been already used, duplicate ignored \relax l.1623 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup licate ignored \relax l.1623 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl icate ignored \relax l.1624 \aliasA{colMeans}{colSums}{colMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i gnored \relax l.1645 \aliasA{rowMeans}{colSums}{rowMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig nored \relax l.1656 \aliasA{rowSums}{colSums}{rowSums} [2212] Underfull \hbox (badness 2922) in paragraph at lines 1710--1714 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i n-her-it-ing from Underfull \hbox (badness 1728) in paragraph at lines 1710--1714 \T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a Underfull \hbox (badness 1237) in paragraph at lines 1721--1724 [][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1 /pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10 v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since [2213] Underfull \hbox (badness 10000) in paragraph at lines 1801--1805 []\T1/pcr/m/n/10 signature(x = "compMatrix", value = "list")\T1/ptm/m/n/10 : se t the [2214] Underfull \hbox (badness 3547) in paragraph at lines 1875--1878 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2215] [2216] [2217] Underfull \hbox (badness 10000) in paragraph at lines 2112--2114 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix ", where = [2218] [2219] Underfull \hbox (badness 10000) in paragraph at lines 2234--2236 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix" , where = Underfull \hbox (badness 3068) in paragraph at lines 2295--2299 \T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10 or sim-i-lar. Of-ten how-ever, more eas-ily via [2220] Underfull \hbox (badness 4713) in paragraph at lines 2330--2332 []\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de -com-po-si-tion of a square [2221] Underfull \hbox (badness 10000) in paragraph at lines 2447--2450 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10 or [2222] Underfull \hbox (badness 10000) in paragraph at lines 2549--2553 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dgTMatrix", ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2549--2553 \T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or [2223] Underfull \hbox (badness 2707) in paragraph at lines 2605--2609 []\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T 1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d gTMatrix" \T1/ptm/m/n/10 (and other Underfull \hbox (badness 2368) in paragraph at lines 2610--2614 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i n more than one pos-si-ble Underfull \hbox (badness 10000) in paragraph at lines 2617--2620 []\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\ T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ; [2224] Underfull \hbox (badness 2689) in paragraph at lines 2673--2675 []\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix. If miss-ing, Underfull \hbox (badness 10000) in paragraph at lines 2677--2682 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 .symDiagonal \T1/ptm/m/n/10 (\T1/pcr/m/n/10 .trDiagonal\T1/ptm/m/n/10 ), the re-sult-ing sparse Underfull \hbox (badness 3482) in paragraph at lines 2677--2682 [][]\T1/pcr/m/n/10 symmetricMatrix[][][] \T1/ptm/m/n/10 (or [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 ) will have slot \T1/pcr/m/n/10 uplo [2225] Underfull \hbox (badness 1097) in paragraph at lines 2700--2703 []\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1 /pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][ ] \T1/ptm/m/n/10 (with ``su-per-class'' Underfull \hbox (badness 1142) in paragraph at lines 2713--2718 [][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de -pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm /m/n/10 ) rep-re-sen-ta-tion of [2226] Underfull \hbox (badness 3646) in paragraph at lines 2951--2954 []\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T 1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][] \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally Underfull \hbox (badness 10000) in paragraph at lines 2973--2974 []\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1 /ptm/m/n/10 : Underfull \hbox (badness 1810) in paragraph at lines 2980--2982 []\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri v-ially im-ple-mented, of Underfull \hbox (badness 10000) in paragraph at lines 2983--2985 []\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv -a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion Underfull \hbox (badness 3803) in paragraph at lines 2986--2990 []\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou p meth-ods re-turn a [2227] Underfull \hbox (badness 1371) in paragraph at lines 2995--3001 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 : the re-sult is from class Underfull \hbox (badness 10000) in paragraph at lines 3002--3006 []\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec t of S3 class Underfull \hbox (badness 2318) in paragraph at lines 3012--3016 [][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr /m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and [2228] [2229] Underfull \hbox (badness 1859) in paragraph at lines 3196--3198 []\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t his group con-tains Underfull \hbox (badness 10000) in paragraph at lines 3243--3245 [][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre fer-able to (and more ef-fi-cient than) [2230] Underfull \hbox (badness 1168) in paragraph at lines 3363--3366 []\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T 1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , via [2231] [2232] Underfull \hbox (badness 4967) in paragraph at lines 3528--3532 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsCMatrix", ...) \T1/ptm/m/n/10 or [2233] Overfull \hbox (2.39853pt too wide) in paragraph at lines 3533--3535 []\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][] \T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 . Underfull \hbox (badness 6364) in paragraph at lines 3575--3578 []\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr /m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves [2234] [2235] Underfull \hbox (badness 10000) in paragraph at lines 3725--3730 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1 /ptm/m/n/10 , by Underfull \hbox (badness 6961) in paragraph at lines 3725--3730 \T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m /n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm /m/n/10 by class Underfull \hbox (badness 10000) in paragraph at lines 3735--3737 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a triv-ial Underfull \hbox (badness 10000) in paragraph at lines 3737--3740 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 : if [2236] Underfull \hbox (badness 4967) in paragraph at lines 3813--3815 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsyMatrix", ...) \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 3852--3855 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 , or Underfull \hbox (badness 1735) in paragraph at lines 3852--3855 \T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing "\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the [2237] Underfull \hbox (badness 10000) in paragraph at lines 3855--3858 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 , or Underfull \hbox (badness 2318) in paragraph at lines 3855--3858 \T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing "\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion Underfull \hbox (badness 6364) in paragraph at lines 3859--3862 []\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr /m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves [2238] Underfull \hbox (badness 4060) in paragraph at lines 3983--3986 []\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse tri-an-gu-lar solve (aka [2239] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4023--4023 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] [2240] Underfull \hbox (badness 3635) in paragraph at lines 4091--4095 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class Underfull \hbox (badness 10000) in paragraph at lines 4100--4103 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma - Underfull \hbox (badness 10000) in paragraph at lines 4100--4103 \T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co m-bi-na-tions, see Underfull \hbox (badness 10000) in paragraph at lines 4105--4109 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1 0 : the [2241] [2242] [2243] [2244] Underfull \hbox (badness 10000) in paragraph at lines 4393--4398 []\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite Tay-lor se-ries [2245] [2246] Overfull \hbox (85.38034pt too wide) in paragraph at lines 4527--4527 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/ Boeing/msc00726.tar.gz"))))[] Overfull \hbox (139.38028pt too wide) in paragraph at lines 4530--4530 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe ll-Boeing/counterx/jgl009.mtx.gz"))))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4534--4534 []\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary dir./folder:[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4537--4537 []\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 4547--4547 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2247] [2248] Underfull \hbox (badness 10000) in paragraph at lines 4702--4704 [][][]\T1/pcr/m/n/10 symmpart[][][] \T1/ptm/m/n/10 for the sym-met-ric part of a ma-trix, or the co-er-cions [2249] [2250] Underfull \hbox (badness 10000) in paragraph at lines 4849--4854 []\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1 /ptm/m/n/10 , [2251] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4930--4930 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che cking reasons" Overfull \hbox (20.58041pt too wide) in paragraph at lines 4932--4932 [] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2, dimnames=dns))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4936--4936 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] [2252] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4943--4943 [] \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] [2253] Underfull \hbox (badness 10000) in paragraph at lines 5068--5073 []\T1/ptm/m/n/10 color for the bor-der of each rect-an-gle. \T1/pcr/m/n/10 NA \ T1/ptm/m/n/10 means Underfull \hbox (badness 10000) in paragraph at lines 5068--5073 \T1/ptm/m/n/10 no bor-der is drawn. When \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 as by de-fault, Underfull \hbox (badness 2644) in paragraph at lines 5068--5073 \T1/pcr/m/n/10 border.col <- if(lwd < .01) NA else NULL \T1/ptm/m/n/10 is used. Con- Underfull \hbox (badness 4108) in paragraph at lines 5068--5073 \T1/ptm/m/n/10 sider us-ing an opaque color in-stead of \T1/pcr/m/n/10 NULL \T1 /ptm/m/n/10 which cor-re-sponds to [2254] Underfull \hbox (badness 4120) in paragraph at lines 5087--5090 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use Overfull \hbox (15.18042pt too wide) in paragraph at lines 5124--5124 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col /row) indices:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5130--5130 [] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, border.col=NA)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5131--5131 [] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd =2, border.col=NA)[] Overfull \hbox (144.78027pt too wide) in paragraph at lines 5134--5134 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5136--5136 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH ECK_EXTRA")) ||[] [2255] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5143--5143 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a nti-aliasing[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5146--5146 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2256] Underfull \hbox (badness 1817) in paragraph at lines 5235--5244 []\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within the Underfull \hbox (badness 5637) in paragraph at lines 5277--5279 []\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use [2257] Underfull \hbox (badness 3138) in paragraph at lines 5303--5305 []\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the [2258] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5370--5370 [] \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1 , I2)) else TRUE,[] Underfull \hbox (badness 1603) in paragraph at lines 5391--5393 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault, Underfull \hbox (badness 10000) in paragraph at lines 5399--5404 []\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault, Underfull \hbox (badness 10000) in paragraph at lines 5399--5404 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 ) , \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as Underfull \hbox (badness 10000) in paragraph at lines 5399--5404 [][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to [2259] [2260] [2261] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5628--5628 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/ pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] [2262] Underfull \hbox (badness 10000) in paragraph at lines 5709--5712 [][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and Overfull \hbox (9.78043pt too wide) in paragraph at lines 5720--5720 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n ot "formally"[] [2263] Underfull \hbox (badness 1622) in paragraph at lines 5757--5762 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \ T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy /m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ), Underfull \hbox (badness 1418) in paragraph at lines 5757--5762 \T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy /m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m /it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/ m/n/10 is the kro-necker prod-uct [2264] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5818--5818 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1) , c(12L, 4L)),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5819--5819 [] \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2) , c(12L, 4L)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5826--5826 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2265] Underfull \hbox (badness 1062) in paragraph at lines 5955--5958 []\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both [2266] Underfull \hbox (badness 2809) in paragraph at lines 5984--5987 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2267] Underfull \hbox (badness 2635) in paragraph at lines 6096--6101 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 6096--6101 \T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/ pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/ m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 6104--6107 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us e, e.g., [2268] Underfull \hbox (badness 10000) in paragraph at lines 6214--6224 \T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/ n/10 ) or in com-pressed column-oriented form (class Underfull \hbox (badness 1242) in paragraph at lines 6214--6224 [][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/ 10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 -- in [2269] Underfull \hbox (badness 1184) in paragraph at lines 6296--6299 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2270] Underfull \hbox (badness 10000) in paragraph at lines 6394--6397 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2271] Underfull \hbox (badness 10000) in paragraph at lines 6469--6472 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., Overfull \hbox (25.98041pt too wide) in paragraph at lines 6485--6485 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] [2272] Underfull \hbox (badness 2443) in paragraph at lines 6524--6530 []\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][ ]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see Underfull \hbox (badness 1776) in paragraph at lines 6524--6530 [][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr /m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar, Underfull \hbox (badness 1675) in paragraph at lines 6545--6548 []\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth- ods for dif-fer-ent types of ma-tri-ces. Use [2273] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6615--6615 [] \T1/pcr/m/n/9 # q is a 0-based permutation o f the columns[] [2274] [2275] Underfull \hbox (badness 6268) in paragraph at lines 6751--6754 []\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math- e-mat-i-cally''), [2276] Underfull \hbox (badness 5036) in paragraph at lines 6775--6779 []\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1 /ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . How-ever, Underfull \hbox (badness 10000) in paragraph at lines 6775--6779 \T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e mpty'' [][]sparse-Ma-trix[][][], as does [2277]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.6868 \aliasA{det}{Matrix-class}{det} Underfull \hbox (badness 1348) in paragraph at lines 6948--6951 []\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10 diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing Underfull \hbox (badness 10000) in paragraph at lines 6953--6956 []\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \ T1/pcr/m/n/10 value \T1/ptm/m/n/10 is Underfull \hbox (badness 10000) in paragraph at lines 6953--6956 \T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p tm/m/n/10 Ma-trix ob-jects, but only when Underfull \hbox (badness 10000) in paragraph at lines 6971--6974 Underfull \hbox (badness 7326) in paragraph at lines 6981--6983 []\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")\T1/ptm/m/n/10 : This re -lies on a cor-rect [2278]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \relax l.7044 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.crossprod}) has been already used, dup licate ignored \relax l.7152 ...A{crossprod}{matrix-products}{crossprod} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du plicate ignored \relax l.7252 ...tcrossprod}{matrix-products}{tcrossprod} [2279] Underfull \hbox (badness 1881) in paragraph at lines 7350--7356 \T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn [2280pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros sprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7412 \end{Details} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrossprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7412 \end{Details} ] Underfull \hbox (badness 10000) in paragraph at lines 7423--7426 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma - Underfull \hbox (badness 10000) in paragraph at lines 7423--7426 \T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co m-bi-na-tions, see Underfull \hbox (badness 5637) in paragraph at lines 7426--7431 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use Underfull \hbox (badness 10000) in paragraph at lines 7435--7437 []\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r e-turns Underfull \hbox (badness 10000) in paragraph at lines 7437--7439 []\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r e-turns Underfull \hbox (badness 10000) in paragraph at lines 7441--7442 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and [2281] [2282] Underfull \hbox (badness 1062) in paragraph at lines 7622--7625 []\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both [2283] Underfull \hbox (badness 2809) in paragraph at lines 7656--7659 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2284] Underfull \hbox (badness 10000) in paragraph at lines 7708--7710 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <- (X + t(X))/2 \T1/ ptm/m/n/10 should be done, af-ter [2285] Underfull \hbox (badness 1406) in paragraph at lines 7748--7752 []\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b y Jens Oehlschlaegel did not Underfull \hbox (badness 1019) in paragraph at lines 7748--7752 \T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t his sim-pli-fi-ca-tion, now only via [2286] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7846--7846 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a ll in this example[] Underfull \vbox (badness 10000) has occurred while \output is active [2287] Underfull \hbox (badness 2635) in paragraph at lines 7911--7916 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 7911--7916 \T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/ pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/ m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 7919--7922 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us e, e.g., [2288] [2289] Underfull \hbox (badness 10000) in paragraph at lines 8113--8115 []\T1/ptm/m/n/10 fast [2290]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8153 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.8153 \HeaderA{norm}{Matrix Norms}{norm} [2291] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8240--8240 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8241--8241 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8242--8242 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Underfull \hbox (badness 2401) in paragraph at lines 8355--8365 []\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1 0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p tm/m/n/10 , [2292] Underfull \hbox (badness 1184) in paragraph at lines 8426--8429 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2293] Underfull \hbox (badness 10000) in paragraph at lines 8516--8519 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2294] Underfull \hbox (badness 10000) in paragraph at lines 8592--8595 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2295] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8608--8608 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] Overfull \vbox (41.60564pt too high) has occurred while \output is active [2296] Underfull \hbox (badness 10000) in paragraph at lines 8718--8720 []\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe r sig-na-tures (use Underfull \hbox (badness 1596) in paragraph at lines 8734--8736 []\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 : co-er-cion to sparse Underfull \hbox (badness 1721) in paragraph at lines 8740--8744 \T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S ee [2297] [2298] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8819--8819 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8824--8824 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8829--8829 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 8852--8862 []\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T 1/pcr/m/n/10 x \T1/ptm/m/n/10 should Underfull \hbox (badness 10000) in paragraph at lines 8852--8862 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2299] [2300]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.qr}) has been already used, duplicate ignored \relax l.8953 \aliasA{qr}{qr-methods}{qr} Underfull \hbox (badness 5119) in paragraph at lines 8999--9002 []\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma- trix with Overfull \hbox (9.78043pt too wide) in paragraph at lines 9026--9026 []\T1/pcr/m/n/9 stopifnot(identical(dimnames(X), dnX))# some versions changed X\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s dimnames![] [2301] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9037--9037 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n ot supported[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9041--9041 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9058--9058 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9066--9066 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor rect colnames[] [2302] Underfull \hbox (badness 10000) in paragraph at lines 9119--9125 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of Underfull \hbox (badness 10000) in paragraph at lines 9136--9139 []\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p tm/m/n/10 , it cor-re-sponds to [2303] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9208--9208 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/ n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale free"[] [2304] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9229--9229 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war ning+ ~1.5 sec (2013)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 9230--9230 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con siderably faster![] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h as been already used, duplicate ignored \relax l.9249 ... the Reciprocal Condition Number}{rcond} [2305] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9362--9362 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2306] [2307] [2308] Underfull \hbox (badness 10000) in paragraph at lines 9547--9549 []\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably Underfull \hbox (badness 1325) in paragraph at lines 9553--9561 \T1/ptm/m/n/10 gets \T1/pcr/m/n/10 x <- rand.x(nnz) \T1/ptm/m/n/10 and calls [] []\T1/pcr/m/n/10 sparseMatrix[][][](i=i, j=j, x=x, ..)\T1/ptm/m/n/10 . When [2309] [2310] Underfull \hbox (badness 1558) in paragraph at lines 9698--9701 []\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1 0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional [2311] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9760--9760 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9764--9764 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2312]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol ve}) has been already used, duplicate ignored \relax l.9826 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (54.78088pt too wide) in paragraph at lines 9923--9923 [] \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P ", "Pt"), ...)[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9928--9928 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2313] Underfull \hbox (badness 6047) in paragraph at lines 9963--9975 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods Underfull \hbox (badness 10000) in paragraph at lines 9980--9983 []\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via Underfull \hbox (badness 7203) in paragraph at lines 9985--9986 []\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar Underfull \hbox (badness 7851) in paragraph at lines 9989--9996 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 10000) in paragraph at lines 9989--9996 \T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U ses the sparse Underfull \hbox (badness 10000) in paragraph at lines 10002--10012 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 2165) in paragraph at lines 10002--10012 \T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym- [2314] Underfull \hbox (badness 1194) in paragraph at lines 10036--10038 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines Underfull \hbox (badness 10000) in paragraph at lines 10050--10053 []\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 10000) in paragraph at lines 10059--10060 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 10065--10067 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10069--10070 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 10077--10080 [][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1 /ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10095--10095 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i s singular!][] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10099--10099 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2315] Underfull \hbox (badness 10000) in paragraph at lines 10120--10123 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu la and data frame Underfull \hbox (badness 1648) in paragraph at lines 10148--10150 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 10000) in paragraph at lines 10156--10159 []\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co- er-ca-ble to) Underfull \hbox (badness 2591) in paragraph at lines 10156--10159 \T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t rasts to be ap-plied to the [2316] Underfull \hbox (badness 10000) in paragraph at lines 10167--10171 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for Underfull \hbox (badness 2828) in paragraph at lines 10167--10171 \T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m /n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for Underfull \hbox (badness 6592) in paragraph at lines 10178--10180 []\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in -di-cat-ing if the re-sult must be a [2317] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10255--10255 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M) == c(0, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10256--10256 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M) == c(3, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10257--10257 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2318] [2319] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10441--10441 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10442--10442 [] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = FALSE)[] [2320] Underfull \hbox (badness 4621) in paragraph at lines 10482--10486 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m /n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a [2321] Underfull \hbox (badness 10000) in paragraph at lines 10558--10561 []\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][]( *, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10570--10570 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10574--10574 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10575--10575 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10580--10580 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims = c(10,20)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10583--10583 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2322] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10606--10606 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 10607--10607 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10633--10633 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep resentations.[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 10635--10635 [] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack age = "SparseM"))) {[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10637--10637 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] [2323] Underfull \hbox (badness 10000) in paragraph at lines 10730--10738 []\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject of S3 class Underfull \hbox (badness 1325) in paragraph at lines 10751--10755 []\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a [2324] Underfull \hbox (badness 10000) in paragraph at lines 10781--10785 [][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s uch as [][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)\T1/ptm/m/n/10 , or pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha s been already used, duplicate ignored \relax l.10821 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2325] [2326] Underfull \hbox (badness 1430) in paragraph at lines 10951--10953 []\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses Overfull \hbox (58.38037pt too wide) in paragraph at lines 10979--10979 [] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai led in Matrix <= 1.1-0[] Underfull \hbox (badness 5036) in paragraph at lines 11007--11009 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2327] Underfull \hbox (badness 2970) in paragraph at lines 11140--11146 []\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/ 10 "sparseVector" \T1/ptm/m/n/10 has the five ac- Underfull \hbox (badness 3679) in paragraph at lines 11140--11146 \T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec tor"\T1/ptm/m/n/10 , [2328] Underfull \hbox (badness 10000) in paragraph at lines 11191--11194 []\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/ 10 co-erces Underfull \hbox (badness 10000) in paragraph at lines 11213--11216 []\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m /n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list [2329] Underfull \hbox (badness 10000) in paragraph at lines 11231--11236 []\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/ 10 logical[][][] \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 11246--11248 [][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc -tion of sparse vec-tors (apart from [2330] [2331] Underfull \hbox (badness 3525) in paragraph at lines 11364--11368 []\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/ pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/ ptm/m/n/10 , where Underfull \hbox (badness 1831) in paragraph at lines 11371--11377 [][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more u sual con-struc-tor of such ma-tri-ces. Then, [2332] Underfull \hbox (badness 10000) in paragraph at lines 11466--11470 []\T1/pcr/m/n/10 signature(object = "symmetricMatrix")\T1/ptm/m/n/10 : re-turns \T1/ptm/m/it/10 sym-met-ric Underfull \hbox (badness 1043) in paragraph at lines 11466--11470 [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , even when the \T1/pcr/m/n/10 Dimnames \T1/ptm/m/n/10 slot only has row or col-umn names. This Underfull \hbox (badness 10000) in paragraph at lines 11482--11487 []\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/ n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be Underfull \hbox (badness 1259) in paragraph at lines 11482--11487 \T1/pcr/m/n/10 list(NULL, )\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. How-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other Underfull \hbox (badness 2591) in paragraph at lines 11490--11495 \T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 , and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1 /ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or [2333] Underfull \hbox (badness 2057) in paragraph at lines 11562--11564 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., [2334] [2335] Underfull \hbox (badness 6641) in paragraph at lines 11648--11651 []\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm /m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit h Underfull \hbox (badness 5133) in paragraph at lines 11688--11692 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the vir-tual class of all sparse ma-tri-ces coded in Underfull \hbox (badness 2818) in paragraph at lines 11688--11692 \T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c re-ated from it. See [2336] Underfull \hbox (badness 7649) in paragraph at lines 11795--11797 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2337] [2338] [2339] Underfull \hbox (badness 7362) in paragraph at lines 11996--11998 []\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a sparse ma-trix (i.e., of sub-class of [2340] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12034--12034 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 12035--12035 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] [2341] [2342] Underfull \hbox (badness 6910) in paragraph at lines 12285--12287 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2343] [2344] [2345]) (./boot-pkg.tex [2346] Chapter 18. [2347] [2348] [2349] [2350] [2351] [2352] [2353] Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f" , "w"), [2354] Underfull \hbox (badness 1325) in paragraph at lines 568--575 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r e-quired. Pos-si-ble Underfull \hbox (badness 1275) in paragraph at lines 583--588 []\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m ulti-sample prob- Underfull \hbox (badness 1264) in paragraph at lines 583--588 \T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n ored when [2355] Overfull \hbox (43.25928pt too wide) in paragraph at lines 643--649 []\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1 0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0 [2356] Underfull \hbox (badness 6268) in paragraph at lines 797--807 \T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de -fault clus-ter, a sec-ond ap-proach is used if [2357] Underfull \hbox (badness 1881) in paragraph at lines 824--826 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 6493) in paragraph at lines 851--855 [][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 , [2358] Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, data = nuke)[] Underfull \vbox (badness 10000) has occurred while \output is active [2359] [2360] Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 []\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i n-ter- Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 \T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues [2361] Underfull \hbox (badness 1496) in paragraph at lines 1082--1091 []\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari- ance of the Underfull \hbox (badness 2005) in paragraph at lines 1082--1091 \T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i n-ter-vals. If it Underfull \hbox (badness 2343) in paragraph at lines 1082--1091 \T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10 is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to Underfull \hbox (badness 2150) in paragraph at lines 1103--1109 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2362] [2363] [2364] [2365] [2366] Underfull \hbox (badness 1571) in paragraph at lines 1443--1445 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2367] [2368] [2369] [2370] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix( 1,n,2), [2371] [2372] [2373] [2374] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4) + strata(ulcer),[] Underfull \vbox (badness 10000) has occurred while \output is active [2375] Underfull \hbox (badness 6268) in paragraph at lines 2081--2083 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2376] [2377] [2378] [2379] Underfull \hbox (badness 1565) in paragraph at lines 2335--2340 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set Underfull \hbox (badness 4595) in paragraph at lines 2360--2365 \T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis tic \T1/ptm/m/n/10 is called. [2380] Underfull \hbox (badness 1881) in paragraph at lines 2429--2431 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 2057) in paragraph at lines 2437--2438 [][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 , [2381] Underfull \hbox (badness 1077) in paragraph at lines 2533--2537 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n /10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the sam-ple Underfull \hbox (badness 1112) in paragraph at lines 2533--2537 \T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1 0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10 is used. This is mul-ti-plied by [2382] [2383] [2384] [2385] [2386] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25, Overfull \hbox (18.78088pt too wide) in paragraph at lines 2894--2894 []\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25,[] [2387] [2388] [2389] Underfull \hbox (badness 3861) in paragraph at lines 3102--3105 [][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [2390] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1 :ncol(mat)) [2391] [2392] [2393] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling [2394] [2395] [2396] [2397] [2398] [2399] [2400] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835 [] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q = NULL)[] [2401] [2402] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])[] [2403] [2404] [2405] Underfull \hbox (badness 10000) in paragraph at lines 4187--4189 []\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault is [2406] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256 []\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz e data as in [2407] [2408] Underfull \hbox (badness 10000) in paragraph at lines 4359--4361 []\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o f Underfull \hbox (badness 1430) in paragraph at lines 4368--4372 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T 1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to Underfull \hbox (badness 2269) in paragraph at lines 4386--4389 []\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by [2409] [2410] [2411] [2412] [2413] [2414] [2415] [2416] [2417] Underfull \hbox (badness 3000) in paragraph at lines 4956--4959 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2418] [2419] [2420] [2421] Underfull \hbox (badness 2293) in paragraph at lines 5235--5238 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5235--5238 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2422] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat a = grav1[, 2])[] [2423] [2424] [2425] [2426] [2427] [2428] [2429] [2430] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c ity.sp1$spa[1][] [2431] Underfull \hbox (badness 1127) in paragraph at lines 5985--6003 \T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then [2432] Underfull \hbox (badness 2837) in paragraph at lines 6018--6021 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad dle.distn"\T1/ptm/m/n/10 . See the help file for [2433] [2434] [2435] [2436] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and Wright (1991). [2437] [2438] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling Overfull \hbox (20.58041pt too wide) in paragraph at lines 6494--6494 []\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t ilting was used[] [2439] [2440] [2441] Underfull \hbox (badness 1596) in paragraph at lines 6739--6743 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2442] [2443] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899 [] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha = c(0.05, 0.95),[] [2444] [2445] [2446] [2447] [2448] [2449] [2450] [2451]) (./class-pkg.tex [2452] Chapter 19. [2453] [2454] [2455] [2456] [2457] [2458] [2459] [2460] Underfull \hbox (badness 10000) in paragraph at lines 608--610 []\T1/ptm/m/n/10 the size of the code-book. De-faults to [2461] [2462] [2463] [2464] [2465] [2466] [2467] [2468]) (./cluster-pkg.tex Chapter 20. [2469] Underfull \hbox (badness 3098) in paragraph at lines 133--142 []\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u- Underfull \hbox (badness 2253) in paragraph at lines 133--142 \T1/ptm/m/n/10 larly for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is spec-i-fied of longer length than one. Since Underfull \hbox (badness 3323) in paragraph at lines 133--142 \T1/ptm/b/n/10 clus-ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-val id \T1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror Underfull \hbox (badness 10000) in paragraph at lines 133--142 \T1/ptm/m/n/10 as \T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n /10 . Fur-ther, \T1/pcr/m/n/10 method= "single" Underfull \hbox (badness 10000) in paragraph at lines 133--142 \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method = c(.5,.5,0,-.5)\T1/ptm/m/n/10 , and Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--142 \T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/ 10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 . [2470] Underfull \hbox (badness 10000) in paragraph at lines 167--169 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \ T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method = [2471] Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252 [] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met hod = 0.5)[iC]) ,[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 253--253 [] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, -.5))[iC]),[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254 [] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, +.5))[iC]))[] [2472] [2473] Underfull \vbox (badness 10000) has occurred while \output is active [2474] [2475] Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518 [] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot = axes,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 522--522 [] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5, ...)[] [2476] Underfull \hbox (badness 5374) in paragraph at lines 539--541 []\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use d when [2477] Overfull \hbox (66.78088pt too wide) in paragraph at lines 637--637 [] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c orrect.d = TRUE)[] [2478] Underfull \hbox (badness 3078) in paragraph at lines 688--691 []\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem- ory (and hence time), but dis-ables [2479] [2480] Underfull \hbox (badness 2941) in paragraph at lines 778--781 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 816--816 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo r this seed):[] [2481] Underfull \hbox (badness 10000) in paragraph at lines 863--865 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2482] Overfull \hbox (24.78088pt too wide) in paragraph at lines 928--928 [] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code =3), ...)[] [2483] Underfull \hbox (badness 4872) in paragraph at lines 974--976 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 988--992 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2484] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1095--1095 [] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE. factor = SEf)))[] [2485] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1112--1112 []\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras < - TRUE # or FALSE[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1150--1150 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] [2486] Underfull \hbox (badness 4144) in paragraph at lines 1182--1186 []\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m /n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent, e.g., for [2487] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1258--1258 [] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1, cex.txt = cex,[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1264--1264 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2488] [2489] Underfull \hbox (badness 10000) in paragraph at lines 1403--1408 []\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1 0 princomp[][][](*, cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 1451--1454 [2490] Underfull \hbox (badness 10000) in paragraph at lines 1468--1472 [][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 , Overfull \hbox (31.3804pt too wide) in paragraph at lines 1492--1492 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a nd label ellipses[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1502--1502 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2491] Underfull \hbox (badness 5741) in paragraph at lines 1542--1545 []\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der -ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only [2492] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1608--1608 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2493] Underfull \hbox (badness 5008) in paragraph at lines 1725--1733 \T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1 0 w[]^^N[]$\T1/ptm/m/n/10 , where [2494] [2495] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1816--1816 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord ratio = 7)))[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 1835--1835 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2496] [2497] [2498] [2499] Underfull \hbox (badness 10000) in paragraph at lines 2143--2145 []\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as Underfull \hbox (badness 10000) in paragraph at lines 2154--2157 Underfull \hbox (badness 3179) in paragraph at lines 2168--2174 [][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [ ][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips oid \T1/ptm/m/n/10 ob-jects. [2500] [2501] [2502] Underfull \hbox (badness 10000) in paragraph at lines 2326--2329 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par tition.object[][][]\T1/ptm/m/n/10 , [2503] Underfull \hbox (badness 1292) in paragraph at lines 2394--2397 []\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t he num-ber of it-er-a-tions needed and Underfull \hbox (badness 6675) in paragraph at lines 2403--2405 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see Underfull \hbox (badness 10000) in paragraph at lines 2426--2429 [][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n /10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [2504] [2505] [2506] [2507] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2642--2642 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] [2508] [2509] Underfull \hbox (badness 1067) in paragraph at lines 2829--2834 []\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger \T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g o-rithm, whereas [2510] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2888--2888 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2511] [2512] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2991--2991 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2513] [2514] [2515] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3187--3187 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3188--3188 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2516] Underfull \hbox (badness 10000) in paragraph at lines 3255--3258 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n /10 pltree() \T1/ptm/m/n/10 is pro-vided by [2517] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3305--3305 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3306--3306 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2518] [2519] [2520] Underfull \hbox (badness 10000) in paragraph at lines 3491--3494 []\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m /n/10 diss \T1/ptm/m/n/10 com-po-nent as for Underfull \hbox (badness 3471) in paragraph at lines 3491--3494 [][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a [2521] Underfull \hbox (badness 10000) in paragraph at lines 3554--3559 [][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [2522] Underfull \hbox (badness 4621) in paragraph at lines 3616--3621 []\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 1990) in paragraph at lines 3616--3621 \T1/ptm/m/n/10 which dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1 /ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider Underfull \hbox (badness 6268) in paragraph at lines 3628--3631 [][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.agnes[][][]\T1/ptm/m/n/10 , [2523] [2524] [2525] Underfull \hbox (badness 10000) in paragraph at lines 3813--3816 [][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3844--3847 [][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [2526] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3897--3897 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] Underfull \hbox (badness 2035) in paragraph at lines 3908--3910 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1 /pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for [2527] [2528] [2529] [2530] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4101--4101 [] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w idth "* s[i]),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 4103--4103 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] Underfull \hbox (badness 1946) in paragraph at lines 4132--4137 []\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n /10 ; note that the de-fault used to be \T1/pcr/m/n/10 col [2531] Underfull \hbox (badness 10000) in paragraph at lines 4199--4207 \T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by [2532] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4241--4241 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus ter-wise coloring[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4250--4250 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4252--4252 [] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma in")); frame()[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 4255--4255 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol denrod4", "gray20")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4257--4257 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4264--4264 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro wnames == indices[] [2533] [2534] [2535] [2536] [2537] [2538] Underfull \hbox (badness 10000) in paragraph at lines 4622--4628 []\T1/ptm/m/n/10 Our ver-sion of the \T1/pcr/m/n/10 xclara \T1/ptm/m/n/10 is sl ightly more rounded than the one from Underfull \hbox (badness 10000) in paragraph at lines 4638--4640 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side Overfull \hbox (52.98038pt too wide) in paragraph at lines 4651--4651 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10 01:2000}, {2001:3000} Overfull \hbox (9.78043pt too wide) in paragraph at lines 4653--4653 []\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s medoid indices == pam(xclara, 3)$id.med[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4663--4663 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o bservations:[] [2539] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4667--4667 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? - - Robust range:[] [2540]) (./codetools-pkg.tex Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17 [] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = !all,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18 [] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress Undefined,[] [2541] Underfull \hbox (badness 10000) in paragraph at lines 65--70 []\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2542] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2543] [2544] [2545]) (./foreign-pkg.tex [2546] Chapter 22. [2547] Underfull \hbox (badness 1231) in paragraph at lines 67--70 []\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr om, or a Underfull \hbox (badness 6708) in paragraph at lines 78--81 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2548] [2549] Underfull \hbox (badness 3601) in paragraph at lines 235--243 []\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n /10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 , [2550] Overfull \hbox (12.78088pt too wide) in paragraph at lines 296--296 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates = FALSE, [2551] [2552] [2553] Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t o.data.frame,[] [2554] Overfull \hbox (30.78088pt too wide) in paragraph at lines 463--463 [] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen d", "no"),[] Underfull \hbox (badness 10000) in paragraph at lines 506--515 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer- Underfull \hbox (badness 6001) in paragraph at lines 506--515 \T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de- fault), the first orig-i-nal value Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named to Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/pcr/m/n/10 paste0(label, duplicated.value.labels.infix, level)\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 516--519 []\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with du- Underfull \hbox (badness 10000) in paragraph at lines 516--519 \T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault \T1/pcr/m/n/10 "_dupli cated_"\T1/ptm/m/n/10 ) if [2555] Underfull \hbox (badness 10000) in paragraph at lines 551--559 []\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en -[]us / library / ms776446(VS . 85 ) .aspx$[][] Underfull \hbox (badness 7613) in paragraph at lines 569--575 []\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/ m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute [2556] Overfull \hbox (20.58041pt too wide) in paragraph at lines 624--624 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg ument settings.[] Overfull \hbox (112.38031pt too wide) in paragraph at lines 625--625 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2557] Overfull \hbox (9.78043pt too wide) in paragraph at lines 658--658 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ ate variables[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 662--662 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt h=w), "\n"))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 669--669 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, collapse="")[] [2558] [2559] Underfull \hbox (badness 10000) in paragraph at lines 813--814 Overfull \hbox (4.38043pt too wide) in paragraph at lines 823--823 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f oreign")[1])[] [2560] [2561] Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899 [] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G lobalEnv) [2562] Overfull \hbox (0.78088pt too wide) in paragraph at lines 963--963 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute (x))) Underfull \hbox (badness 6708) in paragraph at lines 989--992 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2563] [2564] Underfull \hbox (badness 10000) in paragraph at lines 1073--1074 [][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase / format / data _ types . Overfull \hbox (24.78088pt too wide) in paragraph at lines 1109--1109 [] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", "codes"))[] [2565] Underfull \hbox (badness 1286) in paragraph at lines 1194--1198 []\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates = FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec ts [2566] Underfull \hbox (badness 10000) in paragraph at lines 1267--1273 []\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign: ::writeForeignStata\T1/ptm/m/n/10 , [2567] Underfull \hbox (badness 6725) in paragraph at lines 1293--1296 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef -fect, the dec-i-mal in-di-ca-tor is al-ways set by [2568]) (./lattice-pkg.tex Chapter 23. [2569] [2570] [2571] Overfull \hbox (12.78088pt too wide) in paragraph at lines 286--286 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 290--290 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .xyplot"),[] [2572] Overfull \hbox (42.78088pt too wide) in paragraph at lines 298--298 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul t.dotplot"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 305--305 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.barchart"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 313--313 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.stripplot"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 334--334 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 338--338 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .bwplot"),[] [2573] Underfull \hbox (badness 4060) in paragraph at lines 357--369 []\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a lly of the Underfull \hbox (badness 10000) in paragraph at lines 357--369 \T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ iv-a-lently, \T1/pcr/m/n/10 y ~ x | Underfull \hbox (badness 1028) in paragraph at lines 397--412 \T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot both Underfull \hbox (badness 10000) in paragraph at lines 413--415 []\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum, one can ei-ther set [2574] Underfull \hbox (badness 7631) in paragraph at lines 479--484 []\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \ T1/ptm/m/n/10 in this case may be [2575] [2576] Underfull \hbox (badness 1221) in paragraph at lines 650--658 []\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as ar-gu-ments to [2577] [2578] [2579] [2580] Underfull \hbox (badness 2005) in paragraph at lines 986--998 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of fac-tors will be Underfull \hbox (badness 1199) in paragraph at lines 986--998 \T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a use-ful lay-out. [2581] Underfull \hbox (badness 1661) in paragraph at lines 1099--1105 []\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be num-bers be-tween 0 and 1, giv-ing co-or-di-nates [2582] [2583] Underfull \hbox (badness 1097) in paragraph at lines 1225--1227 []\T1/ptm/m/n/10 Logical flag, whether leg-end should have a Underfull \hbox (badness 1917) in paragraph at lines 1239--1240 []\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to [2584] [2585] [2586] Underfull \hbox (badness 1540) in paragraph at lines 1479--1485 []\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/ 10 plot.trellis[][][]\T1/ptm/m/n/10 , [2587] Underfull \hbox (badness 10000) in paragraph at lines 1566--1583 [][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel .stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 , [2588] Underfull \vbox (badness 10000) has occurred while \output is active [2589] Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671 [] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar dSprays$rowpos))),[] Underfull \hbox (badness 2012) in paragraph at lines 1725--1727 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][] []\T1/ptm/m/n/10 , which may pass them on to [2590] Underfull \hbox (badness 6808) in paragraph at lines 1755--1759 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to Underfull \hbox (badness 10000) in paragraph at lines 1772--1775 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 , etc; see [2591] Underfull \hbox (badness 10000) in paragraph at lines 1825--1827 []\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix An-drews [2592] [2593] [2594] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] Underfull \hbox (badness 10000) in paragraph at lines 2086--2093 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/ m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form Underfull \hbox (badness 1997) in paragraph at lines 2086--2093 \T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra ms or ker-nel den-sity [2595] Underfull \hbox (badness 10000) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t he value of Underfull \hbox (badness 1320) in paragraph at lines 2141--2144 \T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch ecked. If [2596] [2597] [2598] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2349--2349 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .qqmath"),[] Underfull \hbox (badness 4441) in paragraph at lines 2362--2366 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2599] [2600] [2601] Underfull \hbox (badness 4441) in paragraph at lines 2547--2554 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2602] [2603] Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689 [] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev elplot.raster")[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2721--2721 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl ot"),[] [2604] Underfull \hbox (badness 10000) in paragraph at lines 2761--2766 []\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu la of the form \T1/pcr/m/n/10 z ~ x * y [2605] Underfull \hbox (badness 2913) in paragraph at lines 2791--2796 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 2791--2796 \T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p tm/m/n/10 must have the same lengths as Underfull \hbox (badness 6758) in paragraph at lines 2877--2881 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be Underfull \hbox (badness 7576) in paragraph at lines 2877--2881 \T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast er[][][]\T1/ptm/m/n/10 . See also Underfull \hbox (badness 10000) in paragraph at lines 2883--2885 []\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T 1/ptm/m/n/10 when [2606] Underfull \hbox (badness 1609) in paragraph at lines 2935--2941 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti ons should be used, Underfull \hbox (badness 2772) in paragraph at lines 2935--2941 \T1/ptm/m/n/10 both for the false color im-age and the color key (if present). Ef- Underfull \hbox (badness 1400) in paragraph at lines 2935--2941 \T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 changes the de-fault panel func-tion from Underfull \hbox (badness 2486) in paragraph at lines 2959--2963 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2607] [2608] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3060--3060 [] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3061--3061 [] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062 [] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite = TRUE),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3073--3073 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. cloud"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 3085--3085 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.wireframe"),[] [2609] Underfull \hbox (badness 10000) in paragraph at lines 3110--3118 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo r-mula of the form \T1/pcr/m/n/10 z ~ x Underfull \hbox (badness 2913) in paragraph at lines 3143--3150 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 3143--3150 \T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p tm/m/n/10 must have the same lengths as [2610] [2611] [2612] [2613]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.parallel}) has been already used, duplicate ignored \relax l.3431 \aliasA{parallel}{B\_08\_splom}{parallel} Overfull \hbox (18.78088pt too wide) in paragraph at lines 3473--3473 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. splom"),[] [2614] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3496--3496 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.parallel"),[] [2615] [2616] [2617] [2618] [2619] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3832--3832 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt( var(x))) [2620] Underfull \hbox (badness 10000) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white bg")\T1/ptm/m/n/10 . Underfull \hbox (badness 2435) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2621] [2622] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4052--4052 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict = FALSE) Underfull \hbox (badness 1173) in paragraph at lines 4061--4065 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4088--4090 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when Underfull \hbox (badness 1728) in paragraph at lines 4105--4109 \T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se t-tings (ob-tained by [2623] Underfull \hbox (badness 5161) in paragraph at lines 4170--4174 []\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis .settings \T1/ptm/m/n/10 has not been fi-nal-ized, Underfull \hbox (badness 4913) in paragraph at lines 4170--4174 \T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca n be ob-tained by [2624] [2625] Underfull \hbox (badness 1067) in paragraph at lines 4284--4294 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm /m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 1735) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points Underfull \hbox (badness 10000) in paragraph at lines 4284--4294 \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and Underfull \hbox (badness 5231) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for Underfull \hbox (badness 1701) in paragraph at lines 4309--4312 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot .symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4312--4314 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl ot.polygon \T1/ptm/m/n/10 and [2626] [2627] [2628] [2629] [2630] [2631] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4716--4716 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab = "Height")[] [2632] [2633] Underfull \hbox (badness 10000) in paragraph at lines 4903--4906 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 . [2634] [2635] Underfull \hbox (badness 1442) in paragraph at lines 5035--5038 []\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and [2636] [2637] [2638] [2639] [2640] [2641] Underfull \hbox (badness 3646) in paragraph at lines 5367--5370 [][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f or Overfull \hbox (36.78088pt too wide) in paragraph at lines 5397--5397 [] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh ich.given],[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5398--5398 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which .given],[] [2642] Underfull \hbox (badness 10000) in paragraph at lines 5486--5489 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 2103) in paragraph at lines 5486--5489 \T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef t of pan-els us-ing Underfull \hbox (badness 6412) in paragraph at lines 5503--5509 []\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl y be-cause of the \T1/pcr/m/n/10 style Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive , es-pe-cially when Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm /m/n/10 are small. Tra-di-tional use is as Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 , though this can be [2643] Underfull \hbox (badness 1635) in paragraph at lines 5512--5517 []\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh ich is to draw a strip ap-pro-pri-ate for [2644] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5661--5661 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la bels,[] [2645] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5675--5675 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose "), ...)[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5676--5676 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos e"), ...)[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5679--5679 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location" , "toplevel",[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5682--5682 [] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig ht", "page"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 5684--5684 [] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in side"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5690--5690 [] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi ch.given",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5691--5691 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692 [] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi ch.panel",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5694--5694 [] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co lumn",[] Underfull \hbox (badness 10000) in paragraph at lines 5710--5712 []\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of [2646] Underfull \hbox (badness 2376) in paragraph at lines 5721--5723 []\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point. De-faults to [2647] Underfull \hbox (badness 2538) in paragraph at lines 5846--5850 \T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and Underfull \hbox (badness 4205) in paragraph at lines 5857--5864 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr a pa-ram-e-ters are passed on to Underfull \hbox (badness 4792) in paragraph at lines 5857--5864 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are used (in com-bi-na-tion with [2648] [2649] Underfull \hbox (badness 10000) in paragraph at lines 6010--6014 [][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , [] []\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 , [2650] [2651] Underfull \hbox (badness 4242) in paragraph at lines 6157--6162 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- [2652] [2653] Underfull \hbox (badness 3601) in paragraph at lines 6273--6278 []\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1 0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round Underfull \hbox (badness 2486) in paragraph at lines 6273--6278 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault, the ac-tual box-plot statis-tics are cal-cu-lated us-ing [2654] [2655] Overfull \hbox (60.78088pt too wide) in paragraph at lines 6360--6360 [] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co lors")$palette,[] [2656] Underfull \hbox (badness 1888) in paragraph at lines 6492--6499 \T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col. regions \T1/ptm/m/n/10 a vec-tor of col-ors, and [2657] Underfull \hbox (badness 10000) in paragraph at lines 6549--6552 []\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The Underfull \hbox (badness 1558) in paragraph at lines 6549--6552 \T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v alid color. The [2658] Underfull \hbox (badness 1005) in paragraph at lines 6599--6607 \T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/ 10 z \T1/ptm/m/n/10 are all passed to Underfull \hbox (badness 1571) in paragraph at lines 6599--6607 \T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/ 10 y \T1/ptm/m/n/10 are in- [2659] [2660] [2661] [2662] [2663] Underfull \hbox (badness 1320) in paragraph at lines 6955--6962 []\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan el func-tion that uses the raster draw- Underfull \hbox (badness 1715) in paragraph at lines 6955--6962 \T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more ef-fi-cient. When us-ing [2664] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7025--7025 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] [2665] Underfull \hbox (badness 10000) in paragraph at lines 7055--7059 []\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments to Underfull \hbox (badness 1584) in paragraph at lines 7055--7059 \T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu nc-tion is passed [2666] Underfull \hbox (badness 10000) in paragraph at lines 7160--7163 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by [2667] [2668] Underfull \hbox (badness 2012) in paragraph at lines 7326--7329 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2669] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7372--7372 [] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta ils.n = 50))[] [2670] [2671] Underfull \hbox (badness 2644) in paragraph at lines 7513--7517 \T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on to Underfull \hbox (badness 2772) in paragraph at lines 7526--7529 []\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a list of ar-gu-ments to be sup-plied to Underfull \hbox (badness 4242) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos -si-bly Underfull \hbox (badness 1147) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is co-erced to a list. This al-lows ar- Underfull \hbox (badness 2351) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline = c(0, 1)\T1/ptm/ m/n/10 , which adds the di- Underfull \hbox (badness 1675) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v = 0)\T1 /ptm/m/n/10 , which adds the Underfull \hbox (badness 1769) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol; e.g., [2672] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7596--7596 [] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y = c(1/6, 4/6)),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7606--7606 [] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d raw = FALSE),[] [2673] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7667--7667 [] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam e.type)[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7672--7672 [] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident ifier, name.type)[] [2674] [2675] [2676] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7857--7857 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden tifier = "grid")[] [2677] Underfull \hbox (badness 1436) in paragraph at lines 7912--7918 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for Underfull \hbox (badness 1231) in paragraph at lines 7912--7918 \T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti ngs. The [2678] [2679] [2680] [2681] [2682] [2683] [2684] [2685] Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo se Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1 /pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from [2686] [2687] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8645--8645 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st ack, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8646--8646 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin t, ...)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8658--8658 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr ipts, ...)[] [2688] Underfull \hbox (badness 3118) in paragraph at lines 8677--8680 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1 /ptm/m/n/10 has a dif-fer-ent mean-ing in [2689] Underfull \hbox (badness 1515) in paragraph at lines 8753--8757 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2690] Underfull \hbox (badness 6316) in paragraph at lines 8859--8864 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2691] [2692] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8966--8966 [] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b ottom$labels$labels)[] [2693] [2694] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9105--9105 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su nspot.year)),[] [2695] Overfull \hbox (84.94879pt too wide) in paragraph at lines 9164--9168 []\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr /m/n/10 left, right, left.name, right.name, condition Overfull \hbox (104.63074pt too wide) in paragraph at lines 9164--9168 \T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left, right.x, right.y, left.name , right.x.name, right.y.name, condition [2696] [2697] [2698] [2699] [2700] [2701] [2702] Underfull \hbox (badness 4205) in paragraph at lines 9622--9626 []\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 , Underfull \hbox (badness 4518) in paragraph at lines 9622--9626 \T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 , Underfull \hbox (badness 6300) in paragraph at lines 9627--9630 []\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm" \T1/ptm/m/n/10 , [2703] [2704] [2705]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma} [2706] [2707] [2708] Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 []\T1/ptm/m/n/10 Cause of death. A fac-tor with lev-els \T1/pcr/m/n/10 Alzheime rs\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Cancer\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 Cerebrovascular diseases\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Diabetes \T1/ptm/m/n/10 , \T1/pcr/m/n/10 Flu and pneumonia\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 Heart disease\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower respiratory\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 Nephritis\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Suicide\ T1/ptm/m/n/10 , and [2709] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10088--10088 [] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list( columns = 2),[] [2710]) (./mgcv-pkg.tex Chapter 24. [2711] [2712] Overfull \hbox (6.78088pt too wide) in paragraph at lines 147--147 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL, Overfull \hbox (18.78088pt too wide) in paragraph at lines 150--150 [] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret e=FALSE,[] [2713] Overfull \hbox (72.78088pt too wide) in paragraph at lines 152--152 [] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in tercept=NULL,...)[] Underfull \hbox (badness 1142) in paragraph at lines 171--175 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 196--201 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2714] [2715] [2716] [2717] Underfull \hbox (badness 10000) in paragraph at lines 361--368 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo th.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 361--368 [][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 361--368 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2718] Overfull \hbox (4.38043pt too wide) in paragraph at lines 404--404 []\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2 ,bs=bs,k=k)+[] [2719] [2720] [2721] Underfull \hbox (badness 2922) in paragraph at lines 603--604 []\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/ n/10 and [2722] [2723] [2724] Underfull \hbox (badness 1158) in paragraph at lines 727--729 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2725] Underfull \hbox (badness 1259) in paragraph at lines 790--791 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [2726] [2727] [2728] [2729] [2730] [2731] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1138--1138 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1139--1139 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1145--1145 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct+adhere,[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1152--1152 []\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for this stratum...[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1154--1154 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in d]),type="l",ylim=c(0,1),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1156--1156 [] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind]) ,lwd=2,col=i)[] Underfull \vbox (badness 10000) has occurred while \output is active [2732] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1187--1187 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights= d,data=surv)[] [2733] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1248--1248 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] [2734] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1293--1293 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] [2735] [2736] [2737] [2738] [2739] [2740] [2741] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1750--1750 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2742] [2743] [2744] [2745] [2746] [2747] Underfull \hbox (badness 1052) in paragraph at lines 2125--2133 \T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo oths. Lin-ear func-tion-als of [2748] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2142--2142 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2154--2157 []\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1 0 formula.gam[][][] \T1/ptm/m/n/10 and also Underfull \hbox (badness 1142) in paragraph at lines 2167--2171 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 2193--2198 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2749] [2750] [2751] Underfull \hbox (badness 1043) in paragraph at lines 2356--2362 \T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v en-tion mech-a-nism de-scribed in [2752] [2753] Underfull \hbox (badness 10000) in paragraph at lines 2492--2498 [][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2492--2498 [][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2492--2498 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2754] Underfull \vbox (badness 10000) has occurred while \output is active [2755] Underfull \vbox (badness 10000) has occurred while \output is active [2756] Underfull \vbox (badness 10000) has occurred while \output is active [2757] [2758] [2759] [2760] [2761] [2762] [2763] [2764] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3148--3148 [] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco l(x)),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3151--3151 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] [2765] [2766] [2767] [2768] [2769] [2770] Underfull \hbox (badness 5189) in paragraph at lines 3512--3516 []\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n /10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see [2771] [2772] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3629--3629 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \vbox (badness 10000) has occurred while \output is active [2773] [2774] [2775] Underfull \hbox (badness 1184) in paragraph at lines 3798--3802 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2776] [2777] [2778] [2779] [2780] [2781] [2782] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4244--4244 [] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i d=1)+s(x1,id=1)+[] [2783] [2784] [2785] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4394--4394 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2786] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4488--4488 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR UE,...)[] [2787] Underfull \hbox (badness 1142) in paragraph at lines 4519--4523 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2788] Underfull \hbox (badness 10000) in paragraph at lines 4588--4597 []\T1/ptm/m/n/10 In the event of \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 con-ver-genc e fail-ures, con-sider mod-i-fy-ing [2789] [2790] Underfull \hbox (badness 5970) in paragraph at lines 4705--4711 [][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 1418) in paragraph at lines 4705--4711 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p cr/m/n/10 pdTens[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 gamm4 \T1/ptm/m/n/10 ( [] []$\T1/pcr/m/n/10 https : / / cran . r-[]project . [2791] Underfull \vbox (badness 10000) has occurred while \output is active [2792] [2793] [2794] Underfull \hbox (badness 1577) in paragraph at lines 4985--4988 []\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see [] []\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment Underfull \hbox (badness 2181) in paragraph at lines 4992--4993 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2795] [2796] [2797] [2798] [2799] [2800] [2801] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5396--5396 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2802] [2803] [2804] [2805] [2806] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5720--5720 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, [2807] Overfull \hbox (36.78088pt too wide) in paragraph at lines 5722--5722 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 5743--5747 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2808] [2809] [2810] Underfull \vbox (badness 10000) has occurred while \output is active [2811] [2812] [2813] Overfull \hbox (72.78088pt too wide) in paragraph at lines 6058--6058 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999, all.derivs=FALSE) [2814] [2815] [2816] [2817] Underfull \vbox (badness 10000) has occurred while \output is active [2818] Underfull \vbox (badness 10000) has occurred while \output is active [2819] [2820] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6487--6487 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] [2821] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6514--6514 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2822] [2823] [2824] [2825] [2826] [2827] [2828] [2829] [2830] Underfull \hbox (badness 1242) in paragraph at lines 7057--7058 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2831] [2832] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7144--7144 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [2833] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7207--7207 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate d covariates[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7226--7226 [] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]] ,na.rm=TRUE)[] [2834] [2835] [2836] [2837] [2838] [2839] [2840] [2841] [2842] [2843] [2844] [2845] [2846] [2847] [2848] [2849] [2850] [2851] Underfull \vbox (badness 10000) has occurred while \output is active [2852] [2853] Underfull \hbox (badness 10000) in paragraph at lines 8446--8449 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8446--8449 \T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\ T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 3118) in paragraph at lines 8446--8449 \T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot \T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su mmary.pdIdnot\T1/ptm/m/n/10 . [2854] Underfull \hbox (badness 10000) in paragraph at lines 8502--8505 []\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p tm/m/n/10 , Underfull \hbox (badness 3108) in paragraph at lines 8502--8505 \T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally be [2855] [2856] [2857] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8722--8722 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s cale=-1,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8723--8723 [] \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS E,xlab=NULL,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8726--8726 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [2858] [2859] [2860] Underfull \hbox (badness 1629) in paragraph at lines 8883--8888 \T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is some-times to clone the [2861] [2862] [2863] [2864] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9094--9094 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,...)[] [2865] [2866] Overfull \hbox (6.78088pt too wide) in paragraph at lines 9258--9258 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [2867] [2868] [2869] [2870] Underfull \vbox (badness 10000) has occurred while \output is active [2871] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9526--9526 [] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s mooth deriv i[] [2872] Underfull \hbox (badness 1205) in paragraph at lines 9564--9566 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9564--9566 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 9570--9575 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2873] Underfull \hbox (badness 1205) in paragraph at lines 9654--9656 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9654--9656 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2874] Underfull \hbox (badness 10000) in paragraph at lines 9723--9726 []\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from Underfull \hbox (badness 2057) in paragraph at lines 9723--9726 [][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n /10 are not needed, [2875] [2876] Underfull \hbox (badness 1253) in paragraph at lines 9853--9855 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [2877] [2878] [2879] [2880] Underfull \hbox (badness 1946) in paragraph at lines 10031--10038 []\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef- fects in a GAM in the same Underfull \hbox (badness 2221) in paragraph at lines 10031--10038 \T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre s-sion terms. This method Underfull \hbox (badness 2042) in paragraph at lines 10031--10038 \T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s ee Underfull \hbox (badness 2846) in paragraph at lines 10039--10042 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1 0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n /10 can be used: Underfull \hbox (badness 5862) in paragraph at lines 10039--10042 \T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [2881] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10105--10105 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \hbox (badness 10000) in paragraph at lines 10134--10137 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 , [2882] [2883] [2884] [2885] [2886] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10421--10421 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU LL,pc=NULL) [2887] [2888] [2889] [2890] [2891] [2892] Underfull \hbox (badness 3861) in paragraph at lines 10762--10765 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if Overfull \hbox (36.78088pt too wide) in paragraph at lines 10769--10769 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE, Underfull \hbox (badness 10000) in paragraph at lines 10782--10786 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [2893] Underfull \hbox (badness 10000) in paragraph at lines 10822--10826 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [2894] [2895] [2896] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10963--10963 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$ vectors[,ind]))[] Underfull \hbox (badness 1975) in paragraph at lines 10974--10979 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2897] Underfull \hbox (badness 1803) in paragraph at lines 11051--11055 \T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T 1/ptm/m/n/10 . Underfull \hbox (badness 1502) in paragraph at lines 11063--11075 \T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec Underfull \hbox (badness 2401) in paragraph at lines 11080--11084 \T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able. Plot meth-ods can be Underfull \hbox (badness 2970) in paragraph at lines 11080--11084 \T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/ m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 , [2898] [2899] [2900] Underfull \vbox (badness 10000) has occurred while \output is active [2901] Underfull \hbox (badness 6876) in paragraph at lines 11275--11281 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one or two vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 11316--11317 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2902] [2903] Underfull \hbox (badness 10000) in paragraph at lines 11433--11434 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2904] [2905] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11487--11487 [] \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs, m=c(4,3,0))+[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11499--11499 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11510--11510 [] \T1/pcr/m/n/9 "1st order penalties: red tps; blue bs over (0,1); black bs over (-.5,1.5)")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11511--11511 [] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions and intervals[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11516--11516 [] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i ntervals away[] [2906] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11522--11522 [] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w ild and wide[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11523--11523 [] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/pcr/m/n/9 `\T1/ pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] [2907] Underfull \hbox (badness 10000) in paragraph at lines 11592--11594 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term Underfull \hbox (badness 10000) in paragraph at lines 11592--11594 \T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 s(...,bs="cs", ...) \T1/ptm/m/n/10 or [2908] [2909] Underfull \hbox (badness 10000) in paragraph at lines 11720--11721 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2910] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11801--11801 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first deriv penalty[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11802--11802 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi ed 2nd deriv[] [2911] [2912] [2913] Underfull \hbox (badness 10000) in paragraph at lines 11952--11953 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2914] [2915] [2916] [2917] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12191--12191 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [2918] Underfull \hbox (badness 10000) in paragraph at lines 12252--12254 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2919] [2920] Underfull \vbox (badness 10000) has occurred while \output is active [2921] Underfull \hbox (badness 10000) in paragraph at lines 12411--12414 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method a smooth spec-i-fi-ca-tion ob- Underfull \hbox (badness 3312) in paragraph at lines 12411--12414 \T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs=" re",)\T1/ptm/m/n/10 . For the Underfull \hbox (badness 7099) in paragraph at lines 12411--12414 \T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr /m/n/10 "random.effect" [2922] [2923] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12493--12493 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] Underfull \hbox (badness 10000) in paragraph at lines 12538--12544 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 2698) in paragraph at lines 12538--12544 \T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1 /pcr/m/n/10 gam \T1/ptm/m/n/10 for- [2924] [2925] [2926] Underfull \vbox (badness 10000) has occurred while \output is active [2927] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12752--12752 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] Underfull \vbox (badness 10000) has occurred while \output is active [2928] [2929] Underfull \hbox (badness 10000) in paragraph at lines 12855--12863 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the sphere, via terms like Underfull \hbox (badness 10000) in paragraph at lines 12881--12882 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2930] [2931] [2932] [2933] Underfull \hbox (badness 3396) in paragraph at lines 13142--13145 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any num-ber of vari-ables, spec-i-fied via terms like [2934] Underfull \hbox (badness 10000) in paragraph at lines 13187--13189 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2935] [2936] [2937] [2938] Underfull \hbox (badness 10000) in paragraph at lines 13411--13414 []\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t en pro- Underfull \hbox (badness 3068) in paragraph at lines 13411--13414 \T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see [] []\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas s (see [2939] Underfull \hbox (badness 10000) in paragraph at lines 13444--13448 [][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr /m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression .spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13444--13448 [][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13444--13448 [][]\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 , [2940] [2941] [2942] [2943] [2944] Underfull \hbox (badness 2158) in paragraph at lines 13734--13734 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [2945] Overfull \hbox (48.78088pt too wide) in paragraph at lines 13809--13809 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [2946] [2947] Overfull \hbox (12.78088pt too wide) in paragraph at lines 13943--13943 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [2948] [2949] Underfull \hbox (badness 4846) in paragraph at lines 14074--14077 []\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or es-ti-ma-tors if [2950] [2951] [2952] [2953] [2954] [2955] [2956] [2957] [2958] [2959] [2960] [2961] [2962] [2963] Underfull \hbox (badness 10000) in paragraph at lines 14899--14907 []\T1/ptm/m/n/10 Suppose that \T1/pcr/m/n/10 m=1 \T1/ptm/m/n/10 and you fill an ar-ray us-ing code like Underfull \hbox (badness 10000) in paragraph at lines 14899--14907 \T1/pcr/m/n/10 for(i in 1:K) for(j in i:K) for(k in j:K) for(l in k:K) [2964] [2965] [2966] [2967] Overfull \hbox (24.78088pt too wide) in paragraph at lines 15171--15171 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA LSE, ...)[] [2968] [2969] [2970] [2971] [2972] [2973] Overfull \hbox (20.58041pt too wide) in paragraph at lines 15465--15465 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li near predictor,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15466--15466 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun ded in regions[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15478--15478 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [2974] [2975] [2976]) (./nlme-pkg.tex Chapter 25. [2977] Underfull \hbox (badness 1009) in paragraph at lines 84--93 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [2978] Underfull \hbox (badness 1009) in paragraph at lines 174--183 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [2979] [2980] [2981] [2982] [2983] Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454 [] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [2984] [2985] Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 --------------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n on-sensical!)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 --------------------------- ---------------[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 --------------------------- ---------------[] [2986] [2987] [2988] [2989] [2990] [2991] [2992] [2993] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil lary fissure"),[] [2994] Underfull \hbox (badness 5446) in paragraph at lines 1147--1149 []\T1/ptm/m/n/10 `\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel.h tm\T1/ptm/m/n/10 ', the first edi-tion of [2995] [2996] [2997] [2998] [2999] [3000] [3001] Underfull \hbox (badness 10000) in paragraph at lines 1630--1633 [][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 , [3002] Underfull \hbox (badness 3780) in paragraph at lines 1647--1649 []\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a ted with each com-po-nent of the [3003] [3004] [3005] [3006] [3007] Underfull \hbox (badness 2042) in paragraph at lines 1994--2000 \T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3008] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla pse = "Dog")[] [3009] Underfull \hbox (badness 1132) in paragraph at lines 2144--2146 []\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac ted us-ing the [3010] [3011] Underfull \hbox (badness 4168) in paragraph at lines 2255--2261 [][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize .corStruct[][][]\T1/ptm/m/n/10 , [3012] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2280--2280 [] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3013] [3014] [3015] [3016] [3017] [3018] [3019] [3020] Underfull \hbox (badness 10000) in paragraph at lines 2843--2847 [][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1 /ptm/m/n/10 , [3021] [3022] [3023] [3024] [3025] [3026] [3027] [3028] [3029] [3030] [3031] [3032] Underfull \hbox (badness 6493) in paragraph at lines 3579--3587 [][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [3033] [3034] [3035] [3036] [3037] [3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] Underfull \hbox (badness 10000) in paragraph at lines 5159--5163 [][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [3057] [3058] [3059] [3060] [3061] Underfull \hbox (badness 10000) in paragraph at lines 5476--5480 []\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit- ted in the fit if Underfull \hbox (badness 2671) in paragraph at lines 5476--5480 \T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if \T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 . [3062] [3063] Underfull \hbox (badness 10000) in paragraph at lines 5591--5594 [][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][] []\T1/ptm/m/n/10 , [3064] [3065] [3066] [3067] [3068] [3069] [3070] [3071] [3072] Underfull \hbox (badness 2799) in paragraph at lines 6097--6103 \T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/ ptm/m/n/10 for the random-effects [3073] Underfull \hbox (badness 7133) in paragraph at lines 6158--6162 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \ T1/pcr/m/n/10 model\T1/ptm/m/n/10 , [3074] Underfull \hbox (badness 2057) in paragraph at lines 6242--6253 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 , [3075] Underfull \hbox (badness 10000) in paragraph at lines 6306--6308 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 6338--6338 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3076] [3077] [3078] [3079] Underfull \hbox (badness 7133) in paragraph at lines 6556--6560 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \ T1/pcr/m/n/10 model\T1/ptm/m/n/10 , [3080] Underfull \hbox (badness 10000) in paragraph at lines 6655--6661 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict .gnls[][][]\T1/ptm/m/n/10 , Overfull \hbox (54.78088pt too wide) in paragraph at lines 6682--6682 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min Scale = 0.001, [3081] Underfull \hbox (badness 10000) in paragraph at lines 6720--6722 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3082] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6750--6750 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3083] [3084] [3085] Underfull \hbox (badness 10000) in paragraph at lines 6993--7000 [][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][ ]\T1/ptm/m/n/10 , [3086] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7010--7010 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7018--7018 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7040--7042 []\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou pedData \T1/ptm/m/n/10 ob-ject or a [3087] [3088] [3089] Underfull \hbox (badness 10000) in paragraph at lines 7255--7260 [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl sStruct[][][]\T1/ptm/m/n/10 , [3090] [3091] [3092] Underfull \hbox (badness 10000) in paragraph at lines 7407--7415 []\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial -iza- Underfull \hbox (badness 10000) in paragraph at lines 7407--7415 \T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 1817) in paragraph at lines 7407--7415 \T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 20 EM it-er-a- Underfull \hbox (badness 3118) in paragraph at lines 7430--7433 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 , [3093] [3094] [3095] Underfull \hbox (badness 3354) in paragraph at lines 7645--7647 []\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10 which \T1/ptm/m/n/10 is not equal to [3096] [3097] [3098] [3099] [3100] [3101] Underfull \hbox (badness 1642) in paragraph at lines 8037--8059 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3102] [3103] Underfull \hbox (badness 10000) in paragraph at lines 8157--8174 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme Object[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8157--8174 [][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 , Overfull \hbox (12.78088pt too wide) in paragraph at lines 8200--8200 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] Underfull \hbox (badness 1642) in paragraph at lines 8209--8231 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3104] [3105] [3106] [3107] [3108] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8474--8474 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, Underfull \hbox (badness 10000) in paragraph at lines 8520--8522 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3109] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8558--8558 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h as been already used, duplicate ignored \relax l.8565 \aliasA{sigma}{lmeObject}{sigma} [3110] [3111] [3112] Underfull \hbox (badness 10000) in paragraph at lines 8726--8738 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo r-mula ob-ject of the form [3113] [3114] [3115] [3116] [3117] [3118] [3119] [3120] [3121] Underfull \hbox (badness 10000) in paragraph at lines 9317--9324 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS truct[][][]\T1/ptm/m/n/10 , Overfull \hbox (4.38043pt too wide) in paragraph at lines 9328--9328 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3122] Underfull \hbox (badness 6300) in paragraph at lines 9410--9413 []\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr /m/n/10 lm \T1/ptm/m/n/10 com-po-nents of [3123] [3124] [3125] [3126]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3127] Underfull \hbox (badness 10000) in paragraph at lines 9699--9702 []\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a s Underfull \hbox (badness 3108) in paragraph at lines 9743--9746 []\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive -definite Underfull \hbox (badness 2521) in paragraph at lines 9743--9746 \T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M ust have the same di-men-sions as [3128] [3129] [3130] Underfull \hbox (badness 2435) in paragraph at lines 9917--9922 []\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/ 10 , [3131] [3132] [3133] [3134] [3135] Underfull \hbox (badness 7291) in paragraph at lines 10207--10209 []\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to [3136] [3137] [3138] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10423--10423 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3139] Underfull \hbox (badness 1596) in paragraph at lines 10452--10478 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3140] [3141] [3142] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10628--10628 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3143] [3144] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10779--10779 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] Underfull \hbox (badness 2213) in paragraph at lines 10790--10795 []\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][]\T1/pcr/m/n/10 nlminb [][][] \T1/ptm/m/n/10 (\T1/pcr/m/n/10 iter.max\T1/ptm/m/n/10 ) or the [][]\T1/p cr/m/n/10 nlm[][][] [3145] Underfull \hbox (badness 10000) in paragraph at lines 10812--10816 []\T1/ptm/m/n/10 a log-i-cal value passed as the \T1/pcr/m/n/10 trace \T1/ptm/m /n/10 to Underfull \hbox (badness 10000) in paragraph at lines 10831--10833 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 10867--10867 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3146] [3147] [3148] [3149] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11123--11123 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* message instead of one *each*[] [3150] [3151] [3152] [3153] [3154] [3155] [3156] [3157] [3158] [3159] [3160] [3161] Underfull \hbox (badness 6268) in paragraph at lines 11902--11912 [][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 pdMatrix[][][]\T1/ptm/m/n/10 , [3162] [3163] [3164] [3165] Underfull \hbox (badness 10000) in paragraph at lines 12163--12169 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon struct[][][]\T1/ptm/m/n/10 , [3166] [3167] [3168] [3169] [3170] Underfull \hbox (badness 6876) in paragraph at lines 12485--12487 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i ni-tial-ized \T1/pcr/m/n/10 pdMat \T1/ptm/m/n/10 ob-ject, \T1/pcr/m/n/10 object \T1/ptm/m/n/10 will be con-structed from [3171] [3172] Underfull \hbox (badness 2452) in paragraph at lines 12641--12648 [][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 reStruct[][][]\T1/ptm/m/n/10 , [3173] Underfull \hbox (badness 10000) in paragraph at lines 12706--12712 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re Struct[][][]\T1/ptm/m/n/10 , [3174] [3175] [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] [3187] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13658--13658 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3188] Underfull \hbox (badness 10000) in paragraph at lines 13685--13688 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 6016) in paragraph at lines 13713--13716 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i- zon-tal axis. Underfull \hbox (badness 2653) in paragraph at lines 13713--13716 \T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T 1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and Underfull \hbox (badness 1975) in paragraph at lines 13720--13723 []\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/ ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot Underfull \hbox (badness 1838) in paragraph at lines 13728--13735 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/ 10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner Underfull \hbox (badness 3713) in paragraph at lines 13728--13735 \T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n /10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner [3189] Overfull \hbox (12.78088pt too wide) in paragraph at lines 13785--13785 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] Underfull \hbox (badness 10000) in paragraph at lines 13792--13795 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 2469) in paragraph at lines 13792--13795 \T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v ari-ate and a sin-gle [3190] Underfull \hbox (badness 4582) in paragraph at lines 13820--13823 []\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De -fault is Underfull \hbox (badness 2418) in paragraph at lines 13820--13823 \T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and Underfull \hbox (badness 2990) in paragraph at lines 13824--13827 []\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/ ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot [3191] Underfull \hbox (badness 10000) in paragraph at lines 13900--13903 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa ta\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 1472) in paragraph at lines 13925--13932 \T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3192] Underfull \hbox (badness 10000) in paragraph at lines 13994--13996 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][ ][]\T1/ptm/m/n/10 , [3193] [3194] [3195] [3196] Underfull \hbox (badness 1540) in paragraph at lines 14209--14214 \T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1 /ptm/m/n/10 in-cludes an Underfull \hbox (badness 1215) in paragraph at lines 14256--14258 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [3197] [3198] [3199] [3200] [3201] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14500--14500 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3202] [3203] [3204] [3205] [3206] [3207] [3208] [3209] [3210]pdfTeX warning (e xt4): destination with the same identifier (name{Rfn.random.effects}) has been already used, duplicate ignored \relax l.15153 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15153 ...Extract Random Effects}{random.effects} [3211] [3212] [3213] [3214] [3215] [3216] [3217] [3218] [3219] [3220] Underfull \hbox (badness 1009) in paragraph at lines 15810--15819 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3221] [3222] [3223] Overfull \hbox (66.78088pt too wide) in paragraph at lines 15957--15957 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3224] [3225] [3226] [3227] Underfull \hbox (badness 10000) in paragraph at lines 16235--16253 []\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form Underfull \hbox (badness 1708) in paragraph at lines 16235--16253 \T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+.. .+xn \T1/ptm/m/n/10 spec-i-fy-ing the model [3228] Underfull \hbox (badness 10000) in paragraph at lines 16292--16298 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc t[][][]\T1/ptm/m/n/10 , [3229] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16323--16323 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3230] [3231] [3232] [3233] [3234] [3235] [3236] Underfull \hbox (badness 1728) in paragraph at lines 16812--16815 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3237] [3238] [3239] [3240] [3241] Underfull \hbox (badness 1867) in paragraph at lines 17147--17156 \T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17147--17156 \T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm \T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" Underfull \hbox (badness 10000) in paragraph at lines 17147--17156 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17147--17156 \T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization" [3242] Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu nc-tion: Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m /n/10 varComb\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/ n/10 varConstPower\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m /n/10 varExp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 , [3243] [3244] [3245] [3246] Underfull \hbox (badness 10000) in paragraph at lines 17458--17465 [][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 , [3247] [3248] [3249] [3250] [3251] [3252] [3253] [3254] Underfull \hbox (badness 10000) in paragraph at lines 17993--18003 [][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][] []\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17993--18003 [][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe r[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 3579) in paragraph at lines 18031--18036 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3255] Underfull \hbox (badness 3579) in paragraph at lines 18095--18100 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3256] Underfull \hbox (badness 3579) in paragraph at lines 18158--18163 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3257] Underfull \hbox (badness 1577) in paragraph at lines 18219--18221 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal Underfull \hbox (badness 3579) in paragraph at lines 18221--18226 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3258] Underfull \hbox (badness 3579) in paragraph at lines 18284--18289 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3259] Underfull \hbox (badness 10000) in paragraph at lines 18317--18326 [][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n /10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18317--18326 [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][] []\T1/ptm/m/n/10 , Underfull \hbox (badness 3579) in paragraph at lines 18356--18361 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3260] [3261] [3262] Underfull \hbox (badness 1009) in paragraph at lines 18505--18514 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3263] [3264] Underfull \hbox (badness 1009) in paragraph at lines 18639--18648 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3265] [3266] [3267] [3268] [3269] [3270] [3271] [3272]) (./nnet-pkg.tex Chapter 26. pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.multinom.1}) has been already used, du plicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} [3273] Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70 [] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored = FALSE,[] Underfull \hbox (badness 10000) in paragraph at lines 78--87 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [3274] [3275] [3276] Overfull \hbox (15.18042pt too wide) in paragraph at lines 369--369 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3277] Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c( 0,0,1),50)),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 429--429 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay =5e-4, maxit=200)[] [3278] Underfull \hbox (badness 4013) in paragraph at lines 474--477 \T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if the net was gen-er-ated by [3279] Overfull \hbox (15.18042pt too wide) in paragraph at lines 509--509 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3280]) (./rpart-pkg.tex Chapter 27. [3281] [3282] [3283] [3284] Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse = TRUE, ...)[] [3285] Underfull \hbox (badness 10000) in paragraph at lines 373--377 []\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm /m/n/10 ) or ma-trix of left and right splits [3286] [3287] [3288] Underfull \hbox (badness 1442) in paragraph at lines 591--597 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be at the hor-i-zon-tal plot co-or-di-nates of [3289] [3290] Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] [3291] Underfull \hbox (badness 2941) in paragraph at lines 785--787 []\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice if [3292] Overfull \hbox (25.98041pt too wide) in paragraph at lines 902--902 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] [3293] Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"), ...)[] [3294] [3295] [3296] Underfull \hbox (badness 2310) in paragraph at lines 1113--1116 []\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees all three resid-ual def-i-ni-tions re-duce to Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m ethod, Overfull \hbox (12.78088pt too wide) in paragraph at lines 1164--1164 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] Underfull \hbox (badness 2837) in paragraph at lines 1187--1196 []\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 " poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1 0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method Underfull \hbox (badness 2088) in paragraph at lines 1187--1196 \T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu ess. If \T1/pcr/m/n/10 y Underfull \hbox (badness 1817) in paragraph at lines 1187--1196 \T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2 [3297] Underfull \hbox (badness 2846) in paragraph at lines 1226--1228 []\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1 0 rpart \T1/ptm/m/n/10 al-go-rithm. See [3298] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1286--1286 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c p = 0.01, Overfull \hbox (60.78088pt too wide) in paragraph at lines 1287--1287 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3299] [3300] [3301] [3302] [3303] [3304] Underfull \hbox (badness 1565) in paragraph at lines 1739--1742 []\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val- ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ', [3305] [3306] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3307] [3308] [3309]) (./spatial-pkg.tex [3310] Chapter 28. [3311] [3312] [3313] [3314] [3315] [3316] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3317] [3318] [3319] [3320] [3321] [3322] [3323] [3324] [3325] [3326] [3327] [3328] [3329]) (./survival-pkg.tex [3330] Chapter 29. [3331] [3332] Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data = lung, nmin = 1[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t he last point[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 193--193 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a nd Grambsch.[] [3333] [3334]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.aml}) has been already used, duplicate ignored \relax l.326 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica te ignored \relax l.326 ... Myelogenous Leukemia survival data}{aml} [3335] [3336] Overfull \hbox (9.78043pt too wide) in paragraph at lines 423--423 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da ta = ovarian) Overfull \hbox (4.38043pt too wide) in paragraph at lines 425--425 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d ata=ovarian)[] [3337] Overfull \hbox (6.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog), lung)[] [3338] [3339] Underfull \vbox (badness 10000) has occurred while \output is active [3340] Overfull \hbox (36.78088pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c ohort.size, Overfull \hbox (48.78088pt too wide) in paragraph at lines 662--662 [] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan", "II.Borgan"),[] [3341] [3342] Overfull \hbox (9.78043pt too wide) in paragraph at lines 805--805 [] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz e=stratsizes,[] [3343] [3344] [3345] Underfull \hbox (badness 1097) in paragraph at lines 975--977 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. Overfull \hbox (4.38043pt too wide) in paragraph at lines 995--995 []\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit h large rate[] [3346] [3347] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1110--1110 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat um), data=infert) [3348]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col on}) has been already used, duplicate ignored \relax l.1178 ...erapy for Stage B/C colon cancer}{colon} Underfull \vbox (badness 2698) has occurred while \output is active [3349] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1271--1271 [] \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G 2", "I"),[] [3350] [3351] [3352] [3353] [3354] [3355] Underfull \hbox (badness 1337) in paragraph at lines 1753--1757 [][][]\T1/pcr/m/n/10 coxph.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 coxp h.control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cluster[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 strata[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Surv[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 pspline[][][]\T1/ptm/m/n/10 , [3356] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1808--1808 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3357] [3358] [3359] [3360] [3361] [3362] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2246--2246 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] [3363] [3364] [3365] [3366] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2495--2495 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3367] [3368] [3369] [3370] [3371] Underfull \vbox (badness 2012) has occurred while \output is active [3372] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2812--2812 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) Overfull \hbox (36.7804pt too wide) in paragraph at lines 2848--2848 [] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre ssion", "death")))[] Underfull \hbox (badness 1389) in paragraph at lines 2862--2864 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with [3373] Underfull \hbox (badness 1048) in paragraph at lines 2917--2919 []\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se e the note in [3374] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2995--2995 [] \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3375] [3376] [3377] [3378] [3379] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3241--3241 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3380] [3381] [3382] [3383] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3507--3507 [] \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5" , sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3384] Underfull \vbox (badness 10000) has occurred while \output is active [3385] [3386] [3387] [3388] [3389] [3390] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3924--3924 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3391] [3392] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4119--4119 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3393] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4245--4245 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] [3394] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4253--4253 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3395] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4339--4339 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3396] [3397] Underfull \hbox (badness 1852) in paragraph at lines 4487--4489 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/ n/10 , which is the re-sult of the [3398] [3399] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4622--4622 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me thod, Overfull \hbox (36.78088pt too wide) in paragraph at lines 4623--4623 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3400] [3401] [3402] Overfull \hbox (30.78088pt too wide) in paragraph at lines 4787--4787 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] Underfull \hbox (badness 1540) in paragraph at lines 4842--4845 []\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per -son years if [3403] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4889--4889 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4910--4910 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50 ,60,70,100)) +[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4912--4912 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3404] [3405] [3406] [3407] [3408] Underfull \vbox (badness 2126) has occurred while \output is active [3409] [3410] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5387--5387 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 1043) in paragraph at lines 5399--5402 \T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and [3411] [3412] [3413] [3414] [3415] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5699--5699 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the ta=5), cancer)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 5700--5700 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), cancer)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.5705 ...ata from a soldering experiment}{solder} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.solder.1}) has been already used, dupl icate ignored \relax l.5705 ...ata from a soldering experiment}{solder} [3416] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5811--5811 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3417] [3418] [3419] [3420] [3421] [3422] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6166--6166 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r r =expected,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6167--6167 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3423] [3424] [3425] [3426] Overfull \hbox (54.78088pt too wide) in paragraph at lines 6459--6459 [] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/ 10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/ n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] [3427] [3428] Underfull \vbox (badness 10000) has occurred while \output is active [3429] Underfull \hbox (badness 10000) in paragraph at lines 6722--6729 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 length \T1/ptm/m/n/10 of a \T1/pcr/m/n/10 S urv \T1/ptm/m/n/10 ob-ject is the num-ber of sur-vival times Underfull \hbox (badness 10000) in paragraph at lines 6722--6729 \T1/ptm/m/n/10 it con-tains, not the num-ber of items re-quired to en-code it, e.g., Underfull \hbox (badness 1412) in paragraph at lines 6722--6729 \T1/pcr/m/n/10 x <- Surv(1:4, 5:9, c(1,0,1,0)); length(x) \T1/ptm/m/n/10 has a value of 4. Like- Underfull \hbox (badness 1253) in paragraph at lines 6733--6736 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 median\T1/ptm/m/n/10 , \T1/pcr/m/n/10 quant ile \T1/ptm/m/n/10 and \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 meth-ods first con-st ruct a sur-vival curve us-ing [3430] [3431] Underfull \hbox (badness 10000) in paragraph at lines 6876--6885 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form [3432] Overfull \hbox (36.7804pt too wide) in paragraph at lines 6972--6972 [] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1 , year=accept.dt),[] [3433] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6990--6990 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] Underfull \hbox (badness 1038) in paragraph at lines 7032--7038 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival [3434] Underfull \hbox (badness 3000) in paragraph at lines 7054--7056 []\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab le \T1/ptm/m/n/10 is in units/day, Overfull \hbox (48.78088pt too wide) in paragraph at lines 7084--7084 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3435] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7170--7170 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3436] [3437] [3438] Underfull \hbox (badness 10000) in paragraph at lines 7395--7400 [][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 , [3439] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7416--7416 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3440] [3441] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7633--7633 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3442] [3443] Underfull \hbox (badness 6332) in paragraph at lines 7740--7745 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val- ues are [3444] [3445] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7933--7933 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3446] [3447] [3448] [3449] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8223--8223 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3450] Underfull \hbox (badness 1354) in paragraph at lines 8264--8268 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3451] [3452] Underfull \hbox (badness 2035) in paragraph at lines 8439--8446 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv reg.distributions[][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 8439--8446 \T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/ m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 , Underfull \hbox (badness 1297) in paragraph at lines 8439--8446 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n /10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is [3453] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8515--8515 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3454] Overfull \vbox (31.11076pt too high) has occurred while \output is active [3455] [3456] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8672--8672 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3457] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8804--8804 [] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x ^2*temp -1))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8807--8807 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3458] [3459] [3460] [3461] [3462] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9109--9109 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic al trial plus[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9110--9110 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9116--9116 [] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day , alk.phos))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9118--9118 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3463] [3464] [3465] [3466] [3467] [3468]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.xtfrm.Surv}) has been already used, duplicate i gnored \relax l.9488 ...ting order for Surv objects}{xtfrm.Surv} [3469] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9556--9556 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3470] [3471] [3472]) No file fullrefman.ind. (./fullrefman.aux) ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.tree} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.viewports} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.xyplot.zoo} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ellipsePoints} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ellipse} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.cluster.stats} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.chorizon} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.as.Rul.dsTMatrix.Rul.listw} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.similar.listw} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.nb2listw} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.read.gal} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.matrix.csr} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.SparseM.ontology} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.modelMatrix} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.model.Matrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.nearcor} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.posdefify} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.get.adjacency} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.graph.adjacency} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.graph} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.sqrtm} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.logm} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.showClass} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.loglm1} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.lmrob} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.wilcox.Rul.test} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.spearman.test} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.pSpearman} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.pKendall} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.Kendall} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.cor.fk} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dMatrix} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgCMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ansari.Rul.test} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.showDefault} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getGroupMembers} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.resetGeneric} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.linearizeMlist} has been referenced but does no t exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getGeneric} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getMethodsForDispatch} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.setDataPart} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getDataPart} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.possibleExtends} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.mosaic} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.assoc} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getNamespace} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.asNamespace} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.formalArgs} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.isRematched} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, replaced by a fixed one {/usr/share/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on fullrefman.pdf (3523 pages, 9046834 bytes). Transcript written on fullrefman.log. This is pdfTeXk, Version 3.1415926-1.40.9 (Web2C 7.5.7) %&-line parsing enabled. entering extended mode (./fullrefman.tex LaTeX2e <2005/12/01> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, german-x-2008-06-18, ngerman-x-2008-06-18, ancientgreek, ibycus, ar abic, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danish, dutc h, esperanto, estonian, farsi, finnish, french, galician, german, ngerman, mono greek, greek, hungarian, icelandic, indonesian, interlingua, irish, italian, la tin, mongolian, mongolian2a, bokmal, nynorsk, polish, portuguese, romanian, rus sian, sanskrit, serbian, slovak, slovenian, spanish, swedish, turkish, ukenglis h, ukrainian, uppersorbian, welsh, loaded. (/usr/share/texmf-dist/tex/latex/base/book.cls Document Class: book 2005/09/16 v1.4f Standard LaTeX document class (/usr/share/texmf-dist/tex/latex/base/bk10.clo)) (../../.././share/texmf/tex/latex/Rd.sty (/usr/share/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texmf/tex/latex/latex2html/url.sty) (/usr/share/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texmf-dist/tex/latex/base/ts1enc.def)) (/usr/share/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texmf-dist/tex/latex/base/t1enc.def)) (/usr/share/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texmf/tex/latex/config/color.cfg) (/usr/share/texmf-dist/tex/latex/pdftex-def/pdftex.def)) (/usr/share/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texmf-dist/tex/latex/oberdiek/hycolor.sty (/usr/share/texmf-dist/tex/latex/oberdiek/xcolor-patch.sty)) (/usr/share/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texmf-dist/tex/generic/oberdiek/infwarerr.sty)) (/usr/share/texmf/tex/latex/config/hyperref.cfg) (/usr/share/texmf-dist/tex/latex/oberdiek/kvoptions.sty) Implicit mode ON; LaTeX internals redefined (/usr/share/texmf-dist/tex/generic/oberdiek/bitset.sty (/usr/share/texmf-dist/tex/generic/oberdiek/intcalc.sty) (/usr/share/texmf-dist/tex/generic/oberdiek/bigintcalc.sty (/usr/share/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty))) (/usr/share/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty) (/usr/share/texmf-dist/tex/generic/oberdiek/atbegshi.sty)) *hyperref using default driver hpdftex* (/usr/share/texmf-dist/tex/latex/hyperref/hpdftex.def) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 366. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 366. ) (/usr/share/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texmf-dist/tex/latex/base/utf8.def (/usr/share/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texmf-dist/tex/latex/base/omsenc.dfu) (/usr/share/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texmf/tex/latex/config/graphics.cfg))) (/usr/share/texmf-dist/tex/latex/base/makeidx.sty) Writing index file fullrefman.idx (./fullrefman.aux) (/usr/share/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texmf-dist/tex/context/base/supp-pdf.tex [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texmf-dist/tex/latex/oberdiek/refcount.sty)) (./fullrefman.out) (./fullrefman.out) (/usr/share/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex) (/usr/share/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/usr/shar e/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./fullrefman.toc (/usr/share/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48]) [49] [50] [1] [2] (./base-pkg.tex Chapter 1. Underfull \hbox (badness 4595) in paragraph at lines 40--43 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [3] Underfull \hbox (badness 4168) in paragraph at lines 94--99 []\T1/pcr/m/n/10 .Devices \T1/ptm/m/n/10 is a [][]pairlist[][][] of length-one char-ac-ter vec-tors. The first en-try is al-ways [4] Underfull \hbox (badness 10000) in paragraph at lines 135--141 []\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1/ptm/m/n/10 such that Underfull \hbox (badness 10000) in paragraph at lines 135--141 \T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . It equals \T1/pcr/m/n/10 double.base ^ ulp.digits \T1/ptm/m/n/10 if ei- Underfull \hbox (badness 6236) in paragraph at lines 135--141 \T1/ptm/m/n/10 ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m /n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er-wise, Underfull \hbox (badness 10000) in paragraph at lines 135--141 \T1/ptm/m/n/10 it is \T1/pcr/m/n/10 (double.base ^ double.ulp.digits) / 2\T1/pt m/m/n/10 . Nor-mally Underfull \hbox (badness 10000) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/pcr/m/n/10 x \T1 /ptm/m/n/10 such that \T1/pcr/m/n/10 1 - x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 4328) in paragraph at lines 141--149 \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/pcr/m/n/10 (double.base ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-ma lly Underfull \hbox (badness 10000) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ- Underfull \hbox (badness 10000) in paragraph at lines 152--159 \T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) * [5] [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 339--342 [][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys. info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar, [8] Underfull \hbox (badness 2359) in paragraph at lines 386--389 []\T1/ptm/m/n/10 logical: should \T1/pcr/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [9] [10] Underfull \hbox (badness 1072) in paragraph at lines 534--540 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [11] [12] (/usr/share/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [13] [14] [15] Overfull \hbox (0.78088pt too wide) in paragraph at lines 860--860 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [16] [17] [18] [19] Underfull \hbox (badness 1838) in paragraph at lines 1147--1150 []\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [20] [21] [22] [23] Underfull \hbox (badness 5862) in paragraph at lines 1381--1387 []\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m /n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I t is guar-an-teed that [24] [25] [26] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1639--1639 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] Underfull \hbox (badness 3168) in paragraph at lines 1656--1663 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , set-ting row n ames and con-vert-ing col-umn names Underfull \hbox (badness 3128) in paragraph at lines 1656--1663 \T1/ptm/m/n/10 (to syn-tac-tic names: see [][]\T1/pcr/m/n/10 make.names[][][]\T 1/ptm/m/n/10 ) is op-tional. Note that all Underfull \hbox (badness 6094) in paragraph at lines 1656--1663 \T1/ptm/m/n/10 of \T1/phv/m/n/10 R\T1/ptm/m/n/10 's \T1/ptm/b/n/10 base \T1/ptm /m/n/10 pack-age \T1/pcr/m/n/10 as.data.frame() \T1/ptm/m/n/10 meth-ods use \T1 /pcr/m/n/10 optional Underfull \hbox (badness 10000) in paragraph at lines 1656--1663 \T1/ptm/m/n/10 only for col-umn names treat-ment, ba-si-cally with the mean-ing of Underfull \hbox (badness 10000) in paragraph at lines 1656--1663 [][]\T1/pcr/m/n/10 data.frame[][][](*, check.names = !optional)\T1/ptm/m/n/10 . See also the [27] Underfull \hbox (badness 1303) in paragraph at lines 1667--1670 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [28] Underfull \hbox (badness 10000) in paragraph at lines 1785--1787 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 Date \T1/ptm/m/n/10 ob-ject, or some-thing wh ich can be co-erced by [29] [30] Overfull \hbox (112.38031pt too wide) in paragraph at lines 1922--1922 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] Overfull \hbox (19.13934pt too wide) in paragraph at lines 1957--1959 []\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e nv[][][](x, parent = emptyenv()) Underfull \hbox (badness 10000) in paragraph at lines 1960--1962 []\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2120--2122 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2233--2233 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [36] [37] Underfull \hbox (badness 1107) in paragraph at lines 2366--2368 []\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1 0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see [38] [39] Overfull \hbox (36.78088pt too wide) in paragraph at lines 2533--2533 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse(substitute(what), backt ick=FALSE), [40] [41] [42] Underfull \hbox (badness 5878) in paragraph at lines 2698--2703 []\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to \T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at- Underfull \hbox (badness 10000) in paragraph at lines 2698--2703 \T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3656--3658 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] Overfull \hbox (102.78088pt too wide) in paragraph at lines 3897--3897 [] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [60] [61] [62] [63] Underfull \hbox (badness 4927) in paragraph at lines 4136--4140 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an ob-ject Underfull \hbox (badness 2012) in paragraph at lines 4136--4140 \T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or [64] [65] Underfull \hbox (badness 4595) in paragraph at lines 4280--4283 []\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par -i-son[][][] and [66] [67] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4435--4435 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] [68] Underfull \hbox (badness 1199) in paragraph at lines 4465--4471 []\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na med ar-gu- Underfull \hbox (badness 2573) in paragraph at lines 4476--4479 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [69] Underfull \hbox (badness 10000) in paragraph at lines 4556--4561 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j ust a wrap-per for Underfull \hbox (badness 10000) in paragraph at lines 4556--4561 [][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T his means that it will split ma- Underfull \hbox (badness 2181) in paragraph at lines 4556--4561 \T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter columns to fac-tors un-less [70] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4635--4635 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [71] [72] [73] [74] Underfull \hbox (badness 2521) in paragraph at lines 4888--4890 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [75] [76] [77] [78] [79] [80] Underfull \hbox (badness 10000) in paragraph at lines 5285--5293 []\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [81] [82] [83] [84] [85] [86] [87] [88] Underfull \hbox (badness 1796) in paragraph at lines 5845--5853 []\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / / [89] [90] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6039--6039 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile r, math-library:[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 6041--6041 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6042--6042 []\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows \TS1/pcr/m/n/9 '\T1/pcr /m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[] [91] [92] [93] Underfull \hbox (badness 1635) in paragraph at lines 6208--6211 []\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1 0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class Underfull \hbox (badness 3009) in paragraph at lines 6212--6215 []\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. They can be es-tab-lished us-ing Underfull \hbox (badness 1102) in paragraph at lines 6229--6242 []\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in Underfull \hbox (badness 1308) in paragraph at lines 6243--6251 []\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should [94] [95] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6396--6396 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [96] Overfull \hbox (107.35893pt too wide) in paragraph at lines 6438--6440 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [97] [98] Underfull \hbox (badness 10000) in paragraph at lines 6580--6583 []\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is Underfull \hbox (badness 2057) in paragraph at lines 6580--6583 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T 1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/ 10 host [99] [100] Underfull \hbox (badness 1248) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it Underfull \hbox (badness 10000) in paragraph at lines 6782--6784 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from [101] Underfull \hbox (badness 1067) in paragraph at lines 6824--6831 \T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar ds . freedesktop . org / clipboards-[]spec / [102] [103] Underfull \vbox (badness 10000) has occurred while \output is active [104] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7016--7016 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [105] Underfull \hbox (badness 1231) in paragraph at lines 7141--7147 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [106] [107] [108] [109] Underfull \hbox (badness 10000) in paragraph at lines 7352--7354 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [110] [111] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7497--7497 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] Underfull \hbox (badness 4595) in paragraph at lines 7539--7542 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [112] [113] [114] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7735--7735 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [115] [116] Underfull \hbox (badness 8132) in paragraph at lines 7836--7840 []\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors ? The Underfull \hbox (badness 4543) in paragraph at lines 7836--7840 \T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , but this can be changed by set-ting Underfull \hbox (badness 10000) in paragraph at lines 7855--7865 []\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing Underfull \hbox (badness 1062) in paragraph at lines 7855--7865 [][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that is a generic func-tion, meth-ods can be [117] Overfull \hbox (4.63962pt too wide) in paragraph at lines 7887--7891 []\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors") Underfull \hbox (badness 7451) in paragraph at lines 7926--7936 [][][]\T1/pcr/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col- Underfull \hbox (badness 3449) in paragraph at lines 7926--7936 \T1/ptm/m/n/10 umn names), [][]\T1/pcr/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods and \T1/pcr/m/n/10 I(matrix(..)) \T1/ptm/m/n/10 ex-a m- [118] [119] [120] [121] [122] [123] Underfull \hbox (badness 10000) in paragraph at lines 8358--8370 \T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n /10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8358--8370 \T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59", tz = "UTC") \T1/ptm/m/n/10 will give [124] [125] [126] Underfull \hbox (badness 5802) in paragraph at lines 8585--8589 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10 reads the file byte-by-byte. This al-lows a Underfull \hbox (badness 10000) in paragraph at lines 8620--8621 [][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy / index . [127] [128] [129] Underfull \hbox (badness 10000) in paragraph at lines 8805--8809 []\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu nc-tions should be listed in [130] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8893--8893 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8895--8895 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] [131] Overfull \hbox (60.78088pt too wide) in paragraph at lines 8920--8920 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 8921--8921 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [132] [133] Underfull \hbox (badness 5403) in paragraph at lines 9039--9041 []\T1/pcr/m/n/10 ..deparseOpts \T1/ptm/m/n/10 is the [][]\T1/pcr/m/n/10 charact er[][][] \T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used by Underfull \hbox (badness 6063) in paragraph at lines 9058--9060 []\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][]\T1/pcr/m/n /10 formula[][][]\T1/ptm/m/n/10 s, with [134] Underfull \hbox (badness 1132) in paragraph at lines 9130--9137 \T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to make the re-sult parseable. [135] Underfull \hbox (badness 1603) in paragraph at lines 9266--9269 []\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t er-mi-nant if [136] [137] [138] [139] [140] [141] [142] [143] [144] Underfull \hbox (badness 1917) in paragraph at lines 9872--9877 []\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has [145] Overfull \hbox (36.7804pt too wide) in paragraph at lines 9927--9927 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE RS)))) # recycling[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9928--9928 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [146] [147] Underfull \hbox (badness 1168) in paragraph at lines 10030--10035 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by Underfull \hbox (badness 10000) in paragraph at lines 10069--10075 []\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m /n/10 .. \T1/ptm/m/n/10 and ba-si-cally the same as Underfull \hbox (badness 5403) in paragraph at lines 10076--10079 []\T1/pcr/m/n/10 ...length() \T1/ptm/m/n/10 re-turns the num-ber of ex-pres-sio ns in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . This is the same as [148] [149] [150] Underfull \hbox (badness 2828) in paragraph at lines 10235--10239 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 10235--10239 \T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr /m/n/10 https : / / en . wikipedia . org / wiki / Double _ Overfull \hbox (42.78088pt too wide) in paragraph at lines 10268--10268 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [151] [152] [153] [154] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10483--10483 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [155] Underfull \hbox (badness 1629) in paragraph at lines 10557--10561 []\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re -sult of lazy-loading (when [156] Underfull \hbox (badness 2150) in paragraph at lines 10658--10661 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse [157] Underfull \hbox (badness 3690) in paragraph at lines 10672--10680 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10 anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for Underfull \hbox (badness 10000) in paragraph at lines 10681--10683 []\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent to but faster than Underfull \hbox (badness 3735) in paragraph at lines 10701--10708 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [158] [159] [160] Underfull \hbox (badness 10000) in paragraph at lines 10897--10900 []\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use [161] [162] [163] [164] [165] [166] [167] [168] [169] Underfull \hbox (badness 5288) in paragraph at lines 11594--11596 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of Underfull \hbox (badness 3039) in paragraph at lines 11604--11609 []\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10 dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10 and [170] Underfull \hbox (badness 10000) in paragraph at lines 11664--11666 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [171] [172] Underfull \hbox (badness 4569) in paragraph at lines 11781--11785 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11781--11785 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [173] [174] Underfull \hbox (badness 10000) in paragraph at lines 11896--11898 []\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/ m/n/10 where \T1/ptm/m/n/10 as Underfull \hbox (badness 2790) in paragraph at lines 11939--11941 []\T1/pcr/m/n/10 get0(): \T1/ptm/m/n/10 The object---as from [][]\T1/pcr/m/n/10 get[][][](x, *)\T1/ptm/m/n/10 --- if \T1/pcr/m/n/10 exists(x, *) \T1/ptm/m/n/1 0 is true, oth-er-wise [175] [176] [177] Underfull \hbox (badness 4048) in paragraph at lines 12110--12120 []\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me nt into an ex-pres-sion ob-ject. It is Underfull \hbox (badness 3657) in paragraph at lines 12110--12120 \T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d e-fault method calls [178] [179] [180] Underfull \hbox (badness 5460) in paragraph at lines 12358--12367 []\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l- Underfull \hbox (badness 2221) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes e op-er-a-tions are those Underfull \hbox (badness 2707) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x, inherits = FALSE)\T1/ptm/m/ n/10 . If no match is found then \T1/pcr/m/n/10 NULL Underfull \hbox (badness 2818) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T 1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again, Underfull \hbox (badness 6978) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th is case are those of [181] [182] [183] [184] [185] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12732--12732 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [186] [187] [188] [189] Underfull \hbox (badness 5119) in paragraph at lines 13017--13020 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [190] [191] Underfull \hbox (badness 2221) in paragraph at lines 13178--13187 \T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas s [192] [193] [194] [195] Underfull \hbox (badness 2253) in paragraph at lines 13439--13441 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [196] [197] Underfull \hbox (badness 10000) in paragraph at lines 13554--13556 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m /n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with [198] [199] Underfull \hbox (badness 10000) in paragraph at lines 13704--13706 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [200] [201] Underfull \hbox (badness 10000) in paragraph at lines 13813--13817 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13824--13827 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Overfull \hbox (47.58038pt too wide) in paragraph at lines 13845--13845 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] [202] Overfull \hbox (30.78088pt too wide) in paragraph at lines 13868--13868 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [203] Underfull \hbox (badness 10000) in paragraph at lines 13960--13963 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 13970--13970 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [204] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14045--14045 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] [205] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14074--14074 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, Underfull \hbox (badness 7238) in paragraph at lines 14098--14105 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr /m/n/10 vec\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14098--14105 \T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial , equiv-a-lent to Underfull \hbox (badness 2126) in paragraph at lines 14098--14105 \T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter of fact, the in-ter-nal al-go- Underfull \hbox (badness 3965) in paragraph at lines 14106--14110 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [206] [207] [208] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14269--14269 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 14270--14270 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [209] Underfull \hbox (badness 10000) in paragraph at lines 14349--14353 []\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a Underfull \hbox (badness 1389) in paragraph at lines 14349--14353 \T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m ay not be equiv-a-lent to [210] [211] Overfull \hbox (63.78036pt too wide) in paragraph at lines 14497--14497 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have type symbol (aka name).[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 14500--14500 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [212] Underfull \hbox (badness 1168) in paragraph at lines 14584--14588 []\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real or com-plex vec- Underfull \hbox (badness 2012) in paragraph at lines 14584--14588 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [213] Underfull \hbox (badness 6944) in paragraph at lines 14679--14682 [][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 toString[][][]\T1/ptm/m/n/10 , [214] Overfull \hbox (4.38043pt too wide) in paragraph at lines 14704--14704 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [215] [216] Underfull \hbox (badness 10000) in paragraph at lines 14838--14840 []\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos -si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 14857--14857 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14859--14859 [] \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx = NA,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14862--14862 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)))[] Underfull \hbox (badness 2790) in paragraph at lines 14868--14871 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [217] Underfull \hbox (badness 4254) in paragraph at lines 14884--14892 []\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/ m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied, Underfull \hbox (badness 1024) in paragraph at lines 14899--14903 []\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10 xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m /n/10 "E" \T1/ptm/m/n/10 give [218] Underfull \hbox (badness 10000) in paragraph at lines 14968--14970 []\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 []\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 \T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f g") \T1/ptm/m/n/10 gives Underfull \hbox (badness 10000) in paragraph at lines 14979--14987 []\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti -fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be com-plex (or Underfull \hbox (badness 3601) in paragraph at lines 15013--15017 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 3302) in paragraph at lines 15013--15017 \T1/ptm/m/n/10 within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [219] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15080--15080 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big .mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] [220] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15102--15102 []\T1/pcr/m/n/9 doLC <- FALSE # R warns, so change to TRUE manually if you wan t see the effect[] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] [232] Overfull \hbox (20.58041pt too wide) in paragraph at lines 15920--15920 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [233] Underfull \hbox (badness 2418) in paragraph at lines 16029--16033 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 16036--16039 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/ m/n/10 , then the sin-gle Underfull \hbox (badness 2326) in paragraph at lines 16064--16071 [][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 , [234] [235] [236] [237] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16310--16310 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, Underfull \hbox (badness 1867) in paragraph at lines 16335--16342 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [238] [239] [240] [241] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16603--16603 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Underfull \vbox (badness 10000) has occurred while \output is active [242] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16632--16632 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] [243] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16683--16683 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 16689--16693 []\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o r fixed pat-tern for Underfull \hbox (badness 1028) in paragraph at lines 16689--16693 \T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec- tor. Co-erced by [244] [245] [246] [247] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17048--17048 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z < - c(2, 1:9))) [248] [249] [250] [251] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17302--17302 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [252] [253] [254] Underfull \hbox (badness 2435) in paragraph at lines 17563--17565 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www . unicode . org / reports / tr35 / [255] Underfull \hbox (badness 1867) in paragraph at lines 17605--17612 []\T1/ptm/m/n/10 It is op-tional on Win-dows: if \T1/phv/m/n/10 R \T1/ptm/m/n/1 0 has been built against ICU, it will only be used if Underfull \hbox (badness 1490) in paragraph at lines 17605--17612 \T1/ptm/m/n/10 en-vi-ron-ment vari-able \T1/pcr/m/n/10 R_ICU_LOCALE \T1/ptm/m/n /10 is set or once \T1/pcr/m/n/10 icuSetCollate \T1/ptm/m/n/10 is called to se- Underfull \hbox (badness 1490) in paragraph at lines 17605--17612 \T1/ptm/m/n/10 lect the lo-cale (as ICU and Win-dows dif-fer in their idea of l o-cale names). Note that Underfull \hbox (badness 2285) in paragraph at lines 17620--17622 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 http : / / userguide . icu-[]project . org / Overfull \hbox (9.78043pt too wide) in paragraph at lines 17628--17628 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s ettings, we can only reset to the default.[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17638--17638 [] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p rint(sort(x))[] [256] Overfull \hbox (24.78088pt too wide) in paragraph at lines 17658--17658 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [257] [258] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17792--17792 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17798--17798 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17801--17801 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share an environment:[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17807--17807 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [259] [260] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17934--17934 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u se ifelse(),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17942--17942 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] [261] [262] [263] Underfull \hbox (badness 10000) in paragraph at lines 18147--18149 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/ pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and [264] Underfull \hbox (badness 4217) in paragraph at lines 18231--18240 [][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 2057) in paragraph at lines 18246--18262 [][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [265] [266] [267] [268] [269] [270] Underfull \hbox (badness 4699) in paragraph at lines 18660--18663 []\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , [271] [272] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18783--18783 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [273] [274] Underfull \hbox (badness 4739) in paragraph at lines 18918--18920 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [275] [276] [277] [278] [279] [280] [281] Underfull \hbox (badness 1430) in paragraph at lines 19331--19336 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 19331--19336 \T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 is the same as [282] Underfull \hbox (badness 10000) in paragraph at lines 19392--19397 []\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/ 10 will pro-duce a (``higher Underfull \hbox (badness 10000) in paragraph at lines 19392--19397 \T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe r = FALSE \T1/ptm/m/n/10 would Underfull \hbox (badness 5008) in paragraph at lines 19392--19397 \T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon d to Underfull \hbox (badness 10000) in paragraph at lines 19392--19397 \T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s implify = TRUE\T1/ptm/m/n/10 , re- [283] Underfull \hbox (badness 10000) in paragraph at lines 19452--19459 []\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If Underfull \hbox (badness 6364) in paragraph at lines 19452--19459 \T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth- Underfull \hbox (badness 5064) in paragraph at lines 19452--19459 \T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix with Underfull \hbox (badness 5908) in paragraph at lines 19452--19459 \T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length( X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1 0 with Underfull \hbox (badness 10000) in paragraph at lines 19468--19470 []\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 is equiv-a-lent to [284] Underfull \hbox (badness 1975) in paragraph at lines 19540--19543 []\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to [285] [286] [287] [288] [289] [290] Underfull \hbox (badness 1077) in paragraph at lines 19935--19940 []\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/ n/10 and [291] Underfull \hbox (badness 10000) in paragraph at lines 19949--19956 [][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / [292] Underfull \hbox (badness 10000) in paragraph at lines 20023--20027 []\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory [293] Underfull \hbox (badness 10000) in paragraph at lines 20153--20157 []\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use Underfull \hbox (badness 1454) in paragraph at lines 20153--20157 [][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self [294] [295] Underfull \hbox (badness 10000) in paragraph at lines 20251--20258 [][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/ m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 , [296] [297] Underfull \hbox (badness 10000) in paragraph at lines 20372--20376 []\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10 on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use [298] Underfull \hbox (badness 5161) in paragraph at lines 20442--20447 []\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di s-tributed un-der the Underfull \hbox (badness 6592) in paragraph at lines 20442--20447 \T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c opy of Underfull \hbox (badness 5133) in paragraph at lines 20442--20447 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 20442--20447 \T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 3 of the li-cense can be dis-played by [299] [300] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20609--20609 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20613--20613 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [301] Underfull \hbox (badness 3343) in paragraph at lines 20669--20673 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for many more file han-dling func-tions and [302] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20755--20755 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 20766--20766 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, pr = 0.2))),[] [303] [304] Overfull \hbox (9.78043pt too wide) in paragraph at lines 20877--20877 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the same names ![] Overfull \hbox (74.58035pt too wide) in paragraph at lines 20880--20880 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w / same name in .GlobalEnv[] [305] Underfull \hbox (badness 6380) in paragraph at lines 20925--20930 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- Underfull \hbox (badness 1337) in paragraph at lines 20983--20990 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t ails of the string are system-specific: it might be Underfull \hbox (badness 1960) in paragraph at lines 20983--20990 \T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by \T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, ma-cOS) or Underfull \hbox (badness 1043) in paragraph at lines 20983--20990 \T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in [306] Underfull \hbox (badness 2564) in paragraph at lines 21016--21019 []\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/ ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of Overfull \hbox (4.38043pt too wide) in paragraph at lines 21046--21046 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] [307] Underfull \hbox (badness 1205) in paragraph at lines 21069--21074 \T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form [308] [309] Underfull \hbox (badness 1400) in paragraph at lines 21214--21218 [][][]\T1/pcr/m/n/10 raw[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][]\T1/pcr/m/n/10 do uble[][][] \T1/ptm/m/n/10 (class Overfull \hbox (36.83002pt too wide) in paragraph at lines 21234--21241 []\T1/pcr/m/n/10 isTRUE(x) \T1/ptm/m/n/10 is the same as \T1/pcr/m/n/10 { is.lo gical(x) && length(x) == 1 && !is.na(x) && x }\T1/ptm/m/n/10 ; Underfull \hbox (badness 4886) in paragraph at lines 21234--21241 \T1/ptm/m/n/10 In ear-lier \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions, \T1/pcr/m /n/10 isTRUE <- function(x) identical(x, TRUE)\T1/ptm/m/n/10 , had the [310] [311] Underfull \hbox (badness 2469) in paragraph at lines 21384--21390 []\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s, Underfull \hbox (badness 1939) in paragraph at lines 21384--21390 \T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la -bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri butes in-clud-ing names. Underfull \hbox (badness 10000) in paragraph at lines 21384--21390 \T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true" ) \T1/ptm/m/n/10 are re-garded as true, [312] [313] [314] [315] [316] Underfull \hbox (badness 10000) in paragraph at lines 21701--21703 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [317] [318] [319] [320] [321] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22005--22005 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real = r , imaginary = NA ),[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22006--22006 [] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N aN, imaginary = r ))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 22009--22009 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] [322] [323] Underfull \hbox (badness 1655) in paragraph at lines 22133--22137 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [324] [325] [326] Underfull \hbox (badness 2277) in paragraph at lines 22382--22385 []\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][] \T1/pcr/m/n/10 crossprod[][][]() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tcrossprod() \T1/ptm/m/n/10 are typ-i-cally prefer-able. [327] [328] [329] [330] [331] [332] [333] [334] Underfull \hbox (badness 10000) in paragraph at lines 22867--22873 []\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age space can-not ex-ceed Underfull \hbox (badness 6316) in paragraph at lines 22867--22873 \T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er -ror mes-sage be-gins Underfull \hbox (badness 1484) in paragraph at lines 22899--22907 []\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less the OS's de-fault has been Underfull \hbox (badness 2951) in paragraph at lines 22899--22907 \T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http s : / / www . microsoft . com / whdc / Underfull \hbox (badness 3460) in paragraph at lines 22899--22907 \T1/pcr/m/n/10 system / platform / server / PAE / PAEmem . mspx$[][] \T1/ptm/m/ n/10 and [][]$\T1/pcr/m/n/10 https : / / msdn . microsoft . [335] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22976--22976 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [336] Underfull \hbox (badness 10000) in paragraph at lines 23030--23034 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by. x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng th zero vec- Underfull \hbox (badness 10000) in paragraph at lines 23030--23034 \T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr /m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/ n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i. e., [337] [338] [339] [340] [341] [342] Underfull \hbox (badness 10000) in paragraph at lines 23481--23489 \T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T 1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; [343] [344] Underfull \hbox (badness 3849) in paragraph at lines 23595--23600 []\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na lly to a char-ac-ter vec-tor (so meth-ods for [345] Underfull \hbox (badness 7308) in paragraph at lines 23672--23678 []\T1/ptm/m/n/10 For an [][]\T1/pcr/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/pcr/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 5077) in paragraph at lines 23672--23678 \T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env, all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 10000) in paragraph at lines 23682--23685 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 23682--23685 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as [346] [347] Underfull \hbox (badness 10000) in paragraph at lines 23834--23836 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of [348] [349] [350] [351] Underfull \hbox (badness 6188) in paragraph at lines 24053--24056 []\T1/ptm/m/n/10 optional [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/pcr/m/n/10 print()\T1/ptm/m/n/10 , used by [352] [353] [354] [355] [356] [357] [358] Underfull \hbox (badness 2197) in paragraph at lines 24535--24539 []\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s tartup mes-sages given by Underfull \hbox (badness 4048) in paragraph at lines 24535--24539 \T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use Underfull \hbox (badness 2846) in paragraph at lines 24549--24553 []\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment \T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the pack- Underfull \hbox (badness 1990) in paragraph at lines 24549--24553 \T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p uted pack-age in-for-ma-tion ob-ject and pass this to [359] Underfull \hbox (badness 10000) in paragraph at lines 24642--24648 []\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i t loads to the search path. Underfull \hbox (badness 1168) in paragraph at lines 24642--24648 \T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co n-tain-ing the ex-ported val-ues of a [360] Underfull \hbox (badness 10000) in paragraph at lines 24655--24657 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than Overfull \hbox (4.38043pt too wide) in paragraph at lines 24706--24706 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/ n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] [361] [362] [363] Underfull \hbox (badness 10000) in paragraph at lines 24899--24905 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of Underfull \hbox (badness 10000) in paragraph at lines 24899--24905 [][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type [][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\ T1/ptm/m/n/10 ) and not a fac-tor, Underfull \hbox (badness 10000) in paragraph at lines 24899--24905 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T 1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or [364] Underfull \hbox (badness 4120) in paragraph at lines 24985--24992 []\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/ n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from [365] [366] Underfull \hbox (badness 1694) in paragraph at lines 25121--25124 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [367] [368] [369] [370] Underfull \hbox (badness 1603) in paragraph at lines 25368--25370 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [371] Overfull \hbox (73.28088pt too wide) in paragraph at lines 25491--25499 \T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats", "methods")\T1/ptm/m/n/10 . [372] [373] Underfull \hbox (badness 5475) in paragraph at lines 25628--25638 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 3271) in paragraph at lines 25670--25673 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able Underfull \hbox (badness 10000) in paragraph at lines 25685--25687 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [374] [375] [376] Underfull \hbox (badness 3138) in paragraph at lines 25948--25954 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 2088) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by [377] Underfull \hbox (badness 1194) in paragraph at lines 25961--25964 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 1389) in paragraph at lines 25987--25989 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 10000) in paragraph at lines 25999--26003 []\T1/ptm/m/n/10 string used as the user agent in HTTP(S) re-quests. If Underfull \hbox (badness 6592) in paragraph at lines 25999--26003 \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , re-quests will be made with-out a user agen t header. The de-fault is Underfull \hbox (badness 10000) in paragraph at lines 26004--26010 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 26019--26024 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Overfull \hbox (49.4607pt too wide) in paragraph at lines 26025--26036 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][](type = "both ") Underfull \hbox (badness 1009) in paragraph at lines 26037--26040 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 26047--26059 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see Underfull \hbox (badness 1072) in paragraph at lines 26047--26059 [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 . Pos-si-ble val-ues ar e \T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a [378] Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 \T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a Underfull \hbox (badness 6380) in paragraph at lines 26061--26068 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Overfull \hbox (34.78088pt too wide) in paragraph at lines 26061--26068 \T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [379] [380] [381] [382] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26392--26392 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec, 300X faster[] Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n /10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 \T1/pcr/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A[c(arrayindex.x, arrayindex.y)] [383] [384] [385] [386] [387] Underfull \hbox (badness 4341) in paragraph at lines 26729--26731 []\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 , Underfull \hbox (badness 4518) in paragraph at lines 26765--26771 [][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/ n/10 paste(*, collapse=", ")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with [388] Overfull \hbox (42.18039pt too wide) in paragraph at lines 26787--26787 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as the longest input.[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26799--26799 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] [389] [390] [391] [392] [393] [394] [395] Underfull \hbox (badness 10000) in paragraph at lines 27233--27237 []\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr /m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [396] Underfull \hbox (badness 1796) in paragraph at lines 27299--27302 []\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 27499--27502 []\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print -ing of vec-tors, ma-tri-ces and ar-rays, and op-tion [400] [401] [402] [403] [404] [405] [406] [407] [408] Underfull \hbox (badness 1226) in paragraph at lines 28131--28136 \T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T 1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/ n/10 ncol \T1/ptm/m/n/10 is greater than [409] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28176--28176 [] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = rep(c(0,0,1),2))[] [410] [411] [412] [413] Overfull \hbox (15.18042pt too wide) in paragraph at lines 28442--28442 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3 \u147b\u203c")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28453--28453 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\ U147b\U203c"[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 28459--28459 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm l#Literal-constants[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 28460--28460 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug .cgi?id=16098[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 28463--28463 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] [414] Underfull \hbox (badness 7415) in paragraph at lines 28538--28542 []\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use [415] Overfull \hbox (42.18039pt too wide) in paragraph at lines 28559--28559 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] [416] [417] Underfull \hbox (badness 2418) in paragraph at lines 28718--28729 []\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n ot [418] Underfull \hbox (badness 1248) in paragraph at lines 28852--28859 \T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM Trans-ac-tions on Mod-el-ing and Com-puter Underfull \hbox (badness 10000) in paragraph at lines 28852--28859 \T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS / [419] [420] Underfull \hbox (badness 1533) in paragraph at lines 28968--28971 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [421] Underfull \hbox (badness 1337) in paragraph at lines 29065--29068 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute d, i.e., [422] Overfull \hbox (42.78088pt too wide) in paragraph at lines 29113--29113 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] Underfull \hbox (badness 1038) in paragraph at lines 29131--29142 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [423] Underfull \hbox (badness 10000) in paragraph at lines 29143--29146 []\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal: for \T1/pcr/m/n/10 na.last = TRUE \T1/ptm/m/n/10 and [424] Underfull \hbox (badness 1117) in paragraph at lines 29238--29244 \T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \ T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing [425] [426] [427] [428] [429] [430] Underfull \hbox (badness 4048) in paragraph at lines 29616--29621 []\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor to Underfull \hbox (badness 4582) in paragraph at lines 29616--29621 \T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the mode: Underfull \hbox (badness 1824) in paragraph at lines 29616--29621 \T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 " double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , [431] [432] [433] [434] [435] [436] [437] [438] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30162--30162 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [439] [440] [441] [442] Overfull \hbox (13.9408pt too wide) in paragraph at lines 30448--30450 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( ) * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T 1/ptm/m/n/10 '. [443] [444] [445] Underfull \hbox (badness 7558) in paragraph at lines 30664--30668 []\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1968) in paragraph at lines 30674--30676 []\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P OSIX stan-dard, and the Underfull \hbox (badness 5417) in paragraph at lines 30679--30682 [][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/ ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 ls[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 30683--30685 []\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la urikari . net / tre / documentation / Underfull \hbox (badness 10000) in paragraph at lines 30686--30688 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / [446] [447] [448] [449] [450] [451] Underfull \hbox (badness 10000) in paragraph at lines 31091--31095 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [452] [453] [454] [455] [456] Overfull \hbox (12.78088pt too wide) in paragraph at lines 31422--31422 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 31425--31425 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [457] [458] [459] Underfull \hbox (badness 3375) in paragraph at lines 31653--31660 \T1/ptm/m/n/10 pen if the spec-i-fied row names, i.e., \T1/pcr/m/n/10 value\T1/ ptm/m/n/10 , are in-valid, e.g., du- Underfull \hbox (badness 2359) in paragraph at lines 31653--31660 \T1/ptm/m/n/10 pli-cated or \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 . The de-fault (is back com-pat-i-ble), \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , will sig-nal Underfull \hbox (badness 2582) in paragraph at lines 31653--31660 \T1/ptm/m/n/10 an er-ror, where \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 will ``au-to-m atic'' row names and \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 will call [460] [461] [462] Overfull \hbox (54.78088pt too wide) in paragraph at lines 31806--31806 [] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/ 2 && n > 1e7))[] [463] [464] Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 []\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 \T1/ptm/m/n/10 workspace', i.e., \T1/pcr/m/n/10 save(list = ls(all.names = TRUE ), file = [465] [466] [467] Underfull \hbox (badness 2302) in paragraph at lines 32188--32195 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3815) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [468] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32240--32240 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [469] Underfull \hbox (badness 1158) in paragraph at lines 32344--32349 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if [470] Underfull \hbox (badness 10000) in paragraph at lines 32371--32377 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1953) in paragraph at lines 32371--32377 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o c-tal and hex-adec-i-mal rep-re- [471] Underfull \hbox (badness 10000) in paragraph at lines 32447--32452 []\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by Underfull \hbox (badness 6725) in paragraph at lines 32447--32452 \T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10 will give an empty [472] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32529--32529 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [473] [474] [475] Underfull \hbox (badness 2809) in paragraph at lines 32793--32799 []\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2, ..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment Underfull \hbox (badness 7759) in paragraph at lines 32800--32803 []\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/ n/10 1, 2, ..., length.out \T1/ptm/m/n/10 un-less [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] [487] Underfull \hbox (badness 1735) in paragraph at lines 33605--33611 \T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co n-sole. Mes-sages sent [488] Underfull \hbox (badness 4303) in paragraph at lines 33621--33624 []\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault out-put from [489] [490] [491] [492] Overfull \hbox (66.78088pt too wide) in paragraph at lines 33939--33939 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [493] [494] [495] [496] Overfull \hbox (6.78088pt too wide) in paragraph at lines 34191--34191 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 34193--34193 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] [497] Underfull \hbox (badness 10000) in paragraph at lines 34236--34242 [][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 vec-tor, passed as \T1/pcr/ m/n/10 control \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 deparse[][][]()\T1/ptm/m/n/ 10 , see Underfull \hbox (badness 10000) in paragraph at lines 34236--34242 \T1/ptm/m/n/10 also [][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T 1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard- Underfull \hbox (badness 10000) in paragraph at lines 34236--34242 \T1/ptm/m/n/10 coded to \T1/pcr/m/n/10 "showAttributes"\T1/ptm/m/n/10 , which i s the de-fault cur-rently; Underfull \hbox (badness 2512) in paragraph at lines 34251--34253 []\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s kip if [498] Overfull \hbox (20.58041pt too wide) in paragraph at lines 34347--34347 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [499] [500] [501] Underfull \vbox (badness 10000) has occurred while \output is active [502] [503] Overfull \hbox (4.38043pt too wide) in paragraph at lines 34675--34675 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m /n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 34690--34690 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [504] [505] [506] [507] [508] [509] Overfull \hbox (12.78088pt too wide) in paragraph at lines 35129--35129 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 35130--35130 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [510] [511] [512] [513] Overfull \hbox (63.78036pt too wide) in paragraph at lines 35394--35394 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [514] Underfull \hbox (badness 10000) in paragraph at lines 35478--35488 []\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/ pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want Underfull \hbox (badness 8113) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s tart, in-sert a call Underfull \hbox (badness 10000) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n /10 ' file. For ex-am-ple, Underfull \hbox (badness 6542) in paragraph at lines 35478--35488 \T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta ch no ex-tra pack-ages on Underfull \hbox (badness 5189) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) ( or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi- Underfull \hbox (badness 4193) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/ 10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or [515] Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1496) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be Underfull \hbox (badness 1728) in paragraph at lines 35534--35541 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm /m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment [516] [517] [518] [519] [520] Underfull \hbox (badness 10000) in paragraph at lines 35875--35881 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form at \T1/ptm/m/n/10 meth-ods is [521] [522] [523] Underfull \hbox (badness 1163) in paragraph at lines 36064--36071 []\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10 %OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr /m/n/10 0 <= n <= 6 Underfull \hbox (badness 8132) in paragraph at lines 36064--36071 \T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no t fol-lowed by a digit, it uses the set-ting of [524] [525] [526] [527] Underfull \hbox (badness 1142) in paragraph at lines 36346--36352 []\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1 /ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or Overfull \hbox (0.78088pt too wide) in paragraph at lines 36361--36361 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [528] [529] [530] [531] Overfull \hbox (6.78088pt too wide) in paragraph at lines 36609--36609 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36653--36653 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [532] [533] [534] [535] [536] [537] [538] Overfull \hbox (52.98038pt too wide) in paragraph at lines 37087--37087 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e verything gets added.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 37090--37090 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [539] Underfull \hbox (badness 10000) in paragraph at lines 37141--37148 []\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10 signif[][][]() \T1/ptm/m/n/10 (for Underfull \hbox (badness 10000) in paragraph at lines 37141--37148 \T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][] []() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ). Overfull \hbox (4.38043pt too wide) in paragraph at lines 37192--37192 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [540] [541] [542] [543] Underfull \hbox (badness 2762) in paragraph at lines 37431--37440 \T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there is a match then that el-e-ment is eval-u-ated un-less Underfull \hbox (badness 1466) in paragraph at lines 37431--37440 \T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is eval-u-ated, so for ex-am-ple [544] Overfull \hbox (31.3804pt too wide) in paragraph at lines 37493--37493 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [545] [546] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37658--37658 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS 1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. [547] Overfull \hbox (20.58041pt too wide) in paragraph at lines 37696--37696 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] [548] Underfull \hbox (badness 3219) in paragraph at lines 37745--37750 []\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple Underfull \hbox (badness 1107) in paragraph at lines 37745--37750 \T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr /m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match [549] Underfull \hbox (badness 2452) in paragraph at lines 37835--37838 \T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/ ptm/m/n/10 sys-tem call. The lo-gin name comes Underfull \hbox (badness 10000) in paragraph at lines 37835--37838 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and [550] [551] [552] Underfull \hbox (badness 10000) in paragraph at lines 38022--38026 []\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents \T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n /10 and Underfull \hbox (badness 1584) in paragraph at lines 38037--38040 []\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \ T1/ptm/m/n/10 and [553] [554] Overfull \hbox (25.98041pt too wide) in paragraph at lines 38169--38169 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [555] Overfull \hbox (20.58041pt too wide) in paragraph at lines 38239--38239 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/pcr/ m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used [556] [557] [558] Underfull \hbox (badness 1082) in paragraph at lines 38377--38380 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [559] [560] Underfull \hbox (badness 1038) in paragraph at lines 38564--38567 []\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or [561] [562] [563] [564] [565] [566] Underfull \hbox (badness 1515) in paragraph at lines 38928--38931 []\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc r/m/n/10 stderr = TRUE \T1/ptm/m/n/10 im-plies [567] [568] [569] Underfull \hbox (badness 4096) in paragraph at lines 39169--39172 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[ ][][]\T1/ptm/m/n/10 , [570] [571] Underfull \hbox (badness 10000) in paragraph at lines 39283--39287 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., [572] [573] Overfull \hbox (63.78036pt too wide) in paragraph at lines 39436--39436 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 39438--39438 [] \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr /m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 39440--39440 [] \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n /9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 = NULL ), dim=4, dimnames=list(as.character(2:5)))))[] [574] Underfull \hbox (badness 10000) in paragraph at lines 39453--39455 []\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha t was reg-is-tered ear-lier via [575] Underfull \hbox (badness 10000) in paragraph at lines 39533--39536 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [576] [577] Underfull \hbox (badness 1867) in paragraph at lines 39651--39655 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 5475) in paragraph at lines 39713--39717 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / [578] [579] [580] [581] [582] [583] [584] Underfull \hbox (badness 10000) in paragraph at lines 40131--40138 \T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/ n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', ` \T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ', Underfull \hbox (badness 4467) in paragraph at lines 40187--40196 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn s the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 40187--40196 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, Underfull \hbox (badness 10000) in paragraph at lines 40197--40205 []\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op -tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de- Underfull \hbox (badness 10000) in paragraph at lines 40197--40205 \T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da tabase at Underfull \hbox (badness 1303) in paragraph at lines 40197--40205 \T1/pcr/m/n/10 file.path(R.home("share"), "zoneinfo") \T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 ' [585] Underfull \hbox (badness 1337) in paragraph at lines 40263--40271 \T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 / usr/local/etc\T1/ptm/m/n/10 ' or Underfull \hbox (badness 10000) in paragraph at lines 40272--40275 []\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym -link tar-get name of [586] Underfull \hbox (badness 4429) in paragraph at lines 40329--40331 [][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol- Overfull \hbox (31.3804pt too wide) in paragraph at lines 40338--40338 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [587] [588] [589] Underfull \hbox (badness 10000) in paragraph at lines 40555--40557 []\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal l-ing [590] [591] Overfull \hbox (15.18042pt too wide) in paragraph at lines 40677--40677 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15 g)\n", ncp))),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 40679--40679 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] Underfull \vbox (badness 10000) has occurred while \output is active [592] [593] [594] [595] [596] Underfull \hbox (badness 6542) in paragraph at lines 41041--41043 []\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x )\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and [597] [598] [599] Underfull \hbox (badness 3460) in paragraph at lines 41207--41210 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1708) in paragraph at lines 41214--41222 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e r-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 3713) in paragraph at lines 41214--41222 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ]\T1/pcr/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less Underfull \hbox (badness 10000) in paragraph at lines 41223--41227 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10 tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in- Underfull \hbox (badness 10000) in paragraph at lines 41223--41227 \T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 , some-thing like Underfull \hbox (badness 3281) in paragraph at lines 41223--41227 \T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s im-ple er-ror han-dler func- Underfull \hbox (badness 4859) in paragraph at lines 41244--41249 [][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers and sup-press-ing the print-ing of er-ror mes-sages; [600] Underfull \hbox (badness 3895) in paragraph at lines 41306--41318 []\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in Underfull \hbox (badness 1303) in paragraph at lines 41306--41318 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , [601] [602] [603] Underfull \hbox (badness 10000) in paragraph at lines 41491--41494 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [604] [605] Overfull \hbox (9.78043pt too wide) in paragraph at lines 41628--41628 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [606] [607] [608] [609] [610] [611] Overfull \hbox (4.38043pt too wide) in paragraph at lines 42095--42095 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] [612] Overfull \hbox (20.58041pt too wide) in paragraph at lines 42104--42104 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little- endian platform[] [613] Underfull \hbox (badness 1803) in paragraph at lines 42221--42224 []\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1 0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ), Underfull \hbox (badness 2334) in paragraph at lines 42225--42232 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and [614] Underfull \hbox (badness 4726) in paragraph at lines 42251--42255 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec tor(x, mode = "numeric") \T1/ptm/m/n/10 can be Underfull \hbox (badness 1122) in paragraph at lines 42251--42255 \T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/ 10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x , mode = [615] [616] Underfull \hbox (badness 3668) in paragraph at lines 42440--42442 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [617] [618] Overfull \hbox (36.78088pt too wide) in paragraph at lines 42544--42544 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [619] Overfull \hbox (4.38043pt too wide) in paragraph at lines 42619--42619 []\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n /9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 42627--42627 []\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) # There were 105 warnings ...[] [620] [621] Underfull \hbox (badness 6220) in paragraph at lines 42757--42762 []\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][] (.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true, Underfull \hbox (badness 3098) in paragraph at lines 42757--42762 \T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array Ind() \T1/ptm/m/n/10 (and hence, Underfull \hbox (badness 1533) in paragraph at lines 42757--42762 \T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty, Underfull \hbox (badness 6592) in paragraph at lines 42773--42778 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [622] Underfull \hbox (badness 1603) in paragraph at lines 42792--42796 [][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[] [][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the [623] Underfull \hbox (badness 10000) in paragraph at lines 42857--42860 []\T1/ptm/m/n/10 If this ex-tremum is unique (or empty), the re-sults are the s ame as Underfull \hbox (badness 10000) in paragraph at lines 42857--42860 \T1/ptm/m/n/10 (but more ef-fi-cient than) \T1/pcr/m/n/10 which(x == min(x, na. rm = TRUE)) \T1/ptm/m/n/10 or Underfull \hbox (badness 2818) in paragraph at lines 42863--42869 []\T1/ptm/m/n/10 For a [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with both \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 a nd \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 val-ues, \T1/pcr/m/n/10 which.min(x) \T1/ ptm/m/n/10 and Overfull \hbox (15.18042pt too wide) in paragraph at lines 42898--42898 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [624] [625] Underfull \hbox (badness 1622) in paragraph at lines 42992--42994 []\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer . [626] [627] [628] [629] Underfull \hbox (badness 10000) in paragraph at lines 43260--43265 []\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu nc-tion than [][]\T1/pcr/m/n/10 rank[][][] Underfull \hbox (badness 10000) in paragraph at lines 43260--43265 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to Underfull \hbox (badness 10000) in paragraph at lines 43260--43265 \T1/pcr/m/n/10 rank(x, ties.method = "min", na.last = "keep")\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are [630] Underfull \hbox (badness 2846) in paragraph at lines 43354--43358 []\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [631] Overfull \hbox (4.38043pt too wide) in paragraph at lines 43394--43394 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 43415--43419 []\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard ' reg-exps, in-clud-ing el-e-ments named [632]) (./compiler-pkg.tex Chapter 2. [633] Underfull \hbox (badness 2884) in paragraph at lines 101--115 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 options \T1/ptm/m/n/10 ar-gu-ment can be us ed to con-trol com-piler op-er-a-tion. There are cur- Underfull \hbox (badness 10000) in paragraph at lines 101--115 \T1/ptm/m/n/10 rently four op-tions: \T1/pcr/m/n/10 optimize\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 suppressAll\T1/ptm/m/n/10 , \T1/pcr/m/n/10 suppressUndefined\T1/pt m/m/n/10 , and [634] [635] [636]) (./datasets-pkg.tex Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple te list, use [637] [638] [639] [640] [641] Overfull \hbox (15.18042pt too wide) in paragraph at lines 301--301 [] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang e", cex = 1.2,[] [642] Overfull \hbox (4.38043pt too wide) in paragraph at lines 379--379 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi ven = FALSE)[] Underfull \vbox (badness 1033) has occurred while \output is active [643] [644] [645] [646] [647] Overfull \hbox (66.81013pt too wide) in paragraph at lines 702--705 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [648] [649] Overfull \hbox (66.81013pt too wide) in paragraph at lines 835--838 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [650] [651] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [652] [653] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1146--1149 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [654] [655] [656] [657] [658] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1456--1456 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption time (sec)")[] [659] [660] Underfull \hbox (badness 10000) in paragraph at lines 1541--1544 []\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r evenue\T1/ptm/m/n/10 , Underfull \hbox (badness 2903) in paragraph at lines 1541--1544 \T1/pcr/m/n/10 price.index\T1/ptm/m/n/10 , \T1/pcr/m/n/10 income.level\T1/ptm/m /n/10 , and \T1/pcr/m/n/10 market.potential \T1/ptm/m/n/10 ob-tained from the a bove [661] [662] [663] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1730--1733 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [664] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1824--1824 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil y = binomial())[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1832--1832 [] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum), data = infert)[] [665] [666] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1948--1948 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1949--1949 [] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d ni3[[3]]))))[] [667] [668] [669] [670] Overfull \hbox (66.81013pt too wide) in paragraph at lines 2152--2155 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [671] [672] [673] [674] [675] [676] [677] [678] Overfull \hbox (66.81013pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [679] Overfull \vbox (13.87083pt too high) has occurred while \output is active [680] Underfull \vbox (badness 1789) has occurred while \output is active [681] [682] Overfull \vbox (12.25539pt too high) has occurred while \output is active [683] [684] Overfull \vbox (17.12102pt too high) has occurred while \output is active [685] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3137--3137 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [686] [687] [688] [689] [690] [691] [692] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3594--3594 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [693] [694] Overfull \hbox (66.81013pt too wide) in paragraph at lines 3742--3745 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [695] Overfull \vbox (10.49593pt too high) has occurred while \output is active [696] Underfull \hbox (badness 1173) in paragraph at lines 3876--3880 \T1/ptm/m/it/10 Ed-u-ca-tion\T1/ptm/m/n/10 , \T1/ptm/b/n/10 3\T1/ptm/m/n/10 . [ ][]$\T1/pcr/m/n/10 https : / / www . amstat . org / publications / jse / v3n3 / datasets . Overfull \vbox (27.49593pt too high) has occurred while \output is active [697] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3951--3951 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 3980--3983 []\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www -[]personal . buseco . monash . edu . au / Underfull \hbox (badness 10000) in paragraph at lines 3989--3991 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h ttps : / / web . archive . org / web / Underfull \hbox (badness 10000) in paragraph at lines 3989--3991 \T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma n / sitephotos / [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711]) (./grDevices-pkg.tex [712] Chapter 4. [713] [714] [715] [716] [717] [718] Underfull \hbox (badness 10000) in paragraph at lines 374--382 []\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til e, i.e., close to Underfull \hbox (badness 10000) in paragraph at lines 374--382 [][]\T1/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where [719] Overfull \hbox (6.78088pt too wide) in paragraph at lines 479--479 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [720] [721] [722] [723] [724] [725] [726] [727] [728] Underfull \hbox (badness 5175) in paragraph at lines 1082--1084 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [729] Underfull \hbox (badness 1325) in paragraph at lines 1144--1150 \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 , [730] Underfull \hbox (badness 10000) in paragraph at lines 1185--1187 []\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2 . com / Lab / Graphics / Colors / [731] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1237--1237 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] [732] Underfull \hbox (badness 1173) in paragraph at lines 1279--1282 []\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col- ors that will be used in plot-ting, call-ing [733] [734] [735] Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 []\T1/ptm/m/n/10 character: Which events can be gen-er-ated on Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 \T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 \T1/pcr/m/n/10 c("MouseDown", "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10 , Underfull \hbox (badness 2221) in paragraph at lines 1539--1542 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture, oth-er-wise a ma-trix of color names (for [736] Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 []\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 [][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is [737] [738] [739] Underfull \hbox (badness 1565) in paragraph at lines 1767--1772 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to pro-duce and print a postscript copy. This will not Underfull \hbox (badness 1354) in paragraph at lines 1767--1772 \T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10 for how to set this up. Win-dows users may pre-fer to use [740] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1850--1850 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] [741] Underfull \hbox (badness 1184) in paragraph at lines 1891--1901 []\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m /n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in- Underfull \hbox (badness 2057) in paragraph at lines 1891--1901 \T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p tm/m/n/10 , [742] Underfull \hbox (badness 10000) in paragraph at lines 1996--1998 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [743] [744] Underfull \hbox (badness 6758) in paragraph at lines 2157--2160 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [745] [746] Underfull \hbox (badness 2326) in paragraph at lines 2267--2277 \T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra phicsEventHandlers \T1/ptm/m/n/10 to re-place Underfull \hbox (badness 2318) in paragraph at lines 2267--2277 \T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co m-pat-i-bil-ity with pre-2.12.0 Underfull \hbox (badness 2460) in paragraph at lines 2267--2277 \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e vent han-dlers is to set them us-ing Underfull \hbox (badness 1221) in paragraph at lines 2267--2277 \T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics [747] [748] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2370--2370 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r" , yaxs = "r") {[] Underfull \vbox (badness 10000) has occurred while \output is active [749] [750] [751] [752] [753] [754] Underfull \hbox (badness 10000) in paragraph at lines 2750--2751 Underfull \vbox (badness 10000) has occurred while \output is active [755] [756] [757] [758] [759] [760] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3156--3156 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", scale.in = 255))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3157--3157 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] Underfull \hbox (badness 1210) in paragraph at lines 3188--3190 []\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m /n/10 giv-ing the num-ber of rows and columns, ful-fill-ing [761] Underfull \hbox (badness 10000) in paragraph at lines 3248--3253 []\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [762] [763] [764] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3407--3407 []\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al pha = 1) [765] Underfull \hbox (badness 3525) in paragraph at lines 3514--3517 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as [766] Underfull \hbox (badness 1968) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [767] [768] [769] [770] Underfull \hbox (badness 5939) in paragraph at lines 3822--3827 []\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\ T1/ptm/m/n/10 , [771] [772] [773] [774] [775] Underfull \hbox (badness 7576) in paragraph at lines 4199--4206 \T1/pcr/m/n/10 / / www . adobe . com / products / postscript / pdfs / PLRM . pd f$[][] \T1/ptm/m/n/10 or PDF [][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 3701) in paragraph at lines 4199--4206 \T1/pcr/m/n/10 www . adobe . com / devnet / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i- [776] Underfull \vbox (badness 10000) has occurred while \output is active [777] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4316--4316 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [778] Underfull \hbox (badness 1502) in paragraph at lines 4363--4368 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the type of anti-aliasing (if any) to be [779] [780] Underfull \hbox (badness 1348) in paragraph at lines 4515--4518 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also Underfull \hbox (badness 4765) in paragraph at lines 4525--4527 [][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if Overfull \hbox (9.78043pt too wide) in paragraph at lines 4539--4539 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, height = 768)[] [781] Underfull \hbox (badness 5077) in paragraph at lines 4579--4585 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as Underfull \hbox (badness 1342) in paragraph at lines 4595--4597 []\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [782] Underfull \hbox (badness 1874) in paragraph at lines 4672--4680 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as [783] Underfull \hbox (badness 1755) in paragraph at lines 4739--4741 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [784] [785] Underfull \hbox (badness 7344) in paragraph at lines 4910--4912 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso Underfull \hbox (badness 7397) in paragraph at lines 4921--4925 [][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm /m/n/10 which is called from both [786] [787] Underfull \hbox (badness 1552) in paragraph at lines 5034--5043 \T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG othic"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m /n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW Helvetica"\T1/ptm/m/n/10 ), Underfull \hbox (badness 2221) in paragraph at lines 5044--5046 []\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and [788] Underfull \hbox (badness 4686) in paragraph at lines 5076--5082 \T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap an1Ryumin" \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 5102--5109 []\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / [789] [790] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5203--5203 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [791] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5315--5315 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] Underfull \hbox (badness 1648) in paragraph at lines 5321--5325 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [792] [793] Underfull \hbox (badness 10000) in paragraph at lines 5401--5403 []\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10 for on-screen de-vices and to Underfull \hbox (badness 1072) in paragraph at lines 5437--5443 []\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots due to cor-rupted or du-pli- [794] [795] [796] [797] [798] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5759--5759 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15, sep = "."))[] Underfull \hbox (badness 10000) in paragraph at lines 5772--5775 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [799] [800] [801] [802] [803] [804] [805] Underfull \hbox (badness 1189) in paragraph at lines 6169--6171 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [806] Underfull \hbox (badness 10000) in paragraph at lines 6267--6269 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and Underfull \hbox (badness 10000) in paragraph at lines 6306--6313 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T 1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and Underfull \hbox (badness 2469) in paragraph at lines 6306--6313 \T1/pcr/m/n/10 expression(10^degree)\T1/ptm/m/n/10 ) have been seen on Linux sy s-tems which have the Wine [807] Underfull \hbox (badness 3088) in paragraph at lines 6390--6394 []\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do- Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and [808] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6435--6435 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [809] Underfull \hbox (badness 10000) in paragraph at lines 6467--6470 []\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][ ] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 -- [810] Underfull \hbox (badness 5637) in paragraph at lines 6558--6564 \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n /10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 1721) in paragraph at lines 6591--6594 []\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt p : / / www . schmidt-[]web-[]berlin . de / [811] [812] [813] Underfull \hbox (badness 6157) in paragraph at lines 6748--6751 \T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them via Underfull \hbox (badness 1231) in paragraph at lines 6759--6761 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [814] [815] [816]) (./graphics-pkg.tex Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag es, use [817] [818] [819] [820] Underfull \hbox (badness 1412) in paragraph at lines 287--292 []\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal data. \T1/ptm/m/it/10 SAS User Group In-ter-na- [821] [822] [823] Underfull \hbox (badness 2726) in paragraph at lines 466--472 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark lo-ca-tions are com-puted in-ter-nally (the same way [824] [825] [826] Underfull \hbox (badness 10000) in paragraph at lines 659--663 []\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m /n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or Underfull \hbox (badness 3250) in paragraph at lines 659--663 [][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/ m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1 0 if Underfull \hbox (badness 2735) in paragraph at lines 687--694 []\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [827] Overfull \hbox (4.38043pt too wide) in paragraph at lines 744--744 [] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n intLog = 5))[] [828] [829] Underfull \hbox (badness 1062) in paragraph at lines 853--856 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic h di-vide ad-ja-cent (non-stacked!) bars [830] [831] [832] [833] [834] [835] [836] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1290--1290 [] \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = NULL,[] [837] Underfull \hbox (badness 1024) in paragraph at lines 1335--1343 \T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 cex.lab\T1/ptm/m/n/10 , and Underfull \hbox (badness 1248) in paragraph at lines 1363--1369 \T1/ptm/m/n/10 width, point char-ac-ter, point size ex-pan-sion, color, and bac k-ground Underfull \hbox (badness 6893) in paragraph at lines 1363--1369 \T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su p-presses the point, and Underfull \hbox (badness 3375) in paragraph at lines 1369--1371 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), Overfull \hbox (19.3703pt too wide) in paragraph at lines 1391--1395 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10 xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim = range(at, *) + c(-0.5, 0.5)\T1/ptm/m/n/10 . [838] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1439--1439 []\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi s=..,main=..)")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1440--1440 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi s=..,main=..)")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1446--1446 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill = "grey40",[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1447--1447 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [839] [840] [841] [842] [843] Underfull \hbox (badness 10000) in paragraph at lines 1747--1753 [][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 (and [844] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1784--1784 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1793--1793 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [845] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1876--1876 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [846] [847] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2005--2005 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept h, rows = 1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2010--2010 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [848] [849] [850] [851] [852] Underfull \hbox (badness 1009) in paragraph at lines 2296--2303 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [853] [854] [855] [856] [857] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2624--2624 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [858] [859] Underfull \hbox (badness 5878) in paragraph at lines 2785--2789 \T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T 1/ptm/m/n/10 and in gen-eral sat-isfy Underfull \hbox (badness 10000) in paragraph at lines 2810--2813 []\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1 /ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n /10 or [860] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2838--2838 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2842--2842 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] [861] Underfull \hbox (badness 10000) in paragraph at lines 2894--2897 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as [862] [863] [864] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3091--3091 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL SE, pch = 19, ...)[] Overfull \hbox (79.98035pt too wide) in paragraph at lines 3096--3096 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [865] Underfull \hbox (badness 1755) in paragraph at lines 3161--3165 []\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/ 10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/ n/10 , [866] Underfull \hbox (badness 10000) in paragraph at lines 3236--3241 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3236--3241 [][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3236--3241 [][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/ n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is [867] [868] [869] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3423--3423 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 0, horiz = TRUE)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3442--3442 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3446--3446 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [870] [871] [872] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3623--3623 [] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c ex = 0.8, adj = 0)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3624--3624 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3663--3663 [] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj = c(0, 0.3))[] Underfull \vbox (badness 10000) has occurred while \output is active [873] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3715--3715 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3723--3723 []\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset = .05", inset = .05)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3725--3725 []\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset = .02",inset = .02)[] Underfull \vbox (badness 10000) has occurred while \output is active [874] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3733--3733 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] Underfull \hbox (badness 10000) in paragraph at lines 3796--3800 [][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method ; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for [875] [876] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3907--3907 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [877] Underfull \hbox (badness 1867) in paragraph at lines 3950--3954 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [878] [879] Underfull \hbox (badness 3930) in paragraph at lines 4114--4116 []\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a mul-ti-ple of [880] [881] [882] [883] Underfull \hbox (badness 1924) in paragraph at lines 4400--4405 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [884] Underfull \hbox (badness 1286) in paragraph at lines 4424--4427 \T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 oma \T1/ptm/m/n/10 when chang-ing Underfull \hbox (badness 3229) in paragraph at lines 4432--4437 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [885] [886] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4525--4525 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel = panel.cor,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4530--4530 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4574--4574 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = " blue") # hmm...[] [887] Underfull \hbox (badness 1264) in paragraph at lines 4648--4661 \T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/ m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1 /ptm/m/n/10 , [888] [889] Underfull \hbox (badness 7925) in paragraph at lines 4785--4791 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. [890] [891] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 <"/tmp/B.61K3e5/BUILD/R-3.5.2/build/library/graphics/help/figures/"mai.pdf, id= 29409, 289.08pt x 289.08pt> [892 ] Underfull \hbox (badness 10000) in paragraph at lines 4977--4979 <"/tmp/B.61K3e5/BUILD/R-3.5.2/build/library/graphics/help/figures/"oma.pdf, id= 29423, 259.97125pt x 332.24126pt> [893 ] [894] Underfull \hbox (badness 10000) in paragraph at lines 5167--5169 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [895] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5223--5223 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5224--5224 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] Underfull \vbox (badness 10000) has occurred while \output is active [896] [897] Underfull \hbox (badness 3954) in paragraph at lines 5325--5328 []\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm /m/n/10 co-or-di-nates. Of-ten used with Underfull \hbox (badness 10000) in paragraph at lines 5381--5385 \T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and [898] [899] [900] [901] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5589--5589 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5590--5590 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 5641--5645 []\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing or an er-ror; us-ing, e.g., Underfull \hbox (badness 1024) in paragraph at lines 5641--5645 \T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/ n/10 type = "p" \T1/ptm/m/n/10 for S com- [902] [903] [904] [905] [906] [907] [908] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6068--6068 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6074--6074 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [909] [910] [911] [912] [913] [914] Underfull \hbox (badness 10000) in paragraph at lines 6501--6503 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [915] [916] Underfull \hbox (badness 1028) in paragraph at lines 6595--6597 []\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th is works as a mul-ti-ple of <"/tmp/B.61K3e5/BUILD/R-3.5.2/build/library/graphics/help/figures/"pch.pdf, id= 29833, 361.35pt x 50.1875pt> Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639 [][] [917 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6732--6732 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [918] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6763--6763 [] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab = "", main = main)[] Underfull \vbox (badness 10000) has occurred while \output is active [919] [920] Underfull \hbox (badness 10000) in paragraph at lines 6885--6887 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr Overfull \hbox (15.18042pt too wide) in paragraph at lines 6912--6912 [] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b order = "red")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6918--6918 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [921] Underfull \hbox (badness 2600) in paragraph at lines 6978--6980 []\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/ pcr/m/n/10 "winding" \T1/ptm/m/n/10 or [922] [923] [924] Underfull \hbox (badness 1881) in paragraph at lines 7167--7172 []\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m /n/10 par("fg")\T1/ptm/m/n/10 . Use [925] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7210--7210 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [926] [927] [928] [929] [930] [931] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7597--7597 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7601--7601 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [932] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7613--7613 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [933] [934] [935] [936] [937] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7962--7962 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7965--7965 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] [938] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7969--7969 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [939] [940] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8140--8140 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...) Overfull \hbox (36.78088pt too wide) in paragraph at lines 8141--8141 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [941] [942] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8245--8245 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8256--8261 []\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1 /pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for [943] [944] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8364--8364 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035 , seg.lwd = .8)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8379--8379 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [945] [946] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8510--8510 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [947] [948] [949] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8695--8695 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] Underfull \hbox (badness 10000) in paragraph at lines 8723--8725 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8725--8727 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8757--8763 []\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr /m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m /n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing [950]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8805 \HeaderA{units}{Graphical Units}{units} [951] Underfull \hbox (badness 1205) in paragraph at lines 8870--8872 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [952] [953] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8989--8989 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 2, length = 0.1)[] [954]) (./grid-pkg.tex Chapter 6. [955] [956] [957] [958] [959] [960] Underfull \hbox (badness 10000) in paragraph at lines 385--391 \T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo r ex-am-ple, Underfull \hbox (badness 1024) in paragraph at lines 385--391 \T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f ault be-haviour for grobs is to [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1025--1025 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1027--1027 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1029--1029 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] Underfull \vbox (badness 10000) has occurred while \output is active [971] Underfull \hbox (badness 1430) in paragraph at lines 1074--1079 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [972] [973] [974] Underfull \hbox (badness 3219) in paragraph at lines 1288--1291 []\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject de-scrib-ing a cir-cle), but only [975] [976] [977] [978] [979] [980] [981] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1675--1675 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [982] [983] [984] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1889--1889 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla ck"), name="r1")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1890--1890 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey" ), name="r2")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1891--1891 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [985] Underfull \hbox (badness 2961) in paragraph at lines 1926--1931 []\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 , [986] Underfull \hbox (badness 1430) in paragraph at lines 1985--1990 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- Underfull \hbox (badness 4479) in paragraph at lines 2014--2017 []\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10 to al-low a grob to per-form cus-tom ac-tions and [987] [988] [989] Underfull \hbox (badness 2894) in paragraph at lines 2221--2228 []\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de -scrib-ing a frame), but only [990] [991] [992] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2377--2377 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] Underfull \hbox (badness 1430) in paragraph at lines 2389--2394 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [993] [994] [995] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2590--2590 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2622--2622 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [996] [997] [998] [999] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2864--2864 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [1000] [1001] [1002] [1003] [1004] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3179--3179 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1005] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3275--3275 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] [1006] Underfull \hbox (badness 2799) in paragraph at lines 3309--3315 []\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage " \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see [1007] [1008] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3401--3401 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3408--3408 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1009] [1010] [1011] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3602--3602 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3617--3617 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] Underfull \hbox (badness 1067) in paragraph at lines 4355--4358 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1025] Underfull \hbox (badness 1430) in paragraph at lines 4401--4406 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1026] [1027] [1028] Underfull \hbox (badness 7256) in paragraph at lines 4600--4602 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] Underfull \hbox (badness 10000) in paragraph at lines 5189--5191 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu -ments above are passed to [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] Underfull \hbox (badness 3449) in paragraph at lines 5877--5883 \T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1, "npc") - unit(1, "inches")\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 5877--5883 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1048] [1049] [1050] [1051] [1052] Underfull \hbox (badness 1867) in paragraph at lines 6187--6189 []\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or [1053] Underfull \hbox (badness 10000) in paragraph at lines 6224--6230 [][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV iewport[][][]\T1/ptm/m/n/10 , [1054] [1055] Underfull \hbox (badness 7649) in paragraph at lines 6356--6359 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like [1056] [1057] [1058] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6560--6560 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1059]) (./methods-pkg.tex [1060] Chapter 7. [1061] [1062] Underfull \hbox (badness 1688) in paragraph at lines 166--171 \T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c o-erce meth-ods work. Use [1063] [1064] [1065] Underfull \hbox (badness 1348) in paragraph at lines 392--395 [][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo r-ma-tion about group generic func-tions; [][]Meth- [1066] [1067] Overfull \hbox (15.18042pt too wide) in paragraph at lines 558--558 []\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall y a primitive.[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w ith no arguments[] [1068] Overfull \hbox (4.38043pt too wide) in paragraph at lines 619--619 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho ut arguments[] Underfull \vbox (badness 10000) has occurred while \output is active [1069] Overfull \hbox (25.98041pt too wide) in paragraph at lines 637--637 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th e default method[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 640--640 []\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b y callNextMethod[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the "B0" method[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 672--672 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[ ] Underfull \vbox (badness 10000) has occurred while \output is active [1070] [1071] Underfull \hbox (badness 1546) in paragraph at lines 791--797 []\T1/ptm/m/n/10 A ma-trix (or ma-trix like ob-ject) com-bin-ing the columns (o r rows) of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 . Note Underfull \hbox (badness 3780) in paragraph at lines 791--797 \T1/ptm/m/n/10 that meth-ods must con-struct [][]\T1/pcr/m/n/10 colnames[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 rownames[][][] \T1/ptm/m/n/10 from the co r-re-spond-ing col- Underfull \hbox (badness 1789) in paragraph at lines 791--797 \T1/ptm/m/n/10 umn and row names of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr /m/n/10 y \T1/ptm/m/n/10 (but not from de-pars-ing ar-gu-ment names such as in [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1794--1794 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N umber" method[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1796--1796 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE)) ) # the default[] Underfull \hbox (badness 10000) in paragraph at lines 1838--1840 []\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca lls [1085] [1086] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class [1087] [1088] [1089] Underfull \hbox (badness 1132) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/pcr/m/n/10 where = [1090] [1091] Underfull \hbox (badness 10000) in paragraph at lines 2328--2332 []\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od s dis-patch, call Overfull \hbox (6.78088pt too wide) in paragraph at lines 2360--2360 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F ALSE}:[] [1092] [1093] [1094] Underfull \hbox (badness 3792) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class Underfull \hbox (badness 1194) in paragraph at lines 2605--2609 []\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10 (a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and [1095] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2661--2661 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1096] [1097] [1098] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2880--2880 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1099] [1100] [1101] [1102] [1103] [1104] [1105] Underfull \hbox (badness 10000) in paragraph at lines 3403--3408 []\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu rns the im-plicit generic ver-sion, Underfull \hbox (badness 6268) in paragraph at lines 3403--3408 \T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \ T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents [1106] [1107] Underfull \hbox (badness 10000) in paragraph at lines 3531--3535 []\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class [1108] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Overfull \hbox (28.78088pt too wide) in paragraph at lines 3642--3651 [] [1109] [1110] Overfull \hbox (276.78088pt too wide) in paragraph at lines 3762--3763 [] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 Underfull \hbox (badness 10000) in paragraph at lines 3809--3810 []\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) { [1111] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3828--3829 []\T1/pcr/m/n/10 GPS <- setClass("GPS", slots = c(time = "POSIXt"), contains = "Pos") Overfull \hbox (120.78088pt too wide) in paragraph at lines 3846--3847 []\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") Underfull \hbox (badness 6157) in paragraph at lines 3908--3912 []\T1/ptm/m/n/10 A call to [][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) \T1/ ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to [1112] [1113] [1114] Underfull \hbox (badness 10000) in paragraph at lines 4135--4137 []\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method ex-ists for [1115] [1116] Underfull \hbox (badness 1629) in paragraph at lines 4247--4256 \T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is to mod-ify a field ex-plic-itly by [1117] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4308--4308 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4309--4309 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1118] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4366--4366 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here) [1119] [1120] Underfull \hbox (badness 1033) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T 1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si g-na-ture [1121] Underfull \hbox (badness 2126) in paragraph at lines 4574--4582 []\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the im-por-tant steps: ([][]\T1/pcr/m/n/10 setMethod[][][]()\T1/ptm/m/n/10 , [1122] [1123] [1124] Underfull \hbox (badness 10000) in paragraph at lines 4811--4820 []\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha t eval-u-ates a call to [1125] [1126] [1127] [1128] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5195--5195 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] [1129] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5223--5223 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli er fails here)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5237--5237 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho d for classB[] Underfull \vbox (badness 10000) has occurred while \output is active [1130] [1131] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1132] Underfull \hbox (badness 10000) in paragraph at lines 5463--5465 []\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t er-nally by [1133] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1134] [1135] [1136] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1137] Underfull \hbox (badness 10000) in paragraph at lines 5757--5761 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 5757--5761 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1138] Underfull \hbox (badness 10000) in paragraph at lines 5848--5852 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 5848--5852 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1139] [1140] [1141] [1142] Underfull \hbox (badness 10000) in paragraph at lines 6210--6226 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m /n/10 is equiv-a-lent to in-vok-ing the method [1143] [1144] Underfull \hbox (badness 1248) in paragraph at lines 6343--6347 []\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt m/m/n/10 method car-ries out its own com-pu-ta-tions, Underfull \hbox (badness 1960) in paragraph at lines 6343--6347 \T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per -form stan-dard ini-tial-iza-tion, as shown in the [1145] Underfull \hbox (badness 4647) in paragraph at lines 6498--6500 []\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func- tion re-turned by [1146] Underfull \hbox (badness 1072) in paragraph at lines 6575--6582 []\T1/ptm/m/n/10 Establish a traced ver-sion of method [1147] Underfull \hbox (badness 2875) in paragraph at lines 6647--6656 []\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen se as any S4 class (see Underfull \hbox (badness 1436) in paragraph at lines 6647--6656 [][]\T1/pcr/m/n/10 setValidity[][][]\T1/ptm/m/n/10 ). Such meth-ods are of-ten a good idea; they will be called by call-ing [1148] Underfull \vbox (badness 10000) has occurred while \output is active [1149] [1150] [1151]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1152] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7009--7009 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement version of as().[] Underfull \hbox (badness 2042) in paragraph at lines 7065--7072 \T1/ptm/m/n/10 i-nat-ing all the for-mally de-fined slots and turn-ing off the S4 bit of the ob-ject. With [1153] [1154] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7200--7200 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data = datasets::iris)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7204--7204 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con tains = "mlm")[] [1155]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com plex}) has been already used, duplicate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1156] Underfull \hbox (badness 6708) in paragraph at lines 7309--7321 []\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "cummax"\T1/ptm/m/n/10 , Underfull \hbox (badness 2012) in paragraph at lines 7309--7321 \T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr /m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 , Underfull \hbox (badness 3209) in paragraph at lines 7309--7321 \T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m /n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 , [1157] [1158] Underfull \hbox (badness 1694) in paragraph at lines 7472--7474 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see Underfull \hbox (badness 10000) in paragraph at lines 7496--7499 []\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup erClasses() \T1/ptm/m/n/10 which calls [1159] [1160] Underfull \hbox (badness 10000) in paragraph at lines 7663--7670 []\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method, \T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her- Underfull \hbox (badness 7704) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \ T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the Underfull \hbox (badness 10000) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about it, you'll prob-a-bly agree that you wouldn't Underfull \hbox (badness 5817) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/ n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus, Overfull \hbox (0.78088pt too wide) in paragraph at lines 7663--7670 \T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE )) [1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] Underfull \hbox (badness 1052) in paragraph at lines 8489--8496 []\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it [1172] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8622--8622 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(), [1173] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8697--8697 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1174] [1175] [1176] [1177] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8959--8959 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] [1178] [1179] [1180] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9167--9167 [] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns), "setCount")[] [1181] [1182] Underfull \vbox (badness 2277) has occurred while \output is active [1183] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9429--9429 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo rmal arguments[] [1184] [1185] [1186] [1187] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9737--9737 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre es of freedom[] [1188] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9847--9847 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1189] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9858--9858 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] Underfull \hbox (badness 10000) in paragraph at lines 10556--10558 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function " \T1/ptm/m/n/10 for class Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., Underfull \hbox (badness 1681) in paragraph at lines 10564--10568 \T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends [1199] [1200] [1201] [1202]) (./parallel-pkg.tex Chapter 8. Underfull \hbox (badness 2418) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr /m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1203] Underfull \hbox (badness 4242) in paragraph at lines 96--98 []\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \ T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for [1204] [1205] Underfull \hbox (badness 1024) in paragraph at lines 213--216 []\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10 for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and [1206] Underfull \hbox (badness 10000) in paragraph at lines 318--326 []\T1/ptm/m/n/10 On Sparc So-laris \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/1 0 re-turns the num-ber of phys-i-cal cores and [1207] [1208] Underfull \hbox (badness 10000) in paragraph at lines 443--445 []\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/ 10 Rscript \T1/ptm/m/n/10 such as [1209] [1210] [1211] [1212] Underfull \hbox (badness 1917) in paragraph at lines 742--751 []\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr /m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class Underfull \hbox (badness 1178) in paragraph at lines 742--751 \T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in -herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If [1213] [1214] Overfull \hbox (60.78088pt too wide) in paragraph at lines 824--824 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1215] Underfull \hbox (badness 10000) in paragraph at lines 884--887 []\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T 1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1 \T1/ptm/m/n/10 : for [1216] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1005--1005 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit y.list = affL)[] [1217] Overfull \hbox (63.78036pt too wide) in paragraph at lines 1009--1009 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1218] Underfull \hbox (badness 5388) in paragraph at lines 1119--1124 []\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1 /pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from Underfull \hbox (badness 10000) in paragraph at lines 1143--1151 []\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/ m/n/10 is dif-fer-ent only if [1219] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1180--1180 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] [1220] [1221] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1296--1296 [] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif (N, 1, 28)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1310--1310 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] Underfull \hbox (badness 1577) in paragraph at lines 1339--1342 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1222] Underfull \hbox (badness 3375) in paragraph at lines 1385--1387 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/ n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to [1223] [1224]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1225] [1226] [1227] [1228] [1229] [1230] [1231] Overfull \hbox (4.38043pt too wide) in paragraph at lines 492--492 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl ine = TRUE))[] [1232] [1233] [1234] [1235] Overfull \hbox (25.98041pt too wide) in paragraph at lines 706--706 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, sparse = TRUE)))[] [1236] [1237] [1238]) (./stats-pkg.tex Chapter 10. [1239] Underfull \hbox (badness 2781) in paragraph at lines 65--68 []\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 , [1240] [1241] [1242] [1243] [1244] Overfull \hbox (20.58041pt too wide) in paragraph at lines 417--417 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea rson Chi-square[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 438--438 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE) [1245] [1246] [1247] [1248] [1249] [1250] [1251] Underfull \hbox (badness 1024) in paragraph at lines 847--849 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm \T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] Underfull \hbox (badness 10000) in paragraph at lines 1391--1393 []\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu- ment [1260] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 \T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e r-ror strata of class Underfull \hbox (badness 1490) in paragraph at lines 1508--1512 \T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\ T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \ T1/ptm/m/n/10 meth-ods avail-able for [1261] [1262] [1263] [1264] Underfull \hbox (badness 10000) in paragraph at lines 1773--1777 []\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently, via Underfull \hbox (badness 2197) in paragraph at lines 1773--1777 \T1/pcr/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can han-dle miss- [1265] [1266] Underfull \hbox (badness 4303) in paragraph at lines 1874--1876 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 x \T1/ptm/m/n/10 con-tains miss-ing val-ues, see [][]\T1/pcr/m/n/10 NA[][][]\T1/ptm/m/n/10 , also con-sider us-ing [][]\T1/ pcr/m/n/10 arima[][][]()\T1/ptm/m/n/10 , pos-si-bly with [1267] [1268] [1269] Underfull \hbox (badness 10000) in paragraph at lines 2096--2101 []\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en- sure Underfull \hbox (badness 10000) in paragraph at lines 2096--2101 \T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo r Underfull \hbox (badness 1371) in paragraph at lines 2096--2101 \T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\ T1/ptm/m/n/10 , it has been ad-van-ta-geous Underfull \hbox (badness 1221) in paragraph at lines 2102--2108 []\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num -ber of pa- Underfull \hbox (badness 4608) in paragraph at lines 2102--2108 \T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied. [1270] [1271] Underfull \hbox (badness 3965) in paragraph at lines 2183--2185 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1272] [1273] [1274] Underfull \hbox (badness 1221) in paragraph at lines 2457--2462 []\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num -ber of pa- Underfull \hbox (badness 4608) in paragraph at lines 2457--2462 \T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied. [1275] Underfull \hbox (badness 3965) in paragraph at lines 2534--2536 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1276] [1277] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2679--2679 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1278] [1279] [1280] [1281] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2919--2919 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1282] [1283] [1284] Overfull \hbox (19.88992pt too wide) in paragraph at lines 3128--3130 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of variances"\T1/ptm/m/n/10 . [1285] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3176--3176 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3177--3177 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1286] Underfull \hbox (badness 2726) in paragraph at lines 3260--3276 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1287] [1288] [1289] [1290] [1291] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3568--3568 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1292] [1293] [1294] [1295] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3846--3846 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1296] [1297] [1298] [1299] [1300] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4135--4135 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4136--4136 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1301] [1302] [1303] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4374--4374 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1304] [1305] [1306] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4542--4542 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1307] Underfull \hbox (badness 3989) in paragraph at lines 4634--4641 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1308] [1309] Underfull \hbox (badness 2080) in paragraph at lines 4754--4756 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por t aliased co-ef-fi-cients (see [][]\T1/pcr/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b y de-fault where Underfull \hbox (badness 2050) in paragraph at lines 4757--4763 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 complete \T1/ptm/m/n/10 ar-gu-ment also ex- ists for com-pat-i-bil-ity with [][]\T1/pcr/m/n/10 vcov[][][] \T1/ptm/m/n/10 me th-ods, and \T1/pcr/m/n/10 coef Underfull \hbox (badness 4954) in paragraph at lines 4757--4763 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aov \T1/ptm/m/n/10 meth-ods for other classes should typ-i-cally also keep the \T1/pcr/m/n/10 complete = * Underfull \hbox (badness 4726) in paragraph at lines 4757--4763 \T1/ptm/m/n/10 be-hav-ior in sync. By that, with \T1/pcr/m/n/10 p <- length(coe f(obj, complete = TF))\T1/ptm/m/n/10 , [1310] [1311] [1312] [1313] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5019--5019 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1)) , ci = c(-1,-1))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5021--5021 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci = c(-0.9,0.1))[] [1314] Underfull \hbox (badness 7397) in paragraph at lines 5108--5112 []\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an ar-gu-ment to all these con-trast func-tions, how-ever Underfull \hbox (badness 7326) in paragraph at lines 5108--5112 \T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for [1315] [1316] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5242--5242 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5260--5260 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) Underfull \hbox (badness 2680) in paragraph at lines 5287--5289 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is given by [1317] Underfull \hbox (badness 10000) in paragraph at lines 5292--5294 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m /n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 , [1318] [1319] Underfull \hbox (badness 1436) in paragraph at lines 5470--5475 []\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i ng co-vari-ances Underfull \hbox (badness 1377) in paragraph at lines 5470--5475 \T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi -a-tion of) Underfull \hbox (badness 1448) in paragraph at lines 5470--5475 \T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \ T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/ n/10 , [1320] [1321] [1322] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5668--5668 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1323] Underfull \hbox (badness 1168) in paragraph at lines 5740--5745 []\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and [1324] [1325] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5835--5835 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1326] [1327] [1328] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6020--6020 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1329] [1330] Underfull \hbox (badness 10000) in paragraph at lines 6183--6188 []\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When [1331] [1332] [1333] Underfull \hbox (badness 5954) in paragraph at lines 6379--6381 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1334] Underfull \hbox (badness 2503) in paragraph at lines 6461--6464 []\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 5563) in paragraph at lines 6465--6467 []\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also Underfull \hbox (badness 1655) in paragraph at lines 6468--6473 \T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm /m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1 /phv/m/n/10 R \T1/ptm/m/n/10 3.1.2, [1335] Underfull \hbox (badness 7238) in paragraph at lines 6504--6507 [][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr am[][][] \T1/ptm/m/n/10 and [1336] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6539--6539 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, type = "tr")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6554--6554 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6569--6569 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1337] [1338] [1339] [1340] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6813--6813 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1341] [1342] Underfull \vbox (badness 10000) has occurred while \output is active [1343] [1344] [1345] [1346] Underfull \hbox (badness 10000) in paragraph at lines 7211--7215 \T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/ m/n/10 or [1347] Underfull \hbox (badness 6493) in paragraph at lines 7310--7313 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1348] [1349] Underfull \hbox (badness 10000) in paragraph at lines 7447--7450 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht tps : / / CRAN . R-[]project . org / view = [1350] [1351] [1352] [1353] [1354] [1355] Underfull \hbox (badness 10000) in paragraph at lines 7857--7862 []\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T 1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ..., [1356] [1357] Overfull \hbox (33.6622pt too wide) in paragraph at lines 7995--7997 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log = TRUE)\T1/ptm/m/n/10 . [1358] [1359] [1360] Underfull \hbox (badness 1210) in paragraph at lines 8212--8214 []\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b e sup-plied as named ar-gu-ments to [1361] [1362] [1363] [1364] [1365] [1366] [1367] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8687--8687 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link = "log")) # fails[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8690--8690 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1368] [1369] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8828--8828 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2), .90) # ~= 7e-9[] [1370] Underfull \hbox (badness 1859) in paragraph at lines 8867--8872 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\ T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned, i.e., if [1371] [1372] [1373] Underfull \hbox (badness 2865) in paragraph at lines 9113--9122 []\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/pcr/m/n/10 hybrid = TRUE\T1/ptm/m/n /10 , asymp-totic chi-squared prob-a-bil-i- Underfull \hbox (badness 1331) in paragraph at lines 9113--9122 \T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied ver-sion thereof) spec-i-fied by [1374] [1375] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9255--9255 [] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4 0k", "> 40k"),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 9256--9256 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1376] [1377] [1378] Overfull \hbox (61.88992pt too wide) in paragraph at lines 9435--9437 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1379] [1380] [1381] [1382] [1383] [1384] [1385] Underfull \hbox (badness 2443) in paragraph at lines 9888--9894 [][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment); [1386] [1387] [1388] Underfull \hbox (badness 3758) in paragraph at lines 10101--10104 []\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or [1389] [1390] [1391] [1392] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10337--10337 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10363--10368 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1393] Underfull \hbox (badness 4132) in paragraph at lines 10402--10406 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od [1394] Underfull \hbox (badness 10000) in paragraph at lines 10507--10510 []\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fitted.values \T1/ptm/m/n/10 and [1395] [1396] [1397] Underfull \hbox (badness 2142) in paragraph at lines 10711--10714 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ [1398] Underfull \hbox (badness 1708) in paragraph at lines 10792--10796 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1399] Underfull \hbox (badness 10000) in paragraph at lines 10834--10840 [][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, Underfull \hbox (badness 1418) in paragraph at lines 10872--10877 \T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \ T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (= [1400] [1401] Underfull \hbox (badness 2635) in paragraph at lines 11005--11008 \T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1 /pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1 0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th e [1402] [1403] [1404] Underfull \hbox (badness 1694) in paragraph at lines 11190--11193 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1337) in paragraph at lines 11209--11218 []\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate den-dro-gram is re-ordered ac-cord- Underfull \hbox (badness 3049) in paragraph at lines 11209--11218 \T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos ed by the den-dro-gram, by [1405] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11291--11291 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1406] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11324--11324 [] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 0.1),[] Underfull \hbox (badness 10000) in paragraph at lines 11337--11341 []\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p tm/m/n/10 (the de-fault) or [1407] [1408] [1409] Underfull \hbox (badness 7379) in paragraph at lines 11517--11520 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1410] [1411] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11656--11656 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11671 \aliasA{hat}{influence.measures}{hat} [1412] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11724--11724 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11736--11736 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] [1413] Underfull \hbox (badness 1062) in paragraph at lines 11785--11790 []\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther e to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1414] [1415] Underfull \hbox (badness 3623) in paragraph at lines 11956--11958 []\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max (50*.Machine$double.eps, 0.5e-28) \T1/ptm/m/n/10 if [1416] [1417] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12052--12052 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] [1418] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12145--12145 [] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label = "tobacco",[] [1419] Underfull \hbox (badness 10000) in paragraph at lines 12193--12196 []\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1 /ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is [1420] [1421] [1422] Underfull \hbox (badness 4441) in paragraph at lines 12388--12390 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12395--12397 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1423] Underfull \hbox (badness 4739) in paragraph at lines 12418--12420 []\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^ @ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by [1424] Underfull \hbox (badness 2753) in paragraph at lines 12487--12489 []\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https : / / bugs . r-[]project . org / bugzilla3 / [1425] [1426] Underfull \hbox (badness 1292) in paragraph at lines 12612--12616 \T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion \T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for [1427] Underfull \hbox (badness 10000) in paragraph at lines 12725--12727 []\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/ n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm /m/n/10 of Underfull \hbox (badness 2894) in paragraph at lines 12731--12735 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method Underfull \hbox (badness 1038) in paragraph at lines 12731--12735 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive ( or true), trac-ing in-for-ma-tion on the [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13438--13438 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1439] Underfull \hbox (badness 4518) in paragraph at lines 13481--13486 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1440] [1441] Underfull \hbox (badness 10000) in paragraph at lines 13680--13684 []\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/ 10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10 , [1442] [1443] [1444] Underfull \hbox (badness 6995) in paragraph at lines 13865--13867 [][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had [1445] [1446] Underfull \hbox (badness 1163) in paragraph at lines 14013--14021 \T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual s[][][]\T1/ptm/m/n/10 , [1447] [1448] Underfull \hbox (badness 4518) in paragraph at lines 14133--14138 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1449] [1450] Underfull \hbox (badness 10000) in paragraph at lines 14271--14275 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/pcr/m/n/10 (surface = Underfull \hbox (badness 7133) in paragraph at lines 14271--14275 \T1/pcr/m/n/10 "interpolate", statistics = "approximate")\T1/ptm/m/n/10 : shoul d the [1451] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14319--14319 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14320--14320 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1452] Underfull \hbox (badness 10000) in paragraph at lines 14375--14378 []\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g ent, Underfull \hbox (badness 1715) in paragraph at lines 14375--14378 \T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts [1453] [1454] [1455] [1456] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14663--14663 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14664--14664 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1457] Overfull \hbox (45.6622pt too wide) in paragraph at lines 14714--14716 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l og = TRUE)\T1/ptm/m/n/10 . Overfull \hbox (18.78088pt too wide) in paragraph at lines 14757--14757 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 2726) in paragraph at lines 15164--15167 []\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 , [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] Overfull \hbox (31.3804pt too wide) in paragraph at lines 15879--15879 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1476] [1477] Underfull \hbox (badness 1014) in paragraph at lines 16017--16022 \T1/ptm/m/n/10 those spec-i-fied in \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 which are re-cy-cled to the num-ber of data frame rows. Un-like [1478] Underfull \hbox (badness 1648) in paragraph at lines 16083--16085 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 2591) in paragraph at lines 16097--16106 \T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must sup-ply vari-ables with the same names as would Underfull \hbox (badness 3930) in paragraph at lines 16097--16106 \T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/ ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing [1479] Overfull \hbox (25.98041pt too wide) in paragraph at lines 16165--16165 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b = "contr.poly"))[] [1480] [1481] [1482] [1483] [1484] [1485] [1486] [1487] [1488] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16719--16719 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] [1489] [1490] [1491] Overfull \hbox (25.98041pt too wide) in paragraph at lines 16947--16947 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] Underfull \hbox (badness 2359) in paragraph at lines 17533--17535 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1501] Underfull \vbox (badness 10000) has occurred while \output is active [1502] Underfull \vbox (badness 10000) has occurred while \output is active [1503] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17705--17705 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1504] Underfull \hbox (badness 10000) in paragraph at lines 17785--17789 []\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m /n/10 b0 + [1505] [1506] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17865--17865 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17912--17912 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1507] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17959--17959 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1508] [1509] [1510] [1511] [1512] [1513] [1514] [1515] Underfull \hbox (badness 1248) in paragraph at lines 18450--18453 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1127) in paragraph at lines 18463--18467 \T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 1478) in paragraph at lines 18471--18475 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De -faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and [1516] Underfull \hbox (badness 2042) in paragraph at lines 18529--18531 []\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm /m/n/10 method; see com-po-nent [1517] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18635--18635 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] [1518] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18677--18677 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 18695--18695 []\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 18698--18698 []\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 18718--18718 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), [1519] Overfull \hbox (36.78088pt too wide) in paragraph at lines 18721--18721 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] Underfull \hbox (badness 2564) in paragraph at lines 18756--18767 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u- ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1 0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 , Underfull \hbox (badness 1082) in paragraph at lines 18756--18767 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately \T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm /m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa [1520] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18819--18819 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1521] [1522] [1523] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19044--19044 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1524] Underfull \hbox (badness 1337) in paragraph at lines 19120--19123 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1525] [1526] [1527] [1528] [1529] [1530] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19439--19439 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1531] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19527--19527 [] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist vs Leverage " * h[ii] / (1 - h[ii]))),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 19530--19530 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1532] Underfull \hbox (badness 3049) in paragraph at lines 19609--19613 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1533] [1534] [1535] [1536] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19857--19857 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 4779) in paragraph at lines 19864--19866 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19867--19870 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1537] Underfull \hbox (badness 1107) in paragraph at lines 19925--19927 []\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to [1538] Overfull \hbox (20.58041pt too wide) in paragraph at lines 19980--19980 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] [1539] Overfull \hbox (31.3804pt too wide) in paragraph at lines 19987--19987 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 1, y.intersp = 1)[] Underfull \hbox (badness 10000) in paragraph at lines 20037--20040 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/ m/n/10 which gives Underfull \hbox (badness 10000) in paragraph at lines 20037--20040 \T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for [1540] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20081--20081 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1541] [1542] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20206--20206 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1543] Underfull \hbox (badness 10000) in paragraph at lines 20269--20271 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1544] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20317--20317 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) Underfull \hbox (badness 10000) in paragraph at lines 20372--20374 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 poly(*, simple=TRUE)\T1/ptm/m/n/10 , \T1/pc r/m/n/10 polym(*, coefs=)\T1/ptm/m/n/10 , and [1545] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20409--20409 [] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or just poly():[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 20414--20414 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] Overfull \hbox (25.98041pt too wide) in paragraph at lines 21264--21264 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly equal typically[] [1559] Underfull \hbox (badness 6859) in paragraph at lines 21331--21338 [][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre dict.poly[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 21342--21348 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22080--22080 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1572] [1573] [1574] [1575] [1576] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22364--22364 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 22365--22365 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1577] [1578] [1579] [1580] [1581] Underfull \hbox (badness 1337) in paragraph at lines 22689--22695 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] Overfull \hbox (133.98029pt too wide) in paragraph at lines 23251--23251 [] \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1590] [1591] Underfull \hbox (badness 1028) in paragraph at lines 23392--23395 []\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/ pcr/m/n/10 write() \T1/ptm/m/n/10 and [1592] [1593] Underfull \hbox (badness 10000) in paragraph at lines 23502--23505 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 5091) in paragraph at lines 23502--23505 \T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for ef-fi-ciency if [1594] Underfull \hbox (badness 10000) in paragraph at lines 23557--23559 []\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 reorder[][][]()\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing Underfull \hbox (badness 10000) in paragraph at lines 23619--23621 []\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 relevel[][][]()\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [1595] [1596] Overfull \hbox (9.78043pt too wide) in paragraph at lines 23721--23721 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1597] [1598] [1599] Overfull \hbox (31.3804pt too wide) in paragraph at lines 23941--23941 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1600] [1601] [1602] Underfull \hbox (badness 10000) in paragraph at lines 24087--24090 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has Underfull \hbox (badness 2134) in paragraph at lines 24139--24143 [][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's end point rule and is called by de-fault from [1603] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24152--24152 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1604] [1605] [1606] [1607] [1608] [1609] [1610] Underfull \hbox (badness 6268) in paragraph at lines 24616--24621 [][]\T1/pcr/m/n/10 SSasympOrig[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSbiexp [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 SSfpl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSgompertz[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSmicmen[][][]\T1/ptm/m/n/10 , [1611] Overfull \hbox (58.38037pt too wide) in paragraph at lines 24644--24644 [] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As ym", "xmid", "scal")])[] [1612] [1613] Underfull \hbox (badness 1867) in paragraph at lines 24821--24823 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/pcr/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was [1614] Overfull \hbox (20.58041pt too wide) in paragraph at lines 24870--24870 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] [1615] [1616] [1617] Underfull \hbox (badness 2495) in paragraph at lines 25060--25069 []\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/ m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1 /ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en . [1618] Overfull \hbox (24.78088pt too wide) in paragraph at lines 25142--25142 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] Underfull \hbox (badness 1412) in paragraph at lines 25149--25151 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1619] Overfull \hbox (25.98041pt too wide) in paragraph at lines 25236--25236 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] [1620] Overfull \hbox (84.78088pt too wide) in paragraph at lines 25261--25261 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 25264--25264 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1621] Underfull \hbox (badness 10000) in paragraph at lines 25306--25311 []\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when Underfull \hbox (badness 2435) in paragraph at lines 25306--25311 \T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault ), the num-ber of [1622] Underfull \hbox (badness 2980) in paragraph at lines 25451--25453 []\T1/ptm/m/n/10 the value of \T1/pcr/m/n/10 spar \T1/ptm/m/n/10 com-puted or g iven, un-less it has been given as [1623] Overfull \hbox (18.78088pt too wide) in paragraph at lines 25487--25487 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / tol) ))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25536--25536 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] [1624] Overfull \hbox (47.58038pt too wide) in paragraph at lines 25557--25557 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] Underfull \vbox (badness 10000) has occurred while \output is active [1625] [1626] Overfull \hbox (15.18042pt too wide) in paragraph at lines 25661--25661 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"), sep = " = "),[] [1627] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25728--25728 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1628] [1629] [1630] [1631] [1632] [1633] Overfull \hbox (36.78088pt too wide) in paragraph at lines 26107--26107 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] Underfull \hbox (badness 6477) in paragraph at lines 26161--26164 []\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of an [1634] [1635] Overfull \hbox (31.3804pt too wide) in paragraph at lines 26292--26292 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c ol = 3, n = 1001)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 26293--26293 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] Underfull \vbox (badness 10000) has occurred while \output is active [1636] Underfull \hbox (badness 2922) in paragraph at lines 26362--26367 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1637] Overfull \hbox (9.78043pt too wide) in paragraph at lines 26399--26399 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim = c(-.3, 5),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 26402--26402 [] \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^ {-e^{phi[3]}*~x}}))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 26411--26411 [] \T1/pcr/m/n/9 c(0 , 1 ), 1, length = 0.08, angle = 25); text(0. 5, 1, quote(1))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26412--26412 [] \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3 # (Asym + R0)/2[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 26416--26416 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] [1638] Underfull \hbox (badness 2922) in paragraph at lines 26458--26463 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Underfull \hbox (badness 3240) in paragraph at lines 26470--26473 [][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][] []\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap h show-ing the \T1/pcr/m/n/10 SSasympOff Overfull \hbox (36.7804pt too wide) in paragraph at lines 26491--26491 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log( 0.4), c0 = 3/4)) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26494--26494 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1639] Underfull \hbox (badness 2922) in paragraph at lines 26544--26549 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1640] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26577--26577 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log (log(2)))) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26581--26581 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim = c(-1/4, 5),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 26591--26591 [] \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2), phi[1]), pos=0, las=1)[] Overfull \hbox (106.98032pt too wide) in paragraph at lines 26596--26596 [] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1641] Underfull \hbox (badness 2922) in paragraph at lines 26632--26638 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 26654--26654 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26670--26670 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] [1642] [1643] Overfull \hbox (30.78088pt too wide) in paragraph at lines 26784--26784 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1644] Underfull \hbox (badness 2922) in paragraph at lines 26846--26851 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1645] Overfull \hbox (69.18036pt too wide) in paragraph at lines 26884--26884 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] [1646] Underfull \hbox (badness 2922) in paragraph at lines 26933--26938 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 26964--26964 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = " red", lwd=2)[] [1647] Underfull \hbox (badness 2922) in paragraph at lines 26998--27003 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (25.98041pt too wide) in paragraph at lines 27023--27023 []\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number of iter...: 0" :[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 27027--27027 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR UE), trace = TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27047--27047 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] [1648] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27057--27057 [] \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0, 2.5,3.5), # NB. SSlogis(x = xmid = 2) = 2.5[] Underfull \hbox (badness 2922) in paragraph at lines 27092--27097 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1649] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27114--27114 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 27132--27132 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] [1650] Underfull \hbox (badness 6493) in paragraph at lines 27184--27189 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27211--27211 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27213--27213 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 27216--27216 []\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul l() fit to Chick.6")[] Overfull \hbox (69.18036pt too wide) in paragraph at lines 27219--27219 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1659] [1660] [1661] [1662] [1663] [1664] [1665] Underfull \hbox (badness 3396) in paragraph at lines 28143--28145 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10 , usu-ally, a re-sult of a call to [1666] [1667] [1668] Underfull \hbox (badness 2237) in paragraph at lines 28320--28322 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1669] [1670] Underfull \hbox (badness 2591) in paragraph at lines 28484--28486 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10 , usu-ally the re-sult of a call to [1671] Underfull \hbox (badness 2237) in paragraph at lines 28530--28533 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1672] Overfull \hbox (48.78088pt too wide) in paragraph at lines 28603--28603 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1673] [1674] Underfull \hbox (badness 3407) in paragraph at lines 28711--28715 []\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low) [1675] [1676] Underfull \hbox (badness 1337) in paragraph at lines 28844--28848 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1677] [1678] Underfull \hbox (badness 10000) in paragraph at lines 28961--28964 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for [1679] [1680] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29090--29090 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29118--29118 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1681] Underfull \hbox (badness 1616) in paragraph at lines 29144--29147 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1682] Overfull \hbox (20.58041pt too wide) in paragraph at lines 29223--29223 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1683] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29300--29300 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1684] Underfull \hbox (badness 5050) in paragraph at lines 29336--29341 []\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject is re-turned. The ob-ject it-self is the re-ordered (un-less [1685] Underfull \hbox (badness 2205) in paragraph at lines 29389--29394 []\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a [1686] [1687] [1688] [1689] [1690] [1691] [1692] [1693] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29984--29984 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE) [1694] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29985--29985 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1695] [1696] [1697] [1698] Underfull \hbox (badness 10000) in paragraph at lines 30274--30278 []\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect Underfull \hbox (badness 1596) in paragraph at lines 30274--30278 \T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign( f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at Overfull \hbox (30.78088pt too wide) in paragraph at lines 30285--30285 [] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con v = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30286--30286 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1699] [1700] Overfull \hbox (31.3804pt too wide) in paragraph at lines 30412--30412 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30421--30421 []\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[] [1701] [1702] [1703] [1704] Underfull \hbox (badness 1337) in paragraph at lines 30638--30642 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] Underfull \hbox (badness 1337) in paragraph at lines 31165--31169 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1713] Underfull \hbox (badness 1946) in paragraph at lines 31242--31247 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 (and \T1/pcr/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the Underfull \hbox (badness 5161) in paragraph at lines 31264--31266 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1714] [1715] [1716] [1717] [1718] Overfull \hbox (0.78088pt too wide) in paragraph at lines 31590--31590 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1719] Underfull \hbox (badness 6775) in paragraph at lines 31647--31652 []\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or [1720] Overfull \hbox (47.58038pt too wide) in paragraph at lines 31710--31710 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] [1721]) (./stats4-pkg.tex [1722] Chapter 11. [1723] [1724] [1725] Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192 [] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf)) , log = TRUE))[] [1726] [1727] [1728]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1729] Underfull \hbox (badness 10000) in paragraph at lines 440--443 []\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class [1730] [1731]) (./tcltk-pkg.tex [1732] Chapter 12. [1733] [1734] [1735] [1736] Overfull \hbox (4.38043pt too wide) in paragraph at lines 349--349 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback ref in here[] [1737] [1738] [1739] Underfull \vbox (badness 10000) has occurred while \output is active [1740] Underfull \hbox (badness 1292) in paragraph at lines 664--671 []\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing any Tk or Tcl com-mand by sim-ply run-ning [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] [1749] [1750] [1751] Underfull \hbox (badness 1189) in paragraph at lines 1407--1410 [][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1752]) (./tools-pkg.tex Chapter 13. [1753] Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for new methods.[] [1754] Underfull \hbox (badness 10000) in paragraph at lines 138--140 []\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion which will be eval-u-ated via Underfull \hbox (badness 1253) in paragraph at lines 164--167 []\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1755] Overfull \hbox (4.38043pt too wide) in paragraph at lines 215--215 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch ing warning)[] [1756] Underfull \hbox (badness 5147) in paragraph at lines 285--298 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 Underfull \hbox (badness 4792) in paragraph at lines 285--298 \T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1 0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou- Underfull \hbox (badness 2237) in paragraph at lines 285--298 \T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1 0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 , [1757] Overfull \hbox (42.78088pt too wide) in paragraph at lines 370--370 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta ngle = TRUE, Underfull \hbox (badness 2460) in paragraph at lines 389--391 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1758] [1759] [1760] [1761] [1762] [1763] [1764] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1765] [1766] Overfull \hbox (0.78088pt too wide) in paragraph at lines 901--901 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 956--956 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1767] [1768] Underfull \hbox (badness 1635) in paragraph at lines 1056--1058 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1769] Underfull \hbox (badness 5431) in paragraph at lines 1131--1134 []\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa ssed to Underfull \hbox (badness 4441) in paragraph at lines 1134--1144 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de- [1770] Underfull \hbox (badness 1014) in paragraph at lines 1156--1158 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1162--1164 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1199--1202 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us- Underfull \hbox (badness 10000) in paragraph at lines 1199--1202 \T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p tm/m/n/10 and [1771] Underfull \hbox (badness 10000) in paragraph at lines 1207--1210 []\T1/pcr/m/n/10 check_packages_in_dir \T1/ptm/m/n/10 re-turns an ob-ject in-he r-it-ing from class [1772] [1773] Underfull \hbox (badness 10000) in paragraph at lines 1356--1359 []\T1/pcr/m/n/10 codocClasses \T1/ptm/m/n/10 and \T1/pcr/m/n/10 codocData \T1/p tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1 0 and Underfull \hbox (badness 10000) in paragraph at lines 1377--1379 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1774] [1775] [1776] [1777] [1778] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1679--1679 [] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking To"),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1682--1682 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1689--1694 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 1689--1694 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . [1779] [1780] [1781]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1782] [1783] [1784] [1785] Underfull \hbox (badness 1142) in paragraph at lines 2161--2167 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgRdMacros \T1/ptm/m/n/10 func-tion fi rst looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-ag e Overfull \hbox (101.58032pt too wide) in paragraph at lines 2195--2195 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1786] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2196--2196 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2223--2230 []\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user and site spe-cific com-pi-la- Underfull \hbox (badness 1102) in paragraph at lines 2223--2230 \T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1 0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com- Underfull \hbox (badness 4168) in paragraph at lines 2223--2230 \T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/ m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m /n/10 with [1787] Underfull \hbox (badness 1342) in paragraph at lines 2275--2281 \T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in [1788] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2351--2351 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb ose"))[] Underfull \hbox (badness 7981) in paragraph at lines 2364--2370 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 2364--2370 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . [1789] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2397--2397 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2406--2406 [] \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo ", "Suggests"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2423--2423 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1790] [1791] [1792] [1793] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2688--2688 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1794] Underfull \hbox (badness 2486) in paragraph at lines 2733--2741 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d efined macros may be given in a sep-a-rate file us-ing [1795] [1796] [1797] [1798] [1799] Underfull \hbox (badness 1072) in paragraph at lines 3111--3113 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to r of links, as re-turned by [1800] [1801] [1802] [1803] [1804] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3447--3447 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1805] [1806] [1807] [1808] Underfull \hbox (badness 4108) in paragraph at lines 3691--3698 []\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o n the loop-back in-ter-face [1809] [1810] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3791--3791 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3794--3794 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3811--3813 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , Underfull \hbox (badness 2932) in paragraph at lines 3828--3834 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1811] [1812] Underfull \hbox (badness 7832) in paragraph at lines 3950--3953 []\T1/ptm/m/n/10 Where sup-ported (\T1/pcr/m/n/10 texi2dvi \T1/ptm/m/n/10 5.0 a nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1813] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4025--4025 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] [1814] Underfull \hbox (badness 1137) in paragraph at lines 4048--4050 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1815] [1816] [1817] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4222--4222 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) Underfull \hbox (badness 10000) in paragraph at lines 4233--4236 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and Underfull \hbox (badness 6859) in paragraph at lines 4249--4254 []\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/ m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p tm/m/n/10 ' are up-dated from Underfull \hbox (badness 1184) in paragraph at lines 4257--4263 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po /\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T he Underfull \hbox (badness 2941) in paragraph at lines 4257--4263 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t he pack-age are ex-am-ined to cre-ate a file [1818] Underfull \hbox (badness 10000) in paragraph at lines 4337--4342 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De pendsList Underfull \hbox (badness 10000) in paragraph at lines 4337--4342 \T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i- fied (for in-stance if Underfull \hbox (badness 10000) in paragraph at lines 4337--4342 \T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1 /ptm/m/n/10 ', it would only re-turn [1819] [1820] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4469--4469 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4470--4470 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz")[] Underfull \hbox (badness 3240) in paragraph at lines 4482--4485 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ', [1821] Underfull \hbox (badness 1742) in paragraph at lines 4486--4496 \T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 , Underfull \hbox (badness 1127) in paragraph at lines 4521--4527 []\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4521--4527 \T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file , and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1 0 ', Underfull \hbox (badness 1571) in paragraph at lines 4549--4553 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [1822] [1823] [1824]) (./utils-pkg.tex Chapter 14. Underfull \hbox (badness 1072) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [1825] [1826] [1827] Underfull \hbox (badness 6316) in paragraph at lines 212--216 []\T1/pcr/m/n/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for a si m-i-lar task to \T1/pcr/m/n/10 apropos\T1/ptm/m/n/10 . By de-fault [1828] Overfull \hbox (4.38043pt too wide) in paragraph at lines 256--256 []\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with these names[] [1829] Overfull \hbox (60.78088pt too wide) in paragraph at lines 370--370 [] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No ", "Cancel"))),[] [1830] [1831] [1832] Underfull \hbox (badness 1946) in paragraph at lines 527--531 \T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org / archive / 2011-[]2 / RJournal _ 2011-[]2 _ Overfull \hbox (0.78088pt too wide) in paragraph at lines 577--577 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc es"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 583--583 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 584--584 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 585--585 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] [1833] Overfull \hbox (0.78088pt too wide) in paragraph at lines 586--586 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Underfull \hbox (badness 10000) in paragraph at lines 620--626 []\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10 , \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 4416) in paragraph at lines 620--626 \T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_ package_C_files \T1/ptm/m/n/10 per-form spell check- [1834] Overfull \hbox (0.78088pt too wide) in paragraph at lines 689--689 [] \T1/pcr/m/n/10 ignore_repo_cache = FALSE, max_repo_cache _age,[] [1835] Underfull \hbox (badness 4505) in paragraph at lines 753--759 \T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][](" available_packages_filters") \T1/ptm/m/n/10 and to [1836] Underfull \hbox (badness 1603) in paragraph at lines 870--876 \T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/ pcr/m/n/10 infile \T1/ptm/m/n/10 starts Underfull \hbox (badness 3029) in paragraph at lines 870--876 \T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 -- \T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are [1837] Overfull \hbox (6.78088pt too wide) in paragraph at lines 927--927 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1838] Underfull \hbox (badness 1817) in paragraph at lines 992--999 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1003--1005 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1839] [1840] Underfull \hbox (badness 10000) in paragraph at lines 1111--1114 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1841] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1194--1194 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1842] [1843] [1844] [1845] [1846] Underfull \hbox (badness 1859) in paragraph at lines 1565--1574 []\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b e quite large the com- [1847] [1848] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1666--1666 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] [1849] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1701--1701 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1850] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1847--1847 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1851] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1867--1867 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, Overfull \hbox (6.78088pt too wide) in paragraph at lines 1919--1919 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1852] Underfull \hbox (badness 2213) in paragraph at lines 1953--1956 []\T1/pcr/m/n/10 ind \T1/ptm/m/n/10 chooses a row in the list of cur-rent mir-r ors, by num-ber. It is best used with [1853] [1854] Underfull \hbox (badness 10000) in paragraph at lines 2054--2056 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via Overfull \hbox (36.7804pt too wide) in paragraph at lines 2088--2088 [] \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] [1855] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2111--2111 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] Underfull \hbox (badness 5189) in paragraph at lines 2156--2158 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1856] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2231--2231 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1857] Underfull \hbox (badness 1082) in paragraph at lines 2305--2309 [][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files; [1858] Underfull \hbox (badness 10000) in paragraph at lines 2342--2344 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see Underfull \hbox (badness 1057) in paragraph at lines 2374--2381 \T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w hen [1859] [1860] [1861] Underfull \hbox (badness 10000) in paragraph at lines 2563--2565 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1862] [1863] [1864] [1865] Underfull \hbox (badness 10000) in paragraph at lines 2800--2804 []\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m /n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us- ing Underfull \hbox (badness 5203) in paragraph at lines 2800--2804 [][]\T1/pcr/m/n/10 read.table[][][](..., header = TRUE, as.is=FALSE)\T1/ptm/m/n /10 , and hence re-sult in a Overfull \hbox (133.10922pt too wide) in paragraph at lines 2805--2808 []\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr /m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][ ](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2854--2857 []\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re c-tory of the cur-rent work-ing di-rec-tory, set [1866] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2926--2926 []\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m /n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] [1867] Underfull \hbox (badness 2452) in paragraph at lines 3002--3005 []\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1 /pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources [1868] [1869] [1870] [1871] [1872] [1873] [1874] Underfull \hbox (badness 1072) in paragraph at lines 3484--3492 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [1875] Underfull \hbox (badness 1231) in paragraph at lines 3533--3539 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 3540--3545 []\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method = "libcurl"\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 7595) in paragraph at lines 3540--3545 \T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1 0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents of Underfull \hbox (badness 1331) in paragraph at lines 3540--3545 \T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in brack-ets are op-tional. See [1876] [1877] Underfull \hbox (badness 4660) in paragraph at lines 3662--3665 \T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/ 10 which makes an in-ter-nal call to Underfull \hbox (badness 10000) in paragraph at lines 3686--3688 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down load.file[][][] \T1/ptm/m/n/10 and [1878] [1879] [1880] Underfull \hbox (badness 1565) in paragraph at lines 3871--3875 []\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of Underfull \hbox (badness 10000) in paragraph at lines 3892--3898 []\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i- nal ob-ject if [1881] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3954--3954 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] Overfull \hbox (2.55087pt too wide) in paragraph at lines 3982--3989 \T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n /10 . [1882] [1883] [1884] [1885] [1886] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4309--4309 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1887]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4380 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4380 ...mat Unordered and Ordered Lists}{format} [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] [1901] [1902] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5333--5333 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [1903] Underfull \hbox (badness 10000) in paragraph at lines 5417--5419 []\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[] project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also [1904] Underfull \hbox (badness 1502) in paragraph at lines 5466--5471 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 5466--5471 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1905] [1906] [1907] Underfull \hbox (badness 10000) in paragraph at lines 5639--5648 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, Underfull \hbox (badness 10000) in paragraph at lines 5639--5648 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 ', which can be re-made by [1908] Underfull \hbox (badness 2150) in paragraph at lines 5702--5705 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See Underfull \hbox (badness 5175) in paragraph at lines 5718--5721 []\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search database for sub-se-quent use by [1909] [1910] Underfull \hbox (badness 3118) in paragraph at lines 5839--5841 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for Underfull \hbox (badness 2409) in paragraph at lines 5872--5876 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1911] Underfull \hbox (badness 5091) in paragraph at lines 5976--5978 []\T1/ptm/m/n/10 download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1 /ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL [1912] Overfull \hbox (44.55087pt too wide) in paragraph at lines 5992--5997 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . Overfull \hbox (48.30977pt too wide) in paragraph at lines 6005--6012 []\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", " Imports", "LinkingTo", "Suggests") [1913] Underfull \hbox (badness 10000) in paragraph at lines 6063--6066 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 6063--6066 \T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack -age in-stall. E.g., Underfull \hbox (badness 10000) in paragraph at lines 6122--6126 []\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T 1/ptm/m/n/10 , [1914] Underfull \hbox (badness 2376) in paragraph at lines 6136--6143 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1 0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6136--6143 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 6136--6143 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1314) in paragraph at lines 6195--6202 []\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from [1915] Underfull \hbox (badness 10000) in paragraph at lines 6236--6241 [][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][ ][]\T1/ptm/m/n/10 , Overfull \hbox (25.98041pt too wide) in paragraph at lines 6259--6259 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] [1916] Underfull \hbox (badness 5133) in paragraph at lines 6295--6299 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each pack-age's Underfull \hbox (badness 1983) in paragraph at lines 6309--6312 []\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along Overfull \hbox (9.78043pt too wide) in paragraph at lines 6356--6356 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [1917] [1918] Underfull \hbox (badness 4132) in paragraph at lines 6475--6477 []\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at [1919] [1920] [1921] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6633--6633 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [1922] [1923] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6776--6776 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [1924] Underfull \hbox (badness 10000) in paragraph at lines 6816--6818 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1925] [1926] Underfull \hbox (badness 10000) in paragraph at lines 6957--6959 []\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if Underfull \hbox (badness 10000) in paragraph at lines 6962--6964 []\T1/ptm/m/n/10 typically the re-sult of \T1/pcr/m/n/10 methods(..)\T1/ptm/m/n /10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class [1927] [1928] [1929] Underfull \hbox (badness 1859) in paragraph at lines 7185--7188 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by [1930] Underfull \hbox (badness 1655) in paragraph at lines 7267--7270 []\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db" \T1/ptm/m/n/10 , with [][]\T1/pcr/m/n/10 attributes[][][] "package" \T1/ptm/m/n /10 (and [1931] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7278--7278 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre pl("PR#", Text),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7282--7282 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 7290--7290 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [1932] Underfull \hbox (badness 10000) in paragraph at lines 7375--7379 []\T1/ptm/m/n/10 For all stan-dards, \T1/pcr/m/n/10 unit = "auto" \T1/ptm/m/n/1 0 is also al-lowed. If [1933] [1934] [1935] [1936] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7639--7639 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 7640--7640 [] \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/ %d/%y"),[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 7641--7641 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] [1937] Underfull \hbox (badness 10000) in paragraph at lines 7669--7671 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/pcr /m/n/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 7683--7685 []\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 1259) in paragraph at lines 7691--7696 []\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [1938] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7737--7737 [] \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an d "stats" are[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7738--7738 [] \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[] [1939] [1940] Underfull \hbox (badness 10000) in paragraph at lines 7867--7872 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 7867--7872 [][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els Underfull \hbox (badness 10000) in paragraph at lines 7874--7877 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 7874--7877 [][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els [1941] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7990--7990 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7991--7991 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [1942] [1943] [1944] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8162--8162 [] \T1/pcr/m/n/9 "S original, "),[] [1945] Underfull \hbox (badness 1789) in paragraph at lines 8285--8287 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [1946] Underfull \hbox (badness 10000) in paragraph at lines 8343--8347 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8343--8347 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1947] [1948] Underfull \hbox (badness 10000) in paragraph at lines 8458--8462 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8458--8462 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1949] Underfull \hbox (badness 10000) in paragraph at lines 8523--8527 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8523--8527 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1950] [1951] [1952] [1953] Underfull \hbox (badness 5203) in paragraph at lines 8854--8857 []\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 ex-trac-tor are de-ter-mined by the generic func-tion [1954] [1955] [1956] Underfull \hbox (badness 1776) in paragraph at lines 9080--9087 []\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o f pieces of code, you should set [1957] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9104--9104 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [1958] [1959] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9265--9265 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [1960] [1961] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9446--9446 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 456 98 76 54[] [1962] [1963] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9532--9532 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9535--9535 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 9540--9540 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [1964] Underfull \hbox (badness 1077) in paragraph at lines 9612--9615 []\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL [1965] [1966] [1967] [1968] [1969] [1970] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10052--10052 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [1971] Underfull \hbox (badness 10000) in paragraph at lines 10139--10141 []\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/ m/n/10 in-stead of the de-fault one, use [1972] [1973] Underfull \hbox (badness 2181) in paragraph at lines 10262--10266 []\T1/pcr/m/n/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/pcr/m/n /10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10262--10266 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 10000) in paragraph at lines 10274--10278 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s&oldid = 78252134$[][]\T1/ptm/m/n/10 . [1974] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10292--10292 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10296--10296 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [1975] [1976] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10428--10428 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [1977] Underfull \hbox (badness 1917) in paragraph at lines 10551--10554 []\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari- Underfull \hbox (badness 4328) in paragraph at lines 10551--10554 \T1/ptm/m/n/10 able \T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES\T1/ptm/m/n/10 . If this is set, then it takes prece-dence over [1978] Overfull \hbox (106.98032pt too wide) in paragraph at lines 10574--10574 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] [1979] Underfull \hbox (badness 8075) in paragraph at lines 10637--10639 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\ T1/ptm/m/n/10 s are nicely viewed via [1980] Underfull \hbox (badness 6725) in paragraph at lines 10687--10696 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \ T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first, Underfull \hbox (badness 6428) in paragraph at lines 10687--10696 \T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i- Underfull \hbox (badness 10000) in paragraph at lines 10687--10696 \T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for re-verse al-pha-bet-i-cal or-der, Underfull \hbox (badness 1997) in paragraph at lines 10687--10696 \T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/ n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or [1981] Underfull \hbox (badness 3646) in paragraph at lines 10813--10815 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software / [1982] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10851--10851 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [1983] [1984] [1985] Underfull \hbox (badness 10000) in paragraph at lines 11032--11036 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no w taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 11063--11069 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [1986] Underfull \hbox (badness 2012) in paragraph at lines 11158--11164 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments for fig-ures should be auto-generated. Use [1987] Underfull \hbox (badness 2096) in paragraph at lines 11171--11173 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether EPS fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 2698) in paragraph at lines 11174--11176 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh ether PDF fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 11181--11184 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1067) in paragraph at lines 11185--11188 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether JPEG fig-ures should be gen-er-ated. Ig-nored if Overfull \hbox (6.78088pt too wide) in paragraph at lines 11239--11239 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] [1988] Underfull \hbox (badness 1009) in paragraph at lines 11257--11268 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [1989] Underfull \hbox (badness 2846) in paragraph at lines 11344--11354 \T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault [1990] [1991] Underfull \hbox (badness 10000) in paragraph at lines 11483--11486 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10 R \T1/ptm/m/n/10 was built un- Underfull \hbox (badness 10000) in paragraph at lines 11483--11486 \T1/ptm/m/n/10 der. Where sub-architectures are in use this is of the form Underfull \hbox (badness 10000) in paragraph at lines 11500--11503 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [1992] Underfull \hbox (badness 2158) in paragraph at lines 11579--11582 []\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe -cially: the value is taken from the cur-rent set-ting of [1993] [1994] [1995] Underfull \hbox (badness 3333) in paragraph at lines 11759--11761 []\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file- [1996] [1997] Overfull \hbox (42.78088pt too wide) in paragraph at lines 11924--11924 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] [1998] Underfull \hbox (badness 5970) in paragraph at lines 11957--11960 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive Underfull \hbox (badness 2600) in paragraph at lines 11957--11960 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less Underfull \hbox (badness 1052) in paragraph at lines 11968--11977 \T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][][]\T1/ptm/m/n/10 ) which de-f aults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons ; [1999] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12012--12012 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12043--12043 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo ng" non-ASCII:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12050--12050 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se e 1 (in UTF-8!):[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 12052--12052 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [2000] [2001] [2002] Underfull \hbox (badness 10000) in paragraph at lines 12220--12222 []\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/ 10 ap-ply only to files pro-duced by [2003] [2004] Underfull \hbox (badness 4492) in paragraph at lines 12377--12384 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in Underfull \hbox (badness 6252) in paragraph at lines 12377--12384 \T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/ n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 2452) in paragraph at lines 12377--12384 \T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 ( with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and [2005] [2006] [2007] Underfull \hbox (badness 2020) in paragraph at lines 12539--12555 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl at-forms), Underfull \hbox (badness 1194) in paragraph at lines 12539--12555 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s im-i-lar) and on Win-dows [2008] Underfull \hbox (badness 2809) in paragraph at lines 12659--12663 []\T1/ptm/m/n/10 NetBSD prior to 8.0 used flag `\T1/pcr/m/n/10 --xz\T1/ptm/m/n/ 10 ' rather than `\T1/pcr/m/n/10 -J\T1/ptm/m/n/10 ', so this should be used \T1 /ptm/m/it/10 via Underfull \hbox (badness 1596) in paragraph at lines 12659--12663 \T1/pcr/m/n/10 extra_flags = "--xz" \T1/ptm/m/n/10 rather than \T1/pcr/m/n/10 c ompression = "xz"\T1/ptm/m/n/10 . The com-mands from Underfull \hbox (badness 5022) in paragraph at lines 12674--12678 []\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl e Underfull \hbox (badness 10000) in paragraph at lines 12681--12684 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs . Underfull \hbox (badness 10000) in paragraph at lines 12681--12684 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml#tag _ 20 _ [2009] [2010] [2011] Overfull \hbox (18.78088pt too wide) in paragraph at lines 12846--12846 [] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss "), ...)[] [2012] [2013] [2014] [2015] [2016] [2017] Overfull \hbox (6.78088pt too wide) in paragraph at lines 13230--13230 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 13236--13236 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Underfull \hbox (badness 4467) in paragraph at lines 13257--13259 []\T1/ptm/m/n/10 Download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1 /ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL Underfull \hbox (badness 4660) in paragraph at lines 13270--13274 \T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/ 10 which makes an in-ter-nal call to Overfull \hbox (36.87935pt too wide) in paragraph at lines 13284--13288 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 13290--13295 []\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T 1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be Underfull \hbox (badness 10000) in paragraph at lines 13290--13295 \T1/ptm/m/n/10 passed to [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 and \T1/pcr/m/n/10 ignore_repo_cache\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13290--13295 \T1/pcr/m/n/10 max_repo_cache_age \T1/ptm/m/n/10 and \T1/pcr/m/n/10 noCache \T1 /ptm/m/n/10 to [][]\T1/pcr/m/n/10 available.packages[][][] [2018] Underfull \hbox (badness 1052) in paragraph at lines 13296--13298 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 13326--13331 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined see Underfull \hbox (badness 10000) in paragraph at lines 13326--13331 [][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai lable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 10000) in paragraph at lines 13326--13331 \T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1 /ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 13347--13352 []\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/ 10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with Underfull \hbox (badness 10000) in paragraph at lines 13355--13358 [][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[] [][]\T1/ptm/m/n/10 , [2019] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13409--13409 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c sb/ch3a.txt") [2020] [2021] [2022] Underfull \hbox (badness 10000) in paragraph at lines 13597--13600 [][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi- gnette browser; Overfull \hbox (42.18039pt too wide) in paragraph at lines 13613--13613 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[] [2023] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13680--13680 [] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d ata = DAT)))[] [2024] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13702--13702 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 13721--13721 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2025] Underfull \hbox (badness 1454) in paragraph at lines 13748--13752 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, Underfull \hbox (badness 1715) in paragraph at lines 13773--13776 []\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 13818--13820 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion [2026] Underfull \hbox (badness 3271) in paragraph at lines 13830--13834 \T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1 /ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if [2027] [2028]) [2029] [2030] (./KernSmooth-pkg.tex Chapter 15. [2031] Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat e = TRUE) [2032] [2033] [2034] [2035] [2036] Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun = 0.05, [2037] [2038] [2039] [2040]) (./MASS-pkg.tex Chapter 16. [2041] [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049] [2050] [2051] Overfull \hbox (20.58041pt too wide) in paragraph at lines 774--774 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b eav2$hours/24))[] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] Underfull \hbox (badness 7256) in paragraph at lines 1604--1606 []\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo r [2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2412--2412 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2416--2416 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] [2075] [2076] [2077] [2078] Underfull \hbox (badness 6559) in paragraph at lines 2694--2697 []\T1/ptm/m/n/10 further ar-gu-ments for \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 and graph-i-cal pa-ram-e-ters. Note that [2079] [2080] [2081] Underfull \hbox (badness 10000) in paragraph at lines 2864--2869 \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "geometric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/pt m/m/n/10 , Underfull \hbox (badness 8189) in paragraph at lines 2864--2869 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "negative binomial"\T1 /ptm/m/n/10 , \T1/pcr/m/n/10 "normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Poisson"\ T1/ptm/m/n/10 , Underfull \hbox (badness 3557) in paragraph at lines 2900--2908 []\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start -ing val-ues will be com-puted if Underfull \hbox (badness 3118) in paragraph at lines 2900--2908 \T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied: \T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , [2082] [2083] Underfull \hbox (badness 4686) in paragraph at lines 3032--3034 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds Underfull \hbox (badness 1515) in paragraph at lines 3046--3050 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n /10 cycles \T1/ptm/m/n/10 terms or when a [2084] [2085] [2086] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3227--3227 [] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL SE, ...)[] Underfull \hbox (badness 5817) in paragraph at lines 3234--3236 []\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1 0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with [2087] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3357--3357 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist = "exponential")[] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097] [2098] [2099] Underfull \hbox (badness 1845) in paragraph at lines 4143--4145 []\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm /m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and [2100] [2101] [2102] [2103] [2104] [2105] [2106] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4639--4639 [] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n", ...)[] [2107] [2108] Underfull \hbox (badness 10000) in paragraph at lines 4791--4794 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2109] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4861--4861 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, Underfull \hbox (badness 10000) in paragraph at lines 4869--4872 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2110] [2111] [2112] [2113] [2114] Underfull \hbox (badness 5681) in paragraph at lines 5269--5271 []\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/ n/10 . This is over-ridden if Underfull \hbox (badness 5022) in paragraph at lines 5273--5276 []\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_ \OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10 \OT1/cmr/m/n/10 ()$ \ T1/ptm/m/n/10 func-tions when [2115] Underfull \hbox (badness 1975) in paragraph at lines 5322--5324 []\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in the case of [2116] [2117] [2118] [2119] [2120] [2121] [2122] [2123] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5908--5908 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP ACK = FALSE) [2124] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5969--5969 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/ 10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") [2125] [2126]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.npk}) has been already used, duplicate ignored \relax l.6111 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica te ignored \relax l.6111 ...sical N, P, K Factorial Experiment}{npk} [2127] Underfull \hbox (badness 1783) in paragraph at lines 6229--6233 []\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space. That is [2128] [2129] [2130] [2131] Underfull \vbox (badness 10000) has occurred while \output is active [2132] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6527--6527 [] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb ose = TRUE)))[] [2133] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6615--6615 [] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr ellis"))[] [2134] [2135] [2136] [2137] [2138] [2139] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7054--7054 []\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100 , A=10, B=1))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7071--7071 [] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c auchit"))[] Underfull \hbox (badness 10000) in paragraph at lines 7078--7085 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2140] Underfull \hbox (badness 10000) in paragraph at lines 7094--7096 []\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat Underfull \hbox (badness 3138) in paragraph at lines 7149--7155 []\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c mr/m/n/10 ) = [2141] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7219--7219 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2142] [2143] Underfull \hbox (badness 5091) in paragraph at lines 7328--7331 \T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na nt com-po-nents are used (ex-cept for [2144] [2145] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7458--7458 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam p = "exact")[] [2146] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7523--7523 [] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC V"), ...)[] [2147] [2148] [2149] [2150] [2151] [2152] Underfull \hbox (badness 4686) in paragraph at lines 7961--7963 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds Underfull \hbox (badness 1515) in paragraph at lines 7977--7981 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n /10 cycles \T1/ptm/m/n/10 terms or when a [2153] [2154] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8080--8080 [] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control = NULL)[] Underfull \hbox (badness 1590) in paragraph at lines 8104--8108 []\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if \T1/pcr/m/n /10 NA\T1/ptm/m/n/10 s are found. The [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9483--9483 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS E, ...)[] [2175] Underfull \hbox (badness 1158) in paragraph at lines 9610--9613 []\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els \T1/pcr/m/n/10 "Heavy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Regul" \T1/ptm/m/n/10 (reg-u-larly), [2176] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9692--9692 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub le.eps^0.25) Overfull \hbox (30.78088pt too wide) in paragraph at lines 9694--9694 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double .eps^0.25,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9697--9697 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub le.eps^0.25)[] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189]) (./Matrix-pkg.tex [2190] Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 41--44 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 41--44 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2191] Underfull \hbox (badness 1769) in paragraph at lines 95--98 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2192] Underfull \hbox (badness 2229) in paragraph at lines 159--162 []\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm /m/n/10 ob-jects; here, when the first is Underfull \hbox (badness 1147) in paragraph at lines 159--162 \T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th ese ar-gu-ments will be con-cate-nated to a new [2193] Underfull \hbox (badness 10000) in paragraph at lines 257--260 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 263--265 []\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][ ]sparseVector[][][]"\T1/ptm/m/n/10 's, see [2194] [2195] Overfull \hbox (42.78088pt too wide) in paragraph at lines 488--488 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp arse = TRUE) Underfull \hbox (badness 5147) in paragraph at lines 495--498 []\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal mean-ing as in [2196] Underfull \hbox (badness 5119) in paragraph at lines 508--512 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class Underfull \hbox (badness 4621) in paragraph at lines 512--516 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m /n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a Overfull \hbox (4.38043pt too wide) in paragraph at lines 535--535 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 537--537 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 546--546 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c( 1:3,2:3,3:2)],[] [2197] [2198] Overfull \hbox (52.98038pt too wide) in paragraph at lines 660--660 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd iag() -- for the case of *many* (k x k) matrices:[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(, , ....., ) where each mat_j is a k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 matrix\TS1/pcr/m/n/9 '[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 662--662 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k) matrix of class \code{"\linkS4class{dgCMatrix}"}.[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 675--675 [] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \ T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri x indexing), but elegant?[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 676--676 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 681--681 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim plify=FALSE)[] [2199] Underfull \hbox (badness 3189) in paragraph at lines 732--736 []\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib . [2200] [2201] [2202] Overfull \hbox (72.78088pt too wide) in paragraph at lines 947--947 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2203] Underfull \hbox (badness 10000) in paragraph at lines 1022--1024 []\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n /10 (or equiv-a- Underfull \hbox (badness 10000) in paragraph at lines 1045--1050 []\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of the lower tri- Underfull \hbox (badness 10000) in paragraph at lines 1045--1050 \T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the de-com-po-si-tion. This method is equiv-a-lent to Underfull \hbox (badness 1092) in paragraph at lines 1045--1050 \T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in the above de-scrip-tion of Underfull \hbox (badness 10000) in paragraph at lines 1068--1075 []\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm = "logical") [2204]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho l}) has been already used, duplicate ignored \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic ate ignored \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} [2205pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha s been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' pdfTeX warning (ext4): destina tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' pdfTeX warning (ext4): destina tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' ] [2206] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1266--1266 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2207] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1360--1360 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) Underfull \hbox (badness 2277) in paragraph at lines 1388--1391 []\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer -ent types of ma-tri-ces. Use [2208] Underfull \hbox (badness 1609) in paragraph at lines 1435--1439 []\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion [] []\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra [2209] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so me GOTOblas:[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1476--1476 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 , sep="") ## dQuote() gives bad plots[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1484--1484 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE) , super = c(FALSE,TRUE)))[] [2210] Underfull \hbox (badness 6445) in paragraph at lines 1531--1538 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("Cholesky", ...) \T1/ptm/m/n/10 or Underfull \hbox (badness 3861) in paragraph at lines 1531--1538 \T1/pcr/m/n/10 new("BunchKaufman", ...)\T1/ptm/m/n/10 , etc, or rather by calls of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or Underfull \hbox (badness 1783) in paragraph at lines 1566--1570 []\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1 /ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend Underfull \hbox (badness 1221) in paragraph at lines 1582--1588 \T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 nu-meric [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . Hen ce, for com-pat-i-bil-ity, the \T1/pcr/m/n/10 "Cholesky" \T1/ptm/m/n/10 and [2211]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col Sums}) has been already used, duplicate ignored \relax l.1623 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup licate ignored \relax l.1623 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl icate ignored \relax l.1624 \aliasA{colMeans}{colSums}{colMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i gnored \relax l.1645 \aliasA{rowMeans}{colSums}{rowMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig nored \relax l.1656 \aliasA{rowSums}{colSums}{rowSums} [2212] Underfull \hbox (badness 2922) in paragraph at lines 1710--1714 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i n-her-it-ing from Underfull \hbox (badness 1728) in paragraph at lines 1710--1714 \T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a Underfull \hbox (badness 1237) in paragraph at lines 1721--1724 [][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1 /pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10 v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since [2213] Underfull \hbox (badness 10000) in paragraph at lines 1801--1805 []\T1/pcr/m/n/10 signature(x = "compMatrix", value = "list")\T1/ptm/m/n/10 : se t the [2214] Underfull \hbox (badness 3547) in paragraph at lines 1875--1878 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2215] [2216] [2217] Underfull \hbox (badness 10000) in paragraph at lines 2112--2114 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix ", where = [2218] [2219] Underfull \hbox (badness 10000) in paragraph at lines 2234--2236 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix" , where = Underfull \hbox (badness 3068) in paragraph at lines 2295--2299 \T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10 or sim-i-lar. Of-ten how-ever, more eas-ily via [2220] Underfull \hbox (badness 4713) in paragraph at lines 2330--2332 []\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de -com-po-si-tion of a square [2221] Underfull \hbox (badness 10000) in paragraph at lines 2447--2450 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10 or [2222] Underfull \hbox (badness 10000) in paragraph at lines 2549--2553 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dgTMatrix", ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2549--2553 \T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or [2223] Underfull \hbox (badness 2707) in paragraph at lines 2605--2609 []\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T 1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d gTMatrix" \T1/ptm/m/n/10 (and other Underfull \hbox (badness 2368) in paragraph at lines 2610--2614 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i n more than one pos-si-ble Underfull \hbox (badness 10000) in paragraph at lines 2617--2620 []\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\ T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ; [2224] Underfull \hbox (badness 2689) in paragraph at lines 2673--2675 []\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix. If miss-ing, Underfull \hbox (badness 10000) in paragraph at lines 2677--2682 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 .symDiagonal \T1/ptm/m/n/10 (\T1/pcr/m/n/10 .trDiagonal\T1/ptm/m/n/10 ), the re-sult-ing sparse Underfull \hbox (badness 3482) in paragraph at lines 2677--2682 [][]\T1/pcr/m/n/10 symmetricMatrix[][][] \T1/ptm/m/n/10 (or [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 ) will have slot \T1/pcr/m/n/10 uplo [2225] Underfull \hbox (badness 1097) in paragraph at lines 2700--2703 []\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1 /pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][ ] \T1/ptm/m/n/10 (with ``su-per-class'' Underfull \hbox (badness 1142) in paragraph at lines 2713--2718 [][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de -pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm /m/n/10 ) rep-re-sen-ta-tion of [2226] Underfull \hbox (badness 3646) in paragraph at lines 2951--2954 []\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T 1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][] \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally Underfull \hbox (badness 10000) in paragraph at lines 2973--2974 []\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1 /ptm/m/n/10 : Underfull \hbox (badness 1810) in paragraph at lines 2980--2982 []\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri v-ially im-ple-mented, of Underfull \hbox (badness 10000) in paragraph at lines 2983--2985 []\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv -a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion Underfull \hbox (badness 3803) in paragraph at lines 2986--2990 []\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou p meth-ods re-turn a [2227] Underfull \hbox (badness 1371) in paragraph at lines 2995--3001 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 : the re-sult is from class Underfull \hbox (badness 10000) in paragraph at lines 3002--3006 []\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec t of S3 class Underfull \hbox (badness 2318) in paragraph at lines 3012--3016 [][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr /m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and [2228] [2229] Underfull \hbox (badness 1859) in paragraph at lines 3196--3198 []\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t his group con-tains Underfull \hbox (badness 10000) in paragraph at lines 3243--3245 [][][]\T1/pcr/m/n/10 drop0[][][](x, tol=1e-10) \T1/ptm/m/n/10 is some-times pre fer-able to (and more ef-fi-cient than) [2230] Underfull \hbox (badness 1168) in paragraph at lines 3363--3366 []\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T 1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , via [2231] [2232] Underfull \hbox (badness 4967) in paragraph at lines 3528--3532 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsCMatrix", ...) \T1/ptm/m/n/10 or [2233] Overfull \hbox (2.39853pt too wide) in paragraph at lines 3533--3535 []\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][] \T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 . Underfull \hbox (badness 6364) in paragraph at lines 3575--3578 []\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr /m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves [2234] [2235] Underfull \hbox (badness 10000) in paragraph at lines 3725--3730 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1 /ptm/m/n/10 , by Underfull \hbox (badness 6961) in paragraph at lines 3725--3730 \T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m /n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm /m/n/10 by class Underfull \hbox (badness 10000) in paragraph at lines 3735--3737 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a triv-ial Underfull \hbox (badness 10000) in paragraph at lines 3737--3740 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 : if [2236] Underfull \hbox (badness 4967) in paragraph at lines 3813--3815 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsyMatrix", ...) \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 3852--3855 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 , or Underfull \hbox (badness 1735) in paragraph at lines 3852--3855 \T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing "\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the [2237] Underfull \hbox (badness 10000) in paragraph at lines 3855--3858 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 , or Underfull \hbox (badness 2318) in paragraph at lines 3855--3858 \T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing "\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion Underfull \hbox (badness 6364) in paragraph at lines 3859--3862 []\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr /m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves [2238] Underfull \hbox (badness 4060) in paragraph at lines 3983--3986 []\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse tri-an-gu-lar solve (aka [2239] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4023--4023 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] [2240] Underfull \hbox (badness 3635) in paragraph at lines 4091--4095 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class Underfull \hbox (badness 10000) in paragraph at lines 4100--4103 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma - Underfull \hbox (badness 10000) in paragraph at lines 4100--4103 \T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co m-bi-na-tions, see Underfull \hbox (badness 10000) in paragraph at lines 4105--4109 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1 0 : the [2241] [2242] [2243] [2244] Underfull \hbox (badness 10000) in paragraph at lines 4393--4398 []\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite Tay-lor se-ries [2245] [2246] Overfull \hbox (85.38034pt too wide) in paragraph at lines 4527--4527 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/ Boeing/msc00726.tar.gz"))))[] Overfull \hbox (139.38028pt too wide) in paragraph at lines 4530--4530 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe ll-Boeing/counterx/jgl009.mtx.gz"))))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4534--4534 []\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary dir./folder:[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4537--4537 []\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 4547--4547 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2247] [2248] Underfull \hbox (badness 10000) in paragraph at lines 4702--4704 [][][]\T1/pcr/m/n/10 symmpart[][][] \T1/ptm/m/n/10 for the sym-met-ric part of a ma-trix, or the co-er-cions [2249] [2250] Underfull \hbox (badness 10000) in paragraph at lines 4849--4854 []\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1 /ptm/m/n/10 , [2251] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4930--4930 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che cking reasons" Overfull \hbox (20.58041pt too wide) in paragraph at lines 4932--4932 [] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2, dimnames=dns))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4936--4936 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] [2252] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4943--4943 [] \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] [2253] Underfull \hbox (badness 10000) in paragraph at lines 5068--5073 []\T1/ptm/m/n/10 color for the bor-der of each rect-an-gle. \T1/pcr/m/n/10 NA \ T1/ptm/m/n/10 means Underfull \hbox (badness 10000) in paragraph at lines 5068--5073 \T1/ptm/m/n/10 no bor-der is drawn. When \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 as by de-fault, Underfull \hbox (badness 2644) in paragraph at lines 5068--5073 \T1/pcr/m/n/10 border.col <- if(lwd < .01) NA else NULL \T1/ptm/m/n/10 is used. Con- Underfull \hbox (badness 4108) in paragraph at lines 5068--5073 \T1/ptm/m/n/10 sider us-ing an opaque color in-stead of \T1/pcr/m/n/10 NULL \T1 /ptm/m/n/10 which cor-re-sponds to [2254] Underfull \hbox (badness 4120) in paragraph at lines 5087--5090 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use Overfull \hbox (15.18042pt too wide) in paragraph at lines 5124--5124 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col /row) indices:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5130--5130 [] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, border.col=NA)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5131--5131 [] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd =2, border.col=NA)[] Overfull \hbox (144.78027pt too wide) in paragraph at lines 5134--5134 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5136--5136 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH ECK_EXTRA")) ||[] [2255] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5143--5143 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a nti-aliasing[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5146--5146 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2256] Underfull \hbox (badness 1817) in paragraph at lines 5235--5244 []\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within the Underfull \hbox (badness 5637) in paragraph at lines 5277--5279 []\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use [2257] Underfull \hbox (badness 3138) in paragraph at lines 5303--5305 []\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the [2258] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5370--5370 [] \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1 , I2)) else TRUE,[] Underfull \hbox (badness 1603) in paragraph at lines 5391--5393 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault, Underfull \hbox (badness 10000) in paragraph at lines 5399--5404 []\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault, Underfull \hbox (badness 10000) in paragraph at lines 5399--5404 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 ) , \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as Underfull \hbox (badness 10000) in paragraph at lines 5399--5404 [][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to [2259] [2260] [2261] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5628--5628 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/ pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] [2262] Underfull \hbox (badness 10000) in paragraph at lines 5709--5712 [][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and Overfull \hbox (9.78043pt too wide) in paragraph at lines 5720--5720 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n ot "formally"[] [2263] Underfull \hbox (badness 1622) in paragraph at lines 5757--5762 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \ T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy /m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ), Underfull \hbox (badness 1418) in paragraph at lines 5757--5762 \T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy /m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m /it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/ m/n/10 is the kro-necker prod-uct [2264] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5818--5818 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1) , c(12L, 4L)),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5819--5819 [] \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2) , c(12L, 4L)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5826--5826 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2265] Underfull \hbox (badness 1062) in paragraph at lines 5955--5958 []\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both [2266] Underfull \hbox (badness 2809) in paragraph at lines 5984--5987 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2267] Underfull \hbox (badness 2635) in paragraph at lines 6096--6101 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 6096--6101 \T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/ pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/ m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 6104--6107 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us e, e.g., [2268] Underfull \hbox (badness 10000) in paragraph at lines 6214--6224 \T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/ n/10 ) or in com-pressed column-oriented form (class Underfull \hbox (badness 1242) in paragraph at lines 6214--6224 [][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/ 10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 -- in [2269] Underfull \hbox (badness 1184) in paragraph at lines 6296--6299 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2270] Underfull \hbox (badness 10000) in paragraph at lines 6394--6397 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2271] Underfull \hbox (badness 10000) in paragraph at lines 6469--6472 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., Overfull \hbox (25.98041pt too wide) in paragraph at lines 6485--6485 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] [2272] Underfull \hbox (badness 2443) in paragraph at lines 6524--6530 []\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][ ]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see Underfull \hbox (badness 1776) in paragraph at lines 6524--6530 [][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr /m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar, Underfull \hbox (badness 1675) in paragraph at lines 6545--6548 []\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth- ods for dif-fer-ent types of ma-tri-ces. Use [2273] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6615--6615 [] \T1/pcr/m/n/9 # q is a 0-based permutation o f the columns[] [2274] [2275] Underfull \hbox (badness 6268) in paragraph at lines 6751--6754 []\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math- e-mat-i-cally''), [2276] Underfull \hbox (badness 5036) in paragraph at lines 6775--6779 []\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1 /ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . How-ever, Underfull \hbox (badness 10000) in paragraph at lines 6775--6779 \T1/pcr/m/n/10 Matrix(0, nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``e mpty'' [][]sparse-Ma-trix[][][], as does [2277]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.6868 \aliasA{det}{Matrix-class}{det} Underfull \hbox (badness 1348) in paragraph at lines 6948--6951 []\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10 diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing Underfull \hbox (badness 10000) in paragraph at lines 6953--6956 []\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \ T1/pcr/m/n/10 value \T1/ptm/m/n/10 is Underfull \hbox (badness 10000) in paragraph at lines 6953--6956 \T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p tm/m/n/10 Ma-trix ob-jects, but only when Underfull \hbox (badness 10000) in paragraph at lines 6971--6974 Underfull \hbox (badness 7326) in paragraph at lines 6981--6983 []\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")\T1/ptm/m/n/10 : This re -lies on a cor-rect [2278]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \relax l.7044 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.crossprod}) has been already used, dup licate ignored \relax l.7152 ...A{crossprod}{matrix-products}{crossprod} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du plicate ignored \relax l.7252 ...tcrossprod}{matrix-products}{tcrossprod} [2279] Underfull \hbox (badness 1881) in paragraph at lines 7350--7356 \T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn [2280pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros sprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7412 \end{Details} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrossprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7412 \end{Details} ] Underfull \hbox (badness 10000) in paragraph at lines 7423--7426 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")\T1/ptm/m/n/10 : Ma - Underfull \hbox (badness 10000) in paragraph at lines 7423--7426 \T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co m-bi-na-tions, see Underfull \hbox (badness 5637) in paragraph at lines 7426--7431 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use Underfull \hbox (badness 10000) in paragraph at lines 7435--7437 []\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r e-turns Underfull \hbox (badness 10000) in paragraph at lines 7437--7439 []\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r e-turns Underfull \hbox (badness 10000) in paragraph at lines 7441--7442 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and [2281] [2282] Underfull \hbox (badness 1062) in paragraph at lines 7622--7625 []\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both [2283] Underfull \hbox (badness 2809) in paragraph at lines 7656--7659 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2284] Underfull \hbox (badness 10000) in paragraph at lines 7708--7710 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <- (X + t(X))/2 \T1/ ptm/m/n/10 should be done, af-ter [2285] Underfull \hbox (badness 1406) in paragraph at lines 7748--7752 []\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b y Jens Oehlschlaegel did not Underfull \hbox (badness 1019) in paragraph at lines 7748--7752 \T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t his sim-pli-fi-ca-tion, now only via [2286] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7846--7846 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a ll in this example[] Underfull \vbox (badness 10000) has occurred while \output is active [2287] Underfull \hbox (badness 2635) in paragraph at lines 7911--7916 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 7911--7916 \T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/ pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/ m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 7919--7922 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us e, e.g., [2288] [2289] Underfull \hbox (badness 10000) in paragraph at lines 8113--8115 []\T1/ptm/m/n/10 fast [2290]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8153 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.8153 \HeaderA{norm}{Matrix Norms}{norm} [2291] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8240--8240 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8241--8241 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8242--8242 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Underfull \hbox (badness 2401) in paragraph at lines 8355--8365 []\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1 0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p tm/m/n/10 , [2292] Underfull \hbox (badness 1184) in paragraph at lines 8426--8429 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2293] Underfull \hbox (badness 10000) in paragraph at lines 8516--8519 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2294] Underfull \hbox (badness 10000) in paragraph at lines 8592--8595 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2295] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8608--8608 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] Overfull \vbox (41.60564pt too high) has occurred while \output is active [2296] Underfull \hbox (badness 10000) in paragraph at lines 8718--8720 []\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe r sig-na-tures (use Underfull \hbox (badness 1596) in paragraph at lines 8734--8736 []\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 : co-er-cion to sparse Underfull \hbox (badness 1721) in paragraph at lines 8740--8744 \T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S ee [2297] [2298] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8819--8819 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8824--8824 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8829--8829 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 8852--8862 []\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T 1/pcr/m/n/10 x \T1/ptm/m/n/10 should Underfull \hbox (badness 10000) in paragraph at lines 8852--8862 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2299] [2300]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.qr}) has been already used, duplicate ignored \relax l.8953 \aliasA{qr}{qr-methods}{qr} Underfull \hbox (badness 5119) in paragraph at lines 8999--9002 []\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma- trix with Overfull \hbox (9.78043pt too wide) in paragraph at lines 9026--9026 []\T1/pcr/m/n/9 stopifnot(identical(dimnames(X), dnX))# some versions changed X\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s dimnames![] [2301] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9037--9037 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n ot supported[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9041--9041 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9058--9058 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9066--9066 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor rect colnames[] [2302] Underfull \hbox (badness 10000) in paragraph at lines 9119--9125 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of Underfull \hbox (badness 10000) in paragraph at lines 9136--9139 []\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p tm/m/n/10 , it cor-re-sponds to [2303] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9208--9208 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/ n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale free"[] [2304] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9229--9229 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war ning+ ~1.5 sec (2013)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 9230--9230 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con siderably faster![] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h as been already used, duplicate ignored \relax l.9249 ... the Reciprocal Condition Number}{rcond} [2305] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9362--9362 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2306] [2307] [2308] Underfull \hbox (badness 10000) in paragraph at lines 9547--9549 []\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably Underfull \hbox (badness 1325) in paragraph at lines 9553--9561 \T1/ptm/m/n/10 gets \T1/pcr/m/n/10 x <- rand.x(nnz) \T1/ptm/m/n/10 and calls [] []\T1/pcr/m/n/10 sparseMatrix[][][](i=i, j=j, x=x, ..)\T1/ptm/m/n/10 . When [2309] [2310] Underfull \hbox (badness 1558) in paragraph at lines 9698--9701 []\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1 0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional [2311] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9760--9760 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9764--9764 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2312]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol ve}) has been already used, duplicate ignored \relax l.9826 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (54.78088pt too wide) in paragraph at lines 9923--9923 [] \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P ", "Pt"), ...)[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9928--9928 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2313] Underfull \hbox (badness 6047) in paragraph at lines 9963--9975 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods Underfull \hbox (badness 10000) in paragraph at lines 9980--9983 []\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via Underfull \hbox (badness 7203) in paragraph at lines 9985--9986 []\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar Underfull \hbox (badness 7851) in paragraph at lines 9989--9996 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 10000) in paragraph at lines 9989--9996 \T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U ses the sparse Underfull \hbox (badness 10000) in paragraph at lines 10002--10012 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 2165) in paragraph at lines 10002--10012 \T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym- [2314] Underfull \hbox (badness 1194) in paragraph at lines 10036--10038 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines Underfull \hbox (badness 10000) in paragraph at lines 10050--10053 []\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 10000) in paragraph at lines 10059--10060 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 10065--10067 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10069--10070 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 10077--10080 [][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1 /ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10095--10095 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i s singular!][] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10099--10099 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2315] Underfull \hbox (badness 10000) in paragraph at lines 10120--10123 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu la and data frame Underfull \hbox (badness 1648) in paragraph at lines 10148--10150 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 10000) in paragraph at lines 10156--10159 []\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co- er-ca-ble to) Underfull \hbox (badness 2591) in paragraph at lines 10156--10159 \T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t rasts to be ap-plied to the [2316] Underfull \hbox (badness 10000) in paragraph at lines 10167--10171 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for Underfull \hbox (badness 2828) in paragraph at lines 10167--10171 \T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m /n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for Underfull \hbox (badness 6592) in paragraph at lines 10178--10180 []\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in -di-cat-ing if the re-sult must be a [2317] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10255--10255 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M) == c(0, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10256--10256 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M) == c(3, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10257--10257 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2318] [2319] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10441--10441 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10442--10442 [] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = FALSE)[] [2320] Underfull \hbox (badness 4621) in paragraph at lines 10482--10486 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m /n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a [2321] Underfull \hbox (badness 10000) in paragraph at lines 10558--10561 []\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][]( *, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10570--10570 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10574--10574 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10575--10575 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10580--10580 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims = c(10,20)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10583--10583 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2322] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10606--10606 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 10607--10607 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10633--10633 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep resentations.[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 10635--10635 [] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack age = "SparseM"))) {[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10637--10637 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] [2323] Underfull \hbox (badness 10000) in paragraph at lines 10730--10738 []\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject of S3 class Underfull \hbox (badness 1325) in paragraph at lines 10751--10755 []\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a [2324] Underfull \hbox (badness 10000) in paragraph at lines 10781--10785 [][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s uch as [][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)\T1/ptm/m/n/10 , or pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha s been already used, duplicate ignored \relax l.10821 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2325] [2326] Underfull \hbox (badness 1430) in paragraph at lines 10951--10953 []\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses Overfull \hbox (58.38037pt too wide) in paragraph at lines 10979--10979 [] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai led in Matrix <= 1.1-0[] Underfull \hbox (badness 5036) in paragraph at lines 11007--11009 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2327] Underfull \hbox (badness 2970) in paragraph at lines 11140--11146 []\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/ 10 "sparseVector" \T1/ptm/m/n/10 has the five ac- Underfull \hbox (badness 3679) in paragraph at lines 11140--11146 \T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec tor"\T1/ptm/m/n/10 , [2328] Underfull \hbox (badness 10000) in paragraph at lines 11191--11194 []\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/ 10 co-erces Underfull \hbox (badness 10000) in paragraph at lines 11213--11216 []\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m /n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list [2329] Underfull \hbox (badness 10000) in paragraph at lines 11231--11236 []\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/ 10 logical[][][] \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 11246--11248 [][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc -tion of sparse vec-tors (apart from [2330] [2331] Underfull \hbox (badness 3525) in paragraph at lines 11364--11368 []\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/ pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/ ptm/m/n/10 , where Underfull \hbox (badness 1831) in paragraph at lines 11371--11377 [][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more u sual con-struc-tor of such ma-tri-ces. Then, [2332] Underfull \hbox (badness 10000) in paragraph at lines 11466--11470 []\T1/pcr/m/n/10 signature(object = "symmetricMatrix")\T1/ptm/m/n/10 : re-turns \T1/ptm/m/it/10 sym-met-ric Underfull \hbox (badness 1043) in paragraph at lines 11466--11470 [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , even when the \T1/pcr/m/n/10 Dimnames \T1/ptm/m/n/10 slot only has row or col-umn names. This Underfull \hbox (badness 10000) in paragraph at lines 11482--11487 []\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/ n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be Underfull \hbox (badness 1259) in paragraph at lines 11482--11487 \T1/pcr/m/n/10 list(NULL, )\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. How-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other Underfull \hbox (badness 2591) in paragraph at lines 11490--11495 \T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 , and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1 /ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or [2333] Underfull \hbox (badness 2057) in paragraph at lines 11562--11564 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., [2334] [2335] Underfull \hbox (badness 6641) in paragraph at lines 11648--11651 []\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm /m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit h Underfull \hbox (badness 5133) in paragraph at lines 11688--11692 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the vir-tual class of all sparse ma-tri-ces coded in Underfull \hbox (badness 2818) in paragraph at lines 11688--11692 \T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c re-ated from it. See [2336] Underfull \hbox (badness 7649) in paragraph at lines 11795--11797 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2337] [2338] [2339] Underfull \hbox (badness 7362) in paragraph at lines 11996--11998 []\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a sparse ma-trix (i.e., of sub-class of [2340] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12034--12034 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 12035--12035 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] [2341] [2342] Underfull \hbox (badness 6910) in paragraph at lines 12285--12287 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2343] [2344] [2345]) (./boot-pkg.tex [2346] Chapter 18. [2347] [2348] [2349] [2350] [2351] [2352] [2353] Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f" , "w"), [2354] Underfull \hbox (badness 1325) in paragraph at lines 568--575 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r e-quired. Pos-si-ble Underfull \hbox (badness 1275) in paragraph at lines 583--588 []\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m ulti-sample prob- Underfull \hbox (badness 1264) in paragraph at lines 583--588 \T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n ored when [2355] Overfull \hbox (43.25928pt too wide) in paragraph at lines 643--649 []\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1 0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0 [2356] Underfull \hbox (badness 6268) in paragraph at lines 797--807 \T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de -fault clus-ter, a sec-ond ap-proach is used if [2357] Underfull \hbox (badness 1881) in paragraph at lines 824--826 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 6493) in paragraph at lines 851--855 [][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 , [2358] Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, data = nuke)[] Underfull \vbox (badness 10000) has occurred while \output is active [2359] [2360] Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 []\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i n-ter- Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 \T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues [2361] Underfull \hbox (badness 1496) in paragraph at lines 1082--1091 []\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari- ance of the Underfull \hbox (badness 2005) in paragraph at lines 1082--1091 \T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i n-ter-vals. If it Underfull \hbox (badness 2343) in paragraph at lines 1082--1091 \T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10 is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to Underfull \hbox (badness 2150) in paragraph at lines 1103--1109 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2362] [2363] [2364] [2365] [2366] Underfull \hbox (badness 1571) in paragraph at lines 1443--1445 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2367] [2368] [2369] [2370] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix( 1,n,2), [2371] [2372] [2373] [2374] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4) + strata(ulcer),[] Underfull \vbox (badness 10000) has occurred while \output is active [2375] Underfull \hbox (badness 6268) in paragraph at lines 2081--2083 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2376] [2377] [2378] [2379] Underfull \hbox (badness 1565) in paragraph at lines 2335--2340 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set Underfull \hbox (badness 4595) in paragraph at lines 2360--2365 \T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis tic \T1/ptm/m/n/10 is called. [2380] Underfull \hbox (badness 1881) in paragraph at lines 2429--2431 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 2057) in paragraph at lines 2437--2438 [][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 , [2381] Underfull \hbox (badness 1077) in paragraph at lines 2533--2537 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n /10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the sam-ple Underfull \hbox (badness 1112) in paragraph at lines 2533--2537 \T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1 0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10 is used. This is mul-ti-plied by [2382] [2383] [2384] [2385] [2386] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25, Overfull \hbox (18.78088pt too wide) in paragraph at lines 2894--2894 []\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25,[] [2387] [2388] [2389] Underfull \hbox (badness 3861) in paragraph at lines 3102--3105 [][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [2390] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1 :ncol(mat)) [2391] [2392] [2393] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling [2394] [2395] [2396] [2397] [2398] [2399] [2400] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835 [] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q = NULL)[] [2401] [2402] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])[] [2403] [2404] [2405] Underfull \hbox (badness 10000) in paragraph at lines 4187--4189 []\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault is [2406] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256 []\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz e data as in [2407] [2408] Underfull \hbox (badness 10000) in paragraph at lines 4359--4361 []\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o f Underfull \hbox (badness 1430) in paragraph at lines 4368--4372 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T 1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to Underfull \hbox (badness 2269) in paragraph at lines 4386--4389 []\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by [2409] [2410] [2411] [2412] [2413] [2414] [2415] [2416] [2417] Underfull \hbox (badness 3000) in paragraph at lines 4956--4959 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2418] [2419] [2420] [2421] Underfull \hbox (badness 2293) in paragraph at lines 5235--5238 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5235--5238 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2422] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat a = grav1[, 2])[] [2423] [2424] [2425] [2426] [2427] [2428] [2429] [2430] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c ity.sp1$spa[1][] [2431] Underfull \hbox (badness 1127) in paragraph at lines 5985--6003 \T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then [2432] Underfull \hbox (badness 2837) in paragraph at lines 6018--6021 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad dle.distn"\T1/ptm/m/n/10 . See the help file for [2433] [2434] [2435] [2436] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and Wright (1991). [2437] [2438] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling Overfull \hbox (20.58041pt too wide) in paragraph at lines 6494--6494 []\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t ilting was used[] [2439] [2440] [2441] Underfull \hbox (badness 1596) in paragraph at lines 6739--6743 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2442] [2443] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899 [] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha = c(0.05, 0.95),[] [2444] [2445] [2446] [2447] [2448] [2449] [2450] [2451]) (./class-pkg.tex [2452] Chapter 19. [2453] [2454] [2455] [2456] [2457] [2458] [2459] [2460] Underfull \hbox (badness 10000) in paragraph at lines 608--610 []\T1/ptm/m/n/10 the size of the code-book. De-faults to [2461] [2462] [2463] [2464] [2465] [2466] [2467] [2468]) (./cluster-pkg.tex Chapter 20. [2469] Underfull \hbox (badness 3098) in paragraph at lines 133--142 []\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u- Underfull \hbox (badness 2253) in paragraph at lines 133--142 \T1/ptm/m/n/10 larly for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is spec-i-fied of longer length than one. Since Underfull \hbox (badness 3323) in paragraph at lines 133--142 \T1/ptm/b/n/10 clus-ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-val id \T1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror Underfull \hbox (badness 10000) in paragraph at lines 133--142 \T1/ptm/m/n/10 as \T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n /10 . Fur-ther, \T1/pcr/m/n/10 method= "single" Underfull \hbox (badness 10000) in paragraph at lines 133--142 \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method = c(.5,.5,0,-.5)\T1/ptm/m/n/10 , and Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--142 \T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/ 10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 . [2470] Underfull \hbox (badness 10000) in paragraph at lines 167--169 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \ T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method = [2471] Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252 [] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met hod = 0.5)[iC]) ,[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 253--253 [] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, -.5))[iC]),[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254 [] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, +.5))[iC]))[] [2472] [2473] Underfull \vbox (badness 10000) has occurred while \output is active [2474] [2475] Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518 [] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot = axes,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 522--522 [] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5, ...)[] [2476] Underfull \hbox (badness 5374) in paragraph at lines 539--541 []\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use d when [2477] Overfull \hbox (66.78088pt too wide) in paragraph at lines 637--637 [] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c orrect.d = TRUE)[] [2478] Underfull \hbox (badness 3078) in paragraph at lines 688--691 []\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem- ory (and hence time), but dis-ables [2479] [2480] Underfull \hbox (badness 2941) in paragraph at lines 778--781 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 816--816 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo r this seed):[] [2481] Underfull \hbox (badness 10000) in paragraph at lines 863--865 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2482] Overfull \hbox (24.78088pt too wide) in paragraph at lines 928--928 [] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code =3), ...)[] [2483] Underfull \hbox (badness 4872) in paragraph at lines 974--976 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 988--992 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2484] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1095--1095 [] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE. factor = SEf)))[] [2485] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1112--1112 []\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras < - TRUE # or FALSE[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1150--1150 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] [2486] Underfull \hbox (badness 4144) in paragraph at lines 1182--1186 []\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m /n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent, e.g., for [2487] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1258--1258 [] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1, cex.txt = cex,[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1264--1264 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2488] [2489] Underfull \hbox (badness 10000) in paragraph at lines 1403--1408 []\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1 0 princomp[][][](*, cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 1451--1454 [2490] Underfull \hbox (badness 10000) in paragraph at lines 1468--1472 [][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 , Overfull \hbox (31.3804pt too wide) in paragraph at lines 1492--1492 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a nd label ellipses[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1502--1502 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2491] Underfull \hbox (badness 5741) in paragraph at lines 1542--1545 []\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der -ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only [2492] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1608--1608 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2493] Underfull \hbox (badness 5008) in paragraph at lines 1725--1733 \T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1 0 w[]^^N[]$\T1/ptm/m/n/10 , where [2494] [2495] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1816--1816 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord ratio = 7)))[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 1835--1835 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2496] [2497] [2498] [2499] Underfull \hbox (badness 10000) in paragraph at lines 2143--2145 []\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as Underfull \hbox (badness 10000) in paragraph at lines 2154--2157 Underfull \hbox (badness 3179) in paragraph at lines 2168--2174 [][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [ ][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips oid \T1/ptm/m/n/10 ob-jects. [2500] [2501] [2502] Underfull \hbox (badness 10000) in paragraph at lines 2326--2329 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par tition.object[][][]\T1/ptm/m/n/10 , [2503] Underfull \hbox (badness 1292) in paragraph at lines 2394--2397 []\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t he num-ber of it-er-a-tions needed and Underfull \hbox (badness 6675) in paragraph at lines 2403--2405 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see Underfull \hbox (badness 10000) in paragraph at lines 2426--2429 [][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n /10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [2504] [2505] [2506] [2507] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2642--2642 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] [2508] [2509] Underfull \hbox (badness 1067) in paragraph at lines 2829--2834 []\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger \T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g o-rithm, whereas [2510] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2888--2888 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2511] [2512] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2991--2991 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2513] [2514] [2515] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3187--3187 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3188--3188 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2516] Underfull \hbox (badness 10000) in paragraph at lines 3255--3258 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n /10 pltree() \T1/ptm/m/n/10 is pro-vided by [2517] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3305--3305 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3306--3306 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2518] [2519] [2520] Underfull \hbox (badness 10000) in paragraph at lines 3491--3494 []\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m /n/10 diss \T1/ptm/m/n/10 com-po-nent as for Underfull \hbox (badness 3471) in paragraph at lines 3491--3494 [][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a [2521] Underfull \hbox (badness 10000) in paragraph at lines 3554--3559 [][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [2522] Underfull \hbox (badness 4621) in paragraph at lines 3616--3621 []\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 1990) in paragraph at lines 3616--3621 \T1/ptm/m/n/10 which dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1 /ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider Underfull \hbox (badness 6268) in paragraph at lines 3628--3631 [][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.agnes[][][]\T1/ptm/m/n/10 , [2523] [2524] [2525] Underfull \hbox (badness 10000) in paragraph at lines 3813--3816 [][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3844--3847 [][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [2526] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3897--3897 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] Underfull \hbox (badness 2035) in paragraph at lines 3908--3910 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1 /pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for [2527] [2528] [2529] [2530] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4101--4101 [] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w idth "* s[i]),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 4103--4103 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] Underfull \hbox (badness 1946) in paragraph at lines 4132--4137 []\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n /10 ; note that the de-fault used to be \T1/pcr/m/n/10 col [2531] Underfull \hbox (badness 10000) in paragraph at lines 4199--4207 \T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by [2532] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4241--4241 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus ter-wise coloring[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4250--4250 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4252--4252 [] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma in")); frame()[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 4255--4255 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol denrod4", "gray20")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4257--4257 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4264--4264 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro wnames == indices[] [2533] [2534] [2535] [2536] [2537] [2538] Underfull \hbox (badness 10000) in paragraph at lines 4622--4628 []\T1/ptm/m/n/10 Our ver-sion of the \T1/pcr/m/n/10 xclara \T1/ptm/m/n/10 is sl ightly more rounded than the one from Underfull \hbox (badness 10000) in paragraph at lines 4638--4640 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side Overfull \hbox (52.98038pt too wide) in paragraph at lines 4651--4651 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10 01:2000}, {2001:3000} Overfull \hbox (9.78043pt too wide) in paragraph at lines 4653--4653 []\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s medoid indices == pam(xclara, 3)$id.med[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4663--4663 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o bservations:[] [2539] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4667--4667 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? - - Robust range:[] [2540]) (./codetools-pkg.tex Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17 [] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = !all,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18 [] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress Undefined,[] [2541] Underfull \hbox (badness 10000) in paragraph at lines 65--70 []\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2542] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2543] [2544] [2545]) (./foreign-pkg.tex [2546] Chapter 22. [2547] Underfull \hbox (badness 1231) in paragraph at lines 67--70 []\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr om, or a Underfull \hbox (badness 6708) in paragraph at lines 78--81 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2548] [2549] Underfull \hbox (badness 3601) in paragraph at lines 235--243 []\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n /10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 , [2550] Overfull \hbox (12.78088pt too wide) in paragraph at lines 296--296 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates = FALSE, [2551] [2552] [2553] Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t o.data.frame,[] [2554] Overfull \hbox (30.78088pt too wide) in paragraph at lines 463--463 [] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen d", "no"),[] Underfull \hbox (badness 10000) in paragraph at lines 506--515 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer- Underfull \hbox (badness 6001) in paragraph at lines 506--515 \T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de- fault), the first orig-i-nal value Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named to Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/pcr/m/n/10 paste0(label, duplicated.value.labels.infix, level)\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 516--519 []\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with du- Underfull \hbox (badness 10000) in paragraph at lines 516--519 \T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault \T1/pcr/m/n/10 "_dupli cated_"\T1/ptm/m/n/10 ) if [2555] Underfull \hbox (badness 10000) in paragraph at lines 551--559 []\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en -[]us / library / ms776446(VS . 85 ) .aspx$[][] Underfull \hbox (badness 7613) in paragraph at lines 569--575 []\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/ m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute [2556] Overfull \hbox (20.58041pt too wide) in paragraph at lines 624--624 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg ument settings.[] Overfull \hbox (112.38031pt too wide) in paragraph at lines 625--625 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2557] Overfull \hbox (9.78043pt too wide) in paragraph at lines 658--658 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ ate variables[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 662--662 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt h=w), "\n"))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 669--669 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, collapse="")[] [2558] [2559] Underfull \hbox (badness 10000) in paragraph at lines 813--814 Overfull \hbox (4.38043pt too wide) in paragraph at lines 823--823 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f oreign")[1])[] [2560] [2561] Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899 [] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G lobalEnv) [2562] Overfull \hbox (0.78088pt too wide) in paragraph at lines 963--963 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute (x))) Underfull \hbox (badness 6708) in paragraph at lines 989--992 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2563] [2564] Underfull \hbox (badness 10000) in paragraph at lines 1073--1074 [][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase / format / data _ types . Overfull \hbox (24.78088pt too wide) in paragraph at lines 1109--1109 [] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", "codes"))[] [2565] Underfull \hbox (badness 1286) in paragraph at lines 1194--1198 []\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates = FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec ts [2566] Underfull \hbox (badness 10000) in paragraph at lines 1267--1273 []\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign: ::writeForeignStata\T1/ptm/m/n/10 , [2567] Underfull \hbox (badness 6725) in paragraph at lines 1293--1296 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef -fect, the dec-i-mal in-di-ca-tor is al-ways set by [2568]) (./lattice-pkg.tex Chapter 23. [2569] [2570] [2571] Overfull \hbox (12.78088pt too wide) in paragraph at lines 286--286 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 290--290 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .xyplot"),[] [2572] Overfull \hbox (42.78088pt too wide) in paragraph at lines 298--298 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul t.dotplot"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 305--305 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.barchart"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 313--313 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.stripplot"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 334--334 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 338--338 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .bwplot"),[] [2573] Underfull \hbox (badness 4060) in paragraph at lines 357--369 []\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a lly of the Underfull \hbox (badness 10000) in paragraph at lines 357--369 \T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ iv-a-lently, \T1/pcr/m/n/10 y ~ x | Underfull \hbox (badness 1028) in paragraph at lines 397--412 \T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot both Underfull \hbox (badness 10000) in paragraph at lines 413--415 []\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum, one can ei-ther set [2574] Underfull \hbox (badness 7631) in paragraph at lines 479--484 []\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \ T1/ptm/m/n/10 in this case may be [2575] [2576] Underfull \hbox (badness 1221) in paragraph at lines 650--658 []\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as ar-gu-ments to [2577] [2578] [2579] [2580] Underfull \hbox (badness 2005) in paragraph at lines 986--998 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of fac-tors will be Underfull \hbox (badness 1199) in paragraph at lines 986--998 \T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a use-ful lay-out. [2581] Underfull \hbox (badness 1661) in paragraph at lines 1099--1105 []\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be num-bers be-tween 0 and 1, giv-ing co-or-di-nates [2582] [2583] Underfull \hbox (badness 1097) in paragraph at lines 1225--1227 []\T1/ptm/m/n/10 Logical flag, whether leg-end should have a Underfull \hbox (badness 1917) in paragraph at lines 1239--1240 []\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to [2584] [2585] [2586] Underfull \hbox (badness 1540) in paragraph at lines 1479--1485 []\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/ 10 plot.trellis[][][]\T1/ptm/m/n/10 , [2587] Underfull \hbox (badness 10000) in paragraph at lines 1566--1583 [][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel .stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 , [2588] Underfull \vbox (badness 10000) has occurred while \output is active [2589] Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671 [] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar dSprays$rowpos))),[] Underfull \hbox (badness 2012) in paragraph at lines 1725--1727 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][] []\T1/ptm/m/n/10 , which may pass them on to [2590] Underfull \hbox (badness 6808) in paragraph at lines 1755--1759 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to Underfull \hbox (badness 10000) in paragraph at lines 1772--1775 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 , etc; see [2591] Underfull \hbox (badness 10000) in paragraph at lines 1825--1827 []\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix An-drews [2592] [2593] [2594] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] Underfull \hbox (badness 10000) in paragraph at lines 2086--2093 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/ m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form Underfull \hbox (badness 1997) in paragraph at lines 2086--2093 \T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra ms or ker-nel den-sity [2595] Underfull \hbox (badness 10000) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t he value of Underfull \hbox (badness 1320) in paragraph at lines 2141--2144 \T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch ecked. If [2596] [2597] [2598] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2349--2349 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .qqmath"),[] Underfull \hbox (badness 4441) in paragraph at lines 2362--2366 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2599] [2600] [2601] Underfull \hbox (badness 4441) in paragraph at lines 2547--2554 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2602] [2603] Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689 [] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev elplot.raster")[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2721--2721 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl ot"),[] [2604] Underfull \hbox (badness 10000) in paragraph at lines 2761--2766 []\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu la of the form \T1/pcr/m/n/10 z ~ x * y [2605] Underfull \hbox (badness 2913) in paragraph at lines 2791--2796 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 2791--2796 \T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p tm/m/n/10 must have the same lengths as Underfull \hbox (badness 6758) in paragraph at lines 2877--2881 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be Underfull \hbox (badness 7576) in paragraph at lines 2877--2881 \T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][]\T1/pcr/m/n/10 grid.rast er[][][]\T1/ptm/m/n/10 . See also Underfull \hbox (badness 10000) in paragraph at lines 2883--2885 []\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T 1/ptm/m/n/10 when [2606] Underfull \hbox (badness 1609) in paragraph at lines 2935--2941 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti ons should be used, Underfull \hbox (badness 2772) in paragraph at lines 2935--2941 \T1/ptm/m/n/10 both for the false color im-age and the color key (if present). Ef- Underfull \hbox (badness 1400) in paragraph at lines 2935--2941 \T1/ptm/m/n/10 fec-tively, set-ting this to \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 changes the de-fault panel func-tion from Underfull \hbox (badness 2486) in paragraph at lines 2959--2963 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2607] [2608] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3060--3060 [] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3061--3061 [] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062 [] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite = TRUE),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3073--3073 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. cloud"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 3085--3085 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.wireframe"),[] [2609] Underfull \hbox (badness 10000) in paragraph at lines 3110--3118 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo r-mula of the form \T1/pcr/m/n/10 z ~ x Underfull \hbox (badness 2913) in paragraph at lines 3143--3150 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 3143--3150 \T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p tm/m/n/10 must have the same lengths as [2610] [2611] [2612] [2613]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.parallel}) has been already used, duplicate ignored \relax l.3431 \aliasA{parallel}{B\_08\_splom}{parallel} Overfull \hbox (18.78088pt too wide) in paragraph at lines 3473--3473 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. splom"),[] [2614] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3496--3496 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.parallel"),[] [2615] [2616] [2617] [2618] [2619] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3832--3832 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt( var(x))) [2620] Underfull \hbox (badness 10000) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white bg")\T1/ptm/m/n/10 . Underfull \hbox (badness 2435) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2621] [2622] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4052--4052 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict = FALSE) Underfull \hbox (badness 1173) in paragraph at lines 4061--4065 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4088--4090 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when Underfull \hbox (badness 1728) in paragraph at lines 4105--4109 \T1/pcr/m/n/10 theme\T1/ptm/m/n/10 ). These are used to mod-ify the cur-rent se t-tings (ob-tained by [2623] Underfull \hbox (badness 5161) in paragraph at lines 4170--4174 []\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis .settings \T1/ptm/m/n/10 has not been fi-nal-ized, Underfull \hbox (badness 4913) in paragraph at lines 4170--4174 \T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca n be ob-tained by [2624] [2625] Underfull \hbox (badness 1067) in paragraph at lines 4284--4294 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm /m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 1735) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points Underfull \hbox (badness 10000) in paragraph at lines 4284--4294 \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and Underfull \hbox (badness 5231) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for Underfull \hbox (badness 1701) in paragraph at lines 4309--4312 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot .symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4312--4314 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 pl ot.polygon \T1/ptm/m/n/10 and [2626] [2627] [2628] [2629] [2630] [2631] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4716--4716 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab = "Height")[] [2632] [2633] Underfull \hbox (badness 10000) in paragraph at lines 4903--4906 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 . [2634] [2635] Underfull \hbox (badness 1442) in paragraph at lines 5035--5038 []\T1/pcr/m/n/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and [2636] [2637] [2638] [2639] [2640] [2641] Underfull \hbox (badness 3646) in paragraph at lines 5367--5370 [][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f or Overfull \hbox (36.78088pt too wide) in paragraph at lines 5397--5397 [] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh ich.given],[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5398--5398 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which .given],[] [2642] Underfull \hbox (badness 10000) in paragraph at lines 5486--5489 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 2103) in paragraph at lines 5486--5489 \T1/pcr/m/n/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the lef t of pan-els us-ing Underfull \hbox (badness 6412) in paragraph at lines 5503--5509 []\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl y be-cause of the \T1/pcr/m/n/10 style Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive , es-pe-cially when Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm /m/n/10 are small. Tra-di-tional use is as Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 , though this can be [2643] Underfull \hbox (badness 1635) in paragraph at lines 5512--5517 []\T1/pcr/m/n/10 strip.default \T1/ptm/m/n/10 is called for its side-effect, wh ich is to draw a strip ap-pro-pri-ate for [2644] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5661--5661 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la bels,[] [2645] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5675--5675 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose "), ...)[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5676--5676 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos e"), ...)[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5679--5679 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location" , "toplevel",[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5682--5682 [] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig ht", "page"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 5684--5684 [] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in side"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5690--5690 [] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi ch.given",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5691--5691 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692 [] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi ch.panel",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5694--5694 [] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co lumn",[] Underfull \hbox (badness 10000) in paragraph at lines 5710--5712 []\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of [2646] Underfull \hbox (badness 2376) in paragraph at lines 5721--5723 []\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point. De-faults to [2647] Underfull \hbox (badness 2538) in paragraph at lines 5846--5850 \T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and Underfull \hbox (badness 4205) in paragraph at lines 5857--5864 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr a pa-ram-e-ters are passed on to Underfull \hbox (badness 4792) in paragraph at lines 5857--5864 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 trellis.switchFocus\T1/ptm/m/n/10 , these are used (in com-bi-na-tion with [2648] [2649] Underfull \hbox (badness 10000) in paragraph at lines 6010--6014 [][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , [] []\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 , [2650] [2651] Underfull \hbox (badness 4242) in paragraph at lines 6157--6162 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- [2652] [2653] Underfull \hbox (badness 3601) in paragraph at lines 6273--6278 []\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1 0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round Underfull \hbox (badness 2486) in paragraph at lines 6273--6278 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 horizontal=FALSE\T1/ptm/m/n/10 ). By de-fault, the ac-tual box-plot statis-tics are cal-cu-lated us-ing [2654] [2655] Overfull \hbox (60.78088pt too wide) in paragraph at lines 6360--6360 [] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co lors")$palette,[] [2656] Underfull \hbox (badness 1888) in paragraph at lines 6492--6499 \T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col. regions \T1/ptm/m/n/10 a vec-tor of col-ors, and [2657] Underfull \hbox (badness 10000) in paragraph at lines 6549--6552 []\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The Underfull \hbox (badness 1558) in paragraph at lines 6549--6552 \T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v alid color. The [2658] Underfull \hbox (badness 1005) in paragraph at lines 6599--6607 \T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/ 10 z \T1/ptm/m/n/10 are all passed to Underfull \hbox (badness 1571) in paragraph at lines 6599--6607 \T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/ 10 y \T1/ptm/m/n/10 are in- [2659] [2660] [2661] [2662] [2663] Underfull \hbox (badness 1320) in paragraph at lines 6955--6962 []\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan el func-tion that uses the raster draw- Underfull \hbox (badness 1715) in paragraph at lines 6955--6962 \T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more ef-fi-cient. When us-ing [2664] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7025--7025 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] [2665] Underfull \hbox (badness 10000) in paragraph at lines 7055--7059 []\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments to Underfull \hbox (badness 1584) in paragraph at lines 7055--7059 \T1/pcr/m/n/10 diag.panel.splom \T1/ptm/m/n/10 to know what ar-gu-ments this fu nc-tion is passed [2666] Underfull \hbox (badness 10000) in paragraph at lines 7160--7163 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by [2667] [2668] Underfull \hbox (badness 2012) in paragraph at lines 7326--7329 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2669] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7372--7372 [] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta ils.n = 50))[] [2670] [2671] Underfull \hbox (badness 2644) in paragraph at lines 7513--7517 \T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on to Underfull \hbox (badness 2772) in paragraph at lines 7526--7529 []\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a list of ar-gu-ments to be sup-plied to Underfull \hbox (badness 4242) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos -si-bly Underfull \hbox (badness 1147) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is co-erced to a list. This al-lows ar- Underfull \hbox (badness 2351) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline = c(0, 1)\T1/ptm/ m/n/10 , which adds the di- Underfull \hbox (badness 1675) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v = 0)\T1 /ptm/m/n/10 , which adds the Underfull \hbox (badness 1769) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol; e.g., [2672] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7596--7596 [] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y = c(1/6, 4/6)),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7606--7606 [] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d raw = FALSE),[] [2673] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7667--7667 [] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam e.type)[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7672--7672 [] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident ifier, name.type)[] [2674] [2675] [2676] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7857--7857 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden tifier = "grid")[] [2677] Underfull \hbox (badness 1436) in paragraph at lines 7912--7918 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for Underfull \hbox (badness 1231) in paragraph at lines 7912--7918 \T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti ngs. The [2678] [2679] [2680] [2681] [2682] [2683] [2684] [2685] Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo se Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1 /pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from [2686] [2687] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8645--8645 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st ack, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8646--8646 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin t, ...)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8658--8658 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr ipts, ...)[] [2688] Underfull \hbox (badness 3118) in paragraph at lines 8677--8680 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1 /ptm/m/n/10 has a dif-fer-ent mean-ing in [2689] Underfull \hbox (badness 1515) in paragraph at lines 8753--8757 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2690] Underfull \hbox (badness 6316) in paragraph at lines 8859--8864 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2691] [2692] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8966--8966 [] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b ottom$labels$labels)[] [2693] [2694] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9105--9105 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su nspot.year)),[] [2695] Overfull \hbox (84.94879pt too wide) in paragraph at lines 9164--9168 []\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr /m/n/10 left, right, left.name, right.name, condition Overfull \hbox (104.63074pt too wide) in paragraph at lines 9164--9168 \T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left, right.x, right.y, left.name , right.x.name, right.y.name, condition [2696] [2697] [2698] [2699] [2700] [2701] [2702] Underfull \hbox (badness 4205) in paragraph at lines 9622--9626 []\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 , Underfull \hbox (badness 4518) in paragraph at lines 9622--9626 \T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 , Underfull \hbox (badness 6300) in paragraph at lines 9627--9630 []\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm" \T1/ptm/m/n/10 , [2703] [2704] [2705]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma} [2706] [2707] [2708] Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 []\T1/ptm/m/n/10 Cause of death. A fac-tor with lev-els \T1/pcr/m/n/10 Alzheime rs\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Cancer\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 Cerebrovascular diseases\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Diabetes \T1/ptm/m/n/10 , \T1/pcr/m/n/10 Flu and pneumonia\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 Heart disease\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower respiratory\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 Nephritis\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Suicide\ T1/ptm/m/n/10 , and [2709] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10088--10088 [] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list( columns = 2),[] [2710]) (./mgcv-pkg.tex Chapter 24. [2711] [2712] Overfull \hbox (6.78088pt too wide) in paragraph at lines 147--147 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL, Overfull \hbox (18.78088pt too wide) in paragraph at lines 150--150 [] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret e=FALSE,[] [2713] Overfull \hbox (72.78088pt too wide) in paragraph at lines 152--152 [] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in tercept=NULL,...)[] Underfull \hbox (badness 1142) in paragraph at lines 171--175 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 196--201 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2714] [2715] [2716] [2717] Underfull \hbox (badness 10000) in paragraph at lines 361--368 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo th.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 361--368 [][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 361--368 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2718] Overfull \hbox (4.38043pt too wide) in paragraph at lines 404--404 []\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2 ,bs=bs,k=k)+[] [2719] [2720] [2721] Underfull \hbox (badness 2922) in paragraph at lines 603--604 []\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/ n/10 and [2722] [2723] [2724] Underfull \hbox (badness 1158) in paragraph at lines 727--729 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2725] Underfull \hbox (badness 1259) in paragraph at lines 790--791 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [2726] [2727] [2728] [2729] [2730] [2731] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1138--1138 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1139--1139 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1145--1145 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct+adhere,[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1152--1152 []\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for this stratum...[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1154--1154 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in d]),type="l",ylim=c(0,1),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1156--1156 [] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind]) ,lwd=2,col=i)[] Underfull \vbox (badness 10000) has occurred while \output is active [2732] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1187--1187 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights= d,data=surv)[] [2733] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1248--1248 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] [2734] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1293--1293 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] [2735] [2736] [2737] [2738] [2739] [2740] [2741] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1750--1750 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2742] [2743] [2744] [2745] [2746] [2747] Underfull \hbox (badness 1052) in paragraph at lines 2125--2133 \T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo oths. Lin-ear func-tion-als of [2748] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2142--2142 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2154--2157 []\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1 0 formula.gam[][][] \T1/ptm/m/n/10 and also Underfull \hbox (badness 1142) in paragraph at lines 2167--2171 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 2193--2198 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2749] [2750] [2751] Underfull \hbox (badness 1043) in paragraph at lines 2356--2362 \T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v en-tion mech-a-nism de-scribed in [2752] [2753] Underfull \hbox (badness 10000) in paragraph at lines 2492--2498 [][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2492--2498 [][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2492--2498 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2754] Underfull \vbox (badness 10000) has occurred while \output is active [2755] Underfull \vbox (badness 10000) has occurred while \output is active [2756] Underfull \vbox (badness 10000) has occurred while \output is active [2757] [2758] [2759] [2760] [2761] [2762] [2763] [2764] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3148--3148 [] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco l(x)),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3151--3151 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] [2765] [2766] [2767] [2768] [2769] [2770] Underfull \hbox (badness 5189) in paragraph at lines 3512--3516 []\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n /10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see [2771] [2772] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3629--3629 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \vbox (badness 10000) has occurred while \output is active [2773] [2774] [2775] Underfull \hbox (badness 1184) in paragraph at lines 3798--3802 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2776] [2777] [2778] [2779] [2780] [2781] [2782] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4244--4244 [] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i d=1)+s(x1,id=1)+[] [2783] [2784] [2785] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4394--4394 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2786] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4488--4488 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR UE,...)[] [2787] Underfull \hbox (badness 1142) in paragraph at lines 4519--4523 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2788] Underfull \hbox (badness 10000) in paragraph at lines 4588--4597 []\T1/ptm/m/n/10 In the event of \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 con-ver-genc e fail-ures, con-sider mod-i-fy-ing [2789] [2790] Underfull \hbox (badness 5970) in paragraph at lines 4705--4711 [][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 1418) in paragraph at lines 4705--4711 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p cr/m/n/10 pdTens[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 gamm4 \T1/ptm/m/n/10 ( [] []$\T1/pcr/m/n/10 https : / / cran . r-[]project . [2791] Underfull \vbox (badness 10000) has occurred while \output is active [2792] [2793] [2794] Underfull \hbox (badness 1577) in paragraph at lines 4985--4988 []\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see [] []\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment Underfull \hbox (badness 2181) in paragraph at lines 4992--4993 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2795] [2796] [2797] [2798] [2799] [2800] [2801] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5396--5396 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2802] [2803] [2804] [2805] [2806] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5720--5720 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, [2807] Overfull \hbox (36.78088pt too wide) in paragraph at lines 5722--5722 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 5743--5747 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2808] [2809] [2810] Underfull \vbox (badness 10000) has occurred while \output is active [2811] [2812] [2813] Overfull \hbox (72.78088pt too wide) in paragraph at lines 6058--6058 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999, all.derivs=FALSE) [2814] [2815] [2816] [2817] Underfull \vbox (badness 10000) has occurred while \output is active [2818] Underfull \vbox (badness 10000) has occurred while \output is active [2819] [2820] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6487--6487 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] [2821] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6514--6514 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2822] [2823] [2824] [2825] [2826] [2827] [2828] [2829] [2830] Underfull \hbox (badness 1242) in paragraph at lines 7057--7058 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2831] [2832] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7144--7144 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [2833] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7207--7207 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate d covariates[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7226--7226 [] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]] ,na.rm=TRUE)[] [2834] [2835] [2836] [2837] [2838] [2839] [2840] [2841] [2842] [2843] [2844] [2845] [2846] [2847] [2848] [2849] [2850] [2851] Underfull \vbox (badness 10000) has occurred while \output is active [2852] [2853] Underfull \hbox (badness 10000) in paragraph at lines 8446--8449 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8446--8449 \T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\ T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 3118) in paragraph at lines 8446--8449 \T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot \T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su mmary.pdIdnot\T1/ptm/m/n/10 . [2854] Underfull \hbox (badness 10000) in paragraph at lines 8502--8505 []\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p tm/m/n/10 , Underfull \hbox (badness 3108) in paragraph at lines 8502--8505 \T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally be [2855] [2856] [2857] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8722--8722 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s cale=-1,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8723--8723 [] \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS E,xlab=NULL,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8726--8726 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [2858] [2859] [2860] Underfull \hbox (badness 1629) in paragraph at lines 8883--8888 \T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is some-times to clone the [2861] [2862] [2863] [2864] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9094--9094 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,...)[] [2865] [2866] Overfull \hbox (6.78088pt too wide) in paragraph at lines 9258--9258 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [2867] [2868] [2869] [2870] Underfull \vbox (badness 10000) has occurred while \output is active [2871] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9526--9526 [] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s mooth deriv i[] [2872] Underfull \hbox (badness 1205) in paragraph at lines 9564--9566 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9564--9566 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 9570--9575 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2873] Underfull \hbox (badness 1205) in paragraph at lines 9654--9656 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9654--9656 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2874] Underfull \hbox (badness 10000) in paragraph at lines 9723--9726 []\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from Underfull \hbox (badness 2057) in paragraph at lines 9723--9726 [][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n /10 are not needed, [2875] [2876] Underfull \hbox (badness 1253) in paragraph at lines 9853--9855 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [2877] [2878] [2879] [2880] Underfull \hbox (badness 1946) in paragraph at lines 10031--10038 []\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef- fects in a GAM in the same Underfull \hbox (badness 2221) in paragraph at lines 10031--10038 \T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre s-sion terms. This method Underfull \hbox (badness 2042) in paragraph at lines 10031--10038 \T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s ee Underfull \hbox (badness 2846) in paragraph at lines 10039--10042 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1 0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n /10 can be used: Underfull \hbox (badness 5862) in paragraph at lines 10039--10042 \T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [2881] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10105--10105 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \hbox (badness 10000) in paragraph at lines 10134--10137 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 , [2882] [2883] [2884] [2885] [2886] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10421--10421 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU LL,pc=NULL) [2887] [2888] [2889] [2890] [2891] [2892] Underfull \hbox (badness 3861) in paragraph at lines 10762--10765 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if Overfull \hbox (36.78088pt too wide) in paragraph at lines 10769--10769 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE, Underfull \hbox (badness 10000) in paragraph at lines 10782--10786 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [2893] Underfull \hbox (badness 10000) in paragraph at lines 10822--10826 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [2894] [2895] [2896] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10963--10963 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$ vectors[,ind]))[] Underfull \hbox (badness 1975) in paragraph at lines 10974--10979 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2897] Underfull \hbox (badness 1803) in paragraph at lines 11051--11055 \T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T 1/ptm/m/n/10 . Underfull \hbox (badness 1502) in paragraph at lines 11063--11075 \T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec Underfull \hbox (badness 2401) in paragraph at lines 11080--11084 \T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able. Plot meth-ods can be Underfull \hbox (badness 2970) in paragraph at lines 11080--11084 \T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/ m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 , [2898] [2899] [2900] Underfull \vbox (badness 10000) has occurred while \output is active [2901] Underfull \hbox (badness 6876) in paragraph at lines 11275--11281 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one or two vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 11316--11317 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2902] [2903] Underfull \hbox (badness 10000) in paragraph at lines 11433--11434 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2904] [2905] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11487--11487 [] \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs, m=c(4,3,0))+[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11499--11499 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11510--11510 [] \T1/pcr/m/n/9 "1st order penalties: red tps; blue bs over (0,1); black bs over (-.5,1.5)")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11511--11511 [] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions and intervals[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11516--11516 [] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i ntervals away[] [2906] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11522--11522 [] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w ild and wide[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11523--11523 [] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/pcr/m/n/9 `\T1/ pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] [2907] Underfull \hbox (badness 10000) in paragraph at lines 11592--11594 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term Underfull \hbox (badness 10000) in paragraph at lines 11592--11594 \T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 s(...,bs="cs", ...) \T1/ptm/m/n/10 or [2908] [2909] Underfull \hbox (badness 10000) in paragraph at lines 11720--11721 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2910] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11801--11801 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first deriv penalty[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11802--11802 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi ed 2nd deriv[] [2911] [2912] [2913] Underfull \hbox (badness 10000) in paragraph at lines 11952--11953 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2914] [2915] [2916] [2917] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12191--12191 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [2918] Underfull \hbox (badness 10000) in paragraph at lines 12252--12254 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2919] [2920] Underfull \vbox (badness 10000) has occurred while \output is active [2921] Underfull \hbox (badness 10000) in paragraph at lines 12411--12414 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method a smooth spec-i-fi-ca-tion ob- Underfull \hbox (badness 3312) in paragraph at lines 12411--12414 \T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs=" re",)\T1/ptm/m/n/10 . For the Underfull \hbox (badness 7099) in paragraph at lines 12411--12414 \T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr /m/n/10 "random.effect" [2922] [2923] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12493--12493 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] Underfull \hbox (badness 10000) in paragraph at lines 12538--12544 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 2698) in paragraph at lines 12538--12544 \T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1 /pcr/m/n/10 gam \T1/ptm/m/n/10 for- [2924] [2925] [2926] Underfull \vbox (badness 10000) has occurred while \output is active [2927] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12752--12752 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] Underfull \vbox (badness 10000) has occurred while \output is active [2928] [2929] Underfull \hbox (badness 10000) in paragraph at lines 12855--12863 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the sphere, via terms like Underfull \hbox (badness 10000) in paragraph at lines 12881--12882 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2930] [2931] [2932] [2933] Underfull \hbox (badness 3396) in paragraph at lines 13142--13145 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any num-ber of vari-ables, spec-i-fied via terms like [2934] Underfull \hbox (badness 10000) in paragraph at lines 13187--13189 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2935] [2936] [2937] [2938] Underfull \hbox (badness 10000) in paragraph at lines 13411--13414 []\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t en pro- Underfull \hbox (badness 3068) in paragraph at lines 13411--13414 \T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see [] []\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas s (see [2939] Underfull \hbox (badness 10000) in paragraph at lines 13444--13448 [][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr /m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression .spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13444--13448 [][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13444--13448 [][]\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 , [2940] [2941] [2942] [2943] [2944] Underfull \hbox (badness 2158) in paragraph at lines 13734--13734 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [2945] Overfull \hbox (48.78088pt too wide) in paragraph at lines 13809--13809 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [2946] [2947] Overfull \hbox (12.78088pt too wide) in paragraph at lines 13943--13943 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [2948] [2949] Underfull \hbox (badness 4846) in paragraph at lines 14074--14077 []\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or es-ti-ma-tors if [2950] [2951] [2952] [2953] [2954] [2955] [2956] [2957] [2958] [2959] [2960] [2961] [2962] [2963] Underfull \hbox (badness 10000) in paragraph at lines 14899--14907 []\T1/ptm/m/n/10 Suppose that \T1/pcr/m/n/10 m=1 \T1/ptm/m/n/10 and you fill an ar-ray us-ing code like Underfull \hbox (badness 10000) in paragraph at lines 14899--14907 \T1/pcr/m/n/10 for(i in 1:K) for(j in i:K) for(k in j:K) for(l in k:K) [2964] [2965] [2966] [2967] Overfull \hbox (24.78088pt too wide) in paragraph at lines 15171--15171 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA LSE, ...)[] [2968] [2969] [2970] [2971] [2972] [2973] Overfull \hbox (20.58041pt too wide) in paragraph at lines 15465--15465 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li near predictor,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15466--15466 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun ded in regions[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15478--15478 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [2974] [2975] [2976]) (./nlme-pkg.tex Chapter 25. [2977] Underfull \hbox (badness 1009) in paragraph at lines 84--93 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [2978] Underfull \hbox (badness 1009) in paragraph at lines 174--183 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [2979] [2980] [2981] [2982] [2983] Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454 [] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [2984] [2985] Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 --------------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n on-sensical!)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 --------------------------- ---------------[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 --------------------------- ---------------[] [2986] [2987] [2988] [2989] [2990] [2991] [2992] [2993] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil lary fissure"),[] [2994] Underfull \hbox (badness 5446) in paragraph at lines 1147--1149 []\T1/ptm/m/n/10 `\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel.h tm\T1/ptm/m/n/10 ', the first edi-tion of [2995] [2996] [2997] [2998] [2999] [3000] [3001] Underfull \hbox (badness 10000) in paragraph at lines 1630--1633 [][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 , [3002] Underfull \hbox (badness 3780) in paragraph at lines 1647--1649 []\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a ted with each com-po-nent of the [3003] [3004] [3005] [3006] [3007] Underfull \hbox (badness 2042) in paragraph at lines 1994--2000 \T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3008] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla pse = "Dog")[] [3009] Underfull \hbox (badness 1132) in paragraph at lines 2144--2146 []\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac ted us-ing the [3010] [3011] Underfull \hbox (badness 4168) in paragraph at lines 2255--2261 [][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize .corStruct[][][]\T1/ptm/m/n/10 , [3012] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2280--2280 [] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3013] [3014] [3015] [3016] [3017] [3018] [3019] [3020] Underfull \hbox (badness 10000) in paragraph at lines 2843--2847 [][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1 /ptm/m/n/10 , [3021] [3022] [3023] [3024] [3025] [3026] [3027] [3028] [3029] [3030] [3031] [3032] Underfull \hbox (badness 6493) in paragraph at lines 3579--3587 [][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [3033] [3034] [3035] [3036] [3037] [3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] Underfull \hbox (badness 10000) in paragraph at lines 5159--5163 [][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [3057] [3058] [3059] [3060] [3061] Underfull \hbox (badness 10000) in paragraph at lines 5476--5480 []\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit- ted in the fit if Underfull \hbox (badness 2671) in paragraph at lines 5476--5480 \T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if \T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 . [3062] [3063] Underfull \hbox (badness 10000) in paragraph at lines 5591--5594 [][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][] []\T1/ptm/m/n/10 , [3064] [3065] [3066] [3067] [3068] [3069] [3070] [3071] [3072] Underfull \hbox (badness 2799) in paragraph at lines 6097--6103 \T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/ ptm/m/n/10 for the random-effects [3073] Underfull \hbox (badness 7133) in paragraph at lines 6158--6162 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \ T1/pcr/m/n/10 model\T1/ptm/m/n/10 , [3074] Underfull \hbox (badness 2057) in paragraph at lines 6242--6253 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 , [3075] Underfull \hbox (badness 10000) in paragraph at lines 6306--6308 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 6338--6338 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3076] [3077] [3078] [3079] Underfull \hbox (badness 7133) in paragraph at lines 6556--6560 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \ T1/pcr/m/n/10 model\T1/ptm/m/n/10 , [3080] Underfull \hbox (badness 10000) in paragraph at lines 6655--6661 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict .gnls[][][]\T1/ptm/m/n/10 , Overfull \hbox (54.78088pt too wide) in paragraph at lines 6682--6682 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min Scale = 0.001, [3081] Underfull \hbox (badness 10000) in paragraph at lines 6720--6722 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3082] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6750--6750 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3083] [3084] [3085] Underfull \hbox (badness 10000) in paragraph at lines 6993--7000 [][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][ ]\T1/ptm/m/n/10 , [3086] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7010--7010 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7018--7018 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7040--7042 []\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou pedData \T1/ptm/m/n/10 ob-ject or a [3087] [3088] [3089] Underfull \hbox (badness 10000) in paragraph at lines 7255--7260 [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl sStruct[][][]\T1/ptm/m/n/10 , [3090] [3091] [3092] Underfull \hbox (badness 10000) in paragraph at lines 7407--7415 []\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial -iza- Underfull \hbox (badness 10000) in paragraph at lines 7407--7415 \T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 1817) in paragraph at lines 7407--7415 \T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 20 EM it-er-a- Underfull \hbox (badness 3118) in paragraph at lines 7430--7433 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 , [3093] [3094] [3095] Underfull \hbox (badness 3354) in paragraph at lines 7645--7647 []\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10 which \T1/ptm/m/n/10 is not equal to [3096] [3097] [3098] [3099] [3100] [3101] Underfull \hbox (badness 1642) in paragraph at lines 8037--8059 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3102] [3103] Underfull \hbox (badness 10000) in paragraph at lines 8157--8174 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme Object[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8157--8174 [][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 , Overfull \hbox (12.78088pt too wide) in paragraph at lines 8200--8200 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] Underfull \hbox (badness 1642) in paragraph at lines 8209--8231 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3104] [3105] [3106] [3107] [3108] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8474--8474 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, Underfull \hbox (badness 10000) in paragraph at lines 8520--8522 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3109] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8558--8558 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h as been already used, duplicate ignored \relax l.8565 \aliasA{sigma}{lmeObject}{sigma} [3110] [3111] [3112] Underfull \hbox (badness 10000) in paragraph at lines 8726--8738 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo r-mula ob-ject of the form [3113] [3114] [3115] [3116] [3117] [3118] [3119] [3120] [3121] Underfull \hbox (badness 10000) in paragraph at lines 9317--9324 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS truct[][][]\T1/ptm/m/n/10 , Overfull \hbox (4.38043pt too wide) in paragraph at lines 9328--9328 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3122] Underfull \hbox (badness 6300) in paragraph at lines 9410--9413 []\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr /m/n/10 lm \T1/ptm/m/n/10 com-po-nents of [3123] [3124] [3125] [3126]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3127] Underfull \hbox (badness 10000) in paragraph at lines 9699--9702 []\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a s Underfull \hbox (badness 3108) in paragraph at lines 9743--9746 []\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive -definite Underfull \hbox (badness 2521) in paragraph at lines 9743--9746 \T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M ust have the same di-men-sions as [3128] [3129] [3130] Underfull \hbox (badness 2435) in paragraph at lines 9917--9922 []\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/ 10 , [3131] [3132] [3133] [3134] [3135] Underfull \hbox (badness 7291) in paragraph at lines 10207--10209 []\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to [3136] [3137] [3138] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10423--10423 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3139] Underfull \hbox (badness 1596) in paragraph at lines 10452--10478 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3140] [3141] [3142] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10628--10628 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3143] [3144] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10779--10779 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] Underfull \hbox (badness 2213) in paragraph at lines 10790--10795 []\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][]\T1/pcr/m/n/10 nlminb [][][] \T1/ptm/m/n/10 (\T1/pcr/m/n/10 iter.max\T1/ptm/m/n/10 ) or the [][]\T1/p cr/m/n/10 nlm[][][] [3145] Underfull \hbox (badness 10000) in paragraph at lines 10812--10816 []\T1/ptm/m/n/10 a log-i-cal value passed as the \T1/pcr/m/n/10 trace \T1/ptm/m /n/10 to Underfull \hbox (badness 10000) in paragraph at lines 10831--10833 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 10867--10867 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3146] [3147] [3148] [3149] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11123--11123 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* message instead of one *each*[] [3150] [3151] [3152] [3153] [3154] [3155] [3156] [3157] [3158] [3159] [3160] [3161] Underfull \hbox (badness 6268) in paragraph at lines 11902--11912 [][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 pdMatrix[][][]\T1/ptm/m/n/10 , [3162] [3163] [3164] [3165] Underfull \hbox (badness 10000) in paragraph at lines 12163--12169 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon struct[][][]\T1/ptm/m/n/10 , [3166] [3167] [3168] [3169] [3170] Underfull \hbox (badness 6876) in paragraph at lines 12485--12487 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i ni-tial-ized \T1/pcr/m/n/10 pdMat \T1/ptm/m/n/10 ob-ject, \T1/pcr/m/n/10 object \T1/ptm/m/n/10 will be con-structed from [3171] [3172] Underfull \hbox (badness 2452) in paragraph at lines 12641--12648 [][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 reStruct[][][]\T1/ptm/m/n/10 , [3173] Underfull \hbox (badness 10000) in paragraph at lines 12706--12712 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re Struct[][][]\T1/ptm/m/n/10 , [3174] [3175] [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] [3187] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13658--13658 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3188] Underfull \hbox (badness 10000) in paragraph at lines 13685--13688 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 6016) in paragraph at lines 13713--13716 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i- zon-tal axis. Underfull \hbox (badness 2653) in paragraph at lines 13713--13716 \T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T 1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and Underfull \hbox (badness 1975) in paragraph at lines 13720--13723 []\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/ ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot Underfull \hbox (badness 1838) in paragraph at lines 13728--13735 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/ 10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner Underfull \hbox (badness 3713) in paragraph at lines 13728--13735 \T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n /10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner [3189] Overfull \hbox (12.78088pt too wide) in paragraph at lines 13785--13785 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] Underfull \hbox (badness 10000) in paragraph at lines 13792--13795 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 2469) in paragraph at lines 13792--13795 \T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v ari-ate and a sin-gle [3190] Underfull \hbox (badness 4582) in paragraph at lines 13820--13823 []\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De -fault is Underfull \hbox (badness 2418) in paragraph at lines 13820--13823 \T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and Underfull \hbox (badness 2990) in paragraph at lines 13824--13827 []\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/ ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot [3191] Underfull \hbox (badness 10000) in paragraph at lines 13900--13903 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa ta\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 1472) in paragraph at lines 13925--13932 \T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3192] Underfull \hbox (badness 10000) in paragraph at lines 13994--13996 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][ ][]\T1/ptm/m/n/10 , [3193] [3194] [3195] [3196] Underfull \hbox (badness 1540) in paragraph at lines 14209--14214 \T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1 /ptm/m/n/10 in-cludes an Underfull \hbox (badness 1215) in paragraph at lines 14256--14258 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [3197] [3198] [3199] [3200] [3201] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14500--14500 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3202] [3203] [3204] [3205] [3206] [3207] [3208] [3209] [3210]pdfTeX warning (e xt4): destination with the same identifier (name{Rfn.random.effects}) has been already used, duplicate ignored \relax l.15153 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15153 ...Extract Random Effects}{random.effects} [3211] [3212] [3213] [3214] [3215] [3216] [3217] [3218] [3219] [3220] Underfull \hbox (badness 1009) in paragraph at lines 15810--15819 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3221] [3222] [3223] Overfull \hbox (66.78088pt too wide) in paragraph at lines 15957--15957 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3224] [3225] [3226] [3227] Underfull \hbox (badness 10000) in paragraph at lines 16235--16253 []\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form Underfull \hbox (badness 1708) in paragraph at lines 16235--16253 \T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+.. .+xn \T1/ptm/m/n/10 spec-i-fy-ing the model [3228] Underfull \hbox (badness 10000) in paragraph at lines 16292--16298 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc t[][][]\T1/ptm/m/n/10 , [3229] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16323--16323 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3230] [3231] [3232] [3233] [3234] [3235] [3236] Underfull \hbox (badness 1728) in paragraph at lines 16812--16815 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3237] [3238] [3239] [3240] [3241] Underfull \hbox (badness 1867) in paragraph at lines 17147--17156 \T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17147--17156 \T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm \T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" Underfull \hbox (badness 10000) in paragraph at lines 17147--17156 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17147--17156 \T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization" [3242] Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu nc-tion: Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m /n/10 varComb\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/ n/10 varConstPower\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m /n/10 varExp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 , [3243] [3244] [3245] [3246] Underfull \hbox (badness 10000) in paragraph at lines 17458--17465 [][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 , [3247] [3248] [3249] [3250] [3251] [3252] [3253] [3254] Underfull \hbox (badness 10000) in paragraph at lines 17993--18003 [][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][] []\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17993--18003 [][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe r[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 3579) in paragraph at lines 18031--18036 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3255] Underfull \hbox (badness 3579) in paragraph at lines 18095--18100 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3256] Underfull \hbox (badness 3579) in paragraph at lines 18158--18163 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3257] Underfull \hbox (badness 1577) in paragraph at lines 18219--18221 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal Underfull \hbox (badness 3579) in paragraph at lines 18221--18226 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3258] Underfull \hbox (badness 3579) in paragraph at lines 18284--18289 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3259] Underfull \hbox (badness 10000) in paragraph at lines 18317--18326 [][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n /10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18317--18326 [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][] []\T1/ptm/m/n/10 , Underfull \hbox (badness 3579) in paragraph at lines 18356--18361 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3260] [3261] [3262] Underfull \hbox (badness 1009) in paragraph at lines 18505--18514 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3263] [3264] Underfull \hbox (badness 1009) in paragraph at lines 18639--18648 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3265] [3266] [3267] [3268] [3269] [3270] [3271] [3272]) (./nnet-pkg.tex Chapter 26. pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.multinom.1}) has been already used, du plicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} [3273] Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70 [] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored = FALSE,[] Underfull \hbox (badness 10000) in paragraph at lines 78--87 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [3274] [3275] [3276] Overfull \hbox (15.18042pt too wide) in paragraph at lines 369--369 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3277] Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c( 0,0,1),50)),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 429--429 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay =5e-4, maxit=200)[] [3278] Underfull \hbox (badness 4013) in paragraph at lines 474--477 \T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if the net was gen-er-ated by [3279] Overfull \hbox (15.18042pt too wide) in paragraph at lines 509--509 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3280]) (./rpart-pkg.tex Chapter 27. [3281] [3282] [3283] [3284] Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse = TRUE, ...)[] [3285] Underfull \hbox (badness 10000) in paragraph at lines 373--377 []\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm /m/n/10 ) or ma-trix of left and right splits [3286] [3287] [3288] Underfull \hbox (badness 1442) in paragraph at lines 591--597 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be at the hor-i-zon-tal plot co-or-di-nates of [3289] [3290] Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] [3291] Underfull \hbox (badness 2941) in paragraph at lines 785--787 []\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice if [3292] Overfull \hbox (25.98041pt too wide) in paragraph at lines 902--902 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] [3293] Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"), ...)[] [3294] [3295] [3296] Underfull \hbox (badness 2310) in paragraph at lines 1113--1116 []\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees all three resid-ual def-i-ni-tions re-duce to Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m ethod, Overfull \hbox (12.78088pt too wide) in paragraph at lines 1164--1164 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] Underfull \hbox (badness 2837) in paragraph at lines 1187--1196 []\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 " poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1 0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method Underfull \hbox (badness 2088) in paragraph at lines 1187--1196 \T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu ess. If \T1/pcr/m/n/10 y Underfull \hbox (badness 1817) in paragraph at lines 1187--1196 \T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2 [3297] Underfull \hbox (badness 2846) in paragraph at lines 1226--1228 []\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1 0 rpart \T1/ptm/m/n/10 al-go-rithm. See [3298] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1286--1286 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c p = 0.01, Overfull \hbox (60.78088pt too wide) in paragraph at lines 1287--1287 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3299] [3300] [3301] [3302] [3303] [3304] Underfull \hbox (badness 1565) in paragraph at lines 1739--1742 []\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val- ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ', [3305] [3306] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3307] [3308] [3309]) (./spatial-pkg.tex [3310] Chapter 28. [3311] [3312] [3313] [3314] [3315] [3316] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3317] [3318] [3319] [3320] [3321] [3322] [3323] [3324] [3325] [3326] [3327] [3328] [3329]) (./survival-pkg.tex [3330] Chapter 29. [3331] [3332] Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data = lung, nmin = 1[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t he last point[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 193--193 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a nd Grambsch.[] [3333] [3334]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.aml}) has been already used, duplicate ignored \relax l.326 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica te ignored \relax l.326 ... Myelogenous Leukemia survival data}{aml} [3335] [3336] Overfull \hbox (9.78043pt too wide) in paragraph at lines 423--423 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da ta = ovarian) Overfull \hbox (4.38043pt too wide) in paragraph at lines 425--425 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d ata=ovarian)[] [3337] Overfull \hbox (6.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog), lung)[] [3338] [3339] Underfull \vbox (badness 10000) has occurred while \output is active [3340] Overfull \hbox (36.78088pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c ohort.size, Overfull \hbox (48.78088pt too wide) in paragraph at lines 662--662 [] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan", "II.Borgan"),[] [3341] [3342] Overfull \hbox (9.78043pt too wide) in paragraph at lines 805--805 [] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz e=stratsizes,[] [3343] [3344] [3345] Underfull \hbox (badness 1097) in paragraph at lines 975--977 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. Overfull \hbox (4.38043pt too wide) in paragraph at lines 995--995 []\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit h large rate[] [3346] [3347] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1110--1110 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat um), data=infert) [3348]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col on}) has been already used, duplicate ignored \relax l.1178 ...erapy for Stage B/C colon cancer}{colon} Underfull \vbox (badness 2698) has occurred while \output is active [3349] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1271--1271 [] \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G 2", "I"),[] [3350] [3351] [3352] [3353] [3354] [3355] Underfull \hbox (badness 1337) in paragraph at lines 1753--1757 [][][]\T1/pcr/m/n/10 coxph.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 coxp h.control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cluster[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 strata[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Surv[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 pspline[][][]\T1/ptm/m/n/10 , [3356] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1808--1808 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3357] [3358] [3359] [3360] [3361] [3362] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2246--2246 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] [3363] [3364] [3365] [3366] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2495--2495 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3367] [3368] [3369] [3370] [3371] Underfull \vbox (badness 2012) has occurred while \output is active [3372] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2812--2812 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) Overfull \hbox (36.7804pt too wide) in paragraph at lines 2848--2848 [] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre ssion", "death")))[] Underfull \hbox (badness 1389) in paragraph at lines 2862--2864 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with [3373] Underfull \hbox (badness 1048) in paragraph at lines 2917--2919 []\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se e the note in [3374] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2995--2995 [] \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3375] [3376] [3377] [3378] [3379] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3241--3241 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3380] [3381] [3382] [3383] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3507--3507 [] \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5" , sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3384] Underfull \vbox (badness 10000) has occurred while \output is active [3385] [3386] [3387] [3388] [3389] [3390] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3924--3924 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3391] [3392] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4119--4119 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3393] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4245--4245 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] [3394] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4253--4253 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3395] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4339--4339 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3396] [3397] Underfull \hbox (badness 1852) in paragraph at lines 4487--4489 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/ n/10 , which is the re-sult of the [3398] [3399] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4622--4622 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me thod, Overfull \hbox (36.78088pt too wide) in paragraph at lines 4623--4623 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3400] [3401] [3402] Overfull \hbox (30.78088pt too wide) in paragraph at lines 4787--4787 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] Underfull \hbox (badness 1540) in paragraph at lines 4842--4845 []\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per -son years if [3403] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4889--4889 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4910--4910 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50 ,60,70,100)) +[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4912--4912 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3404] [3405] [3406] [3407] [3408] Underfull \vbox (badness 2126) has occurred while \output is active [3409] [3410] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5387--5387 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 1043) in paragraph at lines 5399--5402 \T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and [3411] [3412] [3413] [3414] [3415] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5699--5699 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the ta=5), cancer)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 5700--5700 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), cancer)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.5705 ...ata from a soldering experiment}{solder} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.solder.1}) has been already used, dupl icate ignored \relax l.5705 ...ata from a soldering experiment}{solder} [3416] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5811--5811 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3417] [3418] [3419] [3420] [3421] [3422] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6166--6166 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r r =expected,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6167--6167 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3423] [3424] [3425] [3426] Overfull \hbox (54.78088pt too wide) in paragraph at lines 6459--6459 [] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/ 10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/ n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] [3427] [3428] Underfull \vbox (badness 10000) has occurred while \output is active [3429] Underfull \hbox (badness 10000) in paragraph at lines 6722--6729 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 length \T1/ptm/m/n/10 of a \T1/pcr/m/n/10 S urv \T1/ptm/m/n/10 ob-ject is the num-ber of sur-vival times Underfull \hbox (badness 10000) in paragraph at lines 6722--6729 \T1/ptm/m/n/10 it con-tains, not the num-ber of items re-quired to en-code it, e.g., Underfull \hbox (badness 1412) in paragraph at lines 6722--6729 \T1/pcr/m/n/10 x <- Surv(1:4, 5:9, c(1,0,1,0)); length(x) \T1/ptm/m/n/10 has a value of 4. Like- Underfull \hbox (badness 1253) in paragraph at lines 6733--6736 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 median\T1/ptm/m/n/10 , \T1/pcr/m/n/10 quant ile \T1/ptm/m/n/10 and \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 meth-ods first con-st ruct a sur-vival curve us-ing [3430] [3431] Underfull \hbox (badness 10000) in paragraph at lines 6876--6885 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form [3432] Overfull \hbox (36.7804pt too wide) in paragraph at lines 6972--6972 [] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1 , year=accept.dt),[] [3433] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6990--6990 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] Underfull \hbox (badness 1038) in paragraph at lines 7032--7038 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival [3434] Underfull \hbox (badness 3000) in paragraph at lines 7054--7056 []\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab le \T1/ptm/m/n/10 is in units/day, Overfull \hbox (48.78088pt too wide) in paragraph at lines 7084--7084 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3435] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7170--7170 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3436] [3437] [3438] Underfull \hbox (badness 10000) in paragraph at lines 7395--7400 [][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 , [3439] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7416--7416 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3440] [3441] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7633--7633 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3442] [3443] Underfull \hbox (badness 6332) in paragraph at lines 7740--7745 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val- ues are [3444] [3445] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7933--7933 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3446] [3447] [3448] [3449] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8223--8223 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3450] Underfull \hbox (badness 1354) in paragraph at lines 8264--8268 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3451] [3452] Underfull \hbox (badness 2035) in paragraph at lines 8439--8446 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv reg.distributions[][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 8439--8446 \T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/ m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 , Underfull \hbox (badness 1297) in paragraph at lines 8439--8446 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n /10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is [3453] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8515--8515 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3454] Overfull \vbox (31.11076pt too high) has occurred while \output is active [3455] [3456] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8672--8672 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3457] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8804--8804 [] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x ^2*temp -1))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8807--8807 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3458] [3459] [3460] [3461] [3462] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9109--9109 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic al trial plus[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9110--9110 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9116--9116 [] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day , alk.phos))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9118--9118 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3463] [3464] [3465] [3466] [3467] [3468]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.xtfrm.Surv}) has been already used, duplicate i gnored \relax l.9488 ...ting order for Surv objects}{xtfrm.Surv} [3469] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9556--9556 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3470] [3471] [3472]) No file fullrefman.ind. (./fullrefman.aux) ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.tree} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.viewports} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.xyplot.zoo} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ellipsePoints} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ellipse} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.cluster.stats} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.chorizon} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.as.Rul.dsTMatrix.Rul.listw} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.similar.listw} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.nb2listw} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.read.gal} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.matrix.csr} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.SparseM.ontology} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.modelMatrix} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.model.Matrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.nearcor} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.posdefify} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.get.adjacency} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.graph.adjacency} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.graph} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.sqrtm} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.logm} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.showClass} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.loglm1} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgTMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glht} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.rinvGauss} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.lmrob} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.wilcox.Rul.test} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.spearman.test} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.pSpearman} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.pKendall} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.Kendall} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.cor.fk} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.dMatrix} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.dgCMatrix} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ansari.Rul.test} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.showDefault} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getGroupMembers} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.resetGeneric} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.linearizeMlist} has been referenced but does no t exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getGeneric} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getMethodsForDispatch} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.setDataPart} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getDataPart} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.possibleExtends} has been referenced but does n ot exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.mosaic} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.assoc} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.getNamespace} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.asNamespace} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.formalArgs} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.isRematched} has been referenced but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, replaced by a fixed one {/usr/share/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on fullrefman.pdf (3523 pages, 9046834 bytes). Transcript written on fullrefman.log. make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual' make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc' + exit 0 Executing(%install): env -i TMP=/home/users/builder/tmp HOME=/home/users/builder PATH=/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/users/builder/bin TMPDIR=/tmp/B.61K3e5/BUILD/tmp /bin/sh -e /tmp/B.61K3e5/BUILD/tmp/rpm-tmp.65393 TMP=/home/users/builder/tmp HOME=/home/users/builder PATH=/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/users/builder/bin TMPDIR=/tmp/B.61K3e5/BUILD/tmp + umask 022 + cd /tmp/B.61K3e5/BUILD + /bin/rm '--interactive=never' -rf /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder + /bin/mkdir -p /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder + cd R-3.5.2 + rm -rf /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder + install -d /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/bin /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/share/man/man1 /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/include /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/share/applications /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/share/pixmaps + /usr/bin/make -j4 -C build -j1 install 'DESTDIR=/tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder' make: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/m4' make[1]: Nothing to be done for 'install'. make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/m4' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tools' make[1]: Nothing to be done for 'install'. make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tools' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc' installing doc ... mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/doc make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/html' installing doc/html ... mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/doc/html make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/html' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual' installing doc/manual ... mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/doc/manual mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/doc/manual/images make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc/manual' make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/doc' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/etc' mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/etc installing etc ... make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/etc' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/share' installing share ... mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/share mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/share/R mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/share/dictionaries mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/share/encodings mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/share/java mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/share/licenses mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/share/make mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/share/Rd mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/share/Rd/macros mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/share/sh mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/share/texmf mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/share/texmf/bibtex/bib mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/share/texmf/bibtex/bst mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/share/texmf/tex/latex make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/share' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/scripts' mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/bin make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/scripts' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/include' mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/include make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/include/R_ext' mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/include/R_ext make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/include/R_ext' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/include' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/blas' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/blas' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tre' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tre' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tzone' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/tzone' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/xdr' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/xdr' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/intl' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra/intl' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/extra' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/appl' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/appl' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/nmath' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/nmath' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/unix' x86_64-tld-linux-gcc -I. -I../../src/include -I../../.././src/include -DHAVE_CONFIG_H -O2 -fwrapv -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fPIC -march=x86-64 -Wl,--as-needed -Wl,--no-copy-dt-needed-entries -Wl,-z,relro -Wl,-z,combreloc -DR_HOME='"/usr/lib64/R"' \ -o Rscript ../../.././src/unix/Rscript.c mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/pkgconfig make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/unix' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/bin/exec make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/lib make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/main' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/internet' mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/modules make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/internet' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/lapack' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/lapack' make[3]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/X11' make[3]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules/X11' make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/modules' make[2]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' mkdir -p -- /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library installing packages ... building HTML index ... make[2]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src/library' make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/src' make[1]: Entering directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make[1]: Nothing to be done for 'install'. make[1]: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build/tests' make: Leaving directory '/tmp/B.61K3e5/BUILD/R-3.5.2/build' + install /tmp/B.61K3e5/R.desktop /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/share/applications + install /tmp/B.61K3e5/R.xpm /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/share/pixmaps + ln -sf /usr/lib64/R/lib/libR.so /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64 + mv /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/include /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/include/R + ln -sf /usr/include/R /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/include + >R.files + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/KernSmooth + module=KernSmooth + echo '%dir /usr/lib64/R/library/KernSmooth' + '[' KernSmooth '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/KernSmooth/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/KernSmooth/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/KernSmooth/INDEX + bf=INDEX + echo /usr/lib64/R/library/KernSmooth/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/KernSmooth/Meta + bf=Meta + echo /usr/lib64/R/library/KernSmooth/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/KernSmooth/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/KernSmooth/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/KernSmooth/R + bf=R + echo /usr/lib64/R/library/KernSmooth/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/KernSmooth/help + bf=help + echo /usr/lib64/R/library/KernSmooth/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/KernSmooth/html + bf=html + echo /usr/lib64/R/library/KernSmooth/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/KernSmooth/libs + bf=libs + echo '%dir /usr/lib64/R/library/KernSmooth/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/KernSmooth/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/KernSmooth/po + bf=po + echo '%dir /usr/lib64/R/library/KernSmooth/po' + gen_lang /usr/lib64/R/library/KernSmooth/po + dir=/usr/lib64/R/library/KernSmooth/po + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/KernSmooth/po/de + bd=de + lang=de + echo '%lang(de) /usr/lib64/R/library/KernSmooth/po/de' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/KernSmooth/po/en@quot + bd=en@quot + lang=en + echo '%lang(en) /usr/lib64/R/library/KernSmooth/po/en@quot' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/KernSmooth/po/fr + bd=fr + lang=fr + echo '%lang(fr) /usr/lib64/R/library/KernSmooth/po/fr' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/KernSmooth/po/ko + bd=ko + lang=ko + echo '%lang(ko) /usr/lib64/R/library/KernSmooth/po/ko' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/KernSmooth/po/pl + bd=pl + lang=pl + echo '%lang(pl) /usr/lib64/R/library/KernSmooth/po/pl' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/MASS + module=MASS + echo '%dir /usr/lib64/R/library/MASS' + '[' MASS '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/MASS/CITATION + bf=CITATION + echo /usr/lib64/R/library/MASS/CITATION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/MASS/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/MASS/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/MASS/INDEX + bf=INDEX + echo /usr/lib64/R/library/MASS/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/MASS/Meta + bf=Meta + echo /usr/lib64/R/library/MASS/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/MASS/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/MASS/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/MASS/NEWS + bf=NEWS + echo /usr/lib64/R/library/MASS/NEWS + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/MASS/R + bf=R + echo /usr/lib64/R/library/MASS/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/MASS/data + bf=data + echo /usr/lib64/R/library/MASS/data + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/MASS/help + bf=help + echo /usr/lib64/R/library/MASS/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/MASS/html + bf=html + echo /usr/lib64/R/library/MASS/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/MASS/libs + bf=libs + echo '%dir /usr/lib64/R/library/MASS/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/MASS/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/MASS/po + bf=po + echo '%dir /usr/lib64/R/library/MASS/po' + gen_lang /usr/lib64/R/library/MASS/po + dir=/usr/lib64/R/library/MASS/po + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/MASS/po/de + bd=de + lang=de + echo '%lang(de) /usr/lib64/R/library/MASS/po/de' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/MASS/po/en@quot + bd=en@quot + lang=en + echo '%lang(en) /usr/lib64/R/library/MASS/po/en@quot' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/MASS/po/fr + bd=fr + lang=fr + echo '%lang(fr) /usr/lib64/R/library/MASS/po/fr' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/MASS/po/ko + bd=ko + lang=ko + echo '%lang(ko) /usr/lib64/R/library/MASS/po/ko' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/MASS/po/pl + bd=pl + lang=pl + echo '%lang(pl) /usr/lib64/R/library/MASS/po/pl' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/MASS/scripts + bf=scripts + echo /usr/lib64/R/library/MASS/scripts + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix + module=Matrix + echo '%dir /usr/lib64/R/library/Matrix' + '[' Matrix '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/Copyrights + bf=Copyrights + echo /usr/lib64/R/library/Matrix/Copyrights + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/Matrix/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/Doxyfile + bf=Doxyfile + echo /usr/lib64/R/library/Matrix/Doxyfile + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/INDEX + bf=INDEX + echo /usr/lib64/R/library/Matrix/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/LICENCE + bf=LICENCE + echo /usr/lib64/R/library/Matrix/LICENCE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/Meta + bf=Meta + echo /usr/lib64/R/library/Matrix/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/Matrix/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/NEWS.Rd + bf=NEWS.Rd + echo /usr/lib64/R/library/Matrix/NEWS.Rd + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/R + bf=R + echo /usr/lib64/R/library/Matrix/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/data + bf=data + echo /usr/lib64/R/library/Matrix/data + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/doc + bf=doc + echo /usr/lib64/R/library/Matrix/doc + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/external + bf=external + echo /usr/lib64/R/library/Matrix/external + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/help + bf=help + echo /usr/lib64/R/library/Matrix/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/html + bf=html + echo /usr/lib64/R/library/Matrix/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/include + bf=include + echo /usr/lib64/R/library/Matrix/include + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/libs + bf=libs + echo '%dir /usr/lib64/R/library/Matrix/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/Matrix/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/po + bf=po + echo '%dir /usr/lib64/R/library/Matrix/po' + gen_lang /usr/lib64/R/library/Matrix/po + dir=/usr/lib64/R/library/Matrix/po + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/po/de + bd=de + lang=de + echo '%lang(de) /usr/lib64/R/library/Matrix/po/de' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/po/en@quot + bd=en@quot + lang=en + echo '%lang(en) /usr/lib64/R/library/Matrix/po/en@quot' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/po/fr + bd=fr + lang=fr + echo '%lang(fr) /usr/lib64/R/library/Matrix/po/fr' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/po/ko + bd=ko + lang=ko + echo '%lang(ko) /usr/lib64/R/library/Matrix/po/ko' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/po/pl + bd=pl + lang=pl + echo '%lang(pl) /usr/lib64/R/library/Matrix/po/pl' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/test-tools-1.R + bf=test-tools-1.R + echo /usr/lib64/R/library/Matrix/test-tools-1.R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/test-tools-Matrix.R + bf=test-tools-Matrix.R + echo /usr/lib64/R/library/Matrix/test-tools-Matrix.R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/Matrix/test-tools.R + bf=test-tools.R + echo /usr/lib64/R/library/Matrix/test-tools.R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/base + module=base + echo '%dir /usr/lib64/R/library/base' + '[' base '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/base/CITATION + bf=CITATION + echo /usr/lib64/R/library/base/CITATION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/base/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/base/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/base/INDEX + bf=INDEX + echo /usr/lib64/R/library/base/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/base/Meta + bf=Meta + echo /usr/lib64/R/library/base/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/base/R + bf=R + echo /usr/lib64/R/library/base/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/base/demo + bf=demo + echo /usr/lib64/R/library/base/demo + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/base/help + bf=help + echo /usr/lib64/R/library/base/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/base/html + bf=html + echo /usr/lib64/R/library/base/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/boot + module=boot + echo '%dir /usr/lib64/R/library/boot' + '[' boot '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/boot/CITATION + bf=CITATION + echo /usr/lib64/R/library/boot/CITATION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/boot/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/boot/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/boot/INDEX + bf=INDEX + echo /usr/lib64/R/library/boot/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/boot/Meta + bf=Meta + echo /usr/lib64/R/library/boot/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/boot/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/boot/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/boot/R + bf=R + echo /usr/lib64/R/library/boot/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/boot/bd.q + bf=bd.q + echo /usr/lib64/R/library/boot/bd.q + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/boot/data + bf=data + echo /usr/lib64/R/library/boot/data + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/boot/help + bf=help + echo /usr/lib64/R/library/boot/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/boot/html + bf=html + echo /usr/lib64/R/library/boot/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/boot/po + bf=po + echo '%dir /usr/lib64/R/library/boot/po' + gen_lang /usr/lib64/R/library/boot/po + dir=/usr/lib64/R/library/boot/po + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/boot/po/de + bd=de + lang=de + echo '%lang(de) /usr/lib64/R/library/boot/po/de' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/boot/po/en@quot + bd=en@quot + lang=en + echo '%lang(en) /usr/lib64/R/library/boot/po/en@quot' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/boot/po/fr + bd=fr + lang=fr + echo '%lang(fr) /usr/lib64/R/library/boot/po/fr' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/boot/po/ko + bd=ko + lang=ko + echo '%lang(ko) /usr/lib64/R/library/boot/po/ko' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/boot/po/pl + bd=pl + lang=pl + echo '%lang(pl) /usr/lib64/R/library/boot/po/pl' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/boot/po/ru + bd=ru + lang=ru + echo '%lang(ru) /usr/lib64/R/library/boot/po/ru' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/class + module=class + echo '%dir /usr/lib64/R/library/class' + '[' class '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/class/CITATION + bf=CITATION + echo /usr/lib64/R/library/class/CITATION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/class/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/class/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/class/INDEX + bf=INDEX + echo /usr/lib64/R/library/class/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/class/Meta + bf=Meta + echo /usr/lib64/R/library/class/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/class/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/class/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/class/NEWS + bf=NEWS + echo /usr/lib64/R/library/class/NEWS + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/class/R + bf=R + echo /usr/lib64/R/library/class/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/class/help + bf=help + echo /usr/lib64/R/library/class/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/class/html + bf=html + echo /usr/lib64/R/library/class/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/class/libs + bf=libs + echo '%dir /usr/lib64/R/library/class/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/class/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/class/po + bf=po + echo '%dir /usr/lib64/R/library/class/po' + gen_lang /usr/lib64/R/library/class/po + dir=/usr/lib64/R/library/class/po + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/class/po/de + bd=de + lang=de + echo '%lang(de) /usr/lib64/R/library/class/po/de' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/class/po/en@quot + bd=en@quot + lang=en + echo '%lang(en) /usr/lib64/R/library/class/po/en@quot' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/class/po/fr + bd=fr + lang=fr + echo '%lang(fr) /usr/lib64/R/library/class/po/fr' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/class/po/ko + bd=ko + lang=ko + echo '%lang(ko) /usr/lib64/R/library/class/po/ko' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/class/po/pl + bd=pl + lang=pl + echo '%lang(pl) /usr/lib64/R/library/class/po/pl' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/cluster + module=cluster + echo '%dir /usr/lib64/R/library/cluster' + '[' cluster '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/cluster/CITATION + bf=CITATION + echo /usr/lib64/R/library/cluster/CITATION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/cluster/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/cluster/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/cluster/INDEX + bf=INDEX + echo /usr/lib64/R/library/cluster/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/cluster/Meta + bf=Meta + echo /usr/lib64/R/library/cluster/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/cluster/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/cluster/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/cluster/NEWS.Rd + bf=NEWS.Rd + echo /usr/lib64/R/library/cluster/NEWS.Rd + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/cluster/R + bf=R + echo /usr/lib64/R/library/cluster/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/cluster/data + bf=data + echo /usr/lib64/R/library/cluster/data + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/cluster/help + bf=help + echo /usr/lib64/R/library/cluster/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/cluster/html + bf=html + echo /usr/lib64/R/library/cluster/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/cluster/libs + bf=libs + echo '%dir /usr/lib64/R/library/cluster/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/cluster/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/cluster/po + bf=po + echo '%dir /usr/lib64/R/library/cluster/po' + gen_lang /usr/lib64/R/library/cluster/po + dir=/usr/lib64/R/library/cluster/po + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/cluster/po/de + bd=de + lang=de + echo '%lang(de) /usr/lib64/R/library/cluster/po/de' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/cluster/po/en@quot + bd=en@quot + lang=en + echo '%lang(en) /usr/lib64/R/library/cluster/po/en@quot' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/cluster/po/fr + bd=fr + lang=fr + echo '%lang(fr) /usr/lib64/R/library/cluster/po/fr' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/cluster/po/ko + bd=ko + lang=ko + echo '%lang(ko) /usr/lib64/R/library/cluster/po/ko' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/cluster/po/pl + bd=pl + lang=pl + echo '%lang(pl) /usr/lib64/R/library/cluster/po/pl' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/cluster/test-tools.R + bf=test-tools.R + echo /usr/lib64/R/library/cluster/test-tools.R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/codetools + module=codetools + echo '%dir /usr/lib64/R/library/codetools' + '[' codetools '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/codetools/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/codetools/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/codetools/INDEX + bf=INDEX + echo /usr/lib64/R/library/codetools/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/codetools/Meta + bf=Meta + echo /usr/lib64/R/library/codetools/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/codetools/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/codetools/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/codetools/R + bf=R + echo /usr/lib64/R/library/codetools/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/codetools/help + bf=help + echo /usr/lib64/R/library/codetools/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/codetools/html + bf=html + echo /usr/lib64/R/library/codetools/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/compiler + module=compiler + echo '%dir /usr/lib64/R/library/compiler' + '[' compiler '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/compiler/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/compiler/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/compiler/INDEX + bf=INDEX + echo /usr/lib64/R/library/compiler/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/compiler/Meta + bf=Meta + echo /usr/lib64/R/library/compiler/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/compiler/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/compiler/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/compiler/R + bf=R + echo /usr/lib64/R/library/compiler/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/compiler/help + bf=help + echo /usr/lib64/R/library/compiler/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/compiler/html + bf=html + echo /usr/lib64/R/library/compiler/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/datasets + module=datasets + echo '%dir /usr/lib64/R/library/datasets' + '[' datasets '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/datasets/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/datasets/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/datasets/INDEX + bf=INDEX + echo /usr/lib64/R/library/datasets/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/datasets/Meta + bf=Meta + echo /usr/lib64/R/library/datasets/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/datasets/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/datasets/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/datasets/data + bf=data + echo /usr/lib64/R/library/datasets/data + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/datasets/help + bf=help + echo /usr/lib64/R/library/datasets/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/datasets/html + bf=html + echo /usr/lib64/R/library/datasets/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/foreign + module=foreign + echo '%dir /usr/lib64/R/library/foreign' + '[' foreign '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/foreign/COPYRIGHTS + bf=COPYRIGHTS + echo /usr/lib64/R/library/foreign/COPYRIGHTS + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/foreign/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/foreign/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/foreign/INDEX + bf=INDEX + echo /usr/lib64/R/library/foreign/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/foreign/Meta + bf=Meta + echo /usr/lib64/R/library/foreign/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/foreign/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/foreign/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/foreign/R + bf=R + echo /usr/lib64/R/library/foreign/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/foreign/files + bf=files + echo /usr/lib64/R/library/foreign/files + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/foreign/help + bf=help + echo /usr/lib64/R/library/foreign/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/foreign/html + bf=html + echo /usr/lib64/R/library/foreign/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/foreign/libs + bf=libs + echo '%dir /usr/lib64/R/library/foreign/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/foreign/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/foreign/po + bf=po + echo '%dir /usr/lib64/R/library/foreign/po' + gen_lang /usr/lib64/R/library/foreign/po + dir=/usr/lib64/R/library/foreign/po + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/foreign/po/de + bd=de + lang=de + echo '%lang(de) /usr/lib64/R/library/foreign/po/de' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/foreign/po/en@quot + bd=en@quot + lang=en + echo '%lang(en) /usr/lib64/R/library/foreign/po/en@quot' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/foreign/po/fr + bd=fr + lang=fr + echo '%lang(fr) /usr/lib64/R/library/foreign/po/fr' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/foreign/po/pl + bd=pl + lang=pl + echo '%lang(pl) /usr/lib64/R/library/foreign/po/pl' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grDevices + module=grDevices + echo '%dir /usr/lib64/R/library/grDevices' + '[' grDevices '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grDevices/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/grDevices/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grDevices/INDEX + bf=INDEX + echo /usr/lib64/R/library/grDevices/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grDevices/Meta + bf=Meta + echo /usr/lib64/R/library/grDevices/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grDevices/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/grDevices/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grDevices/R + bf=R + echo /usr/lib64/R/library/grDevices/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grDevices/afm + bf=afm + echo /usr/lib64/R/library/grDevices/afm + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grDevices/demo + bf=demo + echo /usr/lib64/R/library/grDevices/demo + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grDevices/enc + bf=enc + echo /usr/lib64/R/library/grDevices/enc + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grDevices/help + bf=help + echo /usr/lib64/R/library/grDevices/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grDevices/html + bf=html + echo /usr/lib64/R/library/grDevices/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grDevices/icc + bf=icc + echo /usr/lib64/R/library/grDevices/icc + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grDevices/libs + bf=libs + echo '%dir /usr/lib64/R/library/grDevices/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/grDevices/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/graphics + module=graphics + echo '%dir /usr/lib64/R/library/graphics' + '[' graphics '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/graphics/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/graphics/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/graphics/INDEX + bf=INDEX + echo /usr/lib64/R/library/graphics/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/graphics/Meta + bf=Meta + echo /usr/lib64/R/library/graphics/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/graphics/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/graphics/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/graphics/R + bf=R + echo /usr/lib64/R/library/graphics/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/graphics/demo + bf=demo + echo /usr/lib64/R/library/graphics/demo + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/graphics/help + bf=help + echo /usr/lib64/R/library/graphics/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/graphics/html + bf=html + echo /usr/lib64/R/library/graphics/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/graphics/libs + bf=libs + echo '%dir /usr/lib64/R/library/graphics/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/graphics/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grid + module=grid + echo '%dir /usr/lib64/R/library/grid' + '[' grid '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grid/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/grid/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grid/INDEX + bf=INDEX + echo /usr/lib64/R/library/grid/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grid/Meta + bf=Meta + echo /usr/lib64/R/library/grid/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grid/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/grid/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grid/R + bf=R + echo /usr/lib64/R/library/grid/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grid/doc + bf=doc + echo /usr/lib64/R/library/grid/doc + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grid/help + bf=help + echo /usr/lib64/R/library/grid/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grid/html + bf=html + echo /usr/lib64/R/library/grid/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/grid/libs + bf=libs + echo '%dir /usr/lib64/R/library/grid/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/grid/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/lattice + module=lattice + echo '%dir /usr/lib64/R/library/lattice' + '[' lattice '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/lattice/CITATION + bf=CITATION + echo /usr/lib64/R/library/lattice/CITATION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/lattice/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/lattice/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/lattice/INDEX + bf=INDEX + echo /usr/lib64/R/library/lattice/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/lattice/Meta + bf=Meta + echo /usr/lib64/R/library/lattice/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/lattice/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/lattice/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/lattice/NEWS + bf=NEWS + echo /usr/lib64/R/library/lattice/NEWS + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/lattice/R + bf=R + echo /usr/lib64/R/library/lattice/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/lattice/data + bf=data + echo /usr/lib64/R/library/lattice/data + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/lattice/demo + bf=demo + echo /usr/lib64/R/library/lattice/demo + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/lattice/help + bf=help + echo /usr/lib64/R/library/lattice/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/lattice/html + bf=html + echo /usr/lib64/R/library/lattice/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/lattice/libs + bf=libs + echo '%dir /usr/lib64/R/library/lattice/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/lattice/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/lattice/po + bf=po + echo '%dir /usr/lib64/R/library/lattice/po' + gen_lang /usr/lib64/R/library/lattice/po + dir=/usr/lib64/R/library/lattice/po + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/lattice/po/de + bd=de + lang=de + echo '%lang(de) /usr/lib64/R/library/lattice/po/de' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/lattice/po/en@quot + bd=en@quot + lang=en + echo '%lang(en) /usr/lib64/R/library/lattice/po/en@quot' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/lattice/po/fr + bd=fr + lang=fr + echo '%lang(fr) /usr/lib64/R/library/lattice/po/fr' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/lattice/po/ko + bd=ko + lang=ko + echo '%lang(ko) /usr/lib64/R/library/lattice/po/ko' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/lattice/po/pl + bd=pl + lang=pl + echo '%lang(pl) /usr/lib64/R/library/lattice/po/pl' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/methods + module=methods + echo '%dir /usr/lib64/R/library/methods' + '[' methods '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/methods/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/methods/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/methods/INDEX + bf=INDEX + echo /usr/lib64/R/library/methods/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/methods/Meta + bf=Meta + echo /usr/lib64/R/library/methods/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/methods/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/methods/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/methods/R + bf=R + echo /usr/lib64/R/library/methods/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/methods/help + bf=help + echo /usr/lib64/R/library/methods/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/methods/html + bf=html + echo /usr/lib64/R/library/methods/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/methods/libs + bf=libs + echo '%dir /usr/lib64/R/library/methods/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/methods/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/mgcv + module=mgcv + echo '%dir /usr/lib64/R/library/mgcv' + '[' mgcv '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/mgcv/CITATION + bf=CITATION + echo /usr/lib64/R/library/mgcv/CITATION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/mgcv/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/mgcv/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/mgcv/INDEX + bf=INDEX + echo /usr/lib64/R/library/mgcv/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/mgcv/Meta + bf=Meta + echo /usr/lib64/R/library/mgcv/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/mgcv/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/mgcv/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/mgcv/R + bf=R + echo /usr/lib64/R/library/mgcv/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/mgcv/data + bf=data + echo /usr/lib64/R/library/mgcv/data + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/mgcv/help + bf=help + echo /usr/lib64/R/library/mgcv/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/mgcv/html + bf=html + echo /usr/lib64/R/library/mgcv/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/mgcv/libs + bf=libs + echo '%dir /usr/lib64/R/library/mgcv/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/mgcv/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/mgcv/po + bf=po + echo '%dir /usr/lib64/R/library/mgcv/po' + gen_lang /usr/lib64/R/library/mgcv/po + dir=/usr/lib64/R/library/mgcv/po + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/mgcv/po/de + bd=de + lang=de + echo '%lang(de) /usr/lib64/R/library/mgcv/po/de' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/mgcv/po/en@quot + bd=en@quot + lang=en + echo '%lang(en) /usr/lib64/R/library/mgcv/po/en@quot' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/mgcv/po/fr + bd=fr + lang=fr + echo '%lang(fr) /usr/lib64/R/library/mgcv/po/fr' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/mgcv/po/ko + bd=ko + lang=ko + echo '%lang(ko) /usr/lib64/R/library/mgcv/po/ko' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/mgcv/po/pl + bd=pl + lang=pl + echo '%lang(pl) /usr/lib64/R/library/mgcv/po/pl' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme + module=nlme + echo '%dir /usr/lib64/R/library/nlme' + '[' nlme '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme/CITATION + bf=CITATION + echo /usr/lib64/R/library/nlme/CITATION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/nlme/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme/INDEX + bf=INDEX + echo /usr/lib64/R/library/nlme/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme/LICENCE + bf=LICENCE + echo /usr/lib64/R/library/nlme/LICENCE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme/Meta + bf=Meta + echo /usr/lib64/R/library/nlme/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/nlme/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme/R + bf=R + echo /usr/lib64/R/library/nlme/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme/data + bf=data + echo /usr/lib64/R/library/nlme/data + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme/help + bf=help + echo /usr/lib64/R/library/nlme/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme/html + bf=html + echo /usr/lib64/R/library/nlme/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme/libs + bf=libs + echo '%dir /usr/lib64/R/library/nlme/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/nlme/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme/mlbook + bf=mlbook + echo /usr/lib64/R/library/nlme/mlbook + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme/po + bf=po + echo '%dir /usr/lib64/R/library/nlme/po' + gen_lang /usr/lib64/R/library/nlme/po + dir=/usr/lib64/R/library/nlme/po + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme/po/de + bd=de + lang=de + echo '%lang(de) /usr/lib64/R/library/nlme/po/de' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme/po/en@quot + bd=en@quot + lang=en + echo '%lang(en) /usr/lib64/R/library/nlme/po/en@quot' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme/po/fr + bd=fr + lang=fr + echo '%lang(fr) /usr/lib64/R/library/nlme/po/fr' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme/po/ko + bd=ko + lang=ko + echo '%lang(ko) /usr/lib64/R/library/nlme/po/ko' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme/po/pl + bd=pl + lang=pl + echo '%lang(pl) /usr/lib64/R/library/nlme/po/pl' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nlme/scripts + bf=scripts + echo /usr/lib64/R/library/nlme/scripts + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nnet + module=nnet + echo '%dir /usr/lib64/R/library/nnet' + '[' nnet '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nnet/CITATION + bf=CITATION + echo /usr/lib64/R/library/nnet/CITATION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nnet/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/nnet/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nnet/INDEX + bf=INDEX + echo /usr/lib64/R/library/nnet/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nnet/Meta + bf=Meta + echo /usr/lib64/R/library/nnet/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nnet/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/nnet/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nnet/NEWS + bf=NEWS + echo /usr/lib64/R/library/nnet/NEWS + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nnet/R + bf=R + echo /usr/lib64/R/library/nnet/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nnet/help + bf=help + echo /usr/lib64/R/library/nnet/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nnet/html + bf=html + echo /usr/lib64/R/library/nnet/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nnet/libs + bf=libs + echo '%dir /usr/lib64/R/library/nnet/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/nnet/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nnet/po + bf=po + echo '%dir /usr/lib64/R/library/nnet/po' + gen_lang /usr/lib64/R/library/nnet/po + dir=/usr/lib64/R/library/nnet/po + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nnet/po/de + bd=de + lang=de + echo '%lang(de) /usr/lib64/R/library/nnet/po/de' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nnet/po/en@quot + bd=en@quot + lang=en + echo '%lang(en) /usr/lib64/R/library/nnet/po/en@quot' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nnet/po/fr + bd=fr + lang=fr + echo '%lang(fr) /usr/lib64/R/library/nnet/po/fr' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nnet/po/ko + bd=ko + lang=ko + echo '%lang(ko) /usr/lib64/R/library/nnet/po/ko' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/nnet/po/pl + bd=pl + lang=pl + echo '%lang(pl) /usr/lib64/R/library/nnet/po/pl' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/parallel + module=parallel + echo '%dir /usr/lib64/R/library/parallel' + '[' parallel '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/parallel/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/parallel/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/parallel/INDEX + bf=INDEX + echo /usr/lib64/R/library/parallel/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/parallel/Meta + bf=Meta + echo /usr/lib64/R/library/parallel/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/parallel/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/parallel/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/parallel/R + bf=R + echo /usr/lib64/R/library/parallel/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/parallel/doc + bf=doc + echo /usr/lib64/R/library/parallel/doc + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/parallel/help + bf=help + echo /usr/lib64/R/library/parallel/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/parallel/html + bf=html + echo /usr/lib64/R/library/parallel/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/parallel/libs + bf=libs + echo '%dir /usr/lib64/R/library/parallel/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/parallel/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/rpart + module=rpart + echo '%dir /usr/lib64/R/library/rpart' + '[' rpart '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/rpart/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/rpart/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/rpart/INDEX + bf=INDEX + echo /usr/lib64/R/library/rpart/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/rpart/Meta + bf=Meta + echo /usr/lib64/R/library/rpart/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/rpart/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/rpart/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/rpart/NEWS.Rd + bf=NEWS.Rd + echo /usr/lib64/R/library/rpart/NEWS.Rd + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/rpart/R + bf=R + echo /usr/lib64/R/library/rpart/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/rpart/data + bf=data + echo /usr/lib64/R/library/rpart/data + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/rpart/doc + bf=doc + echo /usr/lib64/R/library/rpart/doc + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/rpart/help + bf=help + echo /usr/lib64/R/library/rpart/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/rpart/html + bf=html + echo /usr/lib64/R/library/rpart/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/rpart/libs + bf=libs + echo '%dir /usr/lib64/R/library/rpart/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/rpart/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/rpart/po + bf=po + echo '%dir /usr/lib64/R/library/rpart/po' + gen_lang /usr/lib64/R/library/rpart/po + dir=/usr/lib64/R/library/rpart/po + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/rpart/po/de + bd=de + lang=de + echo '%lang(de) /usr/lib64/R/library/rpart/po/de' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/rpart/po/en@quot + bd=en@quot + lang=en + echo '%lang(en) /usr/lib64/R/library/rpart/po/en@quot' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/rpart/po/fr + bd=fr + lang=fr + echo '%lang(fr) /usr/lib64/R/library/rpart/po/fr' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/rpart/po/ko + bd=ko + lang=ko + echo '%lang(ko) /usr/lib64/R/library/rpart/po/ko' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/rpart/po/pl + bd=pl + lang=pl + echo '%lang(pl) /usr/lib64/R/library/rpart/po/pl' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/rpart/po/ru + bd=ru + lang=ru + echo '%lang(ru) /usr/lib64/R/library/rpart/po/ru' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/spatial + module=spatial + echo '%dir /usr/lib64/R/library/spatial' + '[' spatial '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/spatial/CITATION + bf=CITATION + echo /usr/lib64/R/library/spatial/CITATION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/spatial/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/spatial/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/spatial/INDEX + bf=INDEX + echo /usr/lib64/R/library/spatial/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/spatial/Meta + bf=Meta + echo /usr/lib64/R/library/spatial/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/spatial/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/spatial/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/spatial/NEWS + bf=NEWS + echo /usr/lib64/R/library/spatial/NEWS + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/spatial/PP.files + bf=PP.files + echo /usr/lib64/R/library/spatial/PP.files + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/spatial/R + bf=R + echo /usr/lib64/R/library/spatial/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/spatial/help + bf=help + echo /usr/lib64/R/library/spatial/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/spatial/html + bf=html + echo /usr/lib64/R/library/spatial/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/spatial/libs + bf=libs + echo '%dir /usr/lib64/R/library/spatial/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/spatial/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/spatial/po + bf=po + echo '%dir /usr/lib64/R/library/spatial/po' + gen_lang /usr/lib64/R/library/spatial/po + dir=/usr/lib64/R/library/spatial/po + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/spatial/po/de + bd=de + lang=de + echo '%lang(de) /usr/lib64/R/library/spatial/po/de' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/spatial/po/en@quot + bd=en@quot + lang=en + echo '%lang(en) /usr/lib64/R/library/spatial/po/en@quot' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/spatial/po/fr + bd=fr + lang=fr + echo '%lang(fr) /usr/lib64/R/library/spatial/po/fr' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/spatial/po/ko + bd=ko + lang=ko + echo '%lang(ko) /usr/lib64/R/library/spatial/po/ko' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/spatial/po/pl + bd=pl + lang=pl + echo '%lang(pl) /usr/lib64/R/library/spatial/po/pl' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/spatial/ppdata + bf=ppdata + echo /usr/lib64/R/library/spatial/ppdata + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/splines + module=splines + echo '%dir /usr/lib64/R/library/splines' + '[' splines '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/splines/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/splines/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/splines/INDEX + bf=INDEX + echo /usr/lib64/R/library/splines/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/splines/Meta + bf=Meta + echo /usr/lib64/R/library/splines/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/splines/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/splines/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/splines/R + bf=R + echo /usr/lib64/R/library/splines/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/splines/help + bf=help + echo /usr/lib64/R/library/splines/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/splines/html + bf=html + echo /usr/lib64/R/library/splines/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/splines/libs + bf=libs + echo '%dir /usr/lib64/R/library/splines/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/splines/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats + module=stats + echo '%dir /usr/lib64/R/library/stats' + '[' stats '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats/COPYRIGHTS.modreg + bf=COPYRIGHTS.modreg + echo /usr/lib64/R/library/stats/COPYRIGHTS.modreg + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/stats/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats/INDEX + bf=INDEX + echo /usr/lib64/R/library/stats/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats/Meta + bf=Meta + echo /usr/lib64/R/library/stats/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/stats/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats/R + bf=R + echo /usr/lib64/R/library/stats/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats/SOURCES.ts + bf=SOURCES.ts + echo /usr/lib64/R/library/stats/SOURCES.ts + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats/demo + bf=demo + echo /usr/lib64/R/library/stats/demo + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats/help + bf=help + echo /usr/lib64/R/library/stats/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats/html + bf=html + echo /usr/lib64/R/library/stats/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats/libs + bf=libs + echo '%dir /usr/lib64/R/library/stats/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/stats/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats4 + module=stats4 + echo '%dir /usr/lib64/R/library/stats4' + '[' stats4 '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats4/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/stats4/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats4/INDEX + bf=INDEX + echo /usr/lib64/R/library/stats4/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats4/Meta + bf=Meta + echo /usr/lib64/R/library/stats4/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats4/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/stats4/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats4/R + bf=R + echo /usr/lib64/R/library/stats4/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats4/help + bf=help + echo /usr/lib64/R/library/stats4/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/stats4/html + bf=html + echo /usr/lib64/R/library/stats4/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/survival + module=survival + echo '%dir /usr/lib64/R/library/survival' + '[' survival '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/survival/CITATION + bf=CITATION + echo /usr/lib64/R/library/survival/CITATION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/survival/COPYRIGHTS + bf=COPYRIGHTS + echo /usr/lib64/R/library/survival/COPYRIGHTS + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/survival/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/survival/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/survival/INDEX + bf=INDEX + echo /usr/lib64/R/library/survival/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/survival/Meta + bf=Meta + echo /usr/lib64/R/library/survival/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/survival/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/survival/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/survival/NEWS.Rd + bf=NEWS.Rd + echo /usr/lib64/R/library/survival/NEWS.Rd + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/survival/R + bf=R + echo /usr/lib64/R/library/survival/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/survival/data + bf=data + echo /usr/lib64/R/library/survival/data + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/survival/doc + bf=doc + echo /usr/lib64/R/library/survival/doc + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/survival/help + bf=help + echo /usr/lib64/R/library/survival/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/survival/html + bf=html + echo /usr/lib64/R/library/survival/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/survival/libs + bf=libs + echo '%dir /usr/lib64/R/library/survival/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/survival/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tcltk + module=tcltk + echo '%dir /usr/lib64/R/library/tcltk' + '[' tcltk '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tcltk/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/tcltk/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tcltk/INDEX + bf=INDEX + echo /usr/lib64/R/library/tcltk/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tcltk/Meta + bf=Meta + echo /usr/lib64/R/library/tcltk/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tcltk/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/tcltk/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tcltk/R + bf=R + echo /usr/lib64/R/library/tcltk/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tcltk/demo + bf=demo + echo /usr/lib64/R/library/tcltk/demo + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tcltk/exec + bf=exec + echo /usr/lib64/R/library/tcltk/exec + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tcltk/help + bf=help + echo /usr/lib64/R/library/tcltk/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tcltk/html + bf=html + echo /usr/lib64/R/library/tcltk/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tcltk/libs + bf=libs + echo '%dir /usr/lib64/R/library/tcltk/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/tcltk/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tools + module=tools + echo '%dir /usr/lib64/R/library/tools' + '[' tools '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tools/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/tools/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tools/INDEX + bf=INDEX + echo /usr/lib64/R/library/tools/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tools/Meta + bf=Meta + echo /usr/lib64/R/library/tools/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tools/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/tools/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tools/R + bf=R + echo /usr/lib64/R/library/tools/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tools/help + bf=help + echo /usr/lib64/R/library/tools/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tools/html + bf=html + echo /usr/lib64/R/library/tools/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/tools/libs + bf=libs + echo '%dir /usr/lib64/R/library/tools/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/tools/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations + module=translations + echo '%dir /usr/lib64/R/library/translations' + '[' translations '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/translations/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations/da + bf=da + echo '%lang(da) /usr/lib64/R/library/translations/da' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations/de + bf=de + echo '%lang(de) /usr/lib64/R/library/translations/de' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations/en + bf=en + echo /usr/lib64/R/library/translations/en + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations/en@quot + bf=en@quot + echo /usr/lib64/R/library/translations/en@quot + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations/en_GB + bf=en_GB + echo '%lang(en_GB) /usr/lib64/R/library/translations/en_GB' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations/es + bf=es + echo '%lang(es) /usr/lib64/R/library/translations/es' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations/fa + bf=fa + echo '%lang(fa) /usr/lib64/R/library/translations/fa' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations/fr + bf=fr + echo '%lang(fr) /usr/lib64/R/library/translations/fr' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations/it + bf=it + echo '%lang(it) /usr/lib64/R/library/translations/it' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations/ja + bf=ja + echo '%lang(ja) /usr/lib64/R/library/translations/ja' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations/ko + bf=ko + echo '%lang(ko) /usr/lib64/R/library/translations/ko' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations/nn + bf=nn + echo '%lang(nn) /usr/lib64/R/library/translations/nn' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations/pl + bf=pl + echo '%lang(pl) /usr/lib64/R/library/translations/pl' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations/pt_BR + bf=pt_BR + echo '%lang(pt_BR) /usr/lib64/R/library/translations/pt_BR' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations/ru + bf=ru + echo '%lang(ru) /usr/lib64/R/library/translations/ru' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations/tr + bf=tr + echo '%lang(tr) /usr/lib64/R/library/translations/tr' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations/zh_CN + bf=zh_CN + echo '%lang(zh_CN) /usr/lib64/R/library/translations/zh_CN' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/translations/zh_TW + bf=zh_TW + echo '%lang(zh_TW) /usr/lib64/R/library/translations/zh_TW' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/utils + module=utils + echo '%dir /usr/lib64/R/library/utils' + '[' utils '=' translations ']' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/utils/DESCRIPTION + bf=DESCRIPTION + echo /usr/lib64/R/library/utils/DESCRIPTION + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/utils/INDEX + bf=INDEX + echo /usr/lib64/R/library/utils/INDEX + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/utils/Meta + bf=Meta + echo /usr/lib64/R/library/utils/Meta + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/utils/NAMESPACE + bf=NAMESPACE + echo /usr/lib64/R/library/utils/NAMESPACE + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/utils/R + bf=R + echo /usr/lib64/R/library/utils/R + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/utils/Sweave + bf=Sweave + echo /usr/lib64/R/library/utils/Sweave + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/utils/doc + bf=doc + echo /usr/lib64/R/library/utils/doc + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/utils/help + bf=help + echo /usr/lib64/R/library/utils/help + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/utils/html + bf=html + echo /usr/lib64/R/library/utils/html + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/utils/iconvlist + bf=iconvlist + echo /usr/lib64/R/library/utils/iconvlist + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/utils/libs + bf=libs + echo '%dir /usr/lib64/R/library/utils/libs' + echo '%attr(755,root,root) /usr/lib64/R/library/utils/libs/*.so' + basename /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/library/utils/misc + bf=misc + echo /usr/lib64/R/library/utils/misc + /bin/rm '--interactive=never' /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/doc/COPYING + /bin/rm '--interactive=never' /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/doc/AUTHORS /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/doc/COPYRIGHTS /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/doc/FAQ /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/doc/NEWS.rds /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/doc/THANKS + /bin/rm '--interactive=never' /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/lib64/R/doc/NEWS.pdf + __spec_install_post_strip + set +x Stripping 32 ELF executables...DONE + __spec_install_post_chrpath + set +x Remove RPATH/RUNPATH from 32 executable binaries and shared object files. + __spec_install_post_check_so + set +x Searching for shared objects with unresolved symbols... DONE + __spec_install_post_check_tmpfiles + set +x Checking /var/run <-> tmpfiles.d completeness... DONE + __spec_install_post_compress_docs + set +x Compress man pages: /usr/share/man + __spec_install_post_compress_modules + set +x + __spec_install_post_py_hardlink + set +x Processing files: R-3.5.2-1 Executing(%doc): env -i TMP=/home/users/builder/tmp HOME=/home/users/builder PATH=/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/users/builder/bin TMPDIR=/tmp/B.61K3e5/BUILD/tmp /bin/sh -e /tmp/B.61K3e5/BUILD/tmp/rpm-tmp.66540 + umask 022 + cd /tmp/B.61K3e5/BUILD + cd R-3.5.2 + DOCDIR=/tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/share/doc/R-3.5.2 + export DOCDIR + rm -rf /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/share/doc/R-3.5.2 + /bin/mkdir -p /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/share/doc/R-3.5.2 + /usr/lib/rpm/compress-doc Compressing documentation in /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/share/doc/R-3.5.2... Documentation compressed. + cp -pr README doc/AUTHORS doc/COPYRIGHTS doc/FAQ doc/NEWS doc/NEWS.0 doc/NEWS.1 doc/NEWS.2 doc/RESOURCES doc/THANKS /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/share/doc/R-3.5.2 + /usr/lib/rpm/compress-doc Compressing documentation in /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder/usr/share/doc/R-3.5.2... ./THANKS ./README ./NEWS.2 ./NEWS.0 ./RESOURCES ./FAQ ./NEWS.1 ./COPYRIGHTS ./NEWS ./AUTHORS Documentation compressed. + exit 0 Provides: KernSmooth.so()(64bit) MASS.so()(64bit) Matrix.so()(64bit) R_X11.so()(64bit) R_de.so()(64bit) cairo.so()(64bit) class.so()(64bit) cluster.so()(64bit) foreign.so()(64bit) grDevices.so()(64bit) graphics.so()(64bit) grid.so()(64bit) internet.so()(64bit) lapack.so()(64bit) lattice.so()(64bit) libR.so()(64bit) methods.so()(64bit) mgcv.so()(64bit) nlme.so()(64bit) nnet.so()(64bit) parallel.so()(64bit) pkgconfig(libR) = 3.5.2 rpart.so()(64bit) spatial.so()(64bit) splines.so()(64bit) stats.so()(64bit) survival.so()(64bit) tcltk.so()(64bit) tools.so()(64bit) utils.so()(64bit) Requires(interp): /sbin/ldconfig /sbin/ldconfig Requires(rpmlib): rpmlib(VersionedDependencies) <= 3.0.3-1 Requires(post): /sbin/ldconfig perl-base textutils Requires(postun): /sbin/ldconfig Requires: /bin/sh ld-linux-x86-64.so.2()(64bit) ld-linux-x86-64.so.2(GLIBC_2.2.5)(64bit) libR.so()(64bit) libX11.so.6()(64bit) libXmu.so.6()(64bit) libXt.so.6()(64bit) libblas.so.3()(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.11)(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.15)(64bit) libc.so.6(GLIBC_2.16)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.27)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.6)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_2.8)(64bit) libcairo.so.2()(64bit) libcurl.so.4()(64bit) libdl.so.2()(64bit) libdl.so.2(GLIBC_2.2.5)(64bit) libgobject-2.0.so.0()(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libicui18n.so.63()(64bit) libicuuc.so.63()(64bit) libjpeg.so.8()(64bit) libjpeg.so.8(LIBJPEG_8.0)(64bit) liblapack.so.3()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.23)(64bit) libpango-1.0.so.0()(64bit) libpangocairo-1.0.so.0()(64bit) libpcre.so.1()(64bit) libpng16.so.16()(64bit) libpng16.so.16(PNG16_0)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.2.5)(64bit) libreadline.so.7()(64bit) librt.so.1()(64bit) librt.so.1(GLIBC_2.2.5)(64bit) libtcl8.6.so.0()(64bit) libtiff.so.5()(64bit) libtk8.6.so.0()(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Obsoletes: R-base R-contrib R-recommended Processing files: R-java-tools-3.5.2-1 Checking for unpackaged file(s): /usr/lib/rpm/check-files /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder warning: Installed (but unpackaged) file(s) found: /usr/lib64/R/doc/html/Rlogo.pdf /usr/lib64/R/doc/html/Rlogo.svg Wrote: /tmp/B.61K3e5/RPMS/R-3.5.2-1.x86_64.rpm Wrote: /tmp/B.61K3e5/RPMS/R-java-tools-3.5.2-1.x86_64.rpm Executing(%clean): env -i TMP=/home/users/builder/tmp HOME=/home/users/builder PATH=/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/users/builder/bin TMPDIR=/tmp/B.61K3e5/BUILD/tmp /bin/sh -e /tmp/B.61K3e5/BUILD/tmp/rpm-tmp.90509 + umask 022 + cd /tmp/B.61K3e5/BUILD + cd R-3.5.2 + /bin/rm '--interactive=never' -rf /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder + rm -rf /tmp/B.61K3e5/BUILD/tmp/R-3.5.2-root-builder ended at: Mon Jan 21 12:39:19 2019, done in 0:08:39.920275 + chmod -R u+rwX /tmp/B.61K3e5/BUILD + rm -rf /tmp/B.61K3e5/tmp /tmp/B.61K3e5/BUILD copy rpm files to cache_dir: /spools/ready Creating pndir index of /spools/ready/ (type=dir)... Loading [pndir]previous /spools/ready/packages.ndir.gz... Loading [dir]/spools/ready/... Writing /spools/ready/packages.ndir.gz... Begin-TLD-Builder-Info upgrading packages End-TLD-Builder-Info + rm -rf /tmp/B.61K3e5 Begin-TLD-Builder-Info Build-Time: user:539.75s sys:22.78s real:523.53s (faults io:526 non-io:15750764) Files queued for ftp: 8962 R-java-tools-3.5.2-1.x86_64.rpm 39640549 R-3.5.2-1.x86_64.rpm 106 R-3.5.2-1.src.rpm.uploadinfo warning: Installed (but unpackaged) file(s) found: /usr/lib64/R/doc/html/Rlogo.pdf /usr/lib64/R/doc/html/Rlogo.svg End-TLD-Builder-Info