dpkg-buildpackage -rfakeroot -us -uc -ui -B dpkg-buildpackage: warning: using a gain-root-command while being root dpkg-buildpackage: info: source package r-base dpkg-buildpackage: info: source version 3.5.2-1~stretchcran.0 dpkg-buildpackage: info: source distribution stretch-cran dpkg-buildpackage: info: source changed by Johannes Ranke dpkg-source --before-build r-base-3.5.2 dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean *** clean *** dh_testdir dh_testroot rm -f configure-stamp \ build-stamp build-indep-stamp build-arch-stamp \ make-stamp make-arch-stamp make-indep-stamp \ install-indep-stamp install-arch-stamp \ check-stamp [ ! -f Makefile ] || /usr/bin/make distclean rm -f `find . -name "*~"` rm -rf debian/tmp debian/files* core debian/substvars rm -f doc/html/function.html doc/html/packages.html rm -f modules/*.so src/unix/Rscript dh_clean debian/rules build-arch *** configure *** #automake #autoconf dh_testdir R_SHELL=/bin/bash \ mkdir_p="/bin/mkdir -p" \ MKDIR_P="/bin/mkdir -p" \ R_TEXI2DVICMD=emulation \ R_PAPERSIZE=letter \ R_BROWSER=xdg-open \ R_BZIPCMD=/bin/bzip2 \ R_GZIPCMD="/bin/gzip -n" \ PAGER=/usr/bin/pager \ PERL=/usr/bin/perl \ JAVA_HOME=/usr/lib/jvm/default-java \ R_UNZIPCMD=/usr/bin/unzip \ R_ZIPCMD=/usr/bin/zip \ R_PRINTCMD=/usr/bin/lpr \ TAR=/bin/tar \ LIBnn=lib \ AWK=/usr/bin/awk \ DD=/bin/dd \ GREP=/bin/grep \ FGREP="/bin/grep -F" \ EGREP="/bin/grep -E" \ SED=/bin/sed \ GETWD="/bin/pwd" \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ FC=gfortran \ CFLAGS="-g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ CXXFLAGS="-g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ FFLAGS="-g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong" \ FCFLAGS="-g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong" \ CPPFLAGS= \ LDFLAGS="-Wl,-z,relro" \ FLIBS= \ rsharedir=/usr/share/R/share \ rincludedir=/usr/share/R/include \ rdocdir=/usr/share/R/doc \ ./configure --prefix=/usr \ --with-cairo \ --with-jpeglib \ --with-readline \ --with-tcltk \ --with-system-bzlib \ --with-system-pcre \ --with-system-zlib \ --mandir=/usr/share/man \ --infodir=/usr/share/info \ --datadir=/usr/share/R/share \ --includedir=/usr/share/R/include \ --with-blas \ --with-lapack \ --enable-R-profiling \ --enable-R-shlib \ --enable-memory-profiling \ --without-recommended-packages \ --build arm-linux-gnueabihf configure: WARNING: unrecognized options: --with-system-bzlib, --with-system-pcre, --with-system-zlib checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf loading site script './config.site' loading build-specific script './config.site' checking for pwd... /bin/pwd checking whether builddir is srcdir... yes 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 /usr/bin/pager... /usr/bin/pager checking for /bin/tar... /bin/tar checking for tex... /usr/bin/tex checking for pdftex... /usr/bin/pdftex checking for pdflatex... /usr/bin/pdflatex checking for makeindex... /usr/bin/makeindex 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... found zi4.sty checking for unzip... /usr/bin/unzip checking for zip... /usr/bin/zip checking for gzip... /bin/gzip -n checking for bzip2... /bin/bzip2 using default browser ... xdg-open checking for acroread... no checking for 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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... gcc -std=gnu99 -E defining F77 to be 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 g++ accepts -g... yes checking whether g++ -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g can compile C++ code... yes checking how to run the C++ preprocessor... g++ -E checking whether __attribute__((visibility())) is supported... yes checking whether gcc -std=gnu99 accepts -fvisibility... yes checking whether g++ accepts -fvisibility... yes checking whether gfortran accepts -fvisibility... yes checking for gcc... gcc checking whether we are using the GNU Objective C compiler... no checking whether gcc accepts -g... no checking for Objective C++ compiler... trying some possibilities checking whether g++ can compile ObjC++... no checking whether can compile ObjC++... no no working ObjC++ compiler found checking how to print strings... printf checking for a sed that does not truncate output... (cached) /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc -std=gnu99... /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 arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking for gawk... /usr/bin/awk checking command to parse /usr/bin/nm -B output from gcc -std=gnu99 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 mt... mt checking if mt is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes checking if gcc -std=gnu99 static flag -static works... yes checking if gcc -std=gnu99 supports -c -o file.o... yes checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes checking whether the gcc -std=gnu99 linker (/usr/bin/ld) 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... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) 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... yes 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) 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 gcc -std=gnu99 option to accept ISO C99... none needed checking for gcc -std=gnu99 option to accept ISO Standard C... (cached) none needed checking for inline... inline checking size of int... 4 checking size of long... 4 checking size of long long... 8 checking size of double... 8 checking size of size_t... 4 checking size of long double... 8 checking whether we can compute C Make dependencies... yes, using $(CC) -MM checking whether gcc -std=gnu99 supports -c -o FILE.lo... yes checking for gcc -std=gnu99 option to support OpenMP... -fopenmp checking how to get verbose linking output from gfortran... -v checking for Fortran 77 libraries of gfortran... -L/usr/lib/gcc/arm-linux-gnueabihf/6 -L/usr/lib/gcc/arm-linux-gnueabihf/6/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/6/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lgfortran -lm checking how to get verbose linking output from gcc -std=gnu99... -v checking for C libraries of gcc -std=gnu99... -L/usr/lib/gcc/arm-linux-gnueabihf/6 -L/usr/lib/gcc/arm-linux-gnueabihf/6/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/6/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -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 gcc -std=gnu99 agree on int and double... yes checking whether gfortran and gcc -std=gnu99 agree on double complex... yes checking for gfortran option to support OpenMP... -fopenmp checking whether g++ accepts -M for generating dependencies... yes checking for g++ option to support OpenMP... -fopenmp checking whether we can compute ObjC Make dependencies... no ./configure: line 27539: ::: command not found checking for xmkmf... no checking whether g++ supports C++98 features with -std=gnu++98... yes checking whether g++ supports C++11 features with -std=gnu++11... yes checking whether g++ supports C++14 features with -std=gnu++14... yes checking whether g++ supports C++17 features with -std=gnu++17... no checking whether g++ supports C++17 features with -std=gnu++1z... no checking whether g++ supports C++17 features with -std=c++17... no checking whether g++ supports C++17 features with -std=sun17... no checking whether g++ supports C++17 features with -std=c++1z... no checking whether g++ supports C++17 features with -std=sun1z... no configure: No compiler with C++17 support was found 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... yes 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 whether mktime sets errno... no checking whether mktime works correctly outside 1902-2037... no 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 , headers 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... no checking X11/Xmu/Atoms.h presence... no checking for X11/Xmu/Atoms.h... no checking whether pkg-config knows about cairo and pango... yes checking whether cairo including pango is >= 1.2 and works... yes checking for tclConfig.sh... no checking for tclConfig.sh in library (sub)directories... /usr/lib/tcl8.6/tclConfig.sh checking for tkConfig.sh... no checking for tkConfig.sh in library (sub)directories... /usr/lib/tk8.6/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 for pcre2-config... no checking for curl-config... /usr/bin/curl-config checking libcurl version ... 7.52.1 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... 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(cached) yes checking whether the gfortran linker (/usr/bin/ld) 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 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 ranlib... (cached) 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... 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(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/bash 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 configure: WARNING: unrecognized options: --with-system-bzlib, --with-system-pcre, --with-system-zlib R is now configured for arm-unknown-linux-gnueabihf Source directory: . Installation directory: /usr C compiler: gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g Fortran 77 compiler: gfortran -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong Default C++ compiler: g++ -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g C++98 compiler: g++ -std=gnu++98 -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g C++11 compiler: g++ -std=gnu++11 -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g C++14 compiler: g++ -std=gnu++14 -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g C++17 compiler: Fortran 90/95 compiler: gfortran -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong Obj-C compiler: 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, memory profiling Capabilities skipped: Options not enabled: shared BLAS Recommended packages: no touch configure-stamp *** make-arch *** /usr/bin/make CFLAGS="-g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ CXXFLAGS="-g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \ FFLAGS="-g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong" \ FCFLAGS="-g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong" \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ LDFLAGS="-Wl,-z,relro" \ PKG_BUILT_STAMP="""" \ R_GZIPCMD="/bin/gzip -n" \ R make[1]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/m4' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/tools' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/etc' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/etc' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/share' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/share' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/scripts' creating src/scripts/R.fe make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/scripts' mkdir -p -- ../../bin make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/scripts' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/scripts' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include' mkdir -p -- ../../include make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include/R_ext' mkdir -p -- ../../../include/R_ext make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include/R_ext' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' making regcomp.d from regcomp.c making regerror.d from regerror.c making regexec.d from regexec.c making tre-ast.d from tre-ast.c making tre-compile.d from tre-compile.c making tre-match-approx.d from tre-match-approx.c making tre-match-backtrack.d from tre-match-backtrack.c making tre-match-parallel.d from tre-match-parallel.c making tre-mem.d from tre-mem.c making tre-parse.d from tre-parse.c making tre-stack.d from tre-stack.c making xmalloc.d from xmalloc.c make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c regcomp.c -o regcomp.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c regerror.c -o regerror.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c regexec.c -o regexec.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-ast.c -o tre-ast.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-compile.c -o tre-compile.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-mem.c -o tre-mem.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-parse.c -o tre-parse.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c tre-stack.c -o tre-stack.o gcc -std=gnu99 -I. -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c 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[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' making integrate.d from integrate.c making interv.d from interv.c making maxcol.d from maxcol.c making optim.d from optim.c making pretty.d from pretty.c making uncmin.d from uncmin.c make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c integrate.c -o integrate.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c interv.c -o interv.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c maxcol.c -o maxcol.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c optim.c -o optim.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pretty.c -o pretty.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c uncmin.c -o uncmin.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c dchdc.f -o dchdc.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c dpbfa.f -o dpbfa.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c dpbsl.f -o dpbsl.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c dpoco.f -o dpoco.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c dpodi.f -o dpodi.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c dpofa.f -o dpofa.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c dposl.f -o dposl.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c dqrdc.f -o dqrdc.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c dqrdc2.f -o dqrdc2.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c dqrls.f -o dqrls.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c dqrsl.f -o dqrsl.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c dqrutl.f -o dqrutl.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c dsvdc.f -o dsvdc.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c dtrco.f -o dtrco.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c dtrsl.f -o dtrsl.o 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[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' making mlutils.d from mlutils.c making d1mach.d from d1mach.c making i1mach.d from i1mach.c making fmax2.d from fmax2.c making fmin2.d from fmin2.c making fprec.d from fprec.c making fround.d from fround.c making ftrunc.d from ftrunc.c making sign.d from sign.c making fsign.d from fsign.c making imax2.d from imax2.c making imin2.d from imin2.c making chebyshev.d from chebyshev.c making log1p.d from log1p.c making lgammacor.d from lgammacor.c making gammalims.d from gammalims.c making stirlerr.d from stirlerr.c making bd0.d from bd0.c making gamma.d from gamma.c making lgamma.d from lgamma.c making gamma_cody.d from gamma_cody.c making beta.d from beta.c making lbeta.d from lbeta.c making polygamma.d from polygamma.c making cospi.d from cospi.c making bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_k.d from bessel_k.c making bessel_y.d from bessel_y.c making choose.d from choose.c making snorm.d from snorm.c making sexp.d from sexp.c making dgamma.d from dgamma.c making pgamma.d from pgamma.c making qgamma.d from qgamma.c making rgamma.d from rgamma.c making dbeta.d from dbeta.c making pbeta.d from pbeta.c making qbeta.d from qbeta.c making rbeta.d from rbeta.c making dunif.d from dunif.c making punif.d from punif.c making qunif.d from qunif.c making runif.d from runif.c making dnorm.d from dnorm.c making pnorm.d from pnorm.c making qnorm.d from qnorm.c making rnorm.d from rnorm.c making dlnorm.d from dlnorm.c making plnorm.d from plnorm.c making qlnorm.d from qlnorm.c making rlnorm.d from rlnorm.c making df.d from df.c making pf.d from pf.c making qf.d from qf.c making rf.d from rf.c making dnf.d from dnf.c making dt.d from dt.c making pt.d from pt.c making qt.d from qt.c making rt.d from rt.c making dnt.d from dnt.c making dchisq.d from dchisq.c making pchisq.d from pchisq.c making qchisq.d from qchisq.c making rchisq.d from rchisq.c making rnchisq.d from rnchisq.c making dbinom.d from dbinom.c making pbinom.d from pbinom.c making qbinom.d from qbinom.c making rbinom.d from rbinom.c making rmultinom.d from rmultinom.c making dcauchy.d from dcauchy.c making pcauchy.d from pcauchy.c making qcauchy.d from qcauchy.c making rcauchy.d from rcauchy.c making dexp.d from dexp.c making pexp.d from pexp.c making qexp.d from qexp.c making rexp.d from rexp.c making dgeom.d from dgeom.c making pgeom.d from pgeom.c making qgeom.d from qgeom.c making rgeom.d from rgeom.c making dhyper.d from dhyper.c making phyper.d from phyper.c making qhyper.d from qhyper.c making rhyper.d from rhyper.c making dnbinom.d from dnbinom.c making pnbinom.d from pnbinom.c making qnbinom.d from qnbinom.c making rnbinom.d from rnbinom.c making dpois.d from dpois.c making ppois.d from ppois.c making qpois.d from qpois.c making rpois.d from rpois.c making dweibull.d from dweibull.c making pweibull.d from pweibull.c making qweibull.d from qweibull.c making rweibull.d from rweibull.c making dlogis.d from dlogis.c making plogis.d from plogis.c making qlogis.d from qlogis.c making rlogis.d from rlogis.c making dnchisq.d from dnchisq.c making pnchisq.d from pnchisq.c making qnchisq.d from qnchisq.c making dnbeta.d from dnbeta.c making pnbeta.d from pnbeta.c making qnbeta.d from qnbeta.c making pnf.d from pnf.c making pnt.d from pnt.c making qnf.d from qnf.c making qnt.d from qnt.c making ptukey.d from ptukey.c making qtukey.d from qtukey.c making toms708.d from toms708.c making wilcox.d from wilcox.c making signrank.d from signrank.c make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mlutils.c -o mlutils.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c d1mach.c -o d1mach.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c i1mach.c -o i1mach.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fmax2.c -o fmax2.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fmin2.c -o fmin2.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fprec.c -o fprec.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fround.c -o fround.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ftrunc.c -o ftrunc.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sign.c -o sign.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fsign.c -o fsign.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c imax2.c -o imax2.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c imin2.c -o imin2.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chebyshev.c -o chebyshev.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c log1p.c -o log1p.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lgammacor.c -o lgammacor.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gammalims.c -o gammalims.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stirlerr.c -o stirlerr.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bd0.c -o bd0.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gamma.c -o gamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lgamma.c -o lgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gamma_cody.c -o gamma_cody.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c beta.c -o beta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lbeta.c -o lbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c polygamma.c -o polygamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cospi.c -o cospi.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_i.c -o bessel_i.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_j.c -o bessel_j.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_k.c -o bessel_k.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bessel_y.c -o bessel_y.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c choose.c -o choose.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c snorm.c -o snorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sexp.c -o sexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dgamma.c -o dgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pgamma.c -o pgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qgamma.c -o qgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rgamma.c -o rgamma.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dbeta.c -o dbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pbeta.c -o pbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qbeta.c -o qbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rbeta.c -o rbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dunif.c -o dunif.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c punif.c -o punif.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qunif.c -o qunif.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c runif.c -o runif.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnorm.c -o dnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnorm.c -o pnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnorm.c -o qnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rnorm.c -o rnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dlnorm.c -o dlnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plnorm.c -o plnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qlnorm.c -o qlnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlnorm.c -o rlnorm.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c df.c -o df.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pf.c -o pf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qf.c -o qf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rf.c -o rf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnf.c -o dnf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dt.c -o dt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pt.c -o pt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qt.c -o qt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rt.c -o rt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnt.c -o dnt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dchisq.c -o dchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pchisq.c -o pchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qchisq.c -o qchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rchisq.c -o rchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rnchisq.c -o rnchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dbinom.c -o dbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pbinom.c -o pbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qbinom.c -o qbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rbinom.c -o rbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rmultinom.c -o rmultinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dcauchy.c -o dcauchy.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pcauchy.c -o pcauchy.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qcauchy.c -o qcauchy.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rcauchy.c -o rcauchy.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dexp.c -o dexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pexp.c -o pexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qexp.c -o qexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rexp.c -o rexp.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dgeom.c -o dgeom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pgeom.c -o pgeom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qgeom.c -o qgeom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rgeom.c -o rgeom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dhyper.c -o dhyper.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c phyper.c -o phyper.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qhyper.c -o qhyper.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rhyper.c -o rhyper.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnbinom.c -o dnbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnbinom.c -o pnbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnbinom.c -o qnbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rnbinom.c -o rnbinom.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dpois.c -o dpois.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ppois.c -o ppois.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qpois.c -o qpois.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rpois.c -o rpois.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic 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-D_FORTIFY_SOURCE=2 -g -c rweibull.c -o rweibull.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dlogis.c -o dlogis.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plogis.c -o plogis.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qlogis.c -o qlogis.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rlogis.c -o rlogis.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnchisq.c -o dnchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnchisq.c -o pnchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnchisq.c -o qnchisq.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dnbeta.c -o dnbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnbeta.c -o pnbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnbeta.c -o qnbeta.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnf.c -o pnf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pnt.c -o pnt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnf.c -o qnf.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qnt.c -o qnt.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ptukey.c -o ptukey.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qtukey.c -o qtukey.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c toms708.c -o toms708.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c wilcox.c -o wilcox.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c 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[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' config.status: creating src/unix/Makefile making Rembedded.d from Rembedded.c making dynload.d from dynload.c making system.d from system.c making sys-unix.d from sys-unix.c making sys-std.d from sys-std.c making X11.d from X11.c make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rembedded.c -o Rembedded.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dynload.c -o dynload.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c system.c -o system.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sys-unix.c -o sys-unix.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sys-std.c -o sys-std.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c 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[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-z,relro -DR_HOME='"/root/git/r-backports/stretch/r-base-3.5.2"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' config.status: creating src/main/Makefile making CommandLineArgs.d from CommandLineArgs.c making Rdynload.d from Rdynload.c making Renviron.d from Renviron.c making RNG.d from RNG.c making agrep.d from agrep.c making altrep.d from altrep.c making apply.d from apply.c making arithmetic.d from arithmetic.c making array.d from array.c making attrib.d from attrib.c making bind.d from bind.c making builtin.d from builtin.c making character.d from character.c making coerce.d from coerce.c making colors.d from colors.c making complex.d from complex.c making connections.d from connections.c making context.d from context.c making cum.d from cum.c making dcf.d from dcf.c making datetime.d from datetime.c making debug.d from debug.c making deparse.d from deparse.c making devices.d from devices.c making dotcode.d from dotcode.c making dounzip.d from dounzip.c making dstruct.d from dstruct.c making duplicate.d from duplicate.c making edit.d from edit.c making engine.d from engine.c making envir.d from envir.c making errors.d from errors.c making eval.d from eval.c making format.d from format.c making gevents.d from gevents.c making gram.d from gram.c making gram-ex.d from gram-ex.c making graphics.d from graphics.c making grep.d from grep.c making identical.d from identical.c making inlined.d from inlined.c making inspect.d from inspect.c making internet.d from internet.c making iosupport.d from iosupport.c making lapack.d from lapack.c making list.d from list.c making localecharset.d from localecharset.c making logic.d from logic.c making main.d from main.c making mapply.d from mapply.c making match.d from match.c making memory.d from memory.c making names.d from names.c making objects.d from objects.c making options.d from options.c making paste.d from paste.c making platform.d from platform.c making plot.d from plot.c making plot3d.d from plot3d.c making plotmath.d from plotmath.c making print.d from print.c making printarray.d from printarray.c making printvector.d from printvector.c making printutils.d from printutils.c making qsort.d from qsort.c making radixsort.d from radixsort.c making random.d from random.c making raw.d from raw.c making registration.d from registration.c making relop.d from relop.c making rlocale.d from rlocale.c making saveload.d from saveload.c making scan.d from scan.c making seq.d from seq.c making serialize.d from serialize.c making sort.d from sort.c making source.d from source.c making split.d from split.c making sprintf.d from sprintf.c making startup.d from startup.c making subassign.d from subassign.c making subscript.d from subscript.c making subset.d from subset.c making summary.d from summary.c making sysutils.d from sysutils.c making times.d from times.c making unique.d from unique.c making util.d from util.c making version.d from version.c making g_alab_her.d from g_alab_her.c making g_cntrlify.d from g_cntrlify.c making g_fontdb.d from g_fontdb.c making g_her_glyph.d from g_her_glyph.c making Rmain.d from Rmain.c making alloca.d from alloca.c making mkdtemp.d from mkdtemp.c making strdup.d from strdup.c making strncasecmp.d from strncasecmp.c make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CommandLineArgs.c -o CommandLineArgs.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rdynload.c -o Rdynload.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Renviron.c -o Renviron.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RNG.c -o RNG.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c agrep.c -o agrep.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c altrep.c -o altrep.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c apply.c -o apply.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c arithmetic.c -o arithmetic.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c array.c -o array.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c attrib.c -o attrib.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bind.c -o bind.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c builtin.c -o builtin.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c character.c -o character.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c coerce.c -o coerce.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c colors.c -o colors.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c complex.c -o complex.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c connections.c -o connections.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c context.c -o context.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cum.c -o cum.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dcf.c -o dcf.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c datetime.c -o datetime.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c debug.c -o debug.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c deparse.c -o deparse.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devices.c -o devices.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dotcode.c -o dotcode.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dounzip.c -o dounzip.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dstruct.c -o dstruct.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c duplicate.c -o duplicate.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c edit.c -o edit.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c engine.c -o engine.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c envir.c -o envir.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c errors.c -o errors.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c eval.c -o eval.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c format.c -o format.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gevents.c -o gevents.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gram.c -o gram.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gram-ex.c -o gram-ex.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c graphics.c -o graphics.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c grep.c -o grep.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c identical.c -o identical.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c inlined.c -o inlined.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c inspect.c -o inspect.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c internet.c -o internet.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c iosupport.c -o iosupport.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lapack.c -o lapack.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c list.c -o list.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c localecharset.c -o localecharset.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic 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-fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plotmath.c -o plotmath.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c print.c -o print.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c printarray.c -o printarray.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c printvector.c -o printvector.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c printutils.c -o printutils.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c qsort.c -o qsort.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 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-fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c saveload.c -o saveload.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c scan.c -o scan.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c seq.c -o seq.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c serialize.c -o serialize.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sort.c -o sort.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c source.c -o source.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c split.c -o split.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sprintf.c -o sprintf.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c startup.c -o startup.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c subassign.c -o subassign.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c subscript.c -o subscript.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c subset.c -o subset.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c summary.c -o summary.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sysutils.c -o sysutils.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c times.c -o times.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unique.c -o unique.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.c -o util.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c version.c -o version.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_alab_her.c -o g_alab_her.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_cntrlify.c -o g_cntrlify.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_fontdb.c -o g_fontdb.o gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c g_her_glyph.c -o g_her_glyph.o gfortran -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c xxxpr.f -o xxxpr.o gcc -std=gnu99 -shared -fopenmp -Wl,-z,relro -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 -lblas -lgfortran -lm -lreadline -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/bin/exec mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/lib make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' gcc -std=gnu99 -I../../src/extra -I. -I../../src/include -I../../src/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rmain.c -o Rmain.o gcc -std=gnu99 -Wl,--export-dynamic -fopenmp -L"../../lib" -Wl,-z,relro -o R.bin Rmain.o -lR make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' making Rhttpd.d from Rhttpd.c making Rsock.d from Rsock.c making internet.d from internet.c making libcurl.d from libcurl.c making nanoftp.d from nanoftp.c making nanohttp.d from nanohttp.c making sock.d from sock.c making sockconn.d from sockconn.c make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c Rsock.c -o Rsock.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c internet.c -o internet.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c libcurl.c -o libcurl.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c nanoftp.c -o nanoftp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c nanohttp.c -o nanohttp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c sock.c -o sock.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fvisibility=hidden -c sockconn.c -o sockconn.o gcc -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o nanoftp.o nanohttp.o sock.o sockconn.o -lcurl -lR make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/modules make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' making Lapack.d from Lapack.c make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Lapack.c -o Lapack.o gcc -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro -o lapack.so Lapack.o -lR -llapack -lblas -lgfortran -lm make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' making devX11.d from devX11.c making rotated.d from rotated.c making rbitmap.d from rbitmap.c make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/arm-linux-gnueabihf -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devX11.c -o devX11.o gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/arm-linux-gnueabihf -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rotated.c -o rotated.o gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/arm-linux-gnueabihf -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rbitmap.c -o rbitmap.o gcc -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro -o R_X11.so devX11.o rotated.o rbitmap.o -ltiff -ljpeg -lpng16 -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lR -lm gcc -std=gnu99 -I/usr/include/libpng16 -I/usr/include/arm-linux-gnueabihf -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dataentry.c -o dataentry.o gcc -std=gnu99 -shared -L"../../../lib" -Wl,-z,relro -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 -lX11 -lXt -lR -lm make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' mkdir -p -- ../../library make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/profile' building system startup profile mkdir -p -- ../../../library/base/R make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/profile' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' building package 'translations' mkdir -p -- ../../../library/translations make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' building package 'base' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' mkdir -p -- ../../../library/base/demo make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' building package 'tools' mkdir -p -- ../../../library/tools make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' mkdir -p -- ../../../library/tools/R make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' making text.d from text.c making init.d from init.c making Rmd5.d from Rmd5.c making md5.d from md5.c making signals.d from signals.c making install.d from install.c making getfmts.d from getfmts.c making http.d from http.c making gramLatex.d from gramLatex.c making gramRd.d from gramRd.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c text.c -o text.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rmd5.c -o Rmd5.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c md5.c -o md5.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c signals.c -o signals.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c install.c -o install.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c getfmts.c -o getfmts.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c http.c -o http.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gramLatex.c -o gramLatex.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gramRd.c -o gramRd.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -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[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' building package 'compiler' mkdir -p -- ../../../library/compiler make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' mkdir -p -- ../../../library/compiler/R make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' byte-compiling package 'compiler' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' byte-compiling package 'base' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' byte-compiling package 'tools' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' building package 'utils' mkdir -p -- ../../../library/utils mkdir -p -- ../../../library/utils/doc make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' mkdir -p -- ../../../library/utils/R mkdir -p -- ../../../library/utils/Sweave mkdir -p -- ../../../library/utils/misc make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' making init.d from init.c making io.d from io.c making size.d from size.c making sock.d from sock.c making stubs.d from stubs.c making utils.d from utils.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io.c -o io.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c size.c -o size.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sock.c -o sock.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stubs.c -o stubs.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o utils.so init.o io.o size.o sock.o stubs.o utils.o -L../../../../lib -lR make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' mkdir -p -- ../../../../library/utils/libs make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' byte-compiling package 'utils' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' building package 'grDevices' mkdir -p -- ../../../library/grDevices make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' mkdir -p -- ../../../library/grDevices/R mkdir -p -- ../../../library/grDevices/afm mkdir -p -- ../../../library/grDevices/enc mkdir -p -- ../../../library/grDevices/icc make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' making axis_scales.d from axis_scales.c making chull.d from chull.c making devices.d from devices.c making init.d from init.c making stubs.d from stubs.c making colors.d from colors.c making devCairo.d from devCairo.c making devPicTeX.d from devPicTeX.c making devPS.d from devPS.c making devQuartz.d from devQuartz.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c axis_scales.c -o axis_scales.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chull.c -o chull.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devices.c -o devices.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stubs.c -o stubs.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c colors.c -o colors.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devCairo.c -o devCairo.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devPicTeX.c -o devPicTeX.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devPS.c -o devPS.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c devQuartz.c -o devQuartz.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -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[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' mkdir -p -- ../../../../library/grDevices/libs make[8]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' making cairoBM.d from cairoBM.c make[9]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[10]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' gcc -std=gnu99 -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I../../../../../src/modules/X11 -DHAVE_CONFIG_H -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cairoBM.c -o cairoBM.o gcc -std=gnu99 -shared -L"../../../../../lib" -Wl,-z,relro -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff -ljpeg -lpng16 -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lpng16 -lz -lcairo -L"../../../../../lib" -lR -lm make[10]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[9]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[8]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' byte-compiling package 'grDevices' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' building package 'graphics' mkdir -p -- ../../../library/graphics make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' mkdir -p -- ../../../library/graphics/R make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' making init.d from init.c making base.d from base.c making graphics.d from graphics.c making par.d from par.c making plot.d from plot.c making plot3d.d from plot3d.c making stem.d from stem.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base.c -o base.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c graphics.c -o graphics.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c par.c -o par.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plot.c -o plot.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plot3d.c -o plot3d.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stem.c -o stem.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' mkdir -p -- ../../../../library/graphics/libs make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' byte-compiling package 'graphics' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' building package 'stats' mkdir -p -- ../../../library/stats make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' mkdir -p -- ../../../library/stats/R make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' making init.d from init.c making kmeans.d from kmeans.c making ansari.d from ansari.c making bandwidths.d from bandwidths.c making chisqsim.d from chisqsim.c making d2x2xk.d from d2x2xk.c making fexact.d from fexact.c making kendall.d from kendall.c making ks.d from ks.c making line.d from line.c making smooth.d from smooth.c making prho.d from prho.c making swilk.d from swilk.c making ksmooth.d from ksmooth.c making loessc.d from loessc.c making monoSpl.d from monoSpl.c making isoreg.d from isoreg.c making Srunmed.d from Srunmed.c making dblcen.d from dblcen.c making distance.d from distance.c making hclust-utils.d from hclust-utils.c making nls.d from nls.c making rWishart.d from rWishart.c making HoltWinters.d from HoltWinters.c making PPsum.d from PPsum.c making arima.d from arima.c making burg.d from burg.c making filter.d from filter.c making mAR.d from mAR.c making pacf.d from pacf.c making starma.d from starma.c making port.d from port.c making family.d from family.c making sbart.d from sbart.c making approx.d from approx.c making loglin.d from loglin.c making lowess.d from lowess.c making massdist.d from massdist.c making splines.d from splines.c making lm.d from lm.c making complete_cases.d from complete_cases.c making cov.d from cov.c making deriv.d from deriv.c making fft.d from fft.c making fourier.d from fourier.c making model.d from model.c making optim.d from optim.c making optimize.d from optimize.c making integrate.d from integrate.c making random.d from random.c making distn.d from distn.c making zeroin.d from zeroin.c making rcont.d from rcont.c making influence.d from influence.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c kmeans.c -o kmeans.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ansari.c -o ansari.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bandwidths.c -o bandwidths.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chisqsim.c -o chisqsim.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c d2x2xk.c -o d2x2xk.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fexact.c -o fexact.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c kendall.c -o kendall.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ks.c -o ks.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c line.c -o line.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c smooth.c -o smooth.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c prho.c -o prho.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c swilk.c -o swilk.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ksmooth.c -o ksmooth.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c loessc.c -o loessc.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c monoSpl.c -o monoSpl.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c isoreg.c -o isoreg.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Srunmed.c -o Srunmed.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dblcen.c -o dblcen.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c distance.c -o distance.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c hclust-utils.c -o hclust-utils.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nls.c -o nls.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rWishart.c -o rWishart.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c HoltWinters.c -o HoltWinters.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PPsum.c -o PPsum.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c arima.c -o arima.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c burg.c -o burg.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c filter.c -o filter.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mAR.c -o mAR.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pacf.c -o pacf.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c starma.c -o starma.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c port.c -o port.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c family.c -o family.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sbart.c -o sbart.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c approx.c -o approx.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c loglin.c -o loglin.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lowess.c -o lowess.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c massdist.c -o massdist.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c splines.c -o splines.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lm.c -o lm.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c complete_cases.c -o complete_cases.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cov.c -o cov.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c deriv.c -o deriv.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fft.c -o fft.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fourier.c -o fourier.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c model.c -o model.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c optim.c -o optim.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c optimize.c -o optimize.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c integrate.c -o integrate.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c random.c -o random.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c distn.c -o distn.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c zeroin.c -o zeroin.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rcont.c -o rcont.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fopenmp -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c influence.c -o influence.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c bsplvd.f -o bsplvd.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c bvalue.f -o bvalue.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c bvalus.f -o bvalus.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c loessf.f -o loessf.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c ppr.f -o ppr.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c qsbart.f -o qsbart.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c sgram.f -o sgram.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c sinerp.f -o sinerp.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c sslvrg.f -o sslvrg.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c stxwx.f -o stxwx.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c hclust.f -o hclust.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c kmns.f -o kmns.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c eureka.f -o eureka.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c stl.f -o stl.o gfortran -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c portsrc.f -o portsrc.o gfortran -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -c lminfl.f -o lminfl.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -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 -L../../../../lib -lR make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' mkdir -p -- ../../../../library/stats/libs make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' byte-compiling package 'stats' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' building package 'datasets' mkdir -p -- ../../../library/datasets make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' mkdir -p -- ../../../library/datasets/data make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' building package 'methods' mkdir -p -- ../../../library/methods make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' mkdir -p -- ../../../library/methods/R make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' making do_substitute_direct.d from do_substitute_direct.c making init.d from init.c making methods_list_dispatch.d from methods_list_dispatch.c making slot.d from slot.c making class_support.d from class_support.c making tests.d from tests.c making utils.d from utils.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c do_substitute_direct.c -o do_substitute_direct.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c methods_list_dispatch.c -o methods_list_dispatch.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c slot.c -o slot.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c class_support.c -o class_support.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tests.c -o tests.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -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[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' mkdir -p -- ../../../../library/methods/libs make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' byte-compiling 'methods' initializing class and method definitions ... done make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' building package 'grid' mkdir -p -- ../../../library/grid mkdir -p -- ../../../library/grid/doc make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' mkdir -p -- ../../../library/grid/R make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' making gpar.d from gpar.c making grid.d from grid.c making just.d from just.c making layout.d from layout.c making matrix.d from matrix.c making register.d from register.c making state.d from state.c making unit.d from unit.c making util.d from util.c making viewport.d from viewport.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gpar.c -o gpar.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c grid.c -o grid.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c just.c -o just.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c layout.c -o layout.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c matrix.c -o matrix.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c register.c -o register.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c state.c -o state.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unit.c -o unit.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.c -o util.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c viewport.c -o viewport.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -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[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' mkdir -p -- ../../../../library/grid/libs make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' byte-compiling package 'grid' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' building package 'splines' mkdir -p -- ../../../library/splines make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' mkdir -p -- ../../../library/splines/R make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' making splines.d from splines.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c splines.c -o splines.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o splines.so splines.o -L../../../../lib -lR make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' mkdir -p -- ../../../../library/splines/libs make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' byte-compiling package 'splines' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' building package 'stats4' mkdir -p -- ../../../library/stats4 make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' mkdir -p -- ../../../library/stats4/R make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' byte-compiling package 'stats4' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' building package 'tcltk' mkdir -p -- ../../../library/tcltk/R make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' mkdir -p -- ../../../library/tcltk/exec make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' making init.d from init.c making tcltk.d from tcltk.c making tcltk_unix.d from tcltk_unix.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include/tcl8.6 -I/usr/include/tcl8.6 -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include/tcl8.6 -I/usr/include/tcl8.6 -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tcltk.c -o tcltk.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include/tcl8.6 -I/usr/include/tcl8.6 -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tcltk_unix.c -o tcltk_unix.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib/arm-linux-gnueabihf -ltcl8.6 -L/usr/lib/arm-linux-gnueabihf -ltk8.6 -lX11 -lXss -lXext -lm -L../../../../lib -lR make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' mkdir -p -- ../../../../library/tcltk/libs make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' byte-compiling package 'tcltk' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' building package 'parallel' mkdir -p -- ../../../library/parallel mkdir -p -- ../../../library/parallel/doc make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' mkdir -p -- ../../../library/parallel/R make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' making init.d from init.c making rngstream.d from rngstream.c making fork.d from fork.c gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rngstream.c -o rngstream.o gcc -std=gnu99 -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fork.c -o fork.o gcc -std=gnu99 -shared -L../../../../lib -Wl,-z,relro -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' mkdir -p -- ../../../../library/parallel/libs make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' byte-compiling package 'parallel' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/tests' you should 'make docs' now ... make[1]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2' (cd src/nmath/standalone; \ /usr/bin/make CFLAGS="-g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ CXXFLAGS="-g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ FFLAGS="-g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -D_REENTRANT" \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ R_GZIPCMD="/bin/gzip -n" \ libRmath_la_LDFLAGS=-Wl,-soname,libRmath.so.1 \ shared static ) make[1]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath/standalone' (cd ../../include; /usr/bin/make Rmath.h) make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include' make[2]: 'Rmath.h' is up to date. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include' Copying source files make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath/standalone' making mlutils.d from mlutils.c making d1mach.d from d1mach.c making i1mach.d from i1mach.c making fmax2.d from fmax2.c making fmin2.d from fmin2.c making fprec.d from fprec.c making fround.d from fround.c making ftrunc.d from ftrunc.c making sign.d from sign.c making fsign.d from fsign.c making imax2.d from imax2.c making imin2.d from imin2.c making chebyshev.d from chebyshev.c making log1p.d from log1p.c making lgammacor.d from lgammacor.c making gammalims.d from gammalims.c making stirlerr.d from stirlerr.c making bd0.d from bd0.c making gamma.d from gamma.c making lgamma.d from lgamma.c making gamma_cody.d from gamma_cody.c making beta.d from beta.c making lbeta.d from lbeta.c making polygamma.d from polygamma.c making cospi.d from cospi.c making bessel_i.d from bessel_i.c making bessel_j.d from bessel_j.c making bessel_k.d from bessel_k.c making bessel_y.d from bessel_y.c making choose.d from choose.c making snorm.d from snorm.c making sexp.d from sexp.c making dgamma.d from dgamma.c making pgamma.d from pgamma.c making qgamma.d from qgamma.c making rgamma.d from rgamma.c making dbeta.d from dbeta.c making pbeta.d from pbeta.c making qbeta.d from qbeta.c making rbeta.d from rbeta.c making dunif.d from dunif.c making punif.d from punif.c making qunif.d from qunif.c making runif.d from runif.c making dnorm.d from dnorm.c making pnorm.d from pnorm.c making qnorm.d from qnorm.c making rnorm.d from rnorm.c making dlnorm.d from dlnorm.c making plnorm.d from plnorm.c making qlnorm.d from qlnorm.c making rlnorm.d from rlnorm.c making df.d from df.c making pf.d from pf.c making qf.d from qf.c making rf.d from rf.c making dnf.d from dnf.c making dt.d from dt.c making pt.d from pt.c making qt.d from qt.c making rt.d from rt.c making dnt.d from dnt.c making dchisq.d from dchisq.c making pchisq.d from pchisq.c making qchisq.d from qchisq.c making rchisq.d from rchisq.c making rnchisq.d from rnchisq.c making dbinom.d from dbinom.c making pbinom.d from pbinom.c making qbinom.d from qbinom.c making rbinom.d from rbinom.c making rmultinom.d from rmultinom.c making dcauchy.d from dcauchy.c making pcauchy.d from pcauchy.c making qcauchy.d from qcauchy.c making rcauchy.d from rcauchy.c making dexp.d from dexp.c making pexp.d from pexp.c making qexp.d from qexp.c making rexp.d from rexp.c making dgeom.d from dgeom.c making pgeom.d from pgeom.c making qgeom.d from qgeom.c making rgeom.d from rgeom.c making dhyper.d from dhyper.c making phyper.d from phyper.c making qhyper.d from qhyper.c making rhyper.d from rhyper.c making dnbinom.d from dnbinom.c making pnbinom.d from pnbinom.c making qnbinom.d from qnbinom.c making rnbinom.d from rnbinom.c making dpois.d from dpois.c making ppois.d from ppois.c making qpois.d from qpois.c making rpois.d from rpois.c making dweibull.d from dweibull.c making pweibull.d from pweibull.c making qweibull.d from qweibull.c making rweibull.d from rweibull.c making dlogis.d from dlogis.c making plogis.d from plogis.c making qlogis.d from qlogis.c making rlogis.d from rlogis.c making dnchisq.d from dnchisq.c making pnchisq.d from pnchisq.c making qnchisq.d from qnchisq.c making dnbeta.d from dnbeta.c making pnbeta.d from pnbeta.c making qnbeta.d from qnbeta.c making pnf.d from pnf.c making pnt.d from pnt.c making qnf.d from qnf.c making qnt.d from qnt.c making ptukey.d from ptukey.c making qtukey.d from qtukey.c making toms708.d from toms708.c making wilcox.d from wilcox.c making signrank.d from signrank.c making std_unif.d from std_unif.c make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath/standalone' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath/standalone' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c mlutils.c -o mlutils.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c d1mach.c -o d1mach.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c i1mach.c -o i1mach.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmax2.c -o fmax2.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmin2.c -o fmin2.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fprec.c -o fprec.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fround.c -o fround.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ftrunc.c -o ftrunc.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sign.c -o sign.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fsign.c -o fsign.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imax2.c -o imax2.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imin2.c -o imin2.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c chebyshev.c -o chebyshev.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c log1p.c -o log1p.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgammacor.c -o lgammacor.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gammalims.c -o gammalims.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c stirlerr.c -o stirlerr.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bd0.c -o bd0.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma.c -o gamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgamma.c -o lgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma_cody.c -o gamma_cody.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c beta.c -o beta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lbeta.c -o lbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c polygamma.c -o polygamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c cospi.c -o cospi.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_i.c -o bessel_i.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_j.c -o bessel_j.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_k.c -o bessel_k.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_y.c -o bessel_y.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c choose.c -o choose.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c snorm.c -o snorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sexp.c -o sexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgamma.c -o dgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgamma.c -o pgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgamma.c -o qgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgamma.c -o rgamma.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbeta.c -o dbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbeta.c -o pbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbeta.c -o qbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbeta.c -o rbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dunif.c -o dunif.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c punif.c -o punif.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qunif.c -o qunif.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c runif.c -o runif.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnorm.c -o dnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnorm.c -o pnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnorm.c -o qnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnorm.c -o rnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlnorm.c -o dlnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plnorm.c -o plnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qlnorm.c -o qlnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rlnorm.c -o rlnorm.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c df.c -o df.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pf.c -o pf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qf.c -o qf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rf.c -o rf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnf.c -o dnf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dt.c -o dt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pt.c -o pt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qt.c -o qt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rt.c -o rt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnt.c -o dnt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dchisq.c -o dchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pchisq.c -o pchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qchisq.c -o qchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rchisq.c -o rchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnchisq.c -o rnchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbinom.c -o dbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbinom.c -o pbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbinom.c -o qbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbinom.c -o rbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rmultinom.c -o rmultinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dcauchy.c -o dcauchy.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pcauchy.c -o pcauchy.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qcauchy.c -o qcauchy.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rcauchy.c -o rcauchy.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dexp.c -o dexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pexp.c -o pexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qexp.c -o qexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rexp.c -o rexp.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgeom.c -o dgeom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgeom.c -o pgeom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgeom.c -o qgeom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgeom.c -o rgeom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dhyper.c -o dhyper.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c phyper.c -o phyper.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qhyper.c -o qhyper.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rhyper.c -o rhyper.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnbinom.c -o dnbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnbinom.c -o pnbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnbinom.c -o qnbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnbinom.c -o rnbinom.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dpois.c -o dpois.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ppois.c -o ppois.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qpois.c -o qpois.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rpois.c -o rpois.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dweibull.c -o dweibull.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pweibull.c -o pweibull.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qweibull.c -o qweibull.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rweibull.c -o rweibull.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlogis.c -o dlogis.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plogis.c -o plogis.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qlogis.c -o qlogis.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rlogis.c -o rlogis.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnchisq.c -o dnchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnchisq.c -o pnchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnchisq.c -o qnchisq.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnbeta.c -o dnbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnbeta.c -o pnbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnbeta.c -o qnbeta.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnf.c -o pnf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnt.c -o pnt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnf.c -o qnf.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnt.c -o qnt.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ptukey.c -o ptukey.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qtukey.c -o qtukey.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c toms708.c -o toms708.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c wilcox.c -o wilcox.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c signrank.c -o signrank.lo gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c std_unif.c -o std_unif.lo gcc -std=gnu99 -shared -fopenmp -Wl,-z,relro -o libRmath.so -Wl,-soname,libRmath.so.1 mlutils.lo d1mach.lo i1mach.lo fmax2.lo fmin2.lo fprec.lo fround.lo ftrunc.lo sign.lo fsign.lo imax2.lo imin2.lo chebyshev.lo log1p.lo lgammacor.lo gammalims.lo stirlerr.lo bd0.lo gamma.lo lgamma.lo gamma_cody.lo beta.lo lbeta.lo polygamma.lo cospi.lo bessel_i.lo bessel_j.lo bessel_k.lo bessel_y.lo choose.lo snorm.lo sexp.lo dgamma.lo pgamma.lo qgamma.lo rgamma.lo dbeta.lo pbeta.lo qbeta.lo rbeta.lo dunif.lo punif.lo qunif.lo runif.lo dnorm.lo pnorm.lo qnorm.lo rnorm.lo dlnorm.lo plnorm.lo qlnorm.lo rlnorm.lo df.lo pf.lo qf.lo rf.lo dnf.lo dt.lo pt.lo qt.lo rt.lo dnt.lo dchisq.lo pchisq.lo qchisq.lo rchisq.lo rnchisq.lo dbinom.lo pbinom.lo qbinom.lo rbinom.lo rmultinom.lo dcauchy.lo pcauchy.lo qcauchy.lo rcauchy.lo dexp.lo pexp.lo qexp.lo rexp.lo dgeom.lo pgeom.lo qgeom.lo rgeom.lo dhyper.lo phyper.lo qhyper.lo rhyper.lo dnbinom.lo pnbinom.lo qnbinom.lo rnbinom.lo dpois.lo ppois.lo qpois.lo rpois.lo dweibull.lo pweibull.lo qweibull.lo rweibull.lo dlogis.lo plogis.lo qlogis.lo rlogis.lo dnchisq.lo pnchisq.lo qnchisq.lo dnbeta.lo pnbeta.lo qnbeta.lo pnf.lo pnt.lo qnf.lo qnt.lo ptukey.lo qtukey.lo toms708.lo wilcox.lo signrank.lo std_unif.lo -lm make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath/standalone' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath/standalone' gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c mlutils.c -o mlutils.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c d1mach.c -o d1mach.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c i1mach.c -o i1mach.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmax2.c -o fmax2.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fmin2.c -o fmin2.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fprec.c -o fprec.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fround.c -o fround.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ftrunc.c -o ftrunc.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sign.c -o sign.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c fsign.c -o fsign.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imax2.c -o imax2.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c imin2.c -o imin2.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c chebyshev.c -o chebyshev.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c log1p.c -o log1p.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgammacor.c -o lgammacor.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gammalims.c -o gammalims.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c stirlerr.c -o stirlerr.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bd0.c -o bd0.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma.c -o gamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lgamma.c -o lgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c gamma_cody.c -o gamma_cody.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c beta.c -o beta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c lbeta.c -o lbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c polygamma.c -o polygamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c cospi.c -o cospi.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_i.c -o bessel_i.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_j.c -o bessel_j.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_k.c -o bessel_k.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c bessel_y.c -o bessel_y.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c choose.c -o choose.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c snorm.c -o snorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c sexp.c -o sexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgamma.c -o dgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgamma.c -o pgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgamma.c -o qgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgamma.c -o rgamma.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbeta.c -o dbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbeta.c -o pbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbeta.c -o qbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbeta.c -o rbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dunif.c -o dunif.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c punif.c -o punif.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qunif.c -o qunif.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c runif.c -o runif.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnorm.c -o dnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnorm.c -o pnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnorm.c -o qnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnorm.c -o rnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlnorm.c -o dlnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plnorm.c -o plnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qlnorm.c -o qlnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rlnorm.c -o rlnorm.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c df.c -o df.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pf.c -o pf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qf.c -o qf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rf.c -o rf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnf.c -o dnf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dt.c -o dt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pt.c -o pt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qt.c -o qt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rt.c -o rt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnt.c -o dnt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dchisq.c -o dchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pchisq.c -o pchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qchisq.c -o qchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rchisq.c -o rchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnchisq.c -o rnchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dbinom.c -o dbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pbinom.c -o pbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qbinom.c -o qbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rbinom.c -o rbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rmultinom.c -o rmultinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dcauchy.c -o dcauchy.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pcauchy.c -o pcauchy.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qcauchy.c -o qcauchy.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rcauchy.c -o rcauchy.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dexp.c -o dexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pexp.c -o pexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qexp.c -o qexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rexp.c -o rexp.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dgeom.c -o dgeom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pgeom.c -o pgeom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qgeom.c -o qgeom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rgeom.c -o rgeom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dhyper.c -o dhyper.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c phyper.c -o phyper.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qhyper.c -o qhyper.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rhyper.c -o rhyper.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnbinom.c -o dnbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnbinom.c -o pnbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnbinom.c -o qnbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rnbinom.c -o rnbinom.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dpois.c -o dpois.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ppois.c -o ppois.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qpois.c -o qpois.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rpois.c -o rpois.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dweibull.c -o dweibull.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pweibull.c -o pweibull.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qweibull.c -o qweibull.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rweibull.c -o rweibull.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dlogis.c -o dlogis.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c plogis.c -o plogis.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qlogis.c -o qlogis.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c rlogis.c -o rlogis.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnchisq.c -o dnchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnchisq.c -o pnchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnchisq.c -o qnchisq.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c dnbeta.c -o dnbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnbeta.c -o pnbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnbeta.c -o qnbeta.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnf.c -o pnf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c pnt.c -o pnt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnf.c -o qnf.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qnt.c -o qnt.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c ptukey.c -o ptukey.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c qtukey.c -o qtukey.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c toms708.c -o toms708.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c wilcox.c -o wilcox.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c signrank.c -o signrank.o gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I./.. -DHAVE_CONFIG_H -DMATHLIB_STANDALONE -fopenmp -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -c std_unif.c -o std_unif.o ar -cr libRmath.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 std_unif.o ranlib libRmath.a make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath/standalone' make[1]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath/standalone' R_GZIPCMD="/bin/gzip -n" \ /usr/bin/make docs R_CMD_BUILD_HELP_OPTS="--txt --example" make[1]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/m4' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/tools' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/etc' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/etc' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/share' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/share' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/scripts' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/scripts' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/scripts' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/scripts' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include/R_ext' make[4]: Nothing to be done for 'R'. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include/R_ext' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[5]: 'Makedeps' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[5]: 'libtre.a' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[4]: 'libappl.a' is up to date. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[4]: 'libnmath.a' is up to date. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-z,relro -DR_HOME='"/root/git/r-backports/stretch/r-base-3.5.2"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' /root/git/r-backports/stretch/r-base-3.5.2/lib/libR.so is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' /root/git/r-backports/stretch/r-base-3.5.2/bin/exec/R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[5]: 'R_X11.so' is up to date. make[5]: 'R_de.so' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' /root/git/r-backports/stretch/r-base-3.5.2/modules/R_X11.so is unchanged /root/git/r-backports/stretch/r-base-3.5.2/modules/R_de.so is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/profile' building system startup profile make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/profile' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' building package 'translations' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' building package 'base' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' building package 'tools' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' building package 'compiler' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' building package 'utils' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[9]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[10]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[9]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[8]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' building package 'graphics' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' building package 'stats' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' building package 'datasets' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' building package 'methods' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' building package 'grid' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' building package 'splines' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' building package 'stats4' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' building package 'parallel' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/tests' you should 'make docs' now ... make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' creating doc/NEWS creating doc/NEWS.pdf make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/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 creating doc/manual/R-intro.html creating doc/manual/R-ints.html creating doc/manual/R-lang.html make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' installing parsed Rd make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 compiler parallel make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' building/updating package metadata ... make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' writing package indices make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[1]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2' /usr/bin/make javaconf make[1]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/m4' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/tools' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/etc' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/etc' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/share' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/share' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/scripts' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/scripts' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/scripts' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/scripts' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include/R_ext' make[4]: Nothing to be done for 'R'. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include/R_ext' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[5]: 'Makedeps' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[5]: 'libtre.a' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[4]: 'libappl.a' is up to date. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[4]: 'libnmath.a' is up to date. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-z,relro -DR_HOME='"/root/git/r-backports/stretch/r-base-3.5.2"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' /root/git/r-backports/stretch/r-base-3.5.2/lib/libR.so is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' /root/git/r-backports/stretch/r-base-3.5.2/bin/exec/R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[5]: 'R_X11.so' is up to date. make[5]: 'R_de.so' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' /root/git/r-backports/stretch/r-base-3.5.2/modules/R_X11.so is unchanged /root/git/r-backports/stretch/r-base-3.5.2/modules/R_de.so is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/profile' building system startup profile make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/profile' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' building package 'translations' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' building package 'base' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' building package 'tools' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' building package 'compiler' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' building package 'utils' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[9]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[10]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[9]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[8]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' building package 'graphics' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' building package 'stats' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' building package 'datasets' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' building package 'methods' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' building package 'grid' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' building package 'splines' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' building package 'stats4' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' building package 'parallel' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/tests' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2' configuring Java ... Java interpreter : /usr/lib/jvm/default-java/jre/bin/java Java version : 1.8.0_181 Java home path : /usr/lib/jvm/default-java Java compiler : /usr/lib/jvm/default-java/bin/javac Java headers gen.: /usr/lib/jvm/default-java/bin/javah Java archive tool: /usr/lib/jvm/default-java/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)/jre/lib/arm/client -ljvm make[3]: Entering directory '/tmp/Rjavareconf.BPZjHJ' gcc -std=gnu99 -I"/root/git/r-backports/stretch/r-base-3.5.2/include" -DNDEBUG -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -fpic -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o gcc -std=gnu99 -shared -L/root/git/r-backports/stretch/r-base-3.5.2/lib -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/default-java/jre/lib/arm/client -ljvm -L/root/git/r-backports/stretch/r-base-3.5.2/lib -lR make[3]: Leaving directory '/tmp/Rjavareconf.BPZjHJ' JAVA_HOME : /usr/lib/jvm/default-java Java library path: $(JAVA_HOME)/jre/lib/arm/client JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux JNI linker flags : -L$(JAVA_HOME)/jre/lib/arm/client -ljvm Updating Java configuration in /root/git/r-backports/stretch/r-base-3.5.2 Done. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2' make[1]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2' touch make-arch-stamp *** make-indep *** /usr/bin/make -k docs make[1]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/m4' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/tools' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' make[3]: Nothing to be done for 'R'. make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/etc' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/etc' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/share' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/share' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/scripts' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/scripts' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/scripts' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/scripts' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include/R_ext' make[4]: Nothing to be done for 'R'. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include/R_ext' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[5]: 'Makedeps' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[5]: 'libtre.a' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[4]: 'libappl.a' is up to date. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[4]: 'libnmath.a' is up to date. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-z,relro -DR_HOME='"/root/git/r-backports/stretch/r-base-3.5.2"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' /root/git/r-backports/stretch/r-base-3.5.2/lib/libR.so is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' /root/git/r-backports/stretch/r-base-3.5.2/bin/exec/R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[5]: 'R_X11.so' is up to date. make[5]: 'R_de.so' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' /root/git/r-backports/stretch/r-base-3.5.2/modules/R_X11.so is unchanged /root/git/r-backports/stretch/r-base-3.5.2/modules/R_de.so is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/profile' building system startup profile make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/profile' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' building package 'translations' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' building package 'base' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' building package 'tools' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' building package 'compiler' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' building package 'utils' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[9]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[10]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[9]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[8]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' building package 'graphics' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' building package 'stats' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' building package 'datasets' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' building package 'methods' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' building package 'grid' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' building package 'splines' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' building package 'stats4' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' building package 'parallel' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/tests' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' installing parsed Rd make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 compiler parallel make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' building/updating package metadata ... make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' writing package indices make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[1]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2' (cd doc/manual && /usr/bin/make html) make[1]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' make[1]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' /usr/bin/make info make[1]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-FAQ.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-admin.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-data.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-exts.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-intro.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-ints.texi /usr/bin/texi2any --enable-encoding -D UseExternalXrefs -I. R-lang.texi make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' make[1]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2' (cd doc/manual && \ /usr/bin/make refman.pdf R-admin.pdf R-data.pdf R-exts.pdf \ R-FAQ.pdf R-intro.pdf R-ints.pdf R-lang.pdf) make[1]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' creating doc/manual/version.tex collecting LaTeX docs for package 'base' ... Converting parsed Rd's to LaTeX ........................................... collecting LaTeX docs for package 'tools' ... Converting parsed Rd's to LaTeX ...... collecting LaTeX docs for package 'utils' ... Converting parsed Rd's to LaTeX ............. collecting LaTeX docs for package 'grDevices' ... Converting parsed Rd's to LaTeX ...... collecting LaTeX docs for package 'graphics' ... Converting parsed Rd's to LaTeX ....... collecting LaTeX docs for package 'stats' ... Converting parsed Rd's to LaTeX .............................. collecting LaTeX docs for package 'datasets' ... Converting parsed Rd's to LaTeX ........ collecting LaTeX docs for package 'methods' ... Converting parsed Rd's to LaTeX ........ collecting LaTeX docs for package 'grid' ... Converting parsed Rd's to LaTeX ......... collecting LaTeX docs for package 'splines' ... Converting parsed Rd's to LaTeX . collecting LaTeX docs for package 'stats4' ... Converting parsed Rd's to LaTeX . collecting LaTeX docs for package 'tcltk' ... Converting parsed Rd's to LaTeX . collecting LaTeX docs for package 'compiler' ... Converting parsed Rd's to LaTeX collecting LaTeX docs for package 'parallel' ... Converting parsed Rd's to LaTeX . PDF/LaTeX documentation: reference index ... This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2017/01/01> patch level 3 Babel <3.9r> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (../../share/texmf/tex/latex/Rd.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def)) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe) (/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) Package hyperref Message: Driver (autodetected): hpdftex. 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(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [1] [2] (./base-pkg.tex Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/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/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 386--389 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) 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/zi4/m/n/10 insertions\T1/ptm/m/n/10 ', [9] [10] [11] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 2671) in paragraph at lines 1147--1150 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1922--1922 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [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] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] Underfull \vbox (badness 10000) has occurred while \output is active [51] [52] [53] [54] [55] [56] [57] 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 [58] [59] [60] [61] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3897--3897 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [62] [63] Underfull \hbox (badness 1057) in paragraph at lines 4005--4008 [][][]\T1/zi4/m/n/10 is.language[][][]() \T1/ptm/m/n/10 is also true for calls (but also for [][]\T1/zi4/m/n/10 symbol[][][]\T1/ptm/m/n/10 s and [][]\T1/zi4/m /n/10 expression[][][]\T1/ptm/m/n/10 s where [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] 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 [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6041--6041 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [95] [96] [97] Underfull \hbox (badness 2096) in paragraph at lines 6229--6242 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [98] [99] [100] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6438--6440 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [101] [102] Underfull \hbox (badness 10000) in paragraph at lines 6580--6583 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [103] [104] Underfull \hbox (badness 1442) in paragraph at lines 6762--6768 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a 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 [105] Underfull \hbox (badness 3568) in paragraph at lines 6824--6831 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [106] [107] Underfull \vbox (badness 10000) has occurred while \output is active [108] Underfull \vbox (badness 10000) has occurred while \output is active [109] [110] Underfull \hbox (badness 1077) in paragraph at lines 7141--7147 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7141--7147 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [111] [112] [113] [114] [115] [116] Underfull \hbox (badness 2096) in paragraph at lines 7482--7486 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [117] [118] Underfull \hbox (badness 3000) in paragraph at lines 7575--7577 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7600--7603 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [119] [120] [121] [122] Underfull \hbox (badness 10000) in paragraph at lines 7855--7865 []\T1/zi4/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 [123] Underfull \hbox (badness 4479) in paragraph at lines 7926--7936 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] Underfull \hbox (badness 1394) in paragraph at lines 9685--9690 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [150] [151] [152] [153] [154] [155] Underfull \hbox (badness 1194) in paragraph at lines 10030--10035 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) 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/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [156] [157] [158] Underfull \hbox (badness 1735) in paragraph at lines 10235--10239 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [159] [160] [161] [162] [163] [164] 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 Underfull \hbox (badness 6396) in paragraph at lines 10672--10680 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for [165] Underfull \hbox (badness 2735) 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/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] 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 [182] [183] [184] [185] [186] [187] [188] [189] [190] Underfull \hbox (badness 2698) in paragraph at lines 12358--12367 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/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-lowed Underfull \hbox (badness 4341) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [191] [192] [193] [194] [195] Underfull \vbox (badness 3803) has occurred while \output is active [196] [197] [198] [199] [200] Underfull \hbox (badness 6236) in paragraph at lines 13017--13020 []\T1/ptm/m/n/10 For \T1/zi4/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 [201] [202] [203] [204] [205] [206] 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 [207] Underfull \hbox (badness 1565) in paragraph at lines 13510--13514 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [208] 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/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with [209] [210] Underfull \hbox (badness 1466) in paragraph at lines 13694--13697 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [211] [212] Underfull \hbox (badness 10000) in paragraph at lines 13813--13817 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13824--13827 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [213] [214] [215] [216] [217] 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, [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 4429) 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/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [230] Underfull \hbox (badness 10000) in paragraph at lines 14968--14970 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 []\T1/zi4/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, so [231] Underfull \hbox (badness 10000) in paragraph at lines 15013--15017 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/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 4156) in paragraph at lines 15013--15017 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [232] [233] [234] [235] [236] [237] [238] [239] [240] Underfull \hbox (badness 2452) in paragraph at lines 15605--15609 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15605--15609 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [241] [242] [243] Underfull \hbox (badness 1092) in paragraph at lines 15778--15783 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [244] [245] [246] Underfull \hbox (badness 6741) in paragraph at lines 16029--16033 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [247] [248] [249] [250] [251] 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 [252] [253] [254] [255] Underfull \vbox (badness 10000) has occurred while \output is active [256] [257] [258] Underfull \hbox (badness 3679) in paragraph at lines 16745--16747 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [259] [260] [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 1478) in paragraph at lines 17310--17313 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [267] [268] [269] Underfull \hbox (badness 10000) in paragraph at lines 17563--17565 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] Underfull \hbox (badness 1442) in paragraph at lines 18154--18156 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [280] Underfull \hbox (badness 2452) in paragraph at lines 18246--18262 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [281] [282] [283] [284] [285] [286] [287] Underfull \hbox (badness 1248) in paragraph at lines 18660--18663 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [288] [289] [290] [291] 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 [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] Underfull \hbox (badness 2469) in paragraph at lines 19935--19940 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 19949--19956 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [309] Underfull \hbox (badness 10000) in paragraph at lines 20023--20027 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20023--20027 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [310] [311] Underfull \hbox (badness 1509) in paragraph at lines 20158--20165 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 20158--20165 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 20174--20179 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] Underfull \hbox (badness 1264) 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-ported: Underfull \hbox (badness 4441) in paragraph at lines 20954--20957 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] Underfull \hbox (badness 10000) in paragraph at lines 21701--21703 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] Underfull \hbox (badness 1077) in paragraph at lines 22736--22742 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [352] [353] [354] Underfull \hbox (badness 1484) in paragraph at lines 22899--22907 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [355] [356] [357] [358] [359] Underfull \hbox (badness 2790) in paragraph at lines 23184--23187 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 23184--23187 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [360] [361] [362] [363] Underfull \hbox (badness 1194) in paragraph at lines 23466--23469 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [364] [365] [366] Underfull \hbox (badness 10000) in paragraph at lines 23672--23678 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23672--23678 \T1/ptm/m/n/10 list, i.e., \T1/zi4/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 [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 10000) in paragraph at lines 24053--24056 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [373] [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 10000) in paragraph at lines 24655--24657 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [382] [383] [384] [385] Underfull \hbox (badness 1199) in paragraph at lines 24899--24905 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24899--24905 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [386] [387] [388] [389] [390] [391] [392] [393] Underfull \hbox (badness 1038) in paragraph at lines 25491--25499 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially [394] Underfull \hbox (badness 1881) in paragraph at lines 25500--25503 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 25519--25521 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [395] Underfull \hbox (badness 10000) in paragraph at lines 25628--25638 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25639--25645 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able [396] Underfull \hbox (badness 1968) in paragraph at lines 25675--25680 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment 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 [397] [398] [399] Underfull \hbox (badness 10000) 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/zi4/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/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 25961--25964 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) 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 [400] Underfull \hbox (badness 10000) in paragraph at lines 26019--26024 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 26025--26036 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 26037--26040 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 3713) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 26047--26059 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). Underfull \hbox (badness 2351) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , 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/zi4/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/zi4/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 Underfull \hbox (badness 1874) in paragraph at lines 26061--26068 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [401] [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [406] [407] [408] [409] [410] Underfull \hbox (badness 1735) in paragraph at lines 26724--26728 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [411] [412] [413] [414] [415] [416] [417] [418] [419] [420] Underfull \hbox (badness 2726) in paragraph at lines 27299--27302 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] [431] [432] [433] Underfull \hbox (badness 1052) in paragraph at lines 28131--28136 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [434] [435] [436] [437] [438] Underfull \vbox (badness 10000) has occurred while \output is active [439] [440] [441] [442] [443] [444] [445] [446] 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 [447] [448] Underfull \hbox (badness 1163) in paragraph at lines 29131--29142 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] Underfull \hbox (badness 10000) in paragraph at lines 30664--30668 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 30664--30668 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [473] Underfull \hbox (badness 6188) in paragraph at lines 30686--30688 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [474] [475] [476] [477] [478] [479] [480] [481] Underfull \hbox (badness 1655) in paragraph at lines 31229--31231 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [493] [494] [495] [496] 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 3333) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/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 [497] [498] [499] Underfull \hbox (badness 2261) in paragraph at lines 32344--32349 []\T1/ptm/m/n/10 If \T1/zi4/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 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 [500] Underfull \hbox (badness 10000) in paragraph at lines 32447--32452 []\T1/ptm/m/n/10 Note that since \T1/zi4/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 [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] Underfull \vbox (badness 3803) has occurred while \output is active [540] [541] [542] [543] [544] [545] [546] [547] Underfull \hbox (badness 1072) in paragraph at lines 35489--35493 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 35494--35498 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', 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/zi4/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/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in [548] Underfull \hbox (badness 3343) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 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 Underfull \hbox (badness 1917) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [549] [550] [551] [552] [553] 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/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35875--35881 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] [581] [582] [583] Underfull \hbox (badness 3333) in paragraph at lines 37745--37750 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [584] [585] [586] [587] [588] [589] Underfull \vbox (badness 10000) has occurred while \output is active [590] [591] [592] [593] [594] Underfull \hbox (badness 1472) in paragraph at lines 38377--38380 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] Underfull \vbox (badness 3803) has occurred while \output is active [608] Underfull \hbox (badness 10000) in paragraph at lines 39283--39287 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/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., [609] [610] [611] [612] Underfull \hbox (badness 10000) in paragraph at lines 39533--39536 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [613] [614] Underfull \hbox (badness 10000) in paragraph at lines 39651--39655 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [615] Underfull \hbox (badness 10000) in paragraph at lines 39713--39717 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [616] [617] [618] [619] [620] [621] [622] [623] [624] Underfull \hbox (badness 4013) in paragraph at lines 40326--40328 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [625] [626] [627] [628] [629] [630] Underfull \vbox (badness 10000) has occurred while \output is active [631] [632] [633] [634] [635] [636] [637] [638] 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 1990) in paragraph at lines 41214--41222 []\T1/zi4/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 4846) 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/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [639] [640] [641] [642] 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. [643] [644] [645] [646] Underfull \hbox (badness 1917) in paragraph at lines 41719--41726 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] 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 [658] [659] Underfull \hbox (badness 2401) in paragraph at lines 42568--42572 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [660] [661] [662] Underfull \hbox (badness 2111) in paragraph at lines 42757--42762 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 7362) in paragraph at lines 42773--42778 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [663] [664] [665] [666] [667] [668] [669] [670] [671] Underfull \hbox (badness 5417) in paragraph at lines 43354--43358 []\T1/zi4/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 [672] Underfull \hbox (badness 10000) in paragraph at lines 43415--43419 []\T1/zi4/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 [673] [674]) (./compiler-pkg.tex Chapter 2. [675] [676] [677] [678]) (./datasets-pkg.tex Chapter 3. [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] 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. [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] Overfull \vbox (19.74611pt too high) has occurred while \output is active [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] Underfull \vbox (badness 10000) has occurred while \output is active [747] [748] [749] [750] Underfull \vbox (badness 10000) has occurred while \output is active [751] [752] [753] [754] [755] [756] Overfull \vbox (18.9959pt too high) has occurred while \output is active [757] [758] [759]) (./grDevices-pkg.tex [760] Chapter 4. [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] 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 [778] [779] [780] [781] Underfull \hbox (badness 1852) in paragraph at lines 1279--1282 []\T1/zi4/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 [782] [783] [784] Underfull \hbox (badness 1490) in paragraph at lines 1485--1490 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [787] [788] [789] [790] Underfull \hbox (badness 1325) in paragraph at lines 1891--1901 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [791] [792] 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 [793] [794] [795] 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 [796] [797] [798] [799] [800] [801] [802] [803] [804] Underfull \hbox (badness 10000) in paragraph at lines 2750--2751 [805] [806] [807] [808] [809] [810] [811] [812] Underfull \hbox (badness 10000) in paragraph at lines 3248--3253 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [813] [814] [815] [816] Underfull \hbox (badness 3302) in paragraph at lines 3514--3517 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827] [828] [829] [830] Underfull \hbox (badness 1067) in paragraph at lines 4355--4362 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [831] [832] [833] Underfull \hbox (badness 1789) in paragraph at lines 4595--4597 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [834] Underfull \hbox (badness 1377) in paragraph at lines 4645--4650 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [835] Underfull \hbox (badness 2671) 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/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4721--4728 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, 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 [836] [837] Underfull \hbox (badness 1377) in paragraph at lines 4850--4855 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb" \T1/ptm/m/n/10 (which is RGB+gray) and [838] 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 [839] [840] Underfull \hbox (badness 2035) in paragraph at lines 5034--5043 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [841] Underfull \hbox (badness 10000) in paragraph at lines 5102--5109 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5102--5109 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [842] [843] [844] Underfull \hbox (badness 1546) in paragraph at lines 5244--5252 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [845] 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 [846] [847] [848] [849] [850] [851] [852] Underfull \hbox (badness 10000) in paragraph at lines 5772--5775 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [853] [854] [855] [856] [857] [858] 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 [859] [860] Underfull \hbox (badness 10000) in paragraph at lines 6267--6269 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [861] [862] [863] [864] Underfull \hbox (badness 3780) in paragraph at lines 6558--6564 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [865] [866] [867] Underfull \hbox (badness 2680) in paragraph at lines 6759--6761 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [868] [869] [870]) (./graphics-pkg.tex Chapter 5. [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] Underfull \hbox (badness 10000) in paragraph at lines 687--694 []\T1/zi4/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/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] Underfull \hbox (badness 4634) in paragraph at lines 1262--1265 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] 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 [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] Underfull \vbox (badness 10000) has occurred while \output is active [931] [932] [933] [934] 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 [935] [936] [937] [938] [939] [940] [941] [942] 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 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 [943] [944] [945] [946] [947] Underfull \hbox (badness 10000) 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/zi4/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4785--4791 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [948] [949] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 <"/root/git/r-backports/stretch/r-base-3.5.2/library/graphics/help/figures/"mai .pdf, id=15783, 289.08pt x 289.08pt> [950 ] Underfull \hbox (badness 10000) in paragraph at lines 4977--4979 <"/root/git/r-backports/stretch/r-base-3.5.2/library/graphics/help/figures/"oma .pdf, id=15796, 259.97125pt x 332.24126pt> Underfull \vbox (badness 10000) has occurred while \output is active [951] [952 ] [953] Underfull \hbox (badness 10000) in paragraph at lines 5167--5169 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [954] Underfull \vbox (badness 3803) has occurred while \output is active [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] <"/root/git/r-backports/stretch/r-base-3.5.2/library/graphics/help/figures/"pch .pdf, id=16241, 361.35pt x 50.1875pt> Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639 [][] [977] [978 ] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] Underfull \hbox (badness 1048) in paragraph at lines 7347--7352 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [989] [990] Underfull \hbox (badness 1102) in paragraph at lines 7463--7466 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] Underfull \hbox (badness 1043) in paragraph at lines 8304--8308 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [1005] [1006] [1007] [1008] [1009] [1010] [1011] 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 [1012]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8805 \HeaderA{units}{Graphical Units}{units} [1013] [1014] [1015] [1016]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1017] [1018] [1019] [1020] [1021] [1022] Underfull \hbox (badness 2680) in paragraph at lines 392--395 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] Underfull \hbox (badness 4279) in paragraph at lines 972--981 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] 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 [1090] [1091] [1092] [1093] 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 [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] 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., [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] 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 [1124] [1125] [1126] [1127]) (./methods-pkg.tex [1128] Chapter 7. [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] Underfull \vbox (badness 3803) has occurred while \output is active [1137] Underfull \vbox (badness 10000) has occurred while \output is active [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] Underfull \hbox (badness 1077) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests [1156] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 1981--1986 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1157] [1158] [1159] Underfull \hbox (badness 1242) 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/zi4/m/n/10 where = [1160] [1161] [1162] [1163] [1164] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1165] [1166] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in [1167] Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1168] [1169] [1170] [1171] [1172] [1173] [1174] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1175] [1176] [1177] [1178] [1179] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments [1180] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1181] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [1182] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3846--3847 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] Underfull \hbox (badness 1436) in paragraph at lines 4443--4446 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4472--4478 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1193] Underfull \hbox (badness 1092) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] Underfull \vbox (badness 10000) has occurred while \output is active [1203] [1204] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1205] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1206] 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 [1207] [1208] [1209] [1210] 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 [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1219] [1220] [1221] [1222] Underfull \vbox (badness 10000) has occurred while \output is active [1223] [1224] [1225] [1226]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1227] [1228] [1229]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate 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} [1230] 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 [1231] [1232] [1233] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] Underfull \vbox (badness 10000) has occurred while \output is active [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274] [1275] 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., [1276] [1277] [1278] [1279]) (./parallel-pkg.tex [1280] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] Underfull \hbox (badness 3386) in paragraph at lines 1339--1342 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1302] [1303] [1304]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319]) (./stats-pkg.tex [1320] Chapter 10. [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] Underfull \hbox (badness 1412) in paragraph at lines 847--849 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] Underfull \hbox (badness 2503) in paragraph at lines 1328--1331 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1342] [1343] [1344] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1345] [1346] [1347] [1348] 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 1546) in paragraph at lines 1773--1777 \T1/zi4/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can han-dle miss-ing [1349] [1350] [1351] [1352] [1353] [1354] [1355] 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 [1356] [1357] [1358] [1359] [1360] 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 [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] 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 [1373] [1374] Underfull \hbox (badness 2503) in paragraph at lines 3390--3393 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] 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 = [1395] [1396] Underfull \hbox (badness 3612) in paragraph at lines 4754--4756 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por t aliased co-ef-fi-cients (see [][]\T1/zi4/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b y de-fault where [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] Underfull \hbox (badness 2556) in paragraph at lines 5270--5273 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) 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/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1405] [1406] [1407] [1408] Underfull \hbox (badness 1142) in paragraph at lines 5527--5539 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1409] [1410] [1411] Underfull \hbox (badness 2503) in paragraph at lines 5679--5683 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 8132) in paragraph at lines 6183--6188 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 7081) in paragraph at lines 6461--6464 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6465--6467 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1425] [1426] [1427] [1428] [1429] Underfull \vbox (badness 3803) has occurred while \output is active [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] Underfull \hbox (badness 10000) in paragraph at lines 7310--7313 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 2626) in paragraph at lines 8954--8957 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1465] Underfull \hbox (badness 2503) in paragraph at lines 9061--9065 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1466] Underfull \hbox (badness 2564) 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/zi4/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 [1467] [1468] [1469] [1470] [1471] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9435--9437 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] 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 [1487] [1488] [1489] [1490] [1491] 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 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10730--10733 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1492] 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: [1493] [1494] [1495] [1496] [1497] [1498] 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 1867) in paragraph at lines 11209--11218 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1499] [1500] [1501] [1502] [1503] Underfull \hbox (badness 10000) 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/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1504] [1505] [1506]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} [1507] [1508] Underfull \hbox (badness 1484) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] 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/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1519] [1520] [1521] [1522] [1523] [1524] 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 [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] 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 [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] 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 [1547] [1548] Underfull \hbox (badness 10000) in paragraph at lines 14271--14275 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14278--14280 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] Underfull \hbox (badness 2503) in paragraph at lines 15346--15350 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] Underfull \hbox (badness 1584) in paragraph at lines 15858--15864 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1 /ptm/m/n/10 and [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] 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 [1601] [1602] Underfull \vbox (badness 10000) has occurred while \output is active [1603] Underfull \vbox (badness 10000) has occurred while \output is active [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] Underfull \hbox (badness 1377) in paragraph at lines 18445--18450 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) 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 1454) in paragraph at lines 18463--18467 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18471--18475 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1617] [1618] [1619] Underfull \vbox (badness 10000) has occurred while \output is active [1620] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18695--18695 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18698--18698 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1621] [1622] [1623] [1624] [1625] [1626] 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 [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] 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 [1636] [1637] [1638] [1639] [1640] Underfull \hbox (badness 5563) in paragraph at lines 19864--19866 []\T1/ptm/m/n/10 logical. If \T1/zi4/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 [1641] [1642] [1643] [1644] [1645] [1646] Underfull \hbox (badness 2503) in paragraph at lines 20242--20245 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1647] Underfull \hbox (badness 10000) in paragraph at lines 20269--20271 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] Underfull \hbox (badness 10000) in paragraph at lines 21342--21348 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] 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 [1688] [1689] [1690] [1691] [1692] [1693] [1694] [1695] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23251--23251 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1696] [1697] [1698] [1699] [1700] 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 [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] 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/zi4/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1710] Underfull \hbox (badness 3690) in paragraph at lines 24139--24143 [][][]\T1/zi4/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 [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718] Underfull \hbox (badness 2165) in paragraph at lines 24616--24621 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1719] [1720] [1721] [1722] 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/zi4/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/zi4/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 Underfull \hbox (badness 1132) in paragraph at lines 24834--24838 \T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o f un-de-ter-mined co-ef-fi-cients, e.g., for [1723] [1724] [1725] [1726] [1727] [1728] [1729] Underfull \hbox (badness 10000) in paragraph at lines 25306--25311 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \vbox (badness 10000) has occurred while \output is active [1746] Underfull \hbox (badness 3514) in paragraph at lines 26362--26367 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1747] [1748] Underfull \hbox (badness 3514) in paragraph at lines 26458--26463 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1749] Underfull \hbox (badness 3514) in paragraph at lines 26544--26549 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1750] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26596--26596 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1751] Underfull \hbox (badness 3514) in paragraph at lines 26632--26638 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1752] [1753] [1754] [1755] Underfull \hbox (badness 3514) in paragraph at lines 26846--26851 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1756] [1757] Underfull \hbox (badness 3514) in paragraph at lines 26933--26938 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1758] Underfull \hbox (badness 3514) in paragraph at lines 26998--27003 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1759] [1760] Underfull \hbox (badness 3514) in paragraph at lines 27092--27097 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1761] Underfull \hbox (badness 6691) in paragraph at lines 27184--27189 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] 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/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] [1780] Underfull \hbox (badness 5431) 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/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1781] [1782] [1783] Underfull \hbox (badness 5431) 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/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1784] [1785] [1786] [1787] [1788] [1789] 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 [1790] [1791] 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/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1792] [1793] 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 [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] Underfull \hbox (badness 10000) in paragraph at lines 30274--30278 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect [1813] [1814] [1815] Underfull \vbox (badness 10000) has occurred while \output is active [1816] [1817] [1818] 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 [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] 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 [1828] Underfull \hbox (badness 2142) in paragraph at lines 31242--31247 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/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 [1829] [1830] [1831] [1832] [1833] [1834] Underfull \hbox (badness 10000) in paragraph at lines 31647--31652 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1835] [1836] [1837]) (./stats4-pkg.tex [1838] Chapter 11. [1839] [1840] [1841] [1842] [1843] [1844]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1845] [1846] [1847] [1848]) (./tcltk-pkg.tex Chapter 12. [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \vbox (badness 10000) has occurred while \output is active [1856] Underfull \vbox (badness 10000) has occurred while \output is active [1857] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] [1868] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/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/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1869]) (./tools-pkg.tex [1870] Chapter 13. [1871] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1872] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/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 [1873] [1874] Underfull \hbox (badness 1308) 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 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1875] [1876] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1877] [1878] [1879] [1880] [1881] [1882] [1883] Underfull \vbox (badness 10000) has occurred while \output is active [1884] [1885] [1886] [1887] 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 [1888] 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- [1889] 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-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1199--1202 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1890] [1891] [1892] 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 [1893] [1894] [1895] Underfull \hbox (badness 2293) in paragraph at lines 1551--1553 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1896] [1897] 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 Underfull \hbox (badness 1082) in paragraph at lines 1696--1698 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1898] [1899] [1900] [1901]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1902] [1903] [1904] [1905] [1906] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2195--2195 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1907] [1908] [1909] 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 [1910] [1911] [1912] [1913] [1914] [1915] [1916] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2829. [1917] [1918] [1919] [1920] Underfull \hbox (badness 1424) in paragraph at lines 3111--3113 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1921] [1922] [1923] [1924] [1925] [1926] [1927] [1928] [1929] [1930] [1931] [1932] 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 , [1933] [1934] Underfull \hbox (badness 10000) in paragraph at lines 3950--3953 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1935] [1936] 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 [1937] [1938] [1939] Underfull \hbox (badness 1838) in paragraph at lines 4257--4263 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4257--4263 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1940] Underfull \hbox (badness 5726) in paragraph at lines 4337--4342 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4337--4342 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1941] [1942] [1943] Underfull \hbox (badness 2197) in paragraph at lines 4486--4496 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4486--4496 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1944] 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 [1945] [1946] [1947]) (./utils-pkg.tex [1948] Chapter 14. [1949] Underfull \hbox (badness 2556) 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/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 10000) in paragraph at lines 620--626 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 620--626 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1958] [1959] Underfull \hbox (badness 5847) in paragraph at lines 753--759 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 753--759 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1960] Underfull \hbox (badness 3861) in paragraph at lines 821--826 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1961] [1962] [1963] Underfull \hbox (badness 1430) in paragraph at lines 992--999 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 992--999 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 992--999 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. 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 [1964] [1965] [1966] Underfull \vbox (badness 10000) has occurred while \output is active [1967] [1968] [1969] [1970] [1971] Underfull \hbox (badness 1371) in paragraph at lines 1482--1484 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1972] [1973] [1974] [1975] [1976] [1977] [1978] Underfull \hbox (badness 2057) in paragraph at lines 1959--1961 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1979] [1980] 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/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1981] 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 [1982] [1983] [1984] [1985] Underfull \hbox (badness 1661) in paragraph at lines 2374--2381 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2390--2393 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1986] [1987] [1988] [1989] [1990] [1991] [1992] Underfull \hbox (badness 10000) in paragraph at lines 2800--2804 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2805--2808 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002] Underfull \hbox (badness 1430) 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/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [2003] 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 [2004] [2005] Underfull \hbox (badness 10000) in paragraph at lines 3686--3688 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow nload.file[][][] \T1/ptm/m/n/10 and [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016]pdf TeX warning (ext4): destination with the same identifier (name{Rfn.format}) 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} [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] Underfull \hbox (badness 1371) in paragraph at lines 5377--5379 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [2033] 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 [2034] [2035] [2036] 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, [2037] 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 [2038] [2039] 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 [2040] 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 [2041] Underfull \hbox (badness 1325) in paragraph at lines 5980--5984 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [2042] 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/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2043] Underfull \hbox (badness 3219) in paragraph at lines 6136--6143 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "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 [2044] [2045] Underfull \hbox (badness 10000) in paragraph at lines 6236--6241 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] Underfull \hbox (badness 10000) in paragraph at lines 7669--7671 []\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 7683--7685 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7691--7696 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] 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 [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] [2091] Underfull \hbox (badness 1097) in paragraph at lines 9118--9121 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2092] Underfull \hbox (badness 3000) in paragraph at lines 9254--9259 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2093] [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] Underfull \hbox (badness 2134) in paragraph at lines 9837--9842 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2102] [2103] [2104] [2105] [2106] [2107] [2108] Underfull \hbox (badness 5077) in paragraph at lines 10262--10266 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/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 2469) in paragraph at lines 10274--10278 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 10274--10278 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2109] [2110] [2111] [2112] [2113] Underfull \hbox (badness 4060) in paragraph at lines 10551--10554 []\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 10574--10574 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2114] Underfull \hbox (badness 10000) in paragraph at lines 10637--10639 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2115] [2116] [2117] Underfull \hbox (badness 2150) in paragraph at lines 10813--10815 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2118] [2119] [2120] [2121] Underfull \hbox (badness 10000) in paragraph at lines 11032--11036 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow 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 [2122] [2123] Underfull \hbox (badness 2096) in paragraph at lines 11181--11184 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 11185--11188 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether JPEG fig-ures should be gen-er-ated. Ig-nored if [2124] 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 [2125] [2126] [2127] [2128] [2129] Underfull \hbox (badness 3780) in paragraph at lines 11563--11567 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 11579--11582 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2130] [2131] [2132] [2133] [2134] [2135] Underfull \hbox (badness 2818) in paragraph at lines 11948--11953 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have 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 [2136] [2137] [2138] [2139] [2140] Underfull \hbox (badness 10000) in paragraph at lines 12220--12222 []\T1/ptm/m/n/10 Options other than \T1/zi4/m/sl/10 memory = "none" \T1/ptm/m/n /10 ap-ply only to files pro-duced by [2141] [2142] Underfull \hbox (badness 1057) in paragraph at lines 12377--12384 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in turn, [2143] [2144] [2145] [2146] Underfull \hbox (badness 3612) in paragraph at lines 12659--12663 []\T1/ptm/m/n/10 NetBSD prior to 8.0 used flag `\T1/zi4/m/sl/10 --xz\T1/ptm/m/n /10 ' rather than `\T1/zi4/m/sl/10 -J\T1/ptm/m/n/10 ', so this should be used \ T1/ptm/m/it/10 via Underfull \hbox (badness 6510) in paragraph at lines 12674--12678 []\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a ble Underfull \hbox (badness 10000) in paragraph at lines 12681--12684 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 12681--12684 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] Underfull \hbox (badness 10000) in paragraph at lines 13290--13295 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 3861) in paragraph at lines 13290--13295 [][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n /10 and 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/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av ailable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 1297) in paragraph at lines 13326--13331 \T1/zi4/m/sl/10 available.packages(contriburl = contriburl, method = method) \T 1/ptm/m/n/10 and hence by [2157] Underfull \hbox (badness 10000) in paragraph at lines 13355--13358 [][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [2158] [2159] [2160] [2161] Overfull \hbox (23.85939pt too wide) in paragraph at lines 13597--13600 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](, package = "") [2162] [2163] 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, [2164] 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 [2165] [2166] [2167] [2168]) No file refman.ind. (./refman.aux) Package rerunfilecheck Warning: File `refman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.lmList} 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.survreg} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.stepAIC} has been referenced but does not exist , replaced 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 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Transcript written on refman.log. This is makeindex, version 2.15 [TeX Live 2016] (kpathsea + Thai support). Scanning input file refman.idx.................done (13579 entries accepted, 34 rejected). Sorting entries....................................................................................................................................................done (217268 comparisons). Generating output file refman.ind................done (13394 lines written, 50 warnings). Output written in refman.ind. Transcript written in refman.ilg. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2017/01/01> patch level 3 Babel <3.9r> and hyphenation patterns for 3 language(s) loaded. 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[1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/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/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 386--389 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) 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/zi4/m/n/10 insertions\T1/ptm/m/n/10 ', [9] [10] [11] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 2671) in paragraph at lines 1147--1150 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1922--1922 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [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] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] Underfull \vbox (badness 10000) has occurred while \output is active [51] [52] [53] [54] [55] [56] [57] 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 [58] [59] [60] [61] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3897--3897 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [62] [63] Underfull \hbox (badness 1057) in paragraph at lines 4005--4008 [][][]\T1/zi4/m/n/10 is.language[][][]() \T1/ptm/m/n/10 is also true for calls (but also for [][]\T1/zi4/m/n/10 symbol[][][]\T1/ptm/m/n/10 s and [][]\T1/zi4/m /n/10 expression[][][]\T1/ptm/m/n/10 s where [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] 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 [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6041--6041 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [95] [96] [97] Underfull \hbox (badness 2096) in paragraph at lines 6229--6242 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [98] [99] [100] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6438--6440 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [101] [102] Underfull \hbox (badness 10000) in paragraph at lines 6580--6583 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [103] [104] Underfull \hbox (badness 1442) in paragraph at lines 6762--6768 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a 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 [105] Underfull \hbox (badness 3568) in paragraph at lines 6824--6831 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [106] [107] Underfull \vbox (badness 10000) has occurred while \output is active [108] Underfull \vbox (badness 10000) has occurred while \output is active [109] [110] Underfull \hbox (badness 1077) in paragraph at lines 7141--7147 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater 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- [111] [112] [113] [114] [115] [116] Underfull \hbox (badness 2096) in paragraph at lines 7482--7486 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [117] [118] Underfull \hbox (badness 3000) in paragraph at lines 7575--7577 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7600--7603 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [119] [120] [121] [122] Underfull \hbox (badness 10000) in paragraph at lines 7855--7865 []\T1/zi4/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 [123] Underfull \hbox (badness 4479) in paragraph at lines 7926--7936 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] Underfull \hbox (badness 1394) in paragraph at lines 9685--9690 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [150] [151] [152] [153] [154] [155] Underfull \hbox (badness 1194) in paragraph at lines 10030--10035 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) 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/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [156] [157] [158] Underfull \hbox (badness 1735) in paragraph at lines 10235--10239 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [159] [160] [161] [162] [163] [164] 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 Underfull \hbox (badness 6396) in paragraph at lines 10672--10680 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for [165] Underfull \hbox (badness 2735) 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/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] 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 [182] [183] [184] [185] [186] [187] [188] [189] [190] Underfull \hbox (badness 2698) in paragraph at lines 12358--12367 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/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-lowed Underfull \hbox (badness 4341) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [191] [192] [193] [194] [195] Underfull \vbox (badness 3803) has occurred while \output is active [196] [197] [198] [199] [200] Underfull \hbox (badness 6236) in paragraph at lines 13017--13020 []\T1/ptm/m/n/10 For \T1/zi4/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 [201] [202] [203] [204] [205] [206] 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 [207] Underfull \hbox (badness 1565) in paragraph at lines 13510--13514 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [208] 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/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with [209] [210] Underfull \hbox (badness 1466) in paragraph at lines 13694--13697 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [211] [212] Underfull \hbox (badness 10000) in paragraph at lines 13813--13817 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13824--13827 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [213] [214] [215] [216] [217] 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, [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 4429) 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/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [230] Underfull \hbox (badness 10000) in paragraph at lines 14968--14970 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 []\T1/zi4/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, so [231] Underfull \hbox (badness 10000) in paragraph at lines 15013--15017 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/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 4156) in paragraph at lines 15013--15017 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [232] [233] [234] [235] [236] [237] [238] [239] [240] Underfull \hbox (badness 2452) in paragraph at lines 15605--15609 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15605--15609 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [241] [242] [243] Underfull \hbox (badness 1092) in paragraph at lines 15778--15783 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [244] [245] [246] Underfull \hbox (badness 6741) in paragraph at lines 16029--16033 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [247] [248] [249] [250] [251] 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 [252] [253] [254] [255] Underfull \vbox (badness 10000) has occurred while \output is active [256] [257] [258] Underfull \hbox (badness 3679) in paragraph at lines 16745--16747 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [259] [260] [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 1478) in paragraph at lines 17310--17313 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [267] [268] [269] Underfull \hbox (badness 10000) in paragraph at lines 17563--17565 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] Underfull \hbox (badness 1442) in paragraph at lines 18154--18156 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [280] Underfull \hbox (badness 2452) in paragraph at lines 18246--18262 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [281] [282] [283] [284] [285] [286] [287] Underfull \hbox (badness 1248) in paragraph at lines 18660--18663 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [288] [289] [290] [291] 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 [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] Underfull \hbox (badness 2469) in paragraph at lines 19935--19940 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 19949--19956 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [309] Underfull \hbox (badness 10000) in paragraph at lines 20023--20027 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20023--20027 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [310] [311] Underfull \hbox (badness 1509) in paragraph at lines 20158--20165 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 20158--20165 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 20174--20179 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] Underfull \hbox (badness 1264) 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-ported: Underfull \hbox (badness 4441) in paragraph at lines 20954--20957 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] Underfull \hbox (badness 10000) in paragraph at lines 21701--21703 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] Underfull \hbox (badness 1077) in paragraph at lines 22736--22742 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [352] [353] [354] Underfull \hbox (badness 1484) in paragraph at lines 22899--22907 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [355] [356] [357] [358] [359] Underfull \hbox (badness 2790) in paragraph at lines 23184--23187 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 23184--23187 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [360] [361] [362] [363] Underfull \hbox (badness 1194) in paragraph at lines 23466--23469 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [364] [365] [366] Underfull \hbox (badness 10000) in paragraph at lines 23672--23678 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23672--23678 \T1/ptm/m/n/10 list, i.e., \T1/zi4/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 [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 10000) in paragraph at lines 24053--24056 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [373] [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 10000) in paragraph at lines 24655--24657 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [382] [383] [384] [385] Underfull \hbox (badness 1199) in paragraph at lines 24899--24905 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24899--24905 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [386] [387] [388] [389] [390] [391] [392] [393] Underfull \hbox (badness 1038) in paragraph at lines 25491--25499 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially [394] Underfull \hbox (badness 1881) in paragraph at lines 25500--25503 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 25519--25521 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [395] Underfull \hbox (badness 10000) in paragraph at lines 25628--25638 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25639--25645 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able [396] Underfull \hbox (badness 1968) in paragraph at lines 25675--25680 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment 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 [397] [398] [399] Underfull \hbox (badness 10000) 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/zi4/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/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 25961--25964 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) 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 [400] Underfull \hbox (badness 10000) in paragraph at lines 26019--26024 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 26025--26036 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 26037--26040 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 3713) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 26047--26059 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). Underfull \hbox (badness 2351) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , 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/zi4/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/zi4/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 Underfull \hbox (badness 1874) in paragraph at lines 26061--26068 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [401] [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [406] [407] [408] [409] [410] Underfull \hbox (badness 1735) in paragraph at lines 26724--26728 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [411] [412] [413] [414] [415] [416] [417] [418] [419] [420] Underfull \hbox (badness 2726) in paragraph at lines 27299--27302 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] [431] [432] [433] Underfull \hbox (badness 1052) in paragraph at lines 28131--28136 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [434] [435] [436] [437] [438] Underfull \vbox (badness 10000) has occurred while \output is active [439] [440] [441] [442] [443] [444] [445] [446] 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 [447] [448] Underfull \hbox (badness 1163) in paragraph at lines 29131--29142 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] Underfull \hbox (badness 10000) in paragraph at lines 30664--30668 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 30664--30668 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [473] Underfull \hbox (badness 6188) in paragraph at lines 30686--30688 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [474] [475] [476] [477] [478] [479] [480] [481] Underfull \hbox (badness 1655) in paragraph at lines 31229--31231 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [493] [494] [495] [496] 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 3333) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/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 [497] [498] [499] Underfull \hbox (badness 2261) in paragraph at lines 32344--32349 []\T1/ptm/m/n/10 If \T1/zi4/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 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 [500] Underfull \hbox (badness 10000) in paragraph at lines 32447--32452 []\T1/ptm/m/n/10 Note that since \T1/zi4/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 [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] Underfull \vbox (badness 3803) has occurred while \output is active [540] [541] [542] [543] [544] [545] [546] [547] Underfull \hbox (badness 1072) in paragraph at lines 35489--35493 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 35494--35498 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', 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/zi4/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/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in [548] Underfull \hbox (badness 3343) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 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 Underfull \hbox (badness 1917) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [549] [550] [551] [552] [553] 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/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35875--35881 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] [581] [582] [583] Underfull \hbox (badness 3333) in paragraph at lines 37745--37750 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [584] [585] [586] [587] [588] [589] Underfull \vbox (badness 10000) has occurred while \output is active [590] [591] [592] [593] [594] Underfull \hbox (badness 1472) in paragraph at lines 38377--38380 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] Underfull \vbox (badness 3803) has occurred while \output is active [608] Underfull \hbox (badness 10000) in paragraph at lines 39283--39287 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/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., [609] [610] [611] [612] Underfull \hbox (badness 10000) in paragraph at lines 39533--39536 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [613] [614] Underfull \hbox (badness 10000) in paragraph at lines 39651--39655 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [615] Underfull \hbox (badness 10000) in paragraph at lines 39713--39717 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [616] [617] [618] [619] [620] [621] [622] [623] [624] Underfull \hbox (badness 4013) in paragraph at lines 40326--40328 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [625] [626] [627] [628] [629] [630] Underfull \vbox (badness 10000) has occurred while \output is active [631] [632] [633] [634] [635] [636] [637] [638] 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 1990) in paragraph at lines 41214--41222 []\T1/zi4/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 4846) 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/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [639] [640] [641] [642] 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. [643] [644] [645] [646] Underfull \hbox (badness 1917) in paragraph at lines 41719--41726 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] 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 [658] [659] Underfull \hbox (badness 2401) in paragraph at lines 42568--42572 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [660] [661] [662] Underfull \hbox (badness 2111) in paragraph at lines 42757--42762 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 7362) in paragraph at lines 42773--42778 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [663] [664] [665] [666] [667] [668] [669] [670] [671] Underfull \hbox (badness 5417) in paragraph at lines 43354--43358 []\T1/zi4/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 [672] Underfull \hbox (badness 10000) in paragraph at lines 43415--43419 []\T1/zi4/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 [673] [674]) (./compiler-pkg.tex Chapter 2. [675] [676] [677] [678]) (./datasets-pkg.tex Chapter 3. [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] 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. [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] Overfull \vbox (19.74611pt too high) has occurred while \output is active [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] Underfull \vbox (badness 10000) has occurred while \output is active [747] [748] [749] [750] Underfull \vbox (badness 10000) has occurred while \output is active [751] [752] [753] [754] [755] [756] Overfull \vbox (18.9959pt too high) has occurred while \output is active [757] [758] [759]) (./grDevices-pkg.tex [760] Chapter 4. [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] 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 [778] [779] [780] [781] Underfull \hbox (badness 1852) in paragraph at lines 1279--1282 []\T1/zi4/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 [782] [783] [784] Underfull \hbox (badness 1490) in paragraph at lines 1485--1490 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [787] [788] [789] [790] Underfull \hbox (badness 1325) in paragraph at lines 1891--1901 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [791] [792] 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 [793] [794] [795] 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 [796] [797] [798] [799] [800] [801] [802] [803] [804] Underfull \hbox (badness 10000) in paragraph at lines 2750--2751 [805] [806] [807] [808] [809] [810] [811] [812] Underfull \hbox (badness 10000) in paragraph at lines 3248--3253 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [813] [814] [815] [816] Underfull \hbox (badness 3302) in paragraph at lines 3514--3517 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827] [828] [829] [830] Underfull \hbox (badness 1067) in paragraph at lines 4355--4362 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [831] [832] [833] Underfull \hbox (badness 1789) in paragraph at lines 4595--4597 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [834] Underfull \hbox (badness 1377) in paragraph at lines 4645--4650 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [835] Underfull \hbox (badness 2671) 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/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4721--4728 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, 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 [836] [837] Underfull \hbox (badness 1377) in paragraph at lines 4850--4855 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb" \T1/ptm/m/n/10 (which is RGB+gray) and [838] 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 [839] [840] Underfull \hbox (badness 2035) in paragraph at lines 5034--5043 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [841] Underfull \hbox (badness 10000) in paragraph at lines 5102--5109 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5102--5109 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [842] [843] [844] Underfull \hbox (badness 1546) in paragraph at lines 5244--5252 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [845] 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 [846] [847] [848] [849] [850] [851] [852] Underfull \hbox (badness 10000) in paragraph at lines 5772--5775 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [853] [854] [855] [856] [857] [858] 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 [859] [860] Underfull \hbox (badness 10000) in paragraph at lines 6267--6269 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [861] [862] [863] [864] Underfull \hbox (badness 3780) in paragraph at lines 6558--6564 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [865] [866] [867] Underfull \hbox (badness 2680) in paragraph at lines 6759--6761 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [868] [869] [870]) (./graphics-pkg.tex Chapter 5. [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] Underfull \hbox (badness 10000) in paragraph at lines 687--694 []\T1/zi4/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/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] Underfull \hbox (badness 4634) in paragraph at lines 1262--1265 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] 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 [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] Underfull \vbox (badness 10000) has occurred while \output is active [931] [932] [933] [934] 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 [935] [936] [937] [938] [939] [940] [941] [942] 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 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 [943] [944] [945] [946] [947] Underfull \hbox (badness 10000) 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/zi4/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4785--4791 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [948] [949] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 <"/root/git/r-backports/stretch/r-base-3.5.2/library/graphics/help/figures/"mai .pdf, id=22940, 289.08pt x 289.08pt> [950 ] Underfull \hbox (badness 10000) in paragraph at lines 4977--4979 <"/root/git/r-backports/stretch/r-base-3.5.2/library/graphics/help/figures/"oma .pdf, id=22954, 259.97125pt x 332.24126pt> Underfull \vbox (badness 10000) has occurred while \output is active [951] [952 ] [953] Underfull \hbox (badness 10000) in paragraph at lines 5167--5169 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [954] Underfull \vbox (badness 3803) has occurred while \output is active [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] <"/root/git/r-backports/stretch/r-base-3.5.2/library/graphics/help/figures/"pch .pdf, id=23370, 361.35pt x 50.1875pt> Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639 [][] [977] [978 ] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] Underfull \hbox (badness 1048) in paragraph at lines 7347--7352 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [989] [990] Underfull \hbox (badness 1102) in paragraph at lines 7463--7466 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] Underfull \hbox (badness 1043) in paragraph at lines 8304--8308 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [1005] [1006] [1007] [1008] [1009] [1010] [1011] 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 [1012]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8805 \HeaderA{units}{Graphical Units}{units} [1013] [1014] [1015] [1016]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1017] [1018] [1019] [1020] [1021] [1022] Underfull \hbox (badness 2680) in paragraph at lines 392--395 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] Underfull \hbox (badness 4279) in paragraph at lines 972--981 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] 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 [1090] [1091] [1092] [1093] 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 [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] 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., [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] 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 [1124] [1125] [1126] [1127]) (./methods-pkg.tex [1128] Chapter 7. [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] Underfull \vbox (badness 3803) has occurred while \output is active [1137] Underfull \vbox (badness 10000) has occurred while \output is active [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] Underfull \hbox (badness 1077) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests [1156] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 1981--1986 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1157] [1158] [1159] Underfull \hbox (badness 1242) 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/zi4/m/n/10 where = [1160] [1161] [1162] [1163] [1164] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1165] [1166] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in [1167] Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1168] [1169] [1170] [1171] [1172] [1173] [1174] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1175] [1176] [1177] [1178] [1179] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments [1180] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1181] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [1182] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3846--3847 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] Underfull \hbox (badness 1436) in paragraph at lines 4443--4446 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4472--4478 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1193] Underfull \hbox (badness 1092) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] Underfull \vbox (badness 10000) has occurred while \output is active [1203] [1204] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1205] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1206] 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 [1207] [1208] [1209] [1210] 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 [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1219] [1220] [1221] [1222] Underfull \vbox (badness 10000) has occurred while \output is active [1223] [1224] [1225] [1226]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1227] [1228] [1229]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate 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} [1230] 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 [1231] [1232] [1233] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] Underfull \vbox (badness 10000) has occurred while \output is active [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274] [1275] 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., [1276] [1277] [1278] [1279]) (./parallel-pkg.tex [1280] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] Underfull \hbox (badness 3386) in paragraph at lines 1339--1342 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1302] [1303] [1304]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319]) (./stats-pkg.tex [1320] Chapter 10. [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] Underfull \hbox (badness 1412) in paragraph at lines 847--849 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] Underfull \hbox (badness 2503) in paragraph at lines 1328--1331 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1342] [1343] [1344] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1345] [1346] [1347] [1348] 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 1546) in paragraph at lines 1773--1777 \T1/zi4/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can han-dle miss-ing [1349] [1350] [1351] [1352] [1353] [1354] [1355] 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 [1356] [1357] [1358] [1359] [1360] 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 [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] 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 [1373] [1374] Underfull \hbox (badness 2503) in paragraph at lines 3390--3393 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] 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 = [1395] [1396] Underfull \hbox (badness 3612) in paragraph at lines 4754--4756 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por t aliased co-ef-fi-cients (see [][]\T1/zi4/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b y de-fault where [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] Underfull \hbox (badness 2556) in paragraph at lines 5270--5273 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) 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/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1405] [1406] [1407] [1408] Underfull \hbox (badness 1142) in paragraph at lines 5527--5539 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1409] [1410] [1411] Underfull \hbox (badness 2503) in paragraph at lines 5679--5683 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 8132) in paragraph at lines 6183--6188 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 7081) in paragraph at lines 6461--6464 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6465--6467 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1425] [1426] [1427] [1428] [1429] Underfull \vbox (badness 3803) has occurred while \output is active [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] Underfull \hbox (badness 10000) in paragraph at lines 7310--7313 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 2626) in paragraph at lines 8954--8957 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1465] Underfull \hbox (badness 2503) in paragraph at lines 9061--9065 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1466] Underfull \hbox (badness 2564) 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/zi4/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 [1467] [1468] [1469] [1470] [1471] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9435--9437 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] 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 [1487] [1488] [1489] [1490] [1491] 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 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10730--10733 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1492] 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: [1493] [1494] [1495] [1496] [1497] [1498] 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 1867) in paragraph at lines 11209--11218 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1499] [1500] [1501] [1502] [1503] Underfull \hbox (badness 10000) 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/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1504] [1505] [1506]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} [1507] [1508] Underfull \hbox (badness 1484) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] 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/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1519] [1520] [1521] [1522] [1523] [1524] 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 [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] 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 [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] 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 [1547] [1548] Underfull \hbox (badness 10000) in paragraph at lines 14271--14275 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14278--14280 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] Underfull \hbox (badness 2503) in paragraph at lines 15346--15350 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] Underfull \hbox (badness 1584) in paragraph at lines 15858--15864 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1 /ptm/m/n/10 and [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] 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 [1601] [1602] Underfull \vbox (badness 10000) has occurred while \output is active [1603] Underfull \vbox (badness 10000) has occurred while \output is active [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] Underfull \hbox (badness 1377) in paragraph at lines 18445--18450 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) 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 1454) in paragraph at lines 18463--18467 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18471--18475 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1617] [1618] [1619] Underfull \vbox (badness 10000) has occurred while \output is active [1620] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18695--18695 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18698--18698 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1621] [1622] [1623] [1624] [1625] [1626] 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 [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] 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 [1636] [1637] [1638] [1639] [1640] Underfull \hbox (badness 5563) in paragraph at lines 19864--19866 []\T1/ptm/m/n/10 logical. If \T1/zi4/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 [1641] [1642] [1643] [1644] [1645] [1646] Underfull \hbox (badness 2503) in paragraph at lines 20242--20245 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1647] Underfull \hbox (badness 10000) in paragraph at lines 20269--20271 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] Underfull \hbox (badness 10000) in paragraph at lines 21342--21348 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] 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 [1688] [1689] [1690] [1691] [1692] [1693] [1694] [1695] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23251--23251 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1696] [1697] [1698] [1699] [1700] 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 [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] 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/zi4/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1710] Underfull \hbox (badness 3690) in paragraph at lines 24139--24143 [][][]\T1/zi4/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 [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718] Underfull \hbox (badness 2165) in paragraph at lines 24616--24621 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1719] [1720] [1721] [1722] 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/zi4/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/zi4/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 Underfull \hbox (badness 1132) in paragraph at lines 24834--24838 \T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o f un-de-ter-mined co-ef-fi-cients, e.g., for [1723] [1724] [1725] [1726] [1727] [1728] [1729] Underfull \hbox (badness 10000) in paragraph at lines 25306--25311 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \vbox (badness 10000) has occurred while \output is active [1746] Underfull \hbox (badness 3514) in paragraph at lines 26362--26367 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1747] [1748] Underfull \hbox (badness 3514) in paragraph at lines 26458--26463 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1749] Underfull \hbox (badness 3514) in paragraph at lines 26544--26549 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1750] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26596--26596 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1751] Underfull \hbox (badness 3514) in paragraph at lines 26632--26638 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1752] [1753] [1754] [1755] Underfull \hbox (badness 3514) in paragraph at lines 26846--26851 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1756] [1757] Underfull \hbox (badness 3514) in paragraph at lines 26933--26938 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1758] Underfull \hbox (badness 3514) in paragraph at lines 26998--27003 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1759] [1760] Underfull \hbox (badness 3514) in paragraph at lines 27092--27097 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1761] Underfull \hbox (badness 6691) in paragraph at lines 27184--27189 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] 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/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] [1780] Underfull \hbox (badness 5431) 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/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1781] [1782] [1783] Underfull \hbox (badness 5431) 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/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1784] [1785] [1786] [1787] [1788] [1789] 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 [1790] [1791] 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/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1792] [1793] 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 [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] Underfull \hbox (badness 10000) in paragraph at lines 30274--30278 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect [1813] [1814] [1815] Underfull \vbox (badness 10000) has occurred while \output is active [1816] [1817] [1818] 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 [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] 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 [1828] Underfull \hbox (badness 2142) in paragraph at lines 31242--31247 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/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 [1829] [1830] [1831] [1832] [1833] [1834] Underfull \hbox (badness 10000) in paragraph at lines 31647--31652 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1835] [1836] [1837]) (./stats4-pkg.tex [1838] Chapter 11. [1839] [1840] [1841] [1842] [1843] [1844]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1845] [1846] [1847] [1848]) (./tcltk-pkg.tex Chapter 12. [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \vbox (badness 10000) has occurred while \output is active [1856] Underfull \vbox (badness 10000) has occurred while \output is active [1857] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] [1868] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/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/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1869]) (./tools-pkg.tex [1870] Chapter 13. [1871] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1872] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/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 [1873] [1874] Underfull \hbox (badness 1308) 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 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1875] [1876] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1877] [1878] [1879] [1880] [1881] [1882] [1883] Underfull \vbox (badness 10000) has occurred while \output is active [1884] [1885] [1886] [1887] 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 [1888] 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- [1889] 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-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1199--1202 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1890] [1891] [1892] 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 [1893] [1894] [1895] Underfull \hbox (badness 2293) in paragraph at lines 1551--1553 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1896] [1897] 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 Underfull \hbox (badness 1082) in paragraph at lines 1696--1698 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1898] [1899] [1900] [1901]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1902] [1903] [1904] [1905] [1906] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2195--2195 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1907] [1908] [1909] 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 [1910] [1911] [1912] [1913] [1914] [1915] [1916] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2829. [1917] [1918] [1919] [1920] Underfull \hbox (badness 1424) in paragraph at lines 3111--3113 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1921] [1922] [1923] [1924] [1925] [1926] [1927] [1928] [1929] [1930] [1931] [1932] 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 , [1933] [1934] Underfull \hbox (badness 10000) in paragraph at lines 3950--3953 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1935] [1936] 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 [1937] [1938] [1939] Underfull \hbox (badness 1838) in paragraph at lines 4257--4263 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4257--4263 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1940] Underfull \hbox (badness 5726) in paragraph at lines 4337--4342 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4337--4342 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1941] [1942] [1943] Underfull \hbox (badness 2197) in paragraph at lines 4486--4496 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4486--4496 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1944] 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 [1945] [1946] [1947]) (./utils-pkg.tex [1948] Chapter 14. [1949] Underfull \hbox (badness 2556) 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/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 10000) in paragraph at lines 620--626 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 620--626 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1958] [1959] Underfull \hbox (badness 5847) in paragraph at lines 753--759 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 753--759 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1960] Underfull \hbox (badness 3861) in paragraph at lines 821--826 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1961] [1962] [1963] Underfull \hbox (badness 1430) in paragraph at lines 992--999 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 992--999 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 992--999 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. 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 [1964] [1965] [1966] Underfull \vbox (badness 10000) has occurred while \output is active [1967] [1968] [1969] [1970] [1971] Underfull \hbox (badness 1371) in paragraph at lines 1482--1484 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1972] [1973] [1974] [1975] [1976] [1977] [1978] Underfull \hbox (badness 2057) in paragraph at lines 1959--1961 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1979] [1980] 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/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1981] 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 [1982] [1983] [1984] [1985] Underfull \hbox (badness 1661) in paragraph at lines 2374--2381 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2390--2393 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1986] [1987] [1988] [1989] [1990] [1991] [1992] Underfull \hbox (badness 10000) in paragraph at lines 2800--2804 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2805--2808 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002] Underfull \hbox (badness 1430) 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/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [2003] 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 [2004] [2005] Underfull \hbox (badness 10000) in paragraph at lines 3686--3688 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow nload.file[][][] \T1/ptm/m/n/10 and [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016]pdf TeX warning (ext4): destination with the same identifier (name{Rfn.format}) 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} [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] Underfull \hbox (badness 1371) in paragraph at lines 5377--5379 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [2033] 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 [2034] [2035] [2036] 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, [2037] 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 [2038] [2039] 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 [2040] 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 [2041] Underfull \hbox (badness 1325) in paragraph at lines 5980--5984 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [2042] 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/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2043] Underfull \hbox (badness 3219) in paragraph at lines 6136--6143 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "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 [2044] [2045] Underfull \hbox (badness 10000) in paragraph at lines 6236--6241 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] Underfull \hbox (badness 10000) in paragraph at lines 7669--7671 []\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 7683--7685 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7691--7696 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] 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 [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] [2091] Underfull \hbox (badness 1097) in paragraph at lines 9118--9121 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2092] Underfull \hbox (badness 3000) in paragraph at lines 9254--9259 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2093] [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] Underfull \hbox (badness 2134) in paragraph at lines 9837--9842 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2102] [2103] [2104] [2105] [2106] [2107] [2108] Underfull \hbox (badness 5077) in paragraph at lines 10262--10266 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/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 2469) in paragraph at lines 10274--10278 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 10274--10278 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2109] [2110] [2111] [2112] [2113] Underfull \hbox (badness 4060) in paragraph at lines 10551--10554 []\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 10574--10574 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2114] Underfull \hbox (badness 10000) in paragraph at lines 10637--10639 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. 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Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 11185--11188 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether JPEG fig-ures should be gen-er-ated. Ig-nored if [2124] 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 [2125] [2126] [2127] [2128] [2129] Underfull \hbox (badness 3780) in paragraph at lines 11563--11567 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 11579--11582 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2130] [2131] [2132] [2133] [2134] [2135] Underfull \hbox (badness 2818) in paragraph at lines 11948--11953 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have 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 [2136] [2137] [2138] [2139] [2140] Underfull \hbox (badness 10000) in paragraph at lines 12220--12222 []\T1/ptm/m/n/10 Options other than \T1/zi4/m/sl/10 memory = "none" \T1/ptm/m/n /10 ap-ply only to files pro-duced by [2141] [2142] Underfull \hbox (badness 1057) in paragraph at lines 12377--12384 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in turn, [2143] [2144] [2145] [2146] Underfull \hbox (badness 3612) in paragraph at lines 12659--12663 []\T1/ptm/m/n/10 NetBSD prior to 8.0 used flag `\T1/zi4/m/sl/10 --xz\T1/ptm/m/n /10 ' rather than `\T1/zi4/m/sl/10 -J\T1/ptm/m/n/10 ', so this should be used \ T1/ptm/m/it/10 via Underfull \hbox (badness 6510) in paragraph at lines 12674--12678 []\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a ble Underfull \hbox (badness 10000) in paragraph at lines 12681--12684 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 12681--12684 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] Underfull \hbox (badness 10000) in paragraph at lines 13290--13295 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 3861) in paragraph at lines 13290--13295 [][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n /10 and 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/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av ailable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 1297) in paragraph at lines 13326--13331 \T1/zi4/m/sl/10 available.packages(contriburl = contriburl, method = method) \T 1/ptm/m/n/10 and hence by [2157] Underfull \hbox (badness 10000) in paragraph at lines 13355--13358 [][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [2158] [2159] [2160] [2161] Overfull \hbox (23.85939pt too wide) in paragraph at lines 13597--13600 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](, package = "") [2162] [2163] 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). 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Transcript written on refman.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2017/01/01> patch level 3 Babel <3.9r> and hyphenation patterns for 3 language(s) loaded. 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[1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/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/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 386--389 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) 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/zi4/m/n/10 insertions\T1/ptm/m/n/10 ', [9] [10] [11] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 2671) in paragraph at lines 1147--1150 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1922--1922 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [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] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] Underfull \vbox (badness 10000) has occurred while \output is active [51] [52] [53] [54] [55] [56] [57] 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 [58] [59] [60] [61] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3897--3897 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [62] [63] Underfull \hbox (badness 1057) in paragraph at lines 4005--4008 [][][]\T1/zi4/m/n/10 is.language[][][]() \T1/ptm/m/n/10 is also true for calls (but also for [][]\T1/zi4/m/n/10 symbol[][][]\T1/ptm/m/n/10 s and [][]\T1/zi4/m /n/10 expression[][][]\T1/ptm/m/n/10 s where [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] 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 [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6041--6041 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [95] [96] [97] Underfull \hbox (badness 2096) in paragraph at lines 6229--6242 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [98] [99] [100] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6438--6440 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [101] [102] Underfull \hbox (badness 10000) in paragraph at lines 6580--6583 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [103] [104] Underfull \hbox (badness 1442) in paragraph at lines 6762--6768 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a 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 [105] Underfull \hbox (badness 3568) in paragraph at lines 6824--6831 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [106] [107] Underfull \vbox (badness 10000) has occurred while \output is active [108] Underfull \vbox (badness 10000) has occurred while \output is active [109] [110] Underfull \hbox (badness 1077) in paragraph at lines 7141--7147 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7141--7147 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [111] [112] [113] [114] [115] [116] Underfull \hbox (badness 2096) in paragraph at lines 7482--7486 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [117] [118] Underfull \hbox (badness 3000) in paragraph at lines 7575--7577 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7600--7603 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [119] [120] [121] [122] Underfull \hbox (badness 10000) in paragraph at lines 7855--7865 []\T1/zi4/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 [123] Underfull \hbox (badness 4479) in paragraph at lines 7926--7936 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] Underfull \hbox (badness 1394) in paragraph at lines 9685--9690 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [150] [151] [152] [153] [154] [155] Underfull \hbox (badness 1194) in paragraph at lines 10030--10035 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) 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/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [156] [157] [158] Underfull \hbox (badness 1735) in paragraph at lines 10235--10239 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [159] [160] [161] [162] [163] [164] 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 Underfull \hbox (badness 6396) in paragraph at lines 10672--10680 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for [165] Underfull \hbox (badness 2735) 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/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] 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 [182] [183] [184] [185] [186] [187] [188] [189] [190] Underfull \hbox (badness 2698) in paragraph at lines 12358--12367 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/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-lowed Underfull \hbox (badness 4341) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [191] [192] [193] [194] [195] Underfull \vbox (badness 3803) has occurred while \output is active [196] [197] [198] [199] [200] Underfull \hbox (badness 6236) in paragraph at lines 13017--13020 []\T1/ptm/m/n/10 For \T1/zi4/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 [201] [202] [203] [204] [205] [206] 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 [207] Underfull \hbox (badness 1565) in paragraph at lines 13510--13514 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [208] 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/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with [209] [210] Underfull \hbox (badness 1466) in paragraph at lines 13694--13697 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [211] [212] Underfull \hbox (badness 10000) in paragraph at lines 13813--13817 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13824--13827 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [213] [214] [215] [216] [217] 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, [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 4429) 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/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [230] Underfull \hbox (badness 10000) in paragraph at lines 14968--14970 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 []\T1/zi4/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, so [231] Underfull \hbox (badness 10000) in paragraph at lines 15013--15017 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/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 4156) in paragraph at lines 15013--15017 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [232] [233] [234] [235] [236] [237] [238] [239] [240] Underfull \hbox (badness 2452) in paragraph at lines 15605--15609 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15605--15609 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [241] [242] [243] Underfull \hbox (badness 1092) in paragraph at lines 15778--15783 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [244] [245] [246] Underfull \hbox (badness 6741) in paragraph at lines 16029--16033 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [247] [248] [249] [250] [251] 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 [252] [253] [254] [255] Underfull \vbox (badness 10000) has occurred while \output is active [256] [257] [258] Underfull \hbox (badness 3679) in paragraph at lines 16745--16747 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [259] [260] [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 1478) in paragraph at lines 17310--17313 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [267] [268] [269] Underfull \hbox (badness 10000) in paragraph at lines 17563--17565 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] Underfull \hbox (badness 1442) in paragraph at lines 18154--18156 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [280] Underfull \hbox (badness 2452) in paragraph at lines 18246--18262 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [281] [282] [283] [284] [285] [286] [287] Underfull \hbox (badness 1248) in paragraph at lines 18660--18663 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [288] [289] [290] [291] 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 [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] Underfull \hbox (badness 2469) in paragraph at lines 19935--19940 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 19949--19956 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [309] Underfull \hbox (badness 10000) in paragraph at lines 20023--20027 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20023--20027 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [310] [311] Underfull \hbox (badness 1509) in paragraph at lines 20158--20165 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 20158--20165 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 20174--20179 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] Underfull \hbox (badness 1264) 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-ported: Underfull \hbox (badness 4441) in paragraph at lines 20954--20957 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] Underfull \hbox (badness 10000) in paragraph at lines 21701--21703 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] Underfull \hbox (badness 1077) in paragraph at lines 22736--22742 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [352] [353] [354] Underfull \hbox (badness 1484) in paragraph at lines 22899--22907 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [355] [356] [357] [358] [359] Underfull \hbox (badness 2790) in paragraph at lines 23184--23187 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 23184--23187 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [360] [361] [362] [363] Underfull \hbox (badness 1194) in paragraph at lines 23466--23469 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [364] [365] [366] Underfull \hbox (badness 10000) in paragraph at lines 23672--23678 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23672--23678 \T1/ptm/m/n/10 list, i.e., \T1/zi4/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 [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 10000) in paragraph at lines 24053--24056 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [373] [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 10000) in paragraph at lines 24655--24657 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [382] [383] [384] [385] Underfull \hbox (badness 1199) in paragraph at lines 24899--24905 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24899--24905 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [386] [387] [388] [389] [390] [391] [392] [393] Underfull \hbox (badness 1038) in paragraph at lines 25491--25499 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially [394] Underfull \hbox (badness 1881) in paragraph at lines 25500--25503 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 25519--25521 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [395] Underfull \hbox (badness 10000) in paragraph at lines 25628--25638 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25639--25645 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able [396] Underfull \hbox (badness 1968) in paragraph at lines 25675--25680 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment 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 [397] [398] [399] Underfull \hbox (badness 10000) 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/zi4/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/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 25961--25964 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) 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 [400] Underfull \hbox (badness 10000) in paragraph at lines 26019--26024 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 26025--26036 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 26037--26040 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 3713) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 26047--26059 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). Underfull \hbox (badness 2351) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , 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/zi4/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/zi4/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 Underfull \hbox (badness 1874) in paragraph at lines 26061--26068 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [401] [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [406] [407] [408] [409] [410] Underfull \hbox (badness 1735) in paragraph at lines 26724--26728 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [411] [412] [413] [414] [415] [416] [417] [418] [419] [420] Underfull \hbox (badness 2726) in paragraph at lines 27299--27302 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] [431] [432] [433] Underfull \hbox (badness 1052) in paragraph at lines 28131--28136 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [434] [435] [436] [437] [438] Underfull \vbox (badness 10000) has occurred while \output is active [439] [440] [441] [442] [443] [444] [445] [446] 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 [447] [448] Underfull \hbox (badness 1163) in paragraph at lines 29131--29142 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] Underfull \hbox (badness 10000) in paragraph at lines 30664--30668 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 30664--30668 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [473] Underfull \hbox (badness 6188) in paragraph at lines 30686--30688 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [474] [475] [476] [477] [478] [479] [480] [481] Underfull \hbox (badness 1655) in paragraph at lines 31229--31231 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [493] [494] [495] [496] 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 3333) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/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 [497] [498] [499] Underfull \hbox (badness 2261) in paragraph at lines 32344--32349 []\T1/ptm/m/n/10 If \T1/zi4/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 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 [500] Underfull \hbox (badness 10000) in paragraph at lines 32447--32452 []\T1/ptm/m/n/10 Note that since \T1/zi4/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 [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] Underfull \vbox (badness 3803) has occurred while \output is active [540] [541] [542] [543] [544] [545] [546] [547] Underfull \hbox (badness 1072) in paragraph at lines 35489--35493 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 35494--35498 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', 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/zi4/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/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in [548] Underfull \hbox (badness 3343) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 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 Underfull \hbox (badness 1917) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [549] [550] [551] [552] [553] 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/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35875--35881 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] [581] [582] [583] Underfull \hbox (badness 3333) in paragraph at lines 37745--37750 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [584] [585] [586] [587] [588] [589] Underfull \vbox (badness 10000) has occurred while \output is active [590] [591] [592] [593] [594] Underfull \hbox (badness 1472) in paragraph at lines 38377--38380 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] Underfull \vbox (badness 3803) has occurred while \output is active [608] Underfull \hbox (badness 10000) in paragraph at lines 39283--39287 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/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., [609] [610] [611] [612] Underfull \hbox (badness 10000) in paragraph at lines 39533--39536 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [613] [614] Underfull \hbox (badness 10000) in paragraph at lines 39651--39655 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [615] Underfull \hbox (badness 10000) in paragraph at lines 39713--39717 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [616] [617] [618] [619] [620] [621] [622] [623] [624] Underfull \hbox (badness 4013) in paragraph at lines 40326--40328 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [625] [626] [627] [628] [629] [630] Underfull \vbox (badness 10000) has occurred while \output is active [631] [632] [633] [634] [635] [636] [637] [638] 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 1990) in paragraph at lines 41214--41222 []\T1/zi4/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 4846) 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/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [639] [640] [641] [642] 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. [643] [644] [645] [646] Underfull \hbox (badness 1917) in paragraph at lines 41719--41726 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] 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 [658] [659] Underfull \hbox (badness 2401) in paragraph at lines 42568--42572 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [660] [661] [662] Underfull \hbox (badness 2111) in paragraph at lines 42757--42762 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 7362) in paragraph at lines 42773--42778 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [663] [664] [665] [666] [667] [668] [669] [670] [671] Underfull \hbox (badness 5417) in paragraph at lines 43354--43358 []\T1/zi4/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 [672] Underfull \hbox (badness 10000) in paragraph at lines 43415--43419 []\T1/zi4/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 [673] [674]) (./compiler-pkg.tex Chapter 2. [675] [676] [677] [678]) (./datasets-pkg.tex Chapter 3. [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] 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. [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] Overfull \vbox (19.74611pt too high) has occurred while \output is active [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] Underfull \vbox (badness 10000) has occurred while \output is active [747] [748] [749] [750] Underfull \vbox (badness 10000) has occurred while \output is active [751] [752] [753] [754] [755] [756] Overfull \vbox (18.9959pt too high) has occurred while \output is active [757] [758] [759]) (./grDevices-pkg.tex [760] Chapter 4. [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] 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 [778] [779] [780] [781] Underfull \hbox (badness 1852) in paragraph at lines 1279--1282 []\T1/zi4/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 [782] [783] [784] Underfull \hbox (badness 1490) in paragraph at lines 1485--1490 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [787] [788] [789] [790] Underfull \hbox (badness 1325) in paragraph at lines 1891--1901 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [791] [792] 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 [793] [794] [795] 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 [796] [797] [798] [799] [800] [801] [802] [803] [804] Underfull \hbox (badness 10000) in paragraph at lines 2750--2751 [805] [806] [807] [808] [809] [810] [811] [812] Underfull \hbox (badness 10000) in paragraph at lines 3248--3253 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [813] [814] [815] [816] Underfull \hbox (badness 3302) in paragraph at lines 3514--3517 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827] [828] [829] [830] Underfull \hbox (badness 1067) in paragraph at lines 4355--4362 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [831] [832] [833] Underfull \hbox (badness 1789) in paragraph at lines 4595--4597 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [834] Underfull \hbox (badness 1377) in paragraph at lines 4645--4650 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [835] Underfull \hbox (badness 2671) 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/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4721--4728 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, 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 [836] [837] Underfull \hbox (badness 1377) in paragraph at lines 4850--4855 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb" \T1/ptm/m/n/10 (which is RGB+gray) and [838] 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 [839] [840] Underfull \hbox (badness 2035) in paragraph at lines 5034--5043 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [841] Underfull \hbox (badness 10000) in paragraph at lines 5102--5109 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5102--5109 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [842] [843] [844] Underfull \hbox (badness 1546) in paragraph at lines 5244--5252 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [845] 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 [846] [847] [848] [849] [850] [851] [852] Underfull \hbox (badness 10000) in paragraph at lines 5772--5775 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [853] [854] [855] [856] [857] [858] 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 [859] [860] Underfull \hbox (badness 10000) in paragraph at lines 6267--6269 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [861] [862] [863] [864] Underfull \hbox (badness 3780) in paragraph at lines 6558--6564 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [865] [866] [867] Underfull \hbox (badness 2680) in paragraph at lines 6759--6761 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [868] [869] [870]) (./graphics-pkg.tex Chapter 5. [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] Underfull \hbox (badness 10000) in paragraph at lines 687--694 []\T1/zi4/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/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] Underfull \hbox (badness 4634) in paragraph at lines 1262--1265 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] 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 [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] Underfull \vbox (badness 10000) has occurred while \output is active [931] [932] [933] [934] 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 [935] [936] [937] [938] [939] [940] [941] [942] 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 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 [943] [944] [945] [946] [947] Underfull \hbox (badness 10000) 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/zi4/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4785--4791 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [948] [949] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 <"/root/git/r-backports/stretch/r-base-3.5.2/library/graphics/help/figures/"mai .pdf, id=22946, 289.08pt x 289.08pt> [950 ] Underfull \hbox (badness 10000) in paragraph at lines 4977--4979 <"/root/git/r-backports/stretch/r-base-3.5.2/library/graphics/help/figures/"oma .pdf, id=22960, 259.97125pt x 332.24126pt> Underfull \vbox (badness 10000) has occurred while \output is active [951] [952 ] [953] Underfull \hbox (badness 10000) in paragraph at lines 5167--5169 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [954] Underfull \vbox (badness 3803) has occurred while \output is active [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] <"/root/git/r-backports/stretch/r-base-3.5.2/library/graphics/help/figures/"pch .pdf, id=23376, 361.35pt x 50.1875pt> Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639 [][] [977] [978 ] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] Underfull \hbox (badness 1048) in paragraph at lines 7347--7352 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [989] [990] Underfull \hbox (badness 1102) in paragraph at lines 7463--7466 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] Underfull \hbox (badness 1043) in paragraph at lines 8304--8308 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [1005] [1006] [1007] [1008] [1009] [1010] [1011] 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 [1012]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8805 \HeaderA{units}{Graphical Units}{units} [1013] [1014] [1015] [1016]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1017] [1018] [1019] [1020] [1021] [1022] Underfull \hbox (badness 2680) in paragraph at lines 392--395 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] Underfull \hbox (badness 4279) in paragraph at lines 972--981 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] 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 [1090] [1091] [1092] [1093] 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 [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] 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., [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] 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 [1124] [1125] [1126] [1127]) (./methods-pkg.tex [1128] Chapter 7. [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] Underfull \vbox (badness 3803) has occurred while \output is active [1137] Underfull \vbox (badness 10000) has occurred while \output is active [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] Underfull \hbox (badness 1077) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests [1156] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 1981--1986 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1157] [1158] [1159] Underfull \hbox (badness 1242) 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/zi4/m/n/10 where = [1160] [1161] [1162] [1163] [1164] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1165] [1166] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in [1167] Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1168] [1169] [1170] [1171] [1172] [1173] [1174] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1175] [1176] [1177] [1178] [1179] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments [1180] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1181] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [1182] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3846--3847 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] Underfull \hbox (badness 1436) in paragraph at lines 4443--4446 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4472--4478 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1193] Underfull \hbox (badness 1092) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] Underfull \vbox (badness 10000) has occurred while \output is active [1203] [1204] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1205] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1206] 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 [1207] [1208] [1209] [1210] 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 [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1219] [1220] [1221] [1222] Underfull \vbox (badness 10000) has occurred while \output is active [1223] [1224] [1225] [1226]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1227] [1228] [1229]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate 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} [1230] 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 [1231] [1232] [1233] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] Underfull \vbox (badness 10000) has occurred while \output is active [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274] [1275] 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., [1276] [1277] [1278] [1279]) (./parallel-pkg.tex [1280] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] Underfull \hbox (badness 3386) in paragraph at lines 1339--1342 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1302] [1303] [1304]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319]) (./stats-pkg.tex [1320] Chapter 10. [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] Underfull \hbox (badness 1412) in paragraph at lines 847--849 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] Underfull \hbox (badness 2503) in paragraph at lines 1328--1331 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1342] [1343] [1344] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1345] [1346] [1347] [1348] 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 1546) in paragraph at lines 1773--1777 \T1/zi4/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can han-dle miss-ing [1349] [1350] [1351] [1352] [1353] [1354] [1355] 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 [1356] [1357] [1358] [1359] [1360] 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 [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] 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 [1373] [1374] Underfull \hbox (badness 2503) in paragraph at lines 3390--3393 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] 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 = [1395] [1396] Underfull \hbox (badness 3612) in paragraph at lines 4754--4756 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por t aliased co-ef-fi-cients (see [][]\T1/zi4/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b y de-fault where [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] Underfull \hbox (badness 2556) in paragraph at lines 5270--5273 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) 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/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1405] [1406] [1407] [1408] Underfull \hbox (badness 1142) in paragraph at lines 5527--5539 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1409] [1410] [1411] Underfull \hbox (badness 2503) in paragraph at lines 5679--5683 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 8132) in paragraph at lines 6183--6188 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 7081) in paragraph at lines 6461--6464 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6465--6467 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1425] [1426] [1427] [1428] [1429] Underfull \vbox (badness 3803) has occurred while \output is active [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] Underfull \hbox (badness 10000) in paragraph at lines 7310--7313 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 2626) in paragraph at lines 8954--8957 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1465] Underfull \hbox (badness 2503) in paragraph at lines 9061--9065 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1466] Underfull \hbox (badness 2564) 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/zi4/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 [1467] [1468] [1469] [1470] [1471] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9435--9437 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] 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 [1487] [1488] [1489] [1490] [1491] 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 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10730--10733 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1492] 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: [1493] [1494] [1495] [1496] [1497] [1498] 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 1867) in paragraph at lines 11209--11218 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1499] [1500] [1501] [1502] [1503] Underfull \hbox (badness 10000) 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/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1504] [1505] [1506]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} [1507] [1508] Underfull \hbox (badness 1484) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] 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/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1519] [1520] [1521] [1522] [1523] [1524] 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 [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] 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 [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] 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 [1547] [1548] Underfull \hbox (badness 10000) in paragraph at lines 14271--14275 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14278--14280 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] Underfull \hbox (badness 2503) in paragraph at lines 15346--15350 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] Underfull \hbox (badness 1584) in paragraph at lines 15858--15864 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1 /ptm/m/n/10 and [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] 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 [1601] [1602] Underfull \vbox (badness 10000) has occurred while \output is active [1603] Underfull \vbox (badness 10000) has occurred while \output is active [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] Underfull \hbox (badness 1377) in paragraph at lines 18445--18450 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) 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 1454) in paragraph at lines 18463--18467 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18471--18475 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1617] [1618] [1619] Underfull \vbox (badness 10000) has occurred while \output is active [1620] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18695--18695 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18698--18698 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1621] [1622] [1623] [1624] [1625] [1626] 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 [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] 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 [1636] [1637] [1638] [1639] [1640] Underfull \hbox (badness 5563) in paragraph at lines 19864--19866 []\T1/ptm/m/n/10 logical. If \T1/zi4/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 [1641] [1642] [1643] [1644] [1645] [1646] Underfull \hbox (badness 2503) in paragraph at lines 20242--20245 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1647] Underfull \hbox (badness 10000) in paragraph at lines 20269--20271 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] Underfull \hbox (badness 10000) in paragraph at lines 21342--21348 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] 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 [1688] [1689] [1690] [1691] [1692] [1693] [1694] [1695] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23251--23251 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1696] [1697] [1698] [1699] [1700] 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 [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] 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/zi4/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1710] Underfull \hbox (badness 3690) in paragraph at lines 24139--24143 [][][]\T1/zi4/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 [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718] Underfull \hbox (badness 2165) in paragraph at lines 24616--24621 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1719] [1720] [1721] [1722] 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/zi4/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/zi4/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 Underfull \hbox (badness 1132) in paragraph at lines 24834--24838 \T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o f un-de-ter-mined co-ef-fi-cients, e.g., for [1723] [1724] [1725] [1726] [1727] [1728] [1729] Underfull \hbox (badness 10000) in paragraph at lines 25306--25311 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \vbox (badness 10000) has occurred while \output is active [1746] Underfull \hbox (badness 3514) in paragraph at lines 26362--26367 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1747] [1748] Underfull \hbox (badness 3514) in paragraph at lines 26458--26463 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1749] Underfull \hbox (badness 3514) in paragraph at lines 26544--26549 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1750] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26596--26596 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1751] Underfull \hbox (badness 3514) in paragraph at lines 26632--26638 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1752] [1753] [1754] [1755] Underfull \hbox (badness 3514) in paragraph at lines 26846--26851 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1756] [1757] Underfull \hbox (badness 3514) in paragraph at lines 26933--26938 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1758] Underfull \hbox (badness 3514) in paragraph at lines 26998--27003 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1759] [1760] Underfull \hbox (badness 3514) in paragraph at lines 27092--27097 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1761] Underfull \hbox (badness 6691) in paragraph at lines 27184--27189 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] 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/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] [1780] Underfull \hbox (badness 5431) 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/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1781] [1782] [1783] Underfull \hbox (badness 5431) 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/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1784] [1785] [1786] [1787] [1788] [1789] 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 [1790] [1791] 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/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1792] [1793] 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 [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] Underfull \hbox (badness 10000) in paragraph at lines 30274--30278 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect [1813] [1814] [1815] Underfull \vbox (badness 10000) has occurred while \output is active [1816] [1817] [1818] 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 [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] 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 [1828] Underfull \hbox (badness 2142) in paragraph at lines 31242--31247 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/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 [1829] [1830] [1831] [1832] [1833] [1834] Underfull \hbox (badness 10000) in paragraph at lines 31647--31652 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1835] [1836] [1837]) (./stats4-pkg.tex [1838] Chapter 11. [1839] [1840] [1841] [1842] [1843] [1844]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1845] [1846] [1847] [1848]) (./tcltk-pkg.tex Chapter 12. [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \vbox (badness 10000) has occurred while \output is active [1856] Underfull \vbox (badness 10000) has occurred while \output is active [1857] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] [1868] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/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/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1869]) (./tools-pkg.tex [1870] Chapter 13. [1871] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1872] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/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 [1873] [1874] Underfull \hbox (badness 1308) 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 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1875] [1876] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1877] [1878] [1879] [1880] [1881] [1882] [1883] Underfull \vbox (badness 10000) has occurred while \output is active [1884] [1885] [1886] [1887] 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 [1888] 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- [1889] 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-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1199--1202 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1890] [1891] [1892] 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 [1893] [1894] [1895] Underfull \hbox (badness 2293) in paragraph at lines 1551--1553 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1896] [1897] 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 Underfull \hbox (badness 1082) in paragraph at lines 1696--1698 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1898] [1899] [1900] [1901]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1902] [1903] [1904] [1905] [1906] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2195--2195 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1907] [1908] [1909] 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 [1910] [1911] [1912] [1913] [1914] [1915] [1916] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2829. [1917] [1918] [1919] [1920] Underfull \hbox (badness 1424) in paragraph at lines 3111--3113 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1921] [1922] [1923] [1924] [1925] [1926] [1927] [1928] [1929] [1930] [1931] [1932] 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 , [1933] [1934] Underfull \hbox (badness 10000) in paragraph at lines 3950--3953 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1935] [1936] 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 [1937] [1938] [1939] Underfull \hbox (badness 1838) in paragraph at lines 4257--4263 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4257--4263 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1940] Underfull \hbox (badness 5726) in paragraph at lines 4337--4342 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4337--4342 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1941] [1942] [1943] Underfull \hbox (badness 2197) in paragraph at lines 4486--4496 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4486--4496 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1944] 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 [1945] [1946] [1947]) (./utils-pkg.tex [1948] Chapter 14. [1949] Underfull \hbox (badness 2556) 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/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 10000) in paragraph at lines 620--626 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 620--626 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1958] [1959] Underfull \hbox (badness 5847) in paragraph at lines 753--759 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 753--759 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1960] Underfull \hbox (badness 3861) in paragraph at lines 821--826 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1961] [1962] [1963] Underfull \hbox (badness 1430) in paragraph at lines 992--999 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 992--999 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 992--999 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. 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 [1964] [1965] [1966] Underfull \vbox (badness 10000) has occurred while \output is active [1967] [1968] [1969] [1970] [1971] Underfull \hbox (badness 1371) in paragraph at lines 1482--1484 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1972] [1973] [1974] [1975] [1976] [1977] [1978] Underfull \hbox (badness 2057) in paragraph at lines 1959--1961 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1979] [1980] 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/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1981] 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 [1982] [1983] [1984] [1985] Underfull \hbox (badness 1661) in paragraph at lines 2374--2381 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2390--2393 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1986] [1987] [1988] [1989] [1990] [1991] [1992] Underfull \hbox (badness 10000) in paragraph at lines 2800--2804 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2805--2808 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002] Underfull \hbox (badness 1430) 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/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [2003] 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 [2004] [2005] Underfull \hbox (badness 10000) in paragraph at lines 3686--3688 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow nload.file[][][] \T1/ptm/m/n/10 and [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016]pdf TeX warning (ext4): destination with the same identifier (name{Rfn.format}) 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} [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] Underfull \hbox (badness 1371) in paragraph at lines 5377--5379 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [2033] 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 [2034] [2035] [2036] 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, [2037] 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 [2038] [2039] 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 [2040] 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 [2041] Underfull \hbox (badness 1325) in paragraph at lines 5980--5984 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [2042] 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/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2043] Underfull \hbox (badness 3219) in paragraph at lines 6136--6143 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "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 [2044] [2045] Underfull \hbox (badness 10000) in paragraph at lines 6236--6241 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] Underfull \hbox (badness 10000) in paragraph at lines 7669--7671 []\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 7683--7685 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7691--7696 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] 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 [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] [2091] Underfull \hbox (badness 1097) in paragraph at lines 9118--9121 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2092] Underfull \hbox (badness 3000) in paragraph at lines 9254--9259 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2093] [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] Underfull \hbox (badness 2134) in paragraph at lines 9837--9842 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2102] [2103] [2104] [2105] [2106] [2107] [2108] Underfull \hbox (badness 5077) in paragraph at lines 10262--10266 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/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 2469) in paragraph at lines 10274--10278 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 10274--10278 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2109] [2110] [2111] [2112] [2113] Underfull \hbox (badness 4060) in paragraph at lines 10551--10554 []\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 10574--10574 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2114] Underfull \hbox (badness 10000) in paragraph at lines 10637--10639 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2115] [2116] [2117] Underfull \hbox (badness 2150) in paragraph at lines 10813--10815 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2118] [2119] [2120] [2121] Underfull \hbox (badness 10000) in paragraph at lines 11032--11036 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow 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 [2122] [2123] Underfull \hbox (badness 2096) in paragraph at lines 11181--11184 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 11185--11188 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether JPEG fig-ures should be gen-er-ated. Ig-nored if [2124] 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 [2125] [2126] [2127] [2128] [2129] Underfull \hbox (badness 3780) in paragraph at lines 11563--11567 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 11579--11582 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2130] [2131] [2132] [2133] [2134] [2135] Underfull \hbox (badness 2818) in paragraph at lines 11948--11953 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have 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 [2136] [2137] [2138] [2139] [2140] Underfull \hbox (badness 10000) in paragraph at lines 12220--12222 []\T1/ptm/m/n/10 Options other than \T1/zi4/m/sl/10 memory = "none" \T1/ptm/m/n /10 ap-ply only to files pro-duced by [2141] [2142] Underfull \hbox (badness 1057) in paragraph at lines 12377--12384 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in turn, [2143] [2144] [2145] [2146] Underfull \hbox (badness 3612) in paragraph at lines 12659--12663 []\T1/ptm/m/n/10 NetBSD prior to 8.0 used flag `\T1/zi4/m/sl/10 --xz\T1/ptm/m/n /10 ' rather than `\T1/zi4/m/sl/10 -J\T1/ptm/m/n/10 ', so this should be used \ T1/ptm/m/it/10 via Underfull \hbox (badness 6510) in paragraph at lines 12674--12678 []\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a ble Underfull \hbox (badness 10000) in paragraph at lines 12681--12684 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 12681--12684 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] Underfull \hbox (badness 10000) in paragraph at lines 13290--13295 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 3861) in paragraph at lines 13290--13295 [][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n /10 and 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/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av ailable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 1297) in paragraph at lines 13326--13331 \T1/zi4/m/sl/10 available.packages(contriburl = contriburl, method = method) \T 1/ptm/m/n/10 and hence by [2157] Underfull \hbox (badness 10000) in paragraph at lines 13355--13358 [][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [2158] [2159] [2160] [2161] Overfull \hbox (23.85939pt too wide) in paragraph at lines 13597--13600 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](, package = "") [2162] [2163] 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, [2164] 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 [2165] [2166] [2167] [2168]) (./refman.ind [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] Overfull \hbox (33.3567pt too wide) in paragraph at lines 8658--8660 []\T1/zi4/m/it/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [2218] [2219] [2220] [2221] [2222] [2223] Overfull \hbox (20.8567pt too wide) in paragraph at lines 9958--9960 []\T1/zi4/m/it/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE [2224] [2225] [2226] [2227] [2228] [2229] [2230] Overfull \hbox (5.8567pt too wide) in paragraph at lines 11665--11667 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends Overfull \hbox (5.8567pt too wide) in paragraph at lines 11667--11669 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_results [2231] Overfull \hbox (5.8567pt too wide) in paragraph at lines 11669--11671 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings [2232] [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240]) (./refman.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.lmList} 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.survreg} 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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/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/ texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/usr/share/texlive/texmf-dis t/fonts/enc/dvips/inconsolata/i4-t1-0.enc}< /usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb> Output written on refman.pdf (2271 pages, 6102507 bytes). Transcript written on refman.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-admin.t2d/pdf/xtr/R-ad min.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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.) Writing index file R-admin.vr (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] Cross reference values unknown; you must run TeX again. [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] Chapter 3 [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] 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_ [23] Chapter 5 [24] Chapter 6 [25] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2035--2035 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [26] [27] Underfull \hbox (badness 6842) in paragraph at lines 2229--2240 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- [28] [29] [30] [31] [32] [33] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2702--2702 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2722--2722 []@texttt .../bin/i386/Rcmd check -l @textttsl lib-dir @texttt --extra-arch -- install=check:@textttsl pkg@texttt .log @textttsl pkg[] [34] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2723--2723 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [35] [36] [37] Chapter 8 [38] Chapter 9 [39] [40] [41] [42] Appendix A [43] [44] Overfull \hbox (49.43388pt too wide) in paragraph at lines 3355--3355 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [45] [46] [47] [48] Overfull \hbox (14.94176pt too wide) in paragraph at lines 3626--3626 []@texttt JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.191-1.b12.fc28.x86_6 4/jre[] [49] [50] [51] [52] [53] [54] Appendix B [55] [56] [57] [58] [59] [60] Appendix C [61] [62] [63] [64] [65] [66] Overfull \hbox (78.17732pt too wide) in paragraph at lines 5036--5036 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] Overfull \hbox (72.42863pt too wide) in paragraph at lines 5042--5042 []@texttt CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.s dk/usr/include"[] [67] Overfull \hbox (78.17732pt too wide) in paragraph at lines 5134--5134 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] [68] Overfull \hbox (106.92076pt 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[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5206--5206 []@texttt --enable-memory-profiling --enable-R-framework --x-libraries=/opt/X1 1/lib[] [69] [70] Underfull \hbox (badness 10000) in paragraph at lines 5311--5316 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run Overfull \hbox (20.69044pt too wide) in paragraph at lines 5335--5335 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_191.jdk/Content s/Home[] [71] [72] Overfull \hbox (32.18782pt too wide) in paragraph at lines 5504--5504 []@texttt R_LD_LIBRARY_PATH="/opt/developerstudio12.6/lib:/usr/local/lib:/opt/ csw/lib"[] [73] [74] Underfull \hbox (badness 10000) in paragraph at lines 5613--5619 @texttt LDFLAGS=-L/usr/local/lib/amd64[] @textrm or @texttt LDFLAGS=-L/usr/loca l/lib/sparcv9[] @textrm as Overfull \hbox (26.43913pt too wide) in paragraph at lines 5628--5628 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] 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 [75] [76] [77] [78] Appendix D [79] [80] [81] (Function and variable index) [82] No file R-admin.vrs. (Concept index) [83] No file R-admin.cps. (Environment variable index) [84] No file R-admin.ens. [85] ) (see the transcript file for additional information) Output written on R-admin.pdf (88 pages, 484274 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-admin.t2d/pdf/xtr/R-ad min.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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.) Writing index file R-admin.vr (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-admin.toc [-1] [-2]) [-3] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-admin.toc) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-admin.toc) Chapter 1 (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-admin.aux) Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] Chapter 3 [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] 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_ [23] Chapter 5 [24] Chapter 6 [25] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2035--2035 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [26] [27] Underfull \hbox (badness 6842) in paragraph at lines 2229--2240 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- [28] [29] [30] [31] [32] [33] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2702--2702 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2722--2722 []@texttt .../bin/i386/Rcmd check -l @textttsl lib-dir @texttt --extra-arch -- install=check:@textttsl pkg@texttt .log @textttsl pkg[] [34] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2723--2723 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [35] [36] [37] Chapter 8 [38] Chapter 9 [39] [40] [41] [42] Appendix A [43] [44] Overfull \hbox (49.43388pt too wide) in paragraph at lines 3355--3355 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [45] [46] [47] [48] Overfull \hbox (14.94176pt too wide) in paragraph at lines 3626--3626 []@texttt JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.191-1.b12.fc28.x86_6 4/jre[] [49] [50] [51] [52] [53] [54] Appendix B [55] [56] [57] [58] [59] [60] Appendix C [61] [62] [63] [64] [65] [66] Overfull \hbox (78.17732pt too wide) in paragraph at lines 5036--5036 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] Overfull \hbox (72.42863pt too wide) in paragraph at lines 5042--5042 []@texttt CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.s dk/usr/include"[] [67] Overfull \hbox (78.17732pt too wide) in paragraph at lines 5134--5134 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] [68] Overfull \hbox (106.92076pt 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[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5206--5206 []@texttt --enable-memory-profiling --enable-R-framework --x-libraries=/opt/X1 1/lib[] [69] [70] Underfull \hbox (badness 10000) in paragraph at lines 5311--5316 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run Overfull \hbox (20.69044pt too wide) in paragraph at lines 5335--5335 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_191.jdk/Content s/Home[] [71] [72] Overfull \hbox (32.18782pt too wide) in paragraph at lines 5504--5504 []@texttt R_LD_LIBRARY_PATH="/opt/developerstudio12.6/lib:/usr/local/lib:/opt/ csw/lib"[] [73] [74] Underfull \hbox (badness 10000) in paragraph at lines 5613--5619 @texttt LDFLAGS=-L/usr/local/lib/amd64[] @textrm or @texttt LDFLAGS=-L/usr/loca l/lib/sparcv9[] @textrm as Overfull \hbox (26.43913pt too wide) in paragraph at lines 5628--5628 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] 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 [75] [76] [77] [78] Appendix D [79] [80] [81] (Function and variable index) [82] (Concept index) [83] (Environment variable index) [84] [85] ) (see the transcript file for additional information) Output written on R-admin.pdf (90 pages, 529802 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-admin.t2d/pdf/xtr/R-ad min.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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.) Writing index file R-admin.vr (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-admin.toc [-1] [-2]) [-3] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-admin.toc) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-admin.toc) Chapter 1 (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-admin.aux) Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] Chapter 3 [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] 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_ [23] Chapter 5 [24] Chapter 6 [25] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2035--2035 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [26] [27] Underfull \hbox (badness 6842) in paragraph at lines 2229--2240 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- [28] [29] [30] [31] [32] [33] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2702--2702 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl lib-dir @text tt --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2722--2722 []@texttt .../bin/i386/Rcmd check -l @textttsl lib-dir @texttt --extra-arch -- install=check:@textttsl pkg@texttt .log @textttsl pkg[] [34] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2723--2723 []@texttt .../bin/x64/Rcmd check -l @textttsl lib-dir @texttt --extra-arch --i nstall=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [35] [36] [37] Chapter 8 [38] Chapter 9 [39] [40] [41] [42] Appendix A [43] [44] Overfull \hbox (49.43388pt too wide) in paragraph at lines 3355--3355 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [45] [46] [47] [48] Overfull \hbox (14.94176pt too wide) in paragraph at lines 3626--3626 []@texttt JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.191-1.b12.fc28.x86_6 4/jre[] [49] [50] [51] [52] [53] [54] Appendix B [55] [56] [57] [58] [59] [60] Appendix C [61] [62] [63] [64] [65] [66] Overfull \hbox (78.17732pt too wide) in paragraph at lines 5036--5036 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] Overfull \hbox (72.42863pt too wide) in paragraph at lines 5042--5042 []@texttt CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.s dk/usr/include"[] [67] Overfull \hbox (78.17732pt too wide) in paragraph at lines 5134--5134 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] [68] Overfull \hbox (106.92076pt 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[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5206--5206 []@texttt --enable-memory-profiling --enable-R-framework --x-libraries=/opt/X1 1/lib[] [69] [70] Underfull \hbox (badness 10000) in paragraph at lines 5311--5316 []@textrm To see what com-pat-i-ble ver-sions of Java are cur-rently in-stalled , run Overfull \hbox (20.69044pt too wide) in paragraph at lines 5335--5335 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_191.jdk/Content s/Home[] [71] [72] Overfull \hbox (32.18782pt too wide) in paragraph at lines 5504--5504 []@texttt R_LD_LIBRARY_PATH="/opt/developerstudio12.6/lib:/usr/local/lib:/opt/ csw/lib"[] [73] [74] Underfull \hbox (badness 10000) in paragraph at lines 5613--5619 @texttt LDFLAGS=-L/usr/local/lib/amd64[] @textrm or @texttt LDFLAGS=-L/usr/loca l/lib/sparcv9[] @textrm as Overfull \hbox (26.43913pt too wide) in paragraph at lines 5628--5628 []@texttt JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/s olaris"[] 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 [75] [76] [77] [78] Appendix D [79] [80] [81] (Function and variable index) [82] (Concept index) [83] (Environment variable index) [84] [85] ) (see the transcript file for additional information) Output written on R-admin.pdf (90 pages, 529802 bytes). Transcript written on R-admin.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-data.texi This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-data.t2d/pdf/xtr/R-dat a.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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.) Writing index file R-data.vr (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87 @texttt package=DBI[]@textrm )[][]| Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt org / Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88 @texttt package=dataframes2xls[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 89--89 [][]@textbf foreign Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89 @texttt package=foreign[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 90--90 [][]@textbf gdata Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91 @texttt package=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf rJava Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92 @texttt package=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf RJDBC Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt org / Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt org / Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt org / Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt org / Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Writing index file R-data.cp Cross reference values unknown; you must run TeX again. [4] [5] [6] [7] Chapter 2 [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16] Chapter 4 [17] [18] [19] [20] [21] [22] [23] Chapter 5 [24] Chapter 6 [25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32] Appendix A [33] (Function and variable index) [34] No file R-data.vrs. (Concept index) [35] No file R-data.cps. [36] ) (see the transcript file for additional information) Output written on R-data.pdf (39 pages, 272953 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-data.t2d/pdf/xtr/R-dat a.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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.) Writing index file R-data.vr (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-data.toc [-1]) [-2] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-data.toc) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-data.toc) (Acknowledgements) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-data.aux) Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87 @texttt package=DBI[]@textrm )[][]| Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt org / Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88 @texttt package=dataframes2xls[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 89--89 [][]@textbf foreign Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89 @texttt package=foreign[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 90--90 [][]@textbf gdata Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91 @texttt package=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf rJava Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92 @texttt package=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf RJDBC Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt org / Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt org / Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt org / Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt org / Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Writing index file R-data.cp [4] [5] [6] [7] Chapter 2 [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16] Chapter 4 [17] [18] [19] [20] [21] [22] [23] Chapter 5 [24] Chapter 6 [25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32] Appendix A [33] (Function and variable index) [34] [35] (Concept index) [36] [37] Overfull \vbox (7.16699pt too high) has occurred while \output is active [38] ) (see the transcript file for additional information) Output written on R-data.pdf (42 pages, 312849 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-data.t2d/pdf/xtr/R-dat a.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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.) Writing index file R-data.vr (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-data.toc [-1]) [-2] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-data.toc) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-data.toc) (Acknowledgements) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-data.aux) Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87 @texttt package=DBI[]@textrm )[][]| Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt org / Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88 @texttt package=dataframes2xls[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 89--89 [][]@textbf foreign Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89 @texttt package=foreign[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 90--90 [][]@textbf gdata Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91 @texttt package=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf rJava Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92 @texttt package=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf RJDBC Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt org / Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt org / Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt org / Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt org / Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Writing index file R-data.cp [4] [5] [6] [7] Chapter 2 [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16] Chapter 4 [17] [18] [19] [20] [21] [22] [23] Chapter 5 [24] Chapter 6 [25] Chapter 7 [26] [27] [28] [29] [30] Chapter 8 [31] Chapter 9 [32] Appendix A [33] (Function and variable index) [34] [35] (Concept index) [36] [37] Overfull \vbox (7.16699pt too high) has occurred while \output is active [38] ) (see the transcript file for additional information) Output written on R-data.pdf (42 pages, 312848 bytes). Transcript written on R-data.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-exts.t2d/pdf/xtr/R-ext s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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.) Writing index file R-exts.vr (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Chapter 1 [1] Writing index file R-exts.cp Cross reference values unknown; you must run TeX again. [2] [3] [4] [5] 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] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1917--1917 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [25] [26] [27] [28] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2271--2271 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] [29] Overfull \hbox (53.60722pt too wide) in paragraph at lines 2273--2273 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [30] [31] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2415--2415 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [32] Underfull \hbox (badness 10000) in paragraph at lines 2527--2529 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [33] [34] Overfull \hbox (60.93126pt too wide) in paragraph at lines 2654--2654 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [35] [36] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2799--2801 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] Overfull \hbox (53.86903pt too wide) in paragraph at lines 4635--4635 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 4637--4637 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (65.36641pt 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")[] Overfull \hbox (76.86378pt too wide) in paragraph at lines 4653--4653 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [60] [61] [62] [63] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4951--4951 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [64] [65] [66] Overfull \hbox (30.87428pt too wide) in paragraph at lines 5157--5157 []@texttt abs acos atan calloc ceil div exp fabs floor fmod free log malloc me mcpy[] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5158--5158 []@texttt memset pow printf qsort round sin sprintf sqrt strcmp strcpy strerro r[] [67] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5252--5252 []@texttt erf expm1 fmin fmax lgamma lround loglp round snprintf strcasecmp tr unc[] [68] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5284--5284 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5318--5318 []@texttt #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__) )[] [69] [70] [71] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5546--5546 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [72] [73] [74] Chapter 2 [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] 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 [89] [90] [91] [92] 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 [93] [94] Chapter 3 [95] [96] [97] [98] [99] [100] [101] Overfull \hbox (20.69044pt too wide) in paragraph at lines 7726--7726 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [102] [103] [104] Chapter 4 [105] [106] [107] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8103--8103 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [108] Overfull \hbox (25.25755pt too wide) in paragraph at lines 8144--8144 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [109] Overfull \hbox (20.53261pt too wide) in paragraph at lines 8248--8248 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] [110] Overfull \hbox (38.96663pt too wide) in paragraph at lines 8278--8287 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [111] [112] [113] Overfull \hbox (44.18301pt too wide) in paragraph at lines 8555--8556 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [114] [115] Overfull \hbox (78.17732pt too wide) in paragraph at lines 8688--8688 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Overfull \hbox (29.50735pt too wide) in paragraph at lines 8716--8718 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8729--8729 []@texttt null,object-size,pointer-overflow,return,returns-nonnull-attribute,s hift,[] Overfull \hbox (32.18782pt too wide) in paragraph at lines 8730--8730 []@texttt signed-integer-overflow,unreachable,unsigned-integer-overflow,vla-bo und,vptr[] [116] Underfull \hbox (badness 8151) 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 @texttt -fsanitize=undefined[]@textrm , but can be spec-i-fied sep-a-rately. It adds op-tions [117] Overfull \hbox (72.42863pt 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[] [118] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8896--8896 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8899--8899 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [119] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8978--8978 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [120] [121] Chapter 5 [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] Overfull \hbox (30.87428pt too wide) in paragraph at lines 9946--9946 [] @texttt double *w, int *iper, double *span, double *al pha,[] Overfull \hbox (51.66371pt too wide) in paragraph at lines 9995--9995 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [133] [134] [135] [136] [137] [138] [139] [140] Overfull \hbox (37.93651pt too wide) in paragraph at lines 10574--10574 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11346--11346 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [151] 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 [152] [153] [154] [155] [156] [157] [158] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11929--11929 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [159] [160] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12052--12052 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12057--12057 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12112--12112 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [161] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12124--12124 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [162] Overfull \hbox (26.43913pt too wide) in paragraph at lines 12223--12223 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [163] [164] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12359--12359 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [165] Overfull \hbox (43.6852pt too wide) in paragraph at lines 12440--12440 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [166] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12528--12528 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] Underfull \hbox (badness 10000) in paragraph at lines 13688--13692 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [180] [181] Warning: unbalanced parentheses in @def... [182] Overfull \hbox (26.43913pt too wide) in paragraph at lines 13899--13899 [] @texttt void (*clean)(void *data, Rboolean jump), void *cdata,[] [183] [184] [185] [186] [187] Chapter 7 [188] [189] Chapter 8 [190] [191] [192] Overfull \hbox (43.6852pt too wide) in paragraph at lines 14647--14647 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [193] Overfull \hbox (20.69044pt too wide) in paragraph at lines 14690--14690 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 14706--14706 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [194] [195] [196] [197] Underfull \hbox (badness 10000) in paragraph at lines 14949--14956 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [198] [199] [200] [201] [202] Underfull \hbox (badness 10000) in paragraph at lines 15332--15336 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [203] No file R-exts.vrs. (Concept index) [204] No file R-exts.cps. [205] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl Output written on R-exts.pdf (208 pages, 900949 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-exts.t2d/pdf/xtr/R-ext s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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.) Writing index file R-exts.vr (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-exts.toc [-1] [-2] [-3] [-4]) [-5] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-exts.toc) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-exts.toc) (Acknowledgements) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-exts.aux) Chapter 1 [1] Writing index file R-exts.cp [2] [3] [4] [5] 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] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1917--1917 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [25] [26] [27] [28] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2271--2271 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] [29] Overfull \hbox (53.60722pt too wide) in paragraph at lines 2273--2273 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [30] [31] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2415--2415 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [32] Underfull \hbox (badness 10000) in paragraph at lines 2527--2529 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [33] [34] Overfull \hbox (60.93126pt too wide) in paragraph at lines 2654--2654 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [35] [36] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2799--2801 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] Overfull \hbox (53.86903pt too wide) in paragraph at lines 4635--4635 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 4637--4637 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (65.36641pt 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")[] Overfull \hbox (76.86378pt too wide) in paragraph at lines 4653--4653 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [60] [61] [62] [63] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4951--4951 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [64] [65] [66] Overfull \hbox (30.87428pt too wide) in paragraph at lines 5157--5157 []@texttt abs acos atan calloc ceil div exp fabs floor fmod free log malloc me mcpy[] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5158--5158 []@texttt memset pow printf qsort round sin sprintf sqrt strcmp strcpy strerro r[] [67] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5252--5252 []@texttt erf expm1 fmin fmax lgamma lround loglp round snprintf strcasecmp tr unc[] [68] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5284--5284 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5318--5318 []@texttt #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__) )[] [69] [70] [71] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5546--5546 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [72] [73] [74] Chapter 2 [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] 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 [89] [90] [91] [92] 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 [93] [94] Chapter 3 [95] [96] [97] [98] [99] [100] [101] Overfull \hbox (20.69044pt too wide) in paragraph at lines 7726--7726 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [102] [103] [104] Chapter 4 [105] [106] [107] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8103--8103 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [108] Overfull \hbox (25.25755pt too wide) in paragraph at lines 8144--8144 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [109] Overfull \hbox (20.53261pt too wide) in paragraph at lines 8248--8248 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] [110] Overfull \hbox (38.96663pt too wide) in paragraph at lines 8278--8287 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [111] [112] [113] Overfull \hbox (44.18301pt too wide) in paragraph at lines 8555--8556 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [114] [115] Overfull \hbox (78.17732pt too wide) in paragraph at lines 8688--8688 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Overfull \hbox (29.50735pt too wide) in paragraph at lines 8716--8718 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8729--8729 []@texttt null,object-size,pointer-overflow,return,returns-nonnull-attribute,s hift,[] Overfull \hbox (32.18782pt too wide) in paragraph at lines 8730--8730 []@texttt signed-integer-overflow,unreachable,unsigned-integer-overflow,vla-bo und,vptr[] [116] Underfull \hbox (badness 8151) 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 @texttt -fsanitize=undefined[]@textrm , but can be spec-i-fied sep-a-rately. It adds op-tions [117] Overfull \hbox (72.42863pt 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[] [118] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8896--8896 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8899--8899 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [119] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8978--8978 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [120] [121] Chapter 5 [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] Overfull \hbox (30.87428pt too wide) in paragraph at lines 9946--9946 [] @texttt double *w, int *iper, double *span, double *al pha,[] Overfull \hbox (51.66371pt too wide) in paragraph at lines 9995--9995 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [133] [134] [135] [136] [137] [138] [139] [140] Overfull \hbox (37.93651pt too wide) in paragraph at lines 10574--10574 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11346--11346 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [151] 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 [152] [153] [154] [155] [156] [157] [158] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11929--11929 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [159] [160] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12052--12052 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12057--12057 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12112--12112 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [161] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12124--12124 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [162] Overfull \hbox (26.43913pt too wide) in paragraph at lines 12223--12223 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [163] [164] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12359--12359 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [165] Overfull \hbox (43.6852pt too wide) in paragraph at lines 12440--12440 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [166] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12528--12528 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] Underfull \hbox (badness 10000) in paragraph at lines 13688--13692 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [180] Warning: unbalanced parentheses in @def... [181] [182] Overfull \hbox (26.43913pt too wide) in paragraph at lines 13899--13899 [] @texttt void (*clean)(void *data, Rboolean jump), void *cdata,[] [183] [184] [185] [186] [187] Chapter 7 [188] [189] Chapter 8 [190] [191] [192] Overfull \hbox (43.6852pt too wide) in paragraph at lines 14647--14647 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [193] Overfull \hbox (20.69044pt too wide) in paragraph at lines 14690--14690 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 14706--14706 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [194] [195] [196] [197] Underfull \hbox (badness 10000) in paragraph at lines 14949--14956 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [198] [199] [200] [201] [202] Underfull \hbox (badness 10000) in paragraph at lines 15332--15336 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [203] [204] [205] [206] (Concept index) [207] [208] [209] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss10.pfb> Output written on R-exts.pdf (216 pages, 965353 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-exts.t2d/pdf/xtr/R-ext s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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.) Writing index file R-exts.vr (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-exts.toc [-1] [-2] [-3] [-4]) [-5] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-exts.toc) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-exts.toc) (Acknowledgements) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-exts.aux) Chapter 1 [1] Writing index file R-exts.cp [2] [3] [4] [5] 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] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1917--1917 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [25] [26] [27] [28] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2271--2271 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] [29] Overfull \hbox (53.60722pt too wide) in paragraph at lines 2273--2273 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [30] [31] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2415--2415 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [32] Underfull \hbox (badness 10000) in paragraph at lines 2527--2529 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [33] [34] Overfull \hbox (60.93126pt too wide) in paragraph at lines 2654--2654 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [35] [36] Overfull \hbox (2.98494pt too wide) in paragraph at lines 2799--2801 [][][]@smallrm On sys-tems which use sub-architectures, architecture-specific v er-sions such as @smalltt ~/.R/check.Renviron.i386[] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] Overfull \hbox (53.86903pt too wide) in paragraph at lines 4635--4635 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 4637--4637 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (65.36641pt 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")[] Overfull \hbox (76.86378pt too wide) in paragraph at lines 4653--4653 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [60] [61] [62] [63] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4951--4951 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [64] [65] [66] Overfull \hbox (30.87428pt too wide) in paragraph at lines 5157--5157 []@texttt abs acos atan calloc ceil div exp fabs floor fmod free log malloc me mcpy[] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5158--5158 []@texttt memset pow printf qsort round sin sprintf sqrt strcmp strcpy strerro r[] [67] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5252--5252 []@texttt erf expm1 fmin fmax lgamma lround loglp round snprintf strcasecmp tr unc[] [68] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5284--5284 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5318--5318 []@texttt #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__) )[] [69] [70] [71] Overfull \hbox (13.62822pt too wide) in paragraph at lines 5546--5546 []@texttt #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String )[] [72] [73] [74] Chapter 2 [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] 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 [89] [90] [91] [92] 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 [93] [94] Chapter 3 [95] [96] [97] [98] [99] [100] [101] Overfull \hbox (20.69044pt too wide) in paragraph at lines 7726--7726 [] @texttt as.integer(runif(N, 1, 12)), as.integer(runif(N, 1, 28)))[] [102] [103] [104] Chapter 4 [105] [106] [107] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8103--8103 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [108] Overfull \hbox (25.25755pt too wide) in paragraph at lines 8144--8144 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [109] Overfull \hbox (20.53261pt too wide) in paragraph at lines 8248--8248 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] [110] Overfull \hbox (38.96663pt too wide) in paragraph at lines 8278--8287 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [111] [112] [113] Overfull \hbox (44.18301pt too wide) in paragraph at lines 8555--8556 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [114] [115] Overfull \hbox (78.17732pt too wide) in paragraph at lines 8688--8688 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Overfull \hbox (29.50735pt too wide) in paragraph at lines 8716--8718 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8729--8729 []@texttt null,object-size,pointer-overflow,return,returns-nonnull-attribute,s hift,[] Overfull \hbox (32.18782pt too wide) in paragraph at lines 8730--8730 []@texttt signed-integer-overflow,unreachable,unsigned-integer-overflow,vla-bo und,vptr[] [116] Underfull \hbox (badness 8151) 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 @texttt -fsanitize=undefined[]@textrm , but can be spec-i-fied sep-a-rately. It adds op-tions [117] Overfull \hbox (72.42863pt 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[] [118] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8896--8896 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 8899--8899 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [119] Overfull \hbox (26.43913pt too wide) in paragraph at lines 8978--8978 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [120] [121] Chapter 5 [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] Overfull \hbox (30.87428pt too wide) in paragraph at lines 9946--9946 [] @texttt double *w, int *iper, double *span, double *al pha,[] Overfull \hbox (51.66371pt too wide) in paragraph at lines 9995--9995 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [133] [134] [135] [136] [137] [138] [139] [140] Overfull \hbox (37.93651pt too wide) in paragraph at lines 10574--10574 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11346--11346 [] @texttt if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FAL SE");[] [151] 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 [152] [153] [154] [155] [156] [157] [158] Overfull \hbox (14.94176pt too wide) in paragraph at lines 11929--11929 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [159] [160] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12052--12052 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12057--12057 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12112--12112 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] [161] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12124--12124 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [162] Overfull \hbox (26.43913pt too wide) in paragraph at lines 12223--12223 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [163] [164] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12359--12359 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [165] Overfull \hbox (43.6852pt too wide) in paragraph at lines 12440--12440 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [166] Overfull \hbox (14.94176pt too wide) in paragraph at lines 12528--12528 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_SYMBOL, CE_ANY} cety pe_t;[] Chapter 6 [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] Underfull \hbox (badness 10000) in paragraph at lines 13688--13692 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [180] Warning: unbalanced parentheses in @def... [181] [182] Overfull \hbox (26.43913pt too wide) in paragraph at lines 13899--13899 [] @texttt void (*clean)(void *data, Rboolean jump), void *cdata,[] [183] [184] [185] [186] [187] Chapter 7 [188] [189] Chapter 8 [190] [191] [192] Overfull \hbox (43.6852pt too wide) in paragraph at lines 14647--14647 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [193] Overfull \hbox (20.69044pt too wide) in paragraph at lines 14690--14690 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 14706--14706 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [194] [195] [196] [197] Underfull \hbox (badness 10000) in paragraph at lines 14949--14956 @texttt modules/internet/nanoftp.c[]@textrm , @texttt src/modules/internet/nan ohttp.c[] @textrm and @texttt src/ [198] [199] [200] [201] [202] Underfull \hbox (badness 10000) in paragraph at lines 15332--15336 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [203] [204] [205] [206] (Concept index) [207] [208] [209] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl < /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss10.pfb> Output written on R-exts.pdf (216 pages, 965398 bytes). Transcript written on R-exts.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ. texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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/tex/texinfo/txi-en.tex) [1{/var/lib/texmf/fonts/map/pdftex/up dmap/pdftex.map}] [-1] Chapter 1 Cross reference values unknown; you must run TeX again. [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] Writing index file R-FAQ.fn [40] [41] [42] 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 [43] Chapter 8 [44] Chapter 9 [45] [46] Chapter 10 [47] [48] [49] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (51 pages, 366415 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ. texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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/tex/texinfo/txi-en.tex) [1{/var/lib/texmf/fonts/map/pdftex/up dmap/pdftex.map}] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-FAQ.toc) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-FAQ.toc) Chapter 1 (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] Writing index file R-FAQ.fn [40] [41] [42] 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 [43] Chapter 8 [44] Chapter 9 [45] [46] Chapter 10 [47] [48] [49] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (53 pages, 382769 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ. texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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/tex/texinfo/txi-en.tex) [1{/var/lib/texmf/fonts/map/pdftex/up dmap/pdftex.map}] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-FAQ.toc) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-FAQ.toc) Chapter 1 (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] Writing index file R-FAQ.fn [40] [41] [42] 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 [43] Chapter 8 [44] Chapter 9 [45] [46] Chapter 10 [47] [48] [49] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (53 pages, 382767 bytes). Transcript written on R-FAQ.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-intro.t2d/pdf/xtr/R-in tro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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.) Writing index file R-intro.vr (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Preface) Cross reference values unknown; you must run TeX again. Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] [15] Chapter 4 [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34] Chapter 8 [35] [36] [37] [38] [39] [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Chapter 11 [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] Chapter 12 [67] [68] [69] [70] [71] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5741--5741 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{ n-x})))[] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] Chapter 13 [82] Underfull \hbox (badness 10000) in paragraph at lines 6447--6452 []@textrm Users con-nected to the In-ter-net can use the @texttt install.packag es()[] @textrm and [83] Chapter 14 [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and [86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95] [96] [97] [98] Appendix C [99] [100] Appendix D [101] No file R-intro.vrs. Appendix E [102] No file R-intro.cps. Appendix F [103] [104] ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb> Output written on R-intro.pdf (107 pages, 584239 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-intro.t2d/pdf/xtr/R-in tro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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.) Writing index file R-intro.vr (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-intro.toc) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-intro.toc) (Preface) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-intro.aux) Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] [15] Chapter 4 [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34] Chapter 8 [35] [36] [37] [38] [39] [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Chapter 11 [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] Chapter 12 [67] [68] [69] [70] [71] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5741--5741 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{ n-x})))[] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] Chapter 13 [82] Underfull \hbox (badness 10000) in paragraph at lines 6447--6452 []@textrm Users con-nected to the In-ter-net can use the @texttt install.packag es()[] @textrm and [83] Chapter 14 [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and [86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95] [96] [97] [98] Appendix C [99] [100] Appendix D [101] [102] [103] Appendix E [104] [105] Appendix F [106] [107] ) (see the transcript file for additional information) Output written on R-intro.pdf (113 pages, 633804 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-intro.t2d/pdf/xtr/R-in tro.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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.) Writing index file R-intro.vr (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-intro.toc) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-intro.toc) (Preface) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-intro.aux) Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] [15] Chapter 4 [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34] Chapter 8 [35] [36] [37] [38] [39] [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Chapter 11 [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] Chapter 12 [67] [68] [69] [70] [71] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5741--5741 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{ n-x})))[] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] Chapter 13 [82] Underfull \hbox (badness 10000) in paragraph at lines 6447--6452 []@textrm Users con-nected to the In-ter-net can use the @texttt install.packag es()[] @textrm and [83] Chapter 14 [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and [86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95] [96] [97] [98] Appendix C [99] [100] Appendix D [101] [102] [103] Appendix E [104] [105] Appendix F [106] [107] ) (see the transcript file for additional information) Output written on R-intro.pdf (113 pages, 633859 bytes). Transcript written on R-intro.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-ints.t2d/pdf/xtr/R-int s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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.) Writing index file R-ints.vr (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] Overfull \hbox (49.43388pt too wide) in paragraph at lines 1455--1455 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1456--1456 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt 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 (158.65895pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [19] [20] [21] [22] [23] [24] Chapter 2 [25] Overfull \hbox (26.43913pt too wide) in paragraph at lines 1983--1983 [] @texttt if (!is.character(x)) x <- structure(as.character(x), names = na mes(x))[] [26] [27] [28] [29] Chapter 3 [30] [31] Chapter 4 [32] [33] Chapter 5 [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] Chapter 7 [48] Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [49] Chapter 8 [50] [51] [52] [53] [54] Underfull \hbox (badness 10000) in paragraph at lines 4031--4039 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u sed for Underfull \hbox (badness 7869) in paragraph at lines 4031--4039 @textrm an-a-lyz-ing pack-age code. E.g., use @texttt _R_CHECK_CODETOOLS_PROFI LE_ Underfull \hbox (badness 10000) in paragraph at lines 4031--4039 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [55] [56] [57] [58] [59] Chapter 9 [60] [61] Chapter 10 [62] Chapter 11 [63] Chapter 12 [64] [65] (Function and variable index) [66] [67] No file R-ints.vrs. (Concept index) [68] No file R-ints.cps. [69] ) (see the transcript file for additional information) Output written on R-ints.pdf (72 pages, 397796 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-ints.t2d/pdf/xtr/R-int s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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.) Writing index file R-ints.vr (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-ints.toc [-1] [-2]) [-3] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-ints.toc) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-ints.toc) Chapter 1 (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-ints.aux) Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] Overfull \hbox (49.43388pt too wide) in paragraph at lines 1455--1455 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1456--1456 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt 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 (158.65895pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [19] [20] [21] [22] [23] [24] Chapter 2 [25] Overfull \hbox (26.43913pt too wide) in paragraph at lines 1983--1983 [] @texttt if (!is.character(x)) x <- structure(as.character(x), names = na mes(x))[] [26] [27] [28] [29] Chapter 3 [30] [31] Chapter 4 [32] [33] Chapter 5 [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] Chapter 7 [48] Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [49] Chapter 8 [50] [51] [52] [53] [54] Underfull \hbox (badness 10000) in paragraph at lines 4031--4039 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u sed for Underfull \hbox (badness 7869) in paragraph at lines 4031--4039 @textrm an-a-lyz-ing pack-age code. E.g., use @texttt _R_CHECK_CODETOOLS_PROFI LE_ Underfull \hbox (badness 10000) in paragraph at lines 4031--4039 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [55] [56] [57] [58] [59] Chapter 9 [60] [61] Chapter 10 [62] Chapter 11 [63] Chapter 12 [64] [65] (Function and variable index) [66] [67] [68] (Concept index) [69] [70] ) (see the transcript file for additional information) Output written on R-ints.pdf (75 pages, 447722 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-ints.t2d/pdf/xtr/R-int s.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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.) Writing index file R-ints.vr (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-ints.toc [-1] [-2]) [-3] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-ints.toc) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-ints.toc) Chapter 1 (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-ints.aux) Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] Overfull \hbox (49.43388pt too wide) in paragraph at lines 1455--1455 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1456--1456 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 1457--1457 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (158.65895pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [19] [20] [21] [22] [23] [24] Chapter 2 [25] Overfull \hbox (26.43913pt too wide) in paragraph at lines 1983--1983 [] @texttt if (!is.character(x)) x <- structure(as.character(x), names = na mes(x))[] [26] [27] [28] [29] Chapter 3 [30] [31] Chapter 4 [32] [33] Chapter 5 [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] Chapter 7 [48] Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [49] Chapter 8 [50] [51] [52] [53] [54] Underfull \hbox (badness 10000) in paragraph at lines 4031--4039 @texttt CRAN . R-project . org / package=codetools[]@textrm )[][] func-tions u sed for Underfull \hbox (badness 7869) in paragraph at lines 4031--4039 @textrm an-a-lyz-ing pack-age code. E.g., use @texttt _R_CHECK_CODETOOLS_PROFI LE_ Underfull \hbox (badness 10000) in paragraph at lines 4031--4039 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [55] [56] [57] [58] [59] Chapter 9 [60] [61] Chapter 10 [62] Chapter 11 [63] Chapter 12 [64] [65] (Function and variable index) [66] [67] [68] (Concept index) [69] [70] ) (see the transcript file for additional information) Output written on R-ints.pdf (75 pages, 447719 bytes). Transcript written on R-ints.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-lang.t2d/pdf/xtr/R-lan g.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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.) Writing index file R-lang.vr (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-lang.cp Chapter 2 [1] [2] Cross reference values unknown; you must run TeX again. Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] [8] Chapter 3 [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Chapter 4 [24] [25] [26] [27] [28] Chapter 5 [29] [30] [31] [32] [33] [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] Chapter 7 [44] [45] Chapter 8 [46] [47] Chapter 9 [48] [49] [50] Chapter 10 [51] [52] [53] [54] [55] [56] [57] [58] (Function and Variable Index) [59] No file R-lang.vrs. (Concept Index) [60] No file R-lang.cps. Appendix A [61] [62] ) (see the transcript file for additional information) Output written on R-lang.pdf (65 pages, 330468 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-lang.t2d/pdf/xtr/R-lan g.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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.) Writing index file R-lang.vr (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-lang.toc [-1] [-2]) [-3] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-lang.toc) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-lang.toc) Chapter 1 (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-lang.aux) Writing index file R-lang.cp Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] [8] Chapter 3 [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Chapter 4 [24] [25] [26] [27] [28] Chapter 5 [29] [30] [31] [32] [33] [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] Chapter 7 [44] [45] Chapter 8 [46] [47] Chapter 9 [48] [49] [50] Chapter 10 [51] [52] [53] [54] [55] [56] [57] [58] (Function and Variable Index) [59] [60] (Concept Index) [61] Appendix A [62] Overfull \vbox (22.9195pt too high) has occurred while \output is active [63] [64] ) (see the transcript file for additional information) Output written on R-lang.pdf (69 pages, 379380 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-lang.t2d/pdf/xtr/R-lan g.texi (/usr/share/texmf/tex/texinfo/texinfo.tex Loading texinfo [version 2016-08-16.20]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/root/git/r-backports/stretch/r-base-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.) Writing index file R-lang.vr (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-defs.texi (/usr/share/texmf/tex/texinfo/txi-en.tex)) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/version.texi) [1{/var/li b/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-lang.toc [-1] [-2]) [-3] (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-lang.toc) (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-lang.toc) Chapter 1 (/root/git/r-backports/stretch/r-base-3.5.2/doc/manual/R-lang.aux) Writing index file R-lang.cp Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] [8] Chapter 3 [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Chapter 4 [24] [25] [26] [27] [28] Chapter 5 [29] [30] [31] [32] [33] [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] Chapter 7 [44] [45] Chapter 8 [46] [47] Chapter 9 [48] [49] [50] Chapter 10 [51] [52] [53] [54] [55] [56] [57] [58] (Function and Variable Index) [59] [60] (Concept Index) [61] Appendix A [62] Overfull \vbox (22.9195pt too high) has occurred while \output is active [63] [64] ) (see the transcript file for additional information) Output written on R-lang.pdf (69 pages, 379395 bytes). Transcript written on R-lang.log. make[1]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' /usr/bin/make -k pdf make[1]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' PDF/LaTeX documentation: full reference index ... This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./fullrefman.tex LaTeX2e <2017/01/01> patch level 3 Babel <3.9r> and hyphenation patterns for 3 language(s) loaded. 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(/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/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/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . 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The sim-plest is in [98] [99] [100] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6438--6440 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [101] [102] Underfull \hbox (badness 10000) in paragraph at lines 6580--6583 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [103] [104] Underfull \hbox (badness 1442) in paragraph at lines 6762--6768 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a 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 [105] Underfull \hbox (badness 3568) in paragraph at lines 6824--6831 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [106] [107] Underfull \vbox (badness 10000) has occurred while \output is active [108] Underfull \vbox (badness 10000) has occurred while \output is active [109] [110] Underfull \hbox (badness 1077) in paragraph at lines 7141--7147 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7141--7147 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [111] [112] [113] [114] [115] [116] Underfull \hbox (badness 2096) in paragraph at lines 7482--7486 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [117] [118] Underfull \hbox (badness 3000) in paragraph at lines 7575--7577 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7600--7603 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [119] [120] [121] [122] Underfull \hbox (badness 10000) in paragraph at lines 7855--7865 []\T1/zi4/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 [123] Underfull \hbox (badness 4479) in paragraph at lines 7926--7936 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] Underfull \hbox (badness 1394) in paragraph at lines 9685--9690 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [150] [151] [152] [153] [154] [155] Underfull \hbox (badness 1194) in paragraph at lines 10030--10035 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) 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/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [156] [157] [158] Underfull \hbox (badness 1735) in paragraph at lines 10235--10239 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [159] [160] [161] [162] [163] [164] 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 Underfull \hbox (badness 6396) in paragraph at lines 10672--10680 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for [165] Underfull \hbox (badness 2735) 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/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] 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 [182] [183] [184] [185] [186] [187] [188] [189] [190] Underfull \hbox (badness 2698) in paragraph at lines 12358--12367 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/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-lowed Underfull \hbox (badness 4341) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [191] [192] [193] [194] [195] Underfull \vbox (badness 3803) has occurred while \output is active [196] [197] [198] [199] [200] Underfull \hbox (badness 6236) in paragraph at lines 13017--13020 []\T1/ptm/m/n/10 For \T1/zi4/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 [201] [202] [203] [204] [205] [206] 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 [207] Underfull \hbox (badness 1565) in paragraph at lines 13510--13514 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [208] 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/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with [209] [210] Underfull \hbox (badness 1466) in paragraph at lines 13694--13697 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [211] [212] Underfull \hbox (badness 10000) in paragraph at lines 13813--13817 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13824--13827 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [213] [214] [215] [216] [217] 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, [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 4429) 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/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [230] Underfull \hbox (badness 10000) in paragraph at lines 14968--14970 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 []\T1/zi4/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, so [231] Underfull \hbox (badness 10000) in paragraph at lines 15013--15017 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/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 4156) in paragraph at lines 15013--15017 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [232] [233] [234] [235] [236] [237] [238] [239] [240] Underfull \hbox (badness 2452) in paragraph at lines 15605--15609 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15605--15609 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [241] [242] [243] Underfull \hbox (badness 1092) in paragraph at lines 15778--15783 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [244] [245] [246] Underfull \hbox (badness 6741) in paragraph at lines 16029--16033 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [247] [248] [249] [250] [251] 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 [252] [253] [254] [255] Underfull \vbox (badness 10000) has occurred while \output is active [256] [257] [258] Underfull \hbox (badness 3679) in paragraph at lines 16745--16747 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [259] [260] [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 1478) in paragraph at lines 17310--17313 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [267] [268] [269] Underfull \hbox (badness 10000) in paragraph at lines 17563--17565 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] Underfull \hbox (badness 1442) in paragraph at lines 18154--18156 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [280] Underfull \hbox (badness 2452) in paragraph at lines 18246--18262 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [281] [282] [283] [284] [285] [286] [287] Underfull \hbox (badness 1248) in paragraph at lines 18660--18663 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [288] [289] [290] [291] 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 [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] Underfull \hbox (badness 2469) in paragraph at lines 19935--19940 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 19949--19956 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [309] Underfull \hbox (badness 10000) in paragraph at lines 20023--20027 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20023--20027 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [310] [311] Underfull \hbox (badness 1509) in paragraph at lines 20158--20165 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 20158--20165 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 20174--20179 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] Underfull \hbox (badness 1264) 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-ported: Underfull \hbox (badness 4441) in paragraph at lines 20954--20957 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] Underfull \hbox (badness 10000) in paragraph at lines 21701--21703 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] Underfull \hbox (badness 1077) in paragraph at lines 22736--22742 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [352] [353] [354] Underfull \hbox (badness 1484) in paragraph at lines 22899--22907 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [355] [356] [357] [358] [359] Underfull \hbox (badness 2790) in paragraph at lines 23184--23187 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 23184--23187 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [360] [361] [362] [363] Underfull \hbox (badness 1194) in paragraph at lines 23466--23469 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [364] [365] [366] Underfull \hbox (badness 10000) in paragraph at lines 23672--23678 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23672--23678 \T1/ptm/m/n/10 list, i.e., \T1/zi4/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 [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 10000) in paragraph at lines 24053--24056 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [373] [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 10000) in paragraph at lines 24655--24657 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [382] [383] [384] [385] Underfull \hbox (badness 1199) in paragraph at lines 24899--24905 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24899--24905 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [386] [387] [388] [389] [390] [391] [392] [393] Underfull \hbox (badness 1038) in paragraph at lines 25491--25499 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially [394] Underfull \hbox (badness 1881) in paragraph at lines 25500--25503 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 25519--25521 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [395] Underfull \hbox (badness 10000) in paragraph at lines 25628--25638 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25639--25645 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able [396] Underfull \hbox (badness 1968) in paragraph at lines 25675--25680 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment 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 [397] [398] [399] Underfull \hbox (badness 10000) 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/zi4/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/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 25961--25964 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) 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 [400] Underfull \hbox (badness 10000) in paragraph at lines 26019--26024 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 26025--26036 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 26037--26040 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 3713) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 26047--26059 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). Underfull \hbox (badness 2351) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , 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/zi4/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/zi4/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 Underfull \hbox (badness 1874) in paragraph at lines 26061--26068 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [401] [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [406] [407] [408] [409] [410] Underfull \hbox (badness 1735) in paragraph at lines 26724--26728 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [411] [412] [413] [414] [415] [416] [417] [418] [419] [420] Underfull \hbox (badness 2726) in paragraph at lines 27299--27302 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] [431] [432] [433] Underfull \hbox (badness 1052) in paragraph at lines 28131--28136 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [434] [435] [436] [437] [438] Underfull \vbox (badness 10000) has occurred while \output is active [439] [440] [441] [442] [443] [444] [445] [446] 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 [447] [448] Underfull \hbox (badness 1163) in paragraph at lines 29131--29142 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] Underfull \hbox (badness 10000) in paragraph at lines 30664--30668 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 30664--30668 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [473] Underfull \hbox (badness 6188) in paragraph at lines 30686--30688 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [474] [475] [476] [477] [478] [479] [480] [481] Underfull \hbox (badness 1655) in paragraph at lines 31229--31231 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [493] [494] [495] [496] 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 3333) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/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 [497] [498] [499] Underfull \hbox (badness 2261) in paragraph at lines 32344--32349 []\T1/ptm/m/n/10 If \T1/zi4/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 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 [500] Underfull \hbox (badness 10000) in paragraph at lines 32447--32452 []\T1/ptm/m/n/10 Note that since \T1/zi4/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 [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] Underfull \vbox (badness 3803) has occurred while \output is active [540] [541] [542] [543] [544] [545] [546] [547] Underfull \hbox (badness 1072) in paragraph at lines 35489--35493 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 35494--35498 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', 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/zi4/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/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in [548] Underfull \hbox (badness 3343) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 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 Underfull \hbox (badness 1917) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [549] [550] [551] [552] [553] 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/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35875--35881 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] [581] [582] [583] Underfull \hbox (badness 3333) in paragraph at lines 37745--37750 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [584] [585] [586] [587] [588] [589] Underfull \vbox (badness 10000) has occurred while \output is active [590] [591] [592] [593] [594] Underfull \hbox (badness 1472) in paragraph at lines 38377--38380 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] Underfull \vbox (badness 3803) has occurred while \output is active [608] Underfull \hbox (badness 10000) in paragraph at lines 39283--39287 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/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., [609] [610] [611] [612] Underfull \hbox (badness 10000) in paragraph at lines 39533--39536 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [613] [614] Underfull \hbox (badness 10000) in paragraph at lines 39651--39655 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [615] Underfull \hbox (badness 10000) in paragraph at lines 39713--39717 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [616] [617] [618] [619] [620] [621] [622] [623] [624] Underfull \hbox (badness 4013) in paragraph at lines 40326--40328 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [625] [626] [627] [628] [629] [630] Underfull \vbox (badness 10000) has occurred while \output is active [631] [632] [633] [634] [635] [636] [637] [638] 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 1990) in paragraph at lines 41214--41222 []\T1/zi4/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 4846) 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/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [639] [640] [641] [642] 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. [643] [644] [645] [646] Underfull \hbox (badness 1917) in paragraph at lines 41719--41726 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] 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 [658] [659] Underfull \hbox (badness 2401) in paragraph at lines 42568--42572 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [660] [661] [662] Underfull \hbox (badness 2111) in paragraph at lines 42757--42762 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 7362) in paragraph at lines 42773--42778 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [663] [664] [665] [666] [667] [668] [669] [670] [671] Underfull \hbox (badness 5417) in paragraph at lines 43354--43358 []\T1/zi4/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 [672] Underfull \hbox (badness 10000) in paragraph at lines 43415--43419 []\T1/zi4/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 [673] [674]) (./compiler-pkg.tex Chapter 2. [675] [676] [677] [678]) (./datasets-pkg.tex Chapter 3. [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] 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. [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] Overfull \vbox (19.74611pt too high) has occurred while \output is active [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] Underfull \vbox (badness 10000) has occurred while \output is active [747] [748] [749] [750] Underfull \vbox (badness 10000) has occurred while \output is active [751] [752] [753] [754] [755] [756] Overfull \vbox (18.9959pt too high) has occurred while \output is active [757] [758] [759]) (./grDevices-pkg.tex [760] Chapter 4. [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] 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 [778] [779] [780] [781] Underfull \hbox (badness 1852) in paragraph at lines 1279--1282 []\T1/zi4/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 [782] [783] [784] Underfull \hbox (badness 1490) in paragraph at lines 1485--1490 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [787] [788] [789] [790] Underfull \hbox (badness 1325) in paragraph at lines 1891--1901 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [791] [792] 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 [793] [794] [795] 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 [796] [797] [798] [799] [800] [801] [802] [803] [804] Underfull \hbox (badness 10000) in paragraph at lines 2750--2751 [805] [806] [807] [808] [809] [810] [811] [812] Underfull \hbox (badness 10000) in paragraph at lines 3248--3253 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [813] [814] [815] [816] Underfull \hbox (badness 3302) in paragraph at lines 3514--3517 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827] [828] [829] [830] Underfull \hbox (badness 1067) in paragraph at lines 4355--4362 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [831] [832] [833] Underfull \hbox (badness 1789) in paragraph at lines 4595--4597 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [834] Underfull \hbox (badness 1377) in paragraph at lines 4645--4650 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [835] Underfull \hbox (badness 2671) 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/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4721--4728 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, 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 [836] [837] Underfull \hbox (badness 1377) in paragraph at lines 4850--4855 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb" \T1/ptm/m/n/10 (which is RGB+gray) and [838] 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 [839] [840] Underfull \hbox (badness 2035) in paragraph at lines 5034--5043 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [841] Underfull \hbox (badness 10000) in paragraph at lines 5102--5109 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5102--5109 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [842] [843] [844] Underfull \hbox (badness 1546) in paragraph at lines 5244--5252 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [845] 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 [846] [847] [848] [849] [850] [851] [852] Underfull \hbox (badness 10000) in paragraph at lines 5772--5775 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [853] [854] [855] [856] [857] [858] 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 [859] [860] Underfull \hbox (badness 10000) in paragraph at lines 6267--6269 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [861] [862] [863] [864] Underfull \hbox (badness 3780) in paragraph at lines 6558--6564 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [865] [866] [867] Underfull \hbox (badness 2680) in paragraph at lines 6759--6761 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [868] [869] [870]) (./graphics-pkg.tex Chapter 5. [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] Underfull \hbox (badness 10000) in paragraph at lines 687--694 []\T1/zi4/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/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] Underfull \hbox (badness 4634) in paragraph at lines 1262--1265 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] 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 [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] Underfull \vbox (badness 10000) has occurred while \output is active [931] [932] [933] [934] 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 [935] [936] [937] [938] [939] [940] [941] [942] 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 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 [943] [944] [945] [946] [947] Underfull \hbox (badness 10000) 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/zi4/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4785--4791 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [948] [949] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 <"/root/git/r-backports/stretch/r-base-3.5.2/library/graphics/help/figures/"mai .pdf, id=15783, 289.08pt x 289.08pt> [950 ] Underfull \hbox (badness 10000) in paragraph at lines 4977--4979 <"/root/git/r-backports/stretch/r-base-3.5.2/library/graphics/help/figures/"oma .pdf, id=15796, 259.97125pt x 332.24126pt> Underfull \vbox (badness 10000) has occurred while \output is active [951] [952 ] [953] Underfull \hbox (badness 10000) in paragraph at lines 5167--5169 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [954] Underfull \vbox (badness 3803) has occurred while \output is active [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] <"/root/git/r-backports/stretch/r-base-3.5.2/library/graphics/help/figures/"pch .pdf, id=16241, 361.35pt x 50.1875pt> Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639 [][] [977] [978 ] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] Underfull \hbox (badness 1048) in paragraph at lines 7347--7352 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [989] [990] Underfull \hbox (badness 1102) in paragraph at lines 7463--7466 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] Underfull \hbox (badness 1043) in paragraph at lines 8304--8308 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [1005] [1006] [1007] [1008] [1009] [1010] [1011] 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 [1012]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8805 \HeaderA{units}{Graphical Units}{units} [1013] [1014] [1015] [1016]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1017] [1018] [1019] [1020] [1021] [1022] Underfull \hbox (badness 2680) in paragraph at lines 392--395 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] Underfull \hbox (badness 4279) in paragraph at lines 972--981 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] 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 [1090] [1091] [1092] [1093] 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 [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] 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., [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] 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 [1124] [1125] [1126] [1127]) (./methods-pkg.tex [1128] Chapter 7. [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] Underfull \vbox (badness 3803) has occurred while \output is active [1137] Underfull \vbox (badness 10000) has occurred while \output is active [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] Underfull \hbox (badness 1077) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests [1156] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 1981--1986 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1157] [1158] [1159] Underfull \hbox (badness 1242) 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/zi4/m/n/10 where = [1160] [1161] [1162] [1163] [1164] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1165] [1166] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in [1167] Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1168] [1169] [1170] [1171] [1172] [1173] [1174] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1175] [1176] [1177] [1178] [1179] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments [1180] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1181] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [1182] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3846--3847 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] Underfull \hbox (badness 1436) in paragraph at lines 4443--4446 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4472--4478 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1193] Underfull \hbox (badness 1092) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] Underfull \vbox (badness 10000) has occurred while \output is active [1203] [1204] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1205] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1206] 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 [1207] [1208] [1209] [1210] 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 [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1219] [1220] [1221] [1222] Underfull \vbox (badness 10000) has occurred while \output is active [1223] [1224] [1225] [1226]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1227] [1228] [1229]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate 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} [1230] 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 [1231] [1232] [1233] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] Underfull \vbox (badness 10000) has occurred while \output is active [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274] [1275] 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., [1276] [1277] [1278] [1279]) (./parallel-pkg.tex [1280] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] Underfull \hbox (badness 3386) in paragraph at lines 1339--1342 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1302] [1303] [1304]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319]) (./stats-pkg.tex [1320] Chapter 10. [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] Underfull \hbox (badness 1412) in paragraph at lines 847--849 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] Underfull \hbox (badness 2503) in paragraph at lines 1328--1331 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1342] [1343] [1344] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1345] [1346] [1347] [1348] 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 1546) in paragraph at lines 1773--1777 \T1/zi4/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can han-dle miss-ing [1349] [1350] [1351] [1352] [1353] [1354] [1355] 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 [1356] [1357] [1358] [1359] [1360] 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 [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] 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 [1373] [1374] Underfull \hbox (badness 2503) in paragraph at lines 3390--3393 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] 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 = [1395] [1396] Underfull \hbox (badness 3612) in paragraph at lines 4754--4756 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por t aliased co-ef-fi-cients (see [][]\T1/zi4/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b y de-fault where [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] Underfull \hbox (badness 2556) in paragraph at lines 5270--5273 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) 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/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1405] [1406] [1407] [1408] Underfull \hbox (badness 1142) in paragraph at lines 5527--5539 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1409] [1410] [1411] Underfull \hbox (badness 2503) in paragraph at lines 5679--5683 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 8132) in paragraph at lines 6183--6188 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 7081) in paragraph at lines 6461--6464 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6465--6467 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1425] [1426] [1427] [1428] [1429] Underfull \vbox (badness 3803) has occurred while \output is active [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] Underfull \hbox (badness 10000) in paragraph at lines 7310--7313 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 2626) in paragraph at lines 8954--8957 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1465] Underfull \hbox (badness 2503) in paragraph at lines 9061--9065 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1466] Underfull \hbox (badness 2564) 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/zi4/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 [1467] [1468] [1469] [1470] [1471] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9435--9437 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] 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 [1487] [1488] [1489] [1490] [1491] 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 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10730--10733 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1492] 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: [1493] [1494] [1495] [1496] [1497] [1498] 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 1867) in paragraph at lines 11209--11218 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1499] [1500] [1501] [1502] [1503] Underfull \hbox (badness 10000) 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/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1504] [1505] [1506]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} [1507] [1508] Underfull \hbox (badness 1484) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] 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/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1519] [1520] [1521] [1522] [1523] [1524] 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 [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] 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 [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] 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 [1547] [1548] Underfull \hbox (badness 10000) in paragraph at lines 14271--14275 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14278--14280 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] Underfull \hbox (badness 2503) in paragraph at lines 15346--15350 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] Underfull \hbox (badness 1584) in paragraph at lines 15858--15864 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1 /ptm/m/n/10 and [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] 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 [1601] [1602] Underfull \vbox (badness 10000) has occurred while \output is active [1603] Underfull \vbox (badness 10000) has occurred while \output is active [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] Underfull \hbox (badness 1377) in paragraph at lines 18445--18450 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) 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 1454) in paragraph at lines 18463--18467 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18471--18475 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1617] [1618] [1619] Underfull \vbox (badness 10000) has occurred while \output is active [1620] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18695--18695 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18698--18698 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1621] [1622] [1623] [1624] [1625] [1626] 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 [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] 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 [1636] [1637] [1638] [1639] [1640] Underfull \hbox (badness 5563) in paragraph at lines 19864--19866 []\T1/ptm/m/n/10 logical. If \T1/zi4/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 [1641] [1642] [1643] [1644] [1645] [1646] Underfull \hbox (badness 2503) in paragraph at lines 20242--20245 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1647] Underfull \hbox (badness 10000) in paragraph at lines 20269--20271 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] Underfull \hbox (badness 10000) in paragraph at lines 21342--21348 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] 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 [1688] [1689] [1690] [1691] [1692] [1693] [1694] [1695] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23251--23251 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1696] [1697] [1698] [1699] [1700] 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 [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] 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/zi4/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1710] Underfull \hbox (badness 3690) in paragraph at lines 24139--24143 [][][]\T1/zi4/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 [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718] Underfull \hbox (badness 2165) in paragraph at lines 24616--24621 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1719] [1720] [1721] [1722] 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/zi4/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/zi4/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 Underfull \hbox (badness 1132) in paragraph at lines 24834--24838 \T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o f un-de-ter-mined co-ef-fi-cients, e.g., for [1723] [1724] [1725] [1726] [1727] [1728] [1729] Underfull \hbox (badness 10000) in paragraph at lines 25306--25311 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \vbox (badness 10000) has occurred while \output is active [1746] Underfull \hbox (badness 3514) in paragraph at lines 26362--26367 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1747] [1748] Underfull \hbox (badness 3514) in paragraph at lines 26458--26463 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1749] Underfull \hbox (badness 3514) in paragraph at lines 26544--26549 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1750] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26596--26596 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1751] Underfull \hbox (badness 3514) in paragraph at lines 26632--26638 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1752] [1753] [1754] [1755] Underfull \hbox (badness 3514) in paragraph at lines 26846--26851 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1756] [1757] Underfull \hbox (badness 3514) in paragraph at lines 26933--26938 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1758] Underfull \hbox (badness 3514) in paragraph at lines 26998--27003 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1759] [1760] Underfull \hbox (badness 3514) in paragraph at lines 27092--27097 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1761] Underfull \hbox (badness 6691) in paragraph at lines 27184--27189 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] 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/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] [1780] Underfull \hbox (badness 5431) 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/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1781] [1782] [1783] Underfull \hbox (badness 5431) 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/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1784] [1785] [1786] [1787] [1788] [1789] 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 [1790] [1791] 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/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1792] [1793] 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 [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] Underfull \hbox (badness 10000) in paragraph at lines 30274--30278 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect [1813] [1814] [1815] Underfull \vbox (badness 10000) has occurred while \output is active [1816] [1817] [1818] 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 [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] 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 [1828] Underfull \hbox (badness 2142) in paragraph at lines 31242--31247 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/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 [1829] [1830] [1831] [1832] [1833] [1834] Underfull \hbox (badness 10000) in paragraph at lines 31647--31652 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1835] [1836] [1837]) (./stats4-pkg.tex [1838] Chapter 11. [1839] [1840] [1841] [1842] [1843] [1844]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1845] [1846] [1847] [1848]) (./tcltk-pkg.tex Chapter 12. [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \vbox (badness 10000) has occurred while \output is active [1856] Underfull \vbox (badness 10000) has occurred while \output is active [1857] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] [1868] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/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/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1869]) (./tools-pkg.tex [1870] Chapter 13. [1871] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1872] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/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 [1873] [1874] Underfull \hbox (badness 1308) 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 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1875] [1876] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1877] [1878] [1879] [1880] [1881] [1882] [1883] Underfull \vbox (badness 10000) has occurred while \output is active [1884] [1885] [1886] [1887] 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 [1888] 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- [1889] 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-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1199--1202 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1890] [1891] [1892] 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 [1893] [1894] [1895] Underfull \hbox (badness 2293) in paragraph at lines 1551--1553 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1896] [1897] 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 Underfull \hbox (badness 1082) in paragraph at lines 1696--1698 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1898] [1899] [1900] [1901]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1902] [1903] [1904] [1905] [1906] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2195--2195 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1907] [1908] [1909] 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 [1910] [1911] [1912] [1913] [1914] [1915] [1916] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2829. [1917] [1918] [1919] [1920] Underfull \hbox (badness 1424) in paragraph at lines 3111--3113 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1921] [1922] [1923] [1924] [1925] [1926] [1927] [1928] [1929] [1930] [1931] [1932] 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 , [1933] [1934] Underfull \hbox (badness 10000) in paragraph at lines 3950--3953 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1935] [1936] 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 [1937] [1938] [1939] Underfull \hbox (badness 1838) in paragraph at lines 4257--4263 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4257--4263 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1940] Underfull \hbox (badness 5726) in paragraph at lines 4337--4342 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4337--4342 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1941] [1942] [1943] Underfull \hbox (badness 2197) in paragraph at lines 4486--4496 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4486--4496 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1944] 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 [1945] [1946] [1947]) (./utils-pkg.tex [1948] Chapter 14. [1949] Underfull \hbox (badness 2556) 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/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 10000) in paragraph at lines 620--626 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 620--626 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1958] [1959] Underfull \hbox (badness 5847) in paragraph at lines 753--759 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 753--759 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1960] Underfull \hbox (badness 3861) in paragraph at lines 821--826 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1961] [1962] [1963] Underfull \hbox (badness 1430) in paragraph at lines 992--999 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 992--999 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 992--999 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. 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 [1964] [1965] [1966] Underfull \vbox (badness 10000) has occurred while \output is active [1967] [1968] [1969] [1970] [1971] Underfull \hbox (badness 1371) in paragraph at lines 1482--1484 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1972] [1973] [1974] [1975] [1976] [1977] [1978] Underfull \hbox (badness 2057) in paragraph at lines 1959--1961 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1979] [1980] 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/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1981] 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 [1982] [1983] [1984] [1985] Underfull \hbox (badness 1661) in paragraph at lines 2374--2381 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2390--2393 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1986] [1987] [1988] [1989] [1990] [1991] [1992] Underfull \hbox (badness 10000) in paragraph at lines 2800--2804 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2805--2808 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002] Underfull \hbox (badness 1430) 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/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [2003] 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 [2004] [2005] Underfull \hbox (badness 10000) in paragraph at lines 3686--3688 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow nload.file[][][] \T1/ptm/m/n/10 and [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016]pdf TeX warning (ext4): destination with the same identifier (name{Rfn.format}) 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} [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] Underfull \hbox (badness 1371) in paragraph at lines 5377--5379 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [2033] 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 [2034] [2035] [2036] 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, [2037] 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 [2038] [2039] 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 [2040] 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 [2041] Underfull \hbox (badness 1325) in paragraph at lines 5980--5984 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [2042] 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/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2043] Underfull \hbox (badness 3219) in paragraph at lines 6136--6143 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "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 [2044] [2045] Underfull \hbox (badness 10000) in paragraph at lines 6236--6241 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] Underfull \hbox (badness 10000) in paragraph at lines 7669--7671 []\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 7683--7685 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7691--7696 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] 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 [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] [2091] Underfull \hbox (badness 1097) in paragraph at lines 9118--9121 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2092] Underfull \hbox (badness 3000) in paragraph at lines 9254--9259 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2093] [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] Underfull \hbox (badness 2134) in paragraph at lines 9837--9842 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2102] [2103] [2104] [2105] [2106] [2107] [2108] Underfull \hbox (badness 5077) in paragraph at lines 10262--10266 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/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 2469) in paragraph at lines 10274--10278 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 10274--10278 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2109] [2110] [2111] [2112] [2113] Underfull \hbox (badness 4060) in paragraph at lines 10551--10554 []\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 10574--10574 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2114] Underfull \hbox (badness 10000) in paragraph at lines 10637--10639 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. 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If [2125] [2126] [2127] [2128] [2129] Underfull \hbox (badness 3780) in paragraph at lines 11563--11567 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 11579--11582 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2130] [2131] [2132] [2133] [2134] [2135] Underfull \hbox (badness 2818) in paragraph at lines 11948--11953 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have 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 [2136] [2137] [2138] [2139] [2140] Underfull \hbox (badness 10000) in paragraph at lines 12220--12222 []\T1/ptm/m/n/10 Options other than \T1/zi4/m/sl/10 memory = "none" \T1/ptm/m/n /10 ap-ply only to files pro-duced by [2141] [2142] Underfull \hbox (badness 1057) in paragraph at lines 12377--12384 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in turn, [2143] [2144] [2145] [2146] Underfull \hbox (badness 3612) in paragraph at lines 12659--12663 []\T1/ptm/m/n/10 NetBSD prior to 8.0 used flag `\T1/zi4/m/sl/10 --xz\T1/ptm/m/n /10 ' rather than `\T1/zi4/m/sl/10 -J\T1/ptm/m/n/10 ', so this should be used \ T1/ptm/m/it/10 via Underfull \hbox (badness 6510) in paragraph at lines 12674--12678 []\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a ble Underfull \hbox (badness 10000) in paragraph at lines 12681--12684 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 12681--12684 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] Underfull \hbox (badness 10000) in paragraph at lines 13290--13295 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 3861) in paragraph at lines 13290--13295 [][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n /10 and 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/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av ailable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 1297) in paragraph at lines 13326--13331 \T1/zi4/m/sl/10 available.packages(contriburl = contriburl, method = method) \T 1/ptm/m/n/10 and hence by [2157] Underfull \hbox (badness 10000) in paragraph at lines 13355--13358 [][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [2158] [2159] [2160] [2161] Overfull \hbox (23.85939pt too wide) in paragraph at lines 13597--13600 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](, package = "") [2162] [2163] 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). 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LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.lmList} 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.survreg} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.stepAIC} has been referenced but does not exist , replaced 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 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Transcript written on fullrefman.log. This is makeindex, version 2.15 [TeX Live 2016] (kpathsea + Thai support). Scanning input file fullrefman.idx.................done (13579 entries accepted, 34 rejected). Sorting entries....................................................................................................................................................done (217268 comparisons). Generating output file fullrefman.ind................done (13394 lines written, 50 warnings). Output written in fullrefman.ind. Transcript written in fullrefman.ilg. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./fullrefman.tex LaTeX2e <2017/01/01> patch level 3 Babel <3.9r> and hyphenation patterns for 3 language(s) loaded. 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[1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/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/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 386--389 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) 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/zi4/m/n/10 insertions\T1/ptm/m/n/10 ', [9] [10] [11] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 2671) in paragraph at lines 1147--1150 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1922--1922 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [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] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] Underfull \vbox (badness 10000) has occurred while \output is active [51] [52] [53] [54] [55] [56] [57] 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 [58] [59] [60] [61] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3897--3897 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [62] [63] Underfull \hbox (badness 1057) in paragraph at lines 4005--4008 [][][]\T1/zi4/m/n/10 is.language[][][]() \T1/ptm/m/n/10 is also true for calls (but also for [][]\T1/zi4/m/n/10 symbol[][][]\T1/ptm/m/n/10 s and [][]\T1/zi4/m /n/10 expression[][][]\T1/ptm/m/n/10 s where [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] 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 [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6041--6041 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [95] [96] [97] Underfull \hbox (badness 2096) in paragraph at lines 6229--6242 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [98] [99] [100] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6438--6440 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [101] [102] Underfull \hbox (badness 10000) in paragraph at lines 6580--6583 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [103] [104] Underfull \hbox (badness 1442) in paragraph at lines 6762--6768 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a 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 [105] Underfull \hbox (badness 3568) in paragraph at lines 6824--6831 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [106] [107] Underfull \vbox (badness 10000) has occurred while \output is active [108] Underfull \vbox (badness 10000) has occurred while \output is active [109] [110] Underfull \hbox (badness 1077) in paragraph at lines 7141--7147 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater Underfull \hbox (badness 1231) in paragraph at lines 7141--7147 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [111] [112] [113] [114] [115] [116] Underfull \hbox (badness 2096) in paragraph at lines 7482--7486 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [117] [118] Underfull \hbox (badness 3000) in paragraph at lines 7575--7577 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7600--7603 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [119] [120] [121] [122] Underfull \hbox (badness 10000) in paragraph at lines 7855--7865 []\T1/zi4/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 [123] Underfull \hbox (badness 4479) in paragraph at lines 7926--7936 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] Underfull \hbox (badness 1394) in paragraph at lines 9685--9690 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [150] [151] [152] [153] [154] [155] Underfull \hbox (badness 1194) in paragraph at lines 10030--10035 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) 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/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [156] [157] [158] Underfull \hbox (badness 1735) in paragraph at lines 10235--10239 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [159] [160] [161] [162] [163] [164] 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 Underfull \hbox (badness 6396) in paragraph at lines 10672--10680 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for [165] Underfull \hbox (badness 2735) 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/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] 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 [182] [183] [184] [185] [186] [187] [188] [189] [190] Underfull \hbox (badness 2698) in paragraph at lines 12358--12367 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/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-lowed Underfull \hbox (badness 4341) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [191] [192] [193] [194] [195] Underfull \vbox (badness 3803) has occurred while \output is active [196] [197] [198] [199] [200] Underfull \hbox (badness 6236) in paragraph at lines 13017--13020 []\T1/ptm/m/n/10 For \T1/zi4/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 [201] [202] [203] [204] [205] [206] 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 [207] Underfull \hbox (badness 1565) in paragraph at lines 13510--13514 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [208] 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/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with [209] [210] Underfull \hbox (badness 1466) in paragraph at lines 13694--13697 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [211] [212] Underfull \hbox (badness 10000) in paragraph at lines 13813--13817 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13824--13827 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [213] [214] [215] [216] [217] 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, [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 4429) 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/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [230] Underfull \hbox (badness 10000) in paragraph at lines 14968--14970 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 []\T1/zi4/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, so [231] Underfull \hbox (badness 10000) in paragraph at lines 15013--15017 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/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 4156) in paragraph at lines 15013--15017 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [232] [233] [234] [235] [236] [237] [238] [239] [240] Underfull \hbox (badness 2452) in paragraph at lines 15605--15609 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15605--15609 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [241] [242] [243] Underfull \hbox (badness 1092) in paragraph at lines 15778--15783 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [244] [245] [246] Underfull \hbox (badness 6741) in paragraph at lines 16029--16033 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [247] [248] [249] [250] [251] 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 [252] [253] [254] [255] Underfull \vbox (badness 10000) has occurred while \output is active [256] [257] [258] Underfull \hbox (badness 3679) in paragraph at lines 16745--16747 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [259] [260] [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 1478) in paragraph at lines 17310--17313 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [267] [268] [269] Underfull \hbox (badness 10000) in paragraph at lines 17563--17565 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] Underfull \hbox (badness 1442) in paragraph at lines 18154--18156 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [280] Underfull \hbox (badness 2452) in paragraph at lines 18246--18262 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [281] [282] [283] [284] [285] [286] [287] Underfull \hbox (badness 1248) in paragraph at lines 18660--18663 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [288] [289] [290] [291] 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 [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] Underfull \hbox (badness 2469) in paragraph at lines 19935--19940 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 19949--19956 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [309] Underfull \hbox (badness 10000) in paragraph at lines 20023--20027 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20023--20027 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [310] [311] Underfull \hbox (badness 1509) in paragraph at lines 20158--20165 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 20158--20165 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 20174--20179 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] Underfull \hbox (badness 1264) 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-ported: Underfull \hbox (badness 4441) in paragraph at lines 20954--20957 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] Underfull \hbox (badness 10000) in paragraph at lines 21701--21703 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] Underfull \hbox (badness 1077) in paragraph at lines 22736--22742 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [352] [353] [354] Underfull \hbox (badness 1484) in paragraph at lines 22899--22907 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [355] [356] [357] [358] [359] Underfull \hbox (badness 2790) in paragraph at lines 23184--23187 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 23184--23187 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [360] [361] [362] [363] Underfull \hbox (badness 1194) in paragraph at lines 23466--23469 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [364] [365] [366] Underfull \hbox (badness 10000) in paragraph at lines 23672--23678 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23672--23678 \T1/ptm/m/n/10 list, i.e., \T1/zi4/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 [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 10000) in paragraph at lines 24053--24056 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [373] [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 10000) in paragraph at lines 24655--24657 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [382] [383] [384] [385] Underfull \hbox (badness 1199) in paragraph at lines 24899--24905 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24899--24905 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [386] [387] [388] [389] [390] [391] [392] [393] Underfull \hbox (badness 1038) in paragraph at lines 25491--25499 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially [394] Underfull \hbox (badness 1881) in paragraph at lines 25500--25503 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 25519--25521 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [395] Underfull \hbox (badness 10000) in paragraph at lines 25628--25638 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25639--25645 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able [396] Underfull \hbox (badness 1968) in paragraph at lines 25675--25680 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment 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 [397] [398] [399] Underfull \hbox (badness 10000) 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/zi4/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/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 25961--25964 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) 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 [400] Underfull \hbox (badness 10000) in paragraph at lines 26019--26024 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 26025--26036 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 26037--26040 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 3713) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 26047--26059 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). Underfull \hbox (badness 2351) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , 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/zi4/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/zi4/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 Underfull \hbox (badness 1874) in paragraph at lines 26061--26068 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [401] [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [406] [407] [408] [409] [410] Underfull \hbox (badness 1735) in paragraph at lines 26724--26728 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [411] [412] [413] [414] [415] [416] [417] [418] [419] [420] Underfull \hbox (badness 2726) in paragraph at lines 27299--27302 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] [431] [432] [433] Underfull \hbox (badness 1052) in paragraph at lines 28131--28136 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [434] [435] [436] [437] [438] Underfull \vbox (badness 10000) has occurred while \output is active [439] [440] [441] [442] [443] [444] [445] [446] 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 [447] [448] Underfull \hbox (badness 1163) in paragraph at lines 29131--29142 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] Underfull \hbox (badness 10000) in paragraph at lines 30664--30668 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 30664--30668 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [473] Underfull \hbox (badness 6188) in paragraph at lines 30686--30688 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [474] [475] [476] [477] [478] [479] [480] [481] Underfull \hbox (badness 1655) in paragraph at lines 31229--31231 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [493] [494] [495] [496] 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 3333) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/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 [497] [498] [499] Underfull \hbox (badness 2261) in paragraph at lines 32344--32349 []\T1/ptm/m/n/10 If \T1/zi4/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 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 [500] Underfull \hbox (badness 10000) in paragraph at lines 32447--32452 []\T1/ptm/m/n/10 Note that since \T1/zi4/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 [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] Underfull \vbox (badness 3803) has occurred while \output is active [540] [541] [542] [543] [544] [545] [546] [547] Underfull \hbox (badness 1072) in paragraph at lines 35489--35493 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 35494--35498 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', 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/zi4/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/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in [548] Underfull \hbox (badness 3343) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 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 Underfull \hbox (badness 1917) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [549] [550] [551] [552] [553] 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/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35875--35881 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] [581] [582] [583] Underfull \hbox (badness 3333) in paragraph at lines 37745--37750 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [584] [585] [586] [587] [588] [589] Underfull \vbox (badness 10000) has occurred while \output is active [590] [591] [592] [593] [594] Underfull \hbox (badness 1472) in paragraph at lines 38377--38380 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] Underfull \vbox (badness 3803) has occurred while \output is active [608] Underfull \hbox (badness 10000) in paragraph at lines 39283--39287 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/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., [609] [610] [611] [612] Underfull \hbox (badness 10000) in paragraph at lines 39533--39536 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [613] [614] Underfull \hbox (badness 10000) in paragraph at lines 39651--39655 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [615] Underfull \hbox (badness 10000) in paragraph at lines 39713--39717 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [616] [617] [618] [619] [620] [621] [622] [623] [624] Underfull \hbox (badness 4013) in paragraph at lines 40326--40328 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [625] [626] [627] [628] [629] [630] Underfull \vbox (badness 10000) has occurred while \output is active [631] [632] [633] [634] [635] [636] [637] [638] 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 1990) in paragraph at lines 41214--41222 []\T1/zi4/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 4846) 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/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [639] [640] [641] [642] 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. [643] [644] [645] [646] Underfull \hbox (badness 1917) in paragraph at lines 41719--41726 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] 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 [658] [659] Underfull \hbox (badness 2401) in paragraph at lines 42568--42572 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [660] [661] [662] Underfull \hbox (badness 2111) in paragraph at lines 42757--42762 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 7362) in paragraph at lines 42773--42778 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [663] [664] [665] [666] [667] [668] [669] [670] [671] Underfull \hbox (badness 5417) in paragraph at lines 43354--43358 []\T1/zi4/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 [672] Underfull \hbox (badness 10000) in paragraph at lines 43415--43419 []\T1/zi4/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 [673] [674]) (./compiler-pkg.tex Chapter 2. [675] [676] [677] [678]) (./datasets-pkg.tex Chapter 3. [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] 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. [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] Overfull \vbox (19.74611pt too high) has occurred while \output is active [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] Underfull \vbox (badness 10000) has occurred while \output is active [747] [748] [749] [750] Underfull \vbox (badness 10000) has occurred while \output is active [751] [752] [753] [754] [755] [756] Overfull \vbox (18.9959pt too high) has occurred while \output is active [757] [758] [759]) (./grDevices-pkg.tex [760] Chapter 4. [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] 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 [778] [779] [780] [781] Underfull \hbox (badness 1852) in paragraph at lines 1279--1282 []\T1/zi4/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 [782] [783] [784] Underfull \hbox (badness 1490) in paragraph at lines 1485--1490 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [787] [788] [789] [790] Underfull \hbox (badness 1325) in paragraph at lines 1891--1901 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [791] [792] 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 [793] [794] [795] 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 [796] [797] [798] [799] [800] [801] [802] [803] [804] Underfull \hbox (badness 10000) in paragraph at lines 2750--2751 [805] [806] [807] [808] [809] [810] [811] [812] Underfull \hbox (badness 10000) in paragraph at lines 3248--3253 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [813] [814] [815] [816] Underfull \hbox (badness 3302) in paragraph at lines 3514--3517 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827] [828] [829] [830] Underfull \hbox (badness 1067) in paragraph at lines 4355--4362 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [831] [832] [833] Underfull \hbox (badness 1789) in paragraph at lines 4595--4597 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [834] Underfull \hbox (badness 1377) in paragraph at lines 4645--4650 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [835] Underfull \hbox (badness 2671) 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/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4721--4728 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, 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 [836] [837] Underfull \hbox (badness 1377) in paragraph at lines 4850--4855 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb" \T1/ptm/m/n/10 (which is RGB+gray) and [838] 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 [839] [840] Underfull \hbox (badness 2035) in paragraph at lines 5034--5043 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [841] Underfull \hbox (badness 10000) in paragraph at lines 5102--5109 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5102--5109 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [842] [843] [844] Underfull \hbox (badness 1546) in paragraph at lines 5244--5252 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [845] 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 [846] [847] [848] [849] [850] [851] [852] Underfull \hbox (badness 10000) in paragraph at lines 5772--5775 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [853] [854] [855] [856] [857] [858] 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 [859] [860] Underfull \hbox (badness 10000) in paragraph at lines 6267--6269 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [861] [862] [863] [864] Underfull \hbox (badness 3780) in paragraph at lines 6558--6564 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [865] [866] [867] Underfull \hbox (badness 2680) in paragraph at lines 6759--6761 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [868] [869] [870]) (./graphics-pkg.tex Chapter 5. [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] Underfull \hbox (badness 10000) in paragraph at lines 687--694 []\T1/zi4/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/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] Underfull \hbox (badness 4634) in paragraph at lines 1262--1265 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] 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 [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] Underfull \vbox (badness 10000) has occurred while \output is active [931] [932] [933] [934] 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 [935] [936] [937] [938] [939] [940] [941] [942] 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 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 [943] [944] [945] [946] [947] Underfull \hbox (badness 10000) 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/zi4/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4785--4791 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [948] [949] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 <"/root/git/r-backports/stretch/r-base-3.5.2/library/graphics/help/figures/"mai .pdf, id=22940, 289.08pt x 289.08pt> [950 ] Underfull \hbox (badness 10000) in paragraph at lines 4977--4979 <"/root/git/r-backports/stretch/r-base-3.5.2/library/graphics/help/figures/"oma .pdf, id=22954, 259.97125pt x 332.24126pt> Underfull \vbox (badness 10000) has occurred while \output is active [951] [952 ] [953] Underfull \hbox (badness 10000) in paragraph at lines 5167--5169 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [954] Underfull \vbox (badness 3803) has occurred while \output is active [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] <"/root/git/r-backports/stretch/r-base-3.5.2/library/graphics/help/figures/"pch .pdf, id=23370, 361.35pt x 50.1875pt> Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639 [][] [977] [978 ] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] Underfull \hbox (badness 1048) in paragraph at lines 7347--7352 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [989] [990] Underfull \hbox (badness 1102) in paragraph at lines 7463--7466 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] Underfull \hbox (badness 1043) in paragraph at lines 8304--8308 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [1005] [1006] [1007] [1008] [1009] [1010] [1011] 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 [1012]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8805 \HeaderA{units}{Graphical Units}{units} [1013] [1014] [1015] [1016]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1017] [1018] [1019] [1020] [1021] [1022] Underfull \hbox (badness 2680) in paragraph at lines 392--395 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] Underfull \hbox (badness 4279) in paragraph at lines 972--981 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] 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 [1090] [1091] [1092] [1093] 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 [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] 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., [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] 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 [1124] [1125] [1126] [1127]) (./methods-pkg.tex [1128] Chapter 7. [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] Underfull \vbox (badness 3803) has occurred while \output is active [1137] Underfull \vbox (badness 10000) has occurred while \output is active [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] Underfull \hbox (badness 1077) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests [1156] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 1981--1986 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1157] [1158] [1159] Underfull \hbox (badness 1242) 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/zi4/m/n/10 where = [1160] [1161] [1162] [1163] [1164] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1165] [1166] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in [1167] Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1168] [1169] [1170] [1171] [1172] [1173] [1174] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1175] [1176] [1177] [1178] [1179] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments [1180] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1181] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [1182] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3846--3847 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] Underfull \hbox (badness 1436) in paragraph at lines 4443--4446 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4472--4478 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1193] Underfull \hbox (badness 1092) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] Underfull \vbox (badness 10000) has occurred while \output is active [1203] [1204] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1205] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1206] 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 [1207] [1208] [1209] [1210] 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 [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1219] [1220] [1221] [1222] Underfull \vbox (badness 10000) has occurred while \output is active [1223] [1224] [1225] [1226]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1227] [1228] [1229]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate 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} [1230] 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 [1231] [1232] [1233] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] Underfull \vbox (badness 10000) has occurred while \output is active [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274] [1275] 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., [1276] [1277] [1278] [1279]) (./parallel-pkg.tex [1280] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] Underfull \hbox (badness 3386) in paragraph at lines 1339--1342 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1302] [1303] [1304]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319]) (./stats-pkg.tex [1320] Chapter 10. [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] Underfull \hbox (badness 1412) in paragraph at lines 847--849 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] Underfull \hbox (badness 2503) in paragraph at lines 1328--1331 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1342] [1343] [1344] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1345] [1346] [1347] [1348] 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 1546) in paragraph at lines 1773--1777 \T1/zi4/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can han-dle miss-ing [1349] [1350] [1351] [1352] [1353] [1354] [1355] 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 [1356] [1357] [1358] [1359] [1360] 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 [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] 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 [1373] [1374] Underfull \hbox (badness 2503) in paragraph at lines 3390--3393 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] 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 = [1395] [1396] Underfull \hbox (badness 3612) in paragraph at lines 4754--4756 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por t aliased co-ef-fi-cients (see [][]\T1/zi4/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b y de-fault where [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] Underfull \hbox (badness 2556) in paragraph at lines 5270--5273 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) 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/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1405] [1406] [1407] [1408] Underfull \hbox (badness 1142) in paragraph at lines 5527--5539 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1409] [1410] [1411] Underfull \hbox (badness 2503) in paragraph at lines 5679--5683 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 8132) in paragraph at lines 6183--6188 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 7081) in paragraph at lines 6461--6464 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6465--6467 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1425] [1426] [1427] [1428] [1429] Underfull \vbox (badness 3803) has occurred while \output is active [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] Underfull \hbox (badness 10000) in paragraph at lines 7310--7313 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 2626) in paragraph at lines 8954--8957 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1465] Underfull \hbox (badness 2503) in paragraph at lines 9061--9065 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1466] Underfull \hbox (badness 2564) 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/zi4/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 [1467] [1468] [1469] [1470] [1471] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9435--9437 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] 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 [1487] [1488] [1489] [1490] [1491] 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 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10730--10733 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1492] 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: [1493] [1494] [1495] [1496] [1497] [1498] 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 1867) in paragraph at lines 11209--11218 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1499] [1500] [1501] [1502] [1503] Underfull \hbox (badness 10000) 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/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1504] [1505] [1506]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} [1507] [1508] Underfull \hbox (badness 1484) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] 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/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1519] [1520] [1521] [1522] [1523] [1524] 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 [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] 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 [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] 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 [1547] [1548] Underfull \hbox (badness 10000) in paragraph at lines 14271--14275 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14278--14280 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] Underfull \hbox (badness 2503) in paragraph at lines 15346--15350 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] Underfull \hbox (badness 1584) in paragraph at lines 15858--15864 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1 /ptm/m/n/10 and [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] 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 [1601] [1602] Underfull \vbox (badness 10000) has occurred while \output is active [1603] Underfull \vbox (badness 10000) has occurred while \output is active [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] Underfull \hbox (badness 1377) in paragraph at lines 18445--18450 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) 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 1454) in paragraph at lines 18463--18467 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18471--18475 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1617] [1618] [1619] Underfull \vbox (badness 10000) has occurred while \output is active [1620] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18695--18695 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18698--18698 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1621] [1622] [1623] [1624] [1625] [1626] 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 [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] 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 [1636] [1637] [1638] [1639] [1640] Underfull \hbox (badness 5563) in paragraph at lines 19864--19866 []\T1/ptm/m/n/10 logical. If \T1/zi4/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 [1641] [1642] [1643] [1644] [1645] [1646] Underfull \hbox (badness 2503) in paragraph at lines 20242--20245 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1647] Underfull \hbox (badness 10000) in paragraph at lines 20269--20271 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] Underfull \hbox (badness 10000) in paragraph at lines 21342--21348 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] 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 [1688] [1689] [1690] [1691] [1692] [1693] [1694] [1695] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23251--23251 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1696] [1697] [1698] [1699] [1700] 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 [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] 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/zi4/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1710] Underfull \hbox (badness 3690) in paragraph at lines 24139--24143 [][][]\T1/zi4/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 [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718] Underfull \hbox (badness 2165) in paragraph at lines 24616--24621 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1719] [1720] [1721] [1722] 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/zi4/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/zi4/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 Underfull \hbox (badness 1132) in paragraph at lines 24834--24838 \T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o f un-de-ter-mined co-ef-fi-cients, e.g., for [1723] [1724] [1725] [1726] [1727] [1728] [1729] Underfull \hbox (badness 10000) in paragraph at lines 25306--25311 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \vbox (badness 10000) has occurred while \output is active [1746] Underfull \hbox (badness 3514) in paragraph at lines 26362--26367 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1747] [1748] Underfull \hbox (badness 3514) in paragraph at lines 26458--26463 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1749] Underfull \hbox (badness 3514) in paragraph at lines 26544--26549 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1750] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26596--26596 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1751] Underfull \hbox (badness 3514) in paragraph at lines 26632--26638 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1752] [1753] [1754] [1755] Underfull \hbox (badness 3514) in paragraph at lines 26846--26851 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1756] [1757] Underfull \hbox (badness 3514) in paragraph at lines 26933--26938 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1758] Underfull \hbox (badness 3514) in paragraph at lines 26998--27003 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1759] [1760] Underfull \hbox (badness 3514) in paragraph at lines 27092--27097 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1761] Underfull \hbox (badness 6691) in paragraph at lines 27184--27189 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] 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/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] [1780] Underfull \hbox (badness 5431) 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/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1781] [1782] [1783] Underfull \hbox (badness 5431) 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/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1784] [1785] [1786] [1787] [1788] [1789] 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 [1790] [1791] 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/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1792] [1793] 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 [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] Underfull \hbox (badness 10000) in paragraph at lines 30274--30278 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect [1813] [1814] [1815] Underfull \vbox (badness 10000) has occurred while \output is active [1816] [1817] [1818] 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 [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] 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 [1828] Underfull \hbox (badness 2142) in paragraph at lines 31242--31247 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/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 [1829] [1830] [1831] [1832] [1833] [1834] Underfull \hbox (badness 10000) in paragraph at lines 31647--31652 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1835] [1836] [1837]) (./stats4-pkg.tex [1838] Chapter 11. [1839] [1840] [1841] [1842] [1843] [1844]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1845] [1846] [1847] [1848]) (./tcltk-pkg.tex Chapter 12. [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \vbox (badness 10000) has occurred while \output is active [1856] Underfull \vbox (badness 10000) has occurred while \output is active [1857] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] [1868] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/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/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1869]) (./tools-pkg.tex [1870] Chapter 13. [1871] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1872] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/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 [1873] [1874] Underfull \hbox (badness 1308) 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 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1875] [1876] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1877] [1878] [1879] [1880] [1881] [1882] [1883] Underfull \vbox (badness 10000) has occurred while \output is active [1884] [1885] [1886] [1887] 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 [1888] 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- [1889] 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-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1199--1202 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1890] [1891] [1892] 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 [1893] [1894] [1895] Underfull \hbox (badness 2293) in paragraph at lines 1551--1553 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1896] [1897] 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 Underfull \hbox (badness 1082) in paragraph at lines 1696--1698 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1898] [1899] [1900] [1901]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1902] [1903] [1904] [1905] [1906] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2195--2195 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1907] [1908] [1909] 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 [1910] [1911] [1912] [1913] [1914] [1915] [1916] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2829. [1917] [1918] [1919] [1920] Underfull \hbox (badness 1424) in paragraph at lines 3111--3113 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1921] [1922] [1923] [1924] [1925] [1926] [1927] [1928] [1929] [1930] [1931] [1932] 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 , [1933] [1934] Underfull \hbox (badness 10000) in paragraph at lines 3950--3953 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1935] [1936] 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 [1937] [1938] [1939] Underfull \hbox (badness 1838) in paragraph at lines 4257--4263 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4257--4263 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1940] Underfull \hbox (badness 5726) in paragraph at lines 4337--4342 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4337--4342 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1941] [1942] [1943] Underfull \hbox (badness 2197) in paragraph at lines 4486--4496 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4486--4496 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1944] 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 [1945] [1946] [1947]) (./utils-pkg.tex [1948] Chapter 14. [1949] Underfull \hbox (badness 2556) 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/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 10000) in paragraph at lines 620--626 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 620--626 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1958] [1959] Underfull \hbox (badness 5847) in paragraph at lines 753--759 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 753--759 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1960] Underfull \hbox (badness 3861) in paragraph at lines 821--826 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1961] [1962] [1963] Underfull \hbox (badness 1430) in paragraph at lines 992--999 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 992--999 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 992--999 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. 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 [1964] [1965] [1966] Underfull \vbox (badness 10000) has occurred while \output is active [1967] [1968] [1969] [1970] [1971] Underfull \hbox (badness 1371) in paragraph at lines 1482--1484 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1972] [1973] [1974] [1975] [1976] [1977] [1978] Underfull \hbox (badness 2057) in paragraph at lines 1959--1961 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1979] [1980] 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/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1981] 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 [1982] [1983] [1984] [1985] Underfull \hbox (badness 1661) in paragraph at lines 2374--2381 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2390--2393 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1986] [1987] [1988] [1989] [1990] [1991] [1992] Underfull \hbox (badness 10000) in paragraph at lines 2800--2804 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2805--2808 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002] Underfull \hbox (badness 1430) 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/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [2003] 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 [2004] [2005] Underfull \hbox (badness 10000) in paragraph at lines 3686--3688 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow nload.file[][][] \T1/ptm/m/n/10 and [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016]pdf TeX warning (ext4): destination with the same identifier (name{Rfn.format}) 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} [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] Underfull \hbox (badness 1371) in paragraph at lines 5377--5379 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [2033] 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 [2034] [2035] [2036] 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, [2037] 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 [2038] [2039] 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 [2040] 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 [2041] Underfull \hbox (badness 1325) in paragraph at lines 5980--5984 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [2042] 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/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2043] Underfull \hbox (badness 3219) in paragraph at lines 6136--6143 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "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 [2044] [2045] Underfull \hbox (badness 10000) in paragraph at lines 6236--6241 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] Underfull \hbox (badness 10000) in paragraph at lines 7669--7671 []\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 7683--7685 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7691--7696 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] 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 [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] [2091] Underfull \hbox (badness 1097) in paragraph at lines 9118--9121 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2092] Underfull \hbox (badness 3000) in paragraph at lines 9254--9259 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2093] [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] Underfull \hbox (badness 2134) in paragraph at lines 9837--9842 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2102] [2103] [2104] [2105] [2106] [2107] [2108] Underfull \hbox (badness 5077) in paragraph at lines 10262--10266 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/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 2469) in paragraph at lines 10274--10278 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 10274--10278 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2109] [2110] [2111] [2112] [2113] Underfull \hbox (badness 4060) in paragraph at lines 10551--10554 []\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 10574--10574 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2114] Underfull \hbox (badness 10000) in paragraph at lines 10637--10639 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/zi4/m/sl/10 vignette[][] []\T1/ptm/m/n/10 s are nicely viewed via [2115] [2116] [2117] Underfull \hbox (badness 2150) in paragraph at lines 10813--10815 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2118] [2119] [2120] [2121] Underfull \hbox (badness 10000) in paragraph at lines 11032--11036 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n ow 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 [2122] [2123] Underfull \hbox (badness 2096) in paragraph at lines 11181--11184 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 11185--11188 []\T1/ptm/m/n/10 logical (\T1/zi4/m/sl/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing whether JPEG fig-ures should be gen-er-ated. Ig-nored if [2124] 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 [2125] [2126] [2127] [2128] [2129] Underfull \hbox (badness 3780) in paragraph at lines 11563--11567 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1 /zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via Underfull \hbox (badness 2635) in paragraph at lines 11579--11582 []\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp e-cially: the value is taken from the cur-rent set-ting of [2130] [2131] [2132] [2133] [2134] [2135] Underfull \hbox (badness 2818) in paragraph at lines 11948--11953 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), [] []\T1/zi4/m/sl/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have 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 [2136] [2137] [2138] [2139] [2140] Underfull \hbox (badness 10000) in paragraph at lines 12220--12222 []\T1/ptm/m/n/10 Options other than \T1/zi4/m/sl/10 memory = "none" \T1/ptm/m/n /10 ap-ply only to files pro-duced by [2141] [2142] Underfull \hbox (badness 1057) in paragraph at lines 12377--12384 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in turn, [2143] [2144] [2145] [2146] Underfull \hbox (badness 3612) in paragraph at lines 12659--12663 []\T1/ptm/m/n/10 NetBSD prior to 8.0 used flag `\T1/zi4/m/sl/10 --xz\T1/ptm/m/n /10 ' rather than `\T1/zi4/m/sl/10 -J\T1/ptm/m/n/10 ', so this should be used \ T1/ptm/m/it/10 via Underfull \hbox (badness 6510) in paragraph at lines 12674--12678 []\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a ble Underfull \hbox (badness 10000) in paragraph at lines 12681--12684 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 12681--12684 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] Underfull \hbox (badness 10000) in paragraph at lines 13290--13295 []\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \ T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 3861) in paragraph at lines 13290--13295 [][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n /10 and 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/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 av ailable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 1297) in paragraph at lines 13326--13331 \T1/zi4/m/sl/10 available.packages(contriburl = contriburl, method = method) \T 1/ptm/m/n/10 and hence by [2157] Underfull \hbox (badness 10000) in paragraph at lines 13355--13358 [][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1 0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n /10 , [2158] [2159] [2160] [2161] Overfull \hbox (23.85939pt too wide) in paragraph at lines 13597--13600 [][][]\T1/zi4/m/sl/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi -gnette browser; [][]\T1/zi4/m/sl/10 RShowDoc[][][](, package = "") [2162] [2163] 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, [2164] 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 [2165] [2166] [2167] [2168]) (./fullrefman.ind [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] [2206] [2207] [2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] Overfull \hbox (33.3567pt too wide) in paragraph at lines 8658--8660 []\T1/zi4/m/it/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [2218] [2219] [2220] [2221] [2222] [2223] Overfull \hbox (20.8567pt too wide) in paragraph at lines 9958--9960 []\T1/zi4/m/it/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE [2224] [2225] [2226] [2227] [2228] [2229] [2230] Overfull \hbox (5.8567pt too wide) in paragraph at lines 11665--11667 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends Overfull \hbox (5.8567pt too wide) in paragraph at lines 11667--11669 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_results [2231] Overfull \hbox (5.8567pt too wide) in paragraph at lines 11669--11671 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings [2232] [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240]) (./fullrefman.aux) Package rerunfilecheck Warning: File `fullrefman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.lmList} 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.survreg} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.coxph} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.stepAIC} has been referenced but does not exist , replaced 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 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[1] [2] Underfull \hbox (badness 2547) in paragraph at lines 141--149 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1 /ptm/m/n/10 such that \T1/zi4/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/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/zi4/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [3] [4] [5] Underfull \hbox (badness 1178) in paragraph at lines 297--301 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/ 10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues [6] Underfull \hbox (badness 3977) in paragraph at lines 386--389 []\T1/ptm/m/n/10 logical: should \T1/zi4/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [7] [8] Underfull \hbox (badness 2556) 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/zi4/m/n/10 insertions\T1/ptm/m/n/10 ', [9] [10] [11] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 2671) in paragraph at lines 1147--1150 []\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] Overfull \hbox (26.27782pt too wide) in paragraph at lines 1922--1922 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] [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] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] Underfull \vbox (badness 10000) has occurred while \output is active [51] [52] [53] [54] [55] [56] [57] 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 [58] [59] [60] [61] Overfull \hbox (6.42029pt too wide) in paragraph at lines 3897--3897 [] \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [62] [63] Underfull \hbox (badness 1057) in paragraph at lines 4005--4008 [][][]\T1/zi4/m/n/10 is.language[][][]() \T1/ptm/m/n/10 is also true for calls (but also for [][]\T1/zi4/m/n/10 symbol[][][]\T1/ptm/m/n/10 s and [][]\T1/zi4/m /n/10 expression[][][]\T1/ptm/m/n/10 s where [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] 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 [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6041--6041 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [95] [96] [97] Underfull \hbox (badness 2096) in paragraph at lines 6229--6242 []\T1/ptm/m/n/10 New restarts for \T1/zi4/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in [98] [99] [100] Overfull \hbox (56.34871pt too wide) in paragraph at lines 6438--6440 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa ult", "internal", "wininet", "libcurl")\T1/ptm/m/n/10 : [101] [102] Underfull \hbox (badness 10000) in paragraph at lines 6580--6583 []\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is [103] [104] Underfull \hbox (badness 1442) in paragraph at lines 6762--6768 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move a 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 [105] Underfull \hbox (badness 3568) in paragraph at lines 6824--6831 \T1/zi4/m/n/10 txt$[][]\T1/ptm/m/n/10 ), which can also be spec-i-fied as \T1/z i4/m/n/10 "X11_primary" \T1/ptm/m/n/10 and the sec-ondary se-lec-tion as [106] [107] Underfull \vbox (badness 10000) has occurred while \output is active [108] Underfull \vbox (badness 10000) has occurred while \output is active [109] [110] Underfull \hbox (badness 1077) in paragraph at lines 7141--7147 []\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T 1/ptm/m/n/10 . Con-di-tions of length greater 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- [111] [112] [113] [114] [115] [116] Underfull \hbox (badness 2096) in paragraph at lines 7482--7486 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [117] [118] Underfull \hbox (badness 3000) in paragraph at lines 7575--7577 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0, \T1/zi4/m/n/10 getOption("OutDec") \T1/ptm/m/n/10 is con-sulted when la-bels are con-structed for Underfull \hbox (badness 2351) in paragraph at lines 7600--7603 [][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][ ]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T 1/ptm/m/n/10 , [119] [120] [121] [122] Underfull \hbox (badness 10000) in paragraph at lines 7855--7865 []\T1/zi4/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 [123] Underfull \hbox (badness 4479) in paragraph at lines 7926--7936 [][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col-umn names), [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] Underfull \hbox (badness 1394) in paragraph at lines 9685--9690 []\T1/ptm/m/n/10 Subtraction of date-time ob-jects gives an ob-ject of this cla ss, by call-ing \T1/zi4/m/n/10 difftime \T1/ptm/m/n/10 with [150] [151] [152] [153] [154] [155] Underfull \hbox (badness 1194) in paragraph at lines 10030--10035 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 dontCheck \T1/ptm/m/n/10 func-tion is the s ame as [][]\T1/zi4/m/n/10 identity[][][]\T1/ptm/m/n/10 , but is in-ter-preted b y \T1/zi4/m/n/10 R CMD check Underfull \hbox (badness 1231) 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/z i4/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [156] [157] [158] Underfull \hbox (badness 1735) in paragraph at lines 10235--10239 \T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ zi4/m/n/10 https : / / en . wikipedia . [159] [160] [161] [162] [163] [164] 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 Underfull \hbox (badness 6396) in paragraph at lines 10672--10680 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for [165] Underfull \hbox (badness 2735) 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/zi4/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] 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 [182] [183] [184] [185] [186] [187] [188] [189] [190] Underfull \hbox (badness 2698) in paragraph at lines 12358--12367 []\T1/ptm/m/n/10 Both \T1/zi4/m/n/10 $ \T1/ptm/m/n/10 and \T1/zi4/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-lowed Underfull \hbox (badness 4341) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 and no par-tial match-ing is done. The se-man-tics of these op-e r-a-tions are those of [191] [192] [193] [194] [195] Underfull \vbox (badness 3803) has occurred while \output is active [196] [197] [198] [199] [200] Underfull \hbox (badness 6236) in paragraph at lines 13017--13020 []\T1/ptm/m/n/10 For \T1/zi4/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 [201] [202] [203] [204] [205] [206] 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 [207] Underfull \hbox (badness 1565) in paragraph at lines 13510--13514 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/ 10 , and [208] 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/zi4/m /n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with [209] [210] Underfull \hbox (badness 1466) in paragraph at lines 13694--13697 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/ zi4/m/n/10 file.copy \T1/ptm/m/n/10 and [211] [212] Underfull \hbox (badness 10000) in paragraph at lines 13813--13817 [][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13824--13827 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [213] [214] [215] [216] [217] 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, [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] Underfull \hbox (badness 4429) 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/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for [230] Underfull \hbox (badness 10000) in paragraph at lines 14968--14970 []\T1/ptm/m/n/10 If you set \T1/zi4/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/zi4/m/n/10 mode\T1/ptm/m/n/10 , so Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 []\T1/zi4/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, so [231] Underfull \hbox (badness 10000) in paragraph at lines 15013--15017 []\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/zi4/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 4156) in paragraph at lines 15013--15017 \T1/ptm/m/n/10 within [][]\T1/zi4/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [232] [233] [234] [235] [236] [237] [238] [239] [240] Underfull \hbox (badness 2452) in paragraph at lines 15605--15609 []\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 15605--15609 \T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_ WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and [241] [242] [243] Underfull \hbox (badness 1092) in paragraph at lines 15778--15783 [][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t he DLL has been loaded us-ing [244] [245] [246] Underfull \hbox (badness 6741) in paragraph at lines 16029--16033 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10 , [247] [248] [249] [250] [251] 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 [252] [253] [254] [255] Underfull \vbox (badness 10000) has occurred while \output is active [256] [257] [258] Underfull \hbox (badness 3679) in paragraph at lines 16745--16747 []\T1/ptm/m/n/10 The TRE li-brary of Ville Lau-rikari ([][]$\T1/zi4/m/n/10 http : / / laurikari . net / tre/$[][]\T1/ptm/m/n/10 ) is used ex-cept for [259] [260] [261] [262] [263] [264] [265] [266] Underfull \hbox (badness 1478) in paragraph at lines 17310--17313 []\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [267] [268] [269] Underfull \hbox (badness 10000) in paragraph at lines 17563--17565 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www . unicode . org / reports / tr35 / [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] Underfull \hbox (badness 1442) in paragraph at lines 18154--18156 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see [280] Underfull \hbox (badness 2452) in paragraph at lines 18246--18262 [][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\ T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 , [281] [282] [283] [284] [285] [286] [287] Underfull \hbox (badness 1248) in paragraph at lines 18660--18663 []\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/ m/n/10 , [288] [289] [290] [291] 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 [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] Underfull \hbox (badness 2469) in paragraph at lines 19935--19940 []\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 19949--19956 [][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / [309] Underfull \hbox (badness 10000) in paragraph at lines 20023--20027 []\T1/ptm/m/n/10 By de-fault \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/zi4/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory Underfull \hbox (badness 2460) in paragraph at lines 20023--20027 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/zi4/m/n/ 10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (or `\T 1/zi4/m/n/10 Library/R/\T1/ptm/m/sl/10 x.y\T1/zi4/m/n/10 /library\T1/ptm/m/n/10 ' [310] [311] Underfull \hbox (badness 1509) in paragraph at lines 20158--20165 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /zi4/m/n/10 package \T1/ptm/m/n/10 or \T1/zi4/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack-ages Underfull \hbox (badness 1552) in paragraph at lines 20158--20165 \T1/ptm/m/n/10 Use \T1/zi4/m/n/10 .packages(all = TRUE) \T1/ptm/m/n/10 to ob-ta in just the names of all avail-able pack-ages, and Underfull \hbox (badness 1014) in paragraph at lines 20174--20179 []\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1 0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] Underfull \hbox (badness 1264) 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-ported: Underfull \hbox (badness 4441) in paragraph at lines 20954--20957 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/ m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 , [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] Underfull \hbox (badness 10000) in paragraph at lines 21701--21703 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] Underfull \hbox (badness 1077) in paragraph at lines 22736--22742 \T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][ ]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T 1/zi4/m/n/10 https : / / en . wikipedia . [352] [353] [354] Underfull \hbox (badness 1484) in paragraph at lines 22899--22907 \T1/ptm/m/n/10 to al-low more (up to 3Gb). See [][]$\T1/zi4/m/n/10 https : / / www . microsoft . com / whdc / system / platform / [355] [356] [357] [358] [359] Underfull \hbox (badness 2790) in paragraph at lines 23184--23187 []\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s ages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 23184--23187 \T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m es-sages, so can be sup-pressed by [360] [361] [362] [363] Underfull \hbox (badness 1194) in paragraph at lines 23466--23469 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 . It calls [364] [365] [366] Underfull \hbox (badness 10000) in paragraph at lines 23672--23678 []\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 7379) in paragraph at lines 23672--23678 \T1/ptm/m/n/10 list, i.e., \T1/zi4/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 [367] [368] [369] [370] [371] [372] Underfull \hbox (badness 10000) in paragraph at lines 24053--24056 []\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by [373] [374] [375] [376] [377] [378] [379] [380] [381] Underfull \hbox (badness 10000) in paragraph at lines 24655--24657 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than [382] [383] [384] [385] Underfull \hbox (badness 1199) in paragraph at lines 24899--24905 []\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] \T1/zi4/m/n/10 "numeric" Underfull \hbox (badness 2027) in paragraph at lines 24899--24905 \T1/ptm/m/n/10 ([][]type[][][] \T1/zi4/m/n/10 "double" \T1/ptm/m/n/10 or type \ T1/zi4/m/n/10 "integer"\T1/ptm/m/n/10 ) and not a fac-tor, and \T1/zi4/m/n/10 F ALSE \T1/ptm/m/n/10 oth-er-wise. That is, [386] [387] [388] [389] [390] [391] [392] [393] Underfull \hbox (badness 1038) in paragraph at lines 25491--25499 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini-tially [394] Underfull \hbox (badness 1881) in paragraph at lines 25500--25503 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 25519--25521 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [395] Underfull \hbox (badness 10000) in paragraph at lines 25628--25638 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/zi4/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2142) in paragraph at lines 25639--25645 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able [396] Underfull \hbox (badness 1968) in paragraph at lines 25675--25680 []\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p tm/m/n/10 for print-ing; set by en-vi-ron-ment 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 [397] [398] [399] Underfull \hbox (badness 10000) 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/zi4/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/zi4/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 25948--25954 \T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 10000) in paragraph at lines 25961--25964 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 2689) 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 [400] Underfull \hbox (badness 10000) in paragraph at lines 26019--26024 []\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1629) in paragraph at lines 26025--26036 \T1/ptm/m/n/10 si-ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi 4/m/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use an d Underfull \hbox (badness 7203) in paragraph at lines 26037--26040 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 3713) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Pos-si-ble val-ues are \T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (t he de-fault ex-cept un-der a CRAN ma-cOS build), Underfull \hbox (badness 7944) in paragraph at lines 26047--26059 \T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds). Underfull \hbox (badness 2351) in paragraph at lines 26047--26059 \T1/ptm/m/n/10 Win-dows uses \T1/zi4/m/n/10 "win.binary"\T1/ptm/m/n/10 . (\T1/z i4/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "mac.binary.leo pard"\T1/ptm/m/n/10 , 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/zi4/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/zi4/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 Underfull \hbox (badness 1874) in paragraph at lines 26061--26068 \T1/zi4/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [401] [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/zi4/m/n/10 X \T1/ptm/m/n /10 and \T1/zi4/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/zi4/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 \T1/zi4/m/n/10 c(dim(X), dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] [406] [407] [408] [409] [410] Underfull \hbox (badness 1735) in paragraph at lines 26724--26728 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 paste() \T1/ptm/m/n/10 co-erces [][]\ T1/zi4/m/n/10 NA_character_[][][]\T1/ptm/m/n/10 , the char-ac-ter miss-ing valu e, to \T1/zi4/m/n/10 "NA" \T1/ptm/m/n/10 which [411] [412] [413] [414] [415] [416] [417] [418] [419] [420] Underfull \hbox (badness 2726) in paragraph at lines 27299--27302 []\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] [431] [432] [433] Underfull \hbox (badness 1052) in paragraph at lines 28131--28136 []\T1/zi4/m/n/10 qr.X \T1/ptm/m/n/10 re-turns $\OML/cmm/b/it/10 X$\T1/ptm/m/n/1 0 , the orig-i-nal ma-trix from which the qr ob-ject was con-structed, pro-vide d [434] [435] [436] [437] [438] Underfull \vbox (badness 10000) has occurred while \output is active [439] [440] [441] [442] [443] [444] [445] [446] 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 [447] [448] Underfull \hbox (badness 1163) in paragraph at lines 29131--29142 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469] [470] [471] [472] Underfull \hbox (badness 10000) in paragraph at lines 30664--30668 []\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 30664--30668 \T1/zi4/m/n/10 "(?[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t he matches are also re-turned by name. [473] Underfull \hbox (badness 6188) in paragraph at lines 30686--30688 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / 9699919799 / [474] [475] [476] [477] [478] [479] [480] [481] Underfull \hbox (badness 1655) in paragraph at lines 31229--31231 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm /m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for [482] [483] [484] [485] [486] [487] [488] [489] [490] [491] [492] Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 []\T1/zi4/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent workspace', i.e., [493] [494] [495] [496] 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 3333) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 val-ues. In the case \T1/zi4/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 [497] [498] [499] Underfull \hbox (badness 2261) in paragraph at lines 32344--32349 []\T1/ptm/m/n/10 If \T1/zi4/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 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 [500] Underfull \hbox (badness 10000) in paragraph at lines 32447--32452 []\T1/ptm/m/n/10 Note that since \T1/zi4/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 [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] Underfull \vbox (badness 3803) has occurred while \output is active [540] [541] [542] [543] [544] [545] [546] [547] Underfull \hbox (badness 1072) in paragraph at lines 35489--35493 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by Underfull \hbox (badness 10000) in paragraph at lines 35494--35498 []\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/ 10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 - -no-init-file\T1/ptm/m/n/10 ', 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/zi4/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/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 35522--35528 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in [548] Underfull \hbox (badness 3343) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 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 Underfull \hbox (badness 1917) in paragraph at lines 35534--35541 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [549] [550] [551] [552] [553] 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/zi4/m/n/10 form at \T1/ptm/m/n/10 meth-ods is Underfull \hbox (badness 1264) in paragraph at lines 35875--35881 \T1/zi4/m/n/10 "%Y-%m-%d %H:%M:%S" \T1/ptm/m/n/10 if any el-e-ment has a time c om-po-nent which is [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] [581] [582] [583] Underfull \hbox (badness 3333) in paragraph at lines 37745--37750 []\T1/ptm/m/n/10 If a file-name starts with \T1/zi4/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple [584] [585] [586] [587] [588] [589] Underfull \vbox (badness 10000) has occurred while \output is active [590] [591] [592] [593] [594] Underfull \hbox (badness 1472) in paragraph at lines 38377--38380 []\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [595] [596] [597] [598] [599] [600] [601] [602] [603] [604] [605] [606] [607] Underfull \vbox (badness 3803) has occurred while \output is active [608] Underfull \hbox (badness 10000) in paragraph at lines 39283--39287 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/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., [609] [610] [611] [612] Underfull \hbox (badness 10000) in paragraph at lines 39533--39536 [][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . r-[]project . org / [613] [614] Underfull \hbox (badness 10000) in paragraph at lines 39651--39655 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [615] Underfull \hbox (badness 10000) in paragraph at lines 39713--39717 [][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer . [616] [617] [618] [619] [620] [621] [622] [623] [624] Underfull \hbox (badness 4013) in paragraph at lines 40326--40328 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / www . twinsun . com / tz / tz-[]link . [625] [626] [627] [628] [629] [630] Underfull \vbox (badness 10000) has occurred while \output is active [631] [632] [633] [634] [635] [636] [637] [638] 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 1990) in paragraph at lines 41214--41222 []\T1/zi4/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 4846) 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/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less [639] [640] [641] [642] 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. [643] [644] [645] [646] Underfull \hbox (badness 1917) in paragraph at lines 41719--41726 []\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/ ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] 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 [658] [659] Underfull \hbox (badness 2401) in paragraph at lines 42568--42572 []\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [660] [661] [662] Underfull \hbox (badness 2111) in paragraph at lines 42757--42762 \T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n ot empty, these are used as col-umn names. Underfull \hbox (badness 7362) in paragraph at lines 42773--42778 []\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is [663] [664] [665] [666] [667] [668] [669] [670] [671] Underfull \hbox (badness 5417) in paragraph at lines 43354--43358 []\T1/zi4/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 [672] Underfull \hbox (badness 10000) in paragraph at lines 43415--43419 []\T1/zi4/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 [673] [674]) (./compiler-pkg.tex Chapter 2. [675] [676] [677] [678]) (./datasets-pkg.tex Chapter 3. [679] [680] [681] [682] [683] [684] [685] [686] [687] [688] [689] [690] [691] [692] [693] [694] [695] 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. [696] [697] [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] Overfull \vbox (19.74611pt too high) has occurred while \output is active [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] Underfull \vbox (badness 10000) has occurred while \output is active [747] [748] [749] [750] Underfull \vbox (badness 10000) has occurred while \output is active [751] [752] [753] [754] [755] [756] Overfull \vbox (18.9959pt too high) has occurred while \output is active [757] [758] [759]) (./grDevices-pkg.tex [760] Chapter 4. [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] 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 [778] [779] [780] [781] Underfull \hbox (badness 1852) in paragraph at lines 1279--1282 []\T1/zi4/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 [782] [783] [784] Underfull \hbox (badness 1490) in paragraph at lines 1485--1490 \T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\ T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/ 10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 []\T1/ptm/m/n/10 logical; if \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/10 when [787] [788] [789] [790] Underfull \hbox (badness 1325) in paragraph at lines 1891--1901 \T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/ 10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1 /ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 , [791] [792] 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 [793] [794] [795] 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 [796] [797] [798] [799] [800] [801] [802] [803] [804] Underfull \hbox (badness 10000) in paragraph at lines 2750--2751 [805] [806] [807] [808] [809] [810] [811] [812] Underfull \hbox (badness 10000) in paragraph at lines 3248--3253 []\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [813] [814] [815] [816] Underfull \hbox (badness 3302) in paragraph at lines 3514--3517 []\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as Underfull \hbox (badness 2662) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/zi4/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827] [828] [829] [830] Underfull \hbox (badness 1067) in paragraph at lines 4355--4362 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [831] [832] [833] Underfull \hbox (badness 1789) in paragraph at lines 4595--4597 []\T1/ptm/m/n/10 title string to em-bed as the \T1/zi4/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [834] Underfull \hbox (badness 1377) in paragraph at lines 4645--4650 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [835] Underfull \hbox (badness 2671) 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/zi4/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as Underfull \hbox (badness 1418) in paragraph at lines 4721--4728 \T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4 /m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/ zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm /m/n/10 , Underfull \hbox (badness 2443) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 PostScript de-vice is us-ing URW fonts, you will ob-tain ac-cess to more char-ac-ters and Underfull \hbox (badness 2653) in paragraph at lines 4729--4738 \T1/ptm/m/n/10 more ap-pro-pri-ate met-rics by us-ing these names. To make thes e eas-ier to re-mem-ber, 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 [836] [837] Underfull \hbox (badness 1377) in paragraph at lines 4850--4855 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \ T1/zi4/m/n/10 "rgb" \T1/ptm/m/n/10 (which is RGB+gray) and [838] 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 [839] [840] Underfull \hbox (badness 2035) in paragraph at lines 5034--5043 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/ n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 , [841] Underfull \hbox (badness 10000) in paragraph at lines 5102--5109 []\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4 /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / Underfull \hbox (badness 2189) in paragraph at lines 5102--5109 \T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly . [842] [843] [844] Underfull \hbox (badness 1546) in paragraph at lines 5244--5252 []\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T 1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/ n/10 , [845] 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 [846] [847] [848] [849] [850] [851] [852] Underfull \hbox (badness 10000) in paragraph at lines 5772--5775 []\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [853] [854] [855] [856] [857] [858] 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 [859] [860] Underfull \hbox (badness 10000) in paragraph at lines 6267--6269 []\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [861] [862] [863] [864] Underfull \hbox (badness 3780) in paragraph at lines 6558--6564 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1 0 "AvantGarde"\T1/ptm/m/n/10 , [865] [866] [867] Underfull \hbox (badness 2680) in paragraph at lines 6759--6761 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [868] [869] [870]) (./graphics-pkg.tex Chapter 5. [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] Underfull \hbox (badness 10000) in paragraph at lines 687--694 []\T1/zi4/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/zi4/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] Underfull \hbox (badness 4634) in paragraph at lines 1262--1265 [][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n /10 , [892] [893] [894] [895] [896] [897] [898] [899] [900] [901] [902] [903] [904] [905] [906] [907] [908] 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 [909] [910] [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] [926] [927] [928] [929] [930] Underfull \vbox (badness 10000) has occurred while \output is active [931] [932] [933] [934] 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 [935] [936] [937] [938] [939] [940] [941] [942] 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 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 [943] [944] [945] [946] [947] Underfull \hbox (badness 10000) 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/zi4/m/n /10 (width, height) \T1/ptm/m/n/10 in user co-or-di-nate units. Underfull \hbox (badness 5908) in paragraph at lines 4785--4791 \T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin" ) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that [948] [949] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 <"/root/git/r-backports/stretch/r-base-3.5.2/library/graphics/help/figures/"mai .pdf, id=22946, 289.08pt x 289.08pt> [950 ] Underfull \hbox (badness 10000) in paragraph at lines 4977--4979 <"/root/git/r-backports/stretch/r-base-3.5.2/library/graphics/help/figures/"oma .pdf, id=22960, 259.97125pt x 332.24126pt> Underfull \vbox (badness 10000) has occurred while \output is active [951] [952 ] [953] Underfull \hbox (badness 10000) in paragraph at lines 5167--5169 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [954] Underfull \vbox (badness 3803) has occurred while \output is active [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] [975] [976] <"/root/git/r-backports/stretch/r-base-3.5.2/library/graphics/help/figures/"pch .pdf, id=23376, 361.35pt x 50.1875pt> Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639 [][] [977] [978 ] [979] [980] [981] [982] [983] [984] [985] [986] [987] [988] Underfull \hbox (badness 1048) in paragraph at lines 7347--7352 \T1/ptm/m/n/10 avoided (see the Warn-ings sec-tion be-low). Split-screen mode i s ex-ited by the com-mand [989] [990] Underfull \hbox (badness 1102) in paragraph at lines 7463--7466 []\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d rawn be-tween the point \T1/zi4/m/n/10 (x0[i], y0[i]) \T1/ptm/m/n/10 and the po int [991] [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] Underfull \hbox (badness 1043) in paragraph at lines 8304--8308 []\T1/ptm/m/n/10 For \T1/zi4/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/zi4/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [1005] [1006] [1007] [1008] [1009] [1010] [1011] 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 [1012]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.uni ts}) has been already used, duplicate ignored \relax l.8805 \HeaderA{units}{Graphical Units}{units} [1013] [1014] [1015] [1016]) (./grid-pkg.tex Chapter 6. Underfull \vbox (badness 10000) has occurred while \output is active [1017] [1018] [1019] [1020] [1021] [1022] Underfull \hbox (badness 2680) in paragraph at lines 392--395 []\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1 /zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio n of [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] Underfull \hbox (badness 4279) in paragraph at lines 972--981 [][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m /n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/ 10 unit[][][]\T1/ptm/m/n/10 , [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] 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 [1090] [1091] [1092] [1093] 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 [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] 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., [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] 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 [1124] [1125] [1126] [1127]) (./methods-pkg.tex [1128] Chapter 7. [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] Underfull \vbox (badness 3803) has occurred while \output is active [1137] Underfull \vbox (badness 10000) has occurred while \output is active [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] Underfull \hbox (badness 2237) in paragraph at lines 1385--1387 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \ T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package "\T1/ptm/m/n/10 , also of class [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] Underfull \hbox (badness 1077) in paragraph at lines 1932--1939 []\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob- jects: \T1/zi4/m/n/10 is(x, "refClass") \T1/ptm/m/n/10 tests [1156] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 1981--1986 \T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1 0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the [1157] [1158] [1159] Underfull \hbox (badness 1242) 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/zi4/m/n/10 where = [1160] [1161] [1162] [1163] [1164] Underfull \hbox (badness 10000) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class [1165] [1166] Underfull \hbox (badness 1132) in paragraph at lines 2714--2718 []\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1 0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re -turned re-sult is in [1167] Underfull \hbox (badness 1033) in paragraph at lines 2746--2751 \T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store s the [1168] [1169] [1170] [1171] [1172] [1173] [1174] Underfull \hbox (badness 1102) in paragraph at lines 3303--3305 []\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na me of the pack-age (with-out the ex-tra-ne-ous [1175] [1176] [1177] [1178] [1179] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments [1180] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1181] Overfull \hbox (123.02902pt too wide) in paragraph at lines 3762--3763 [] \T1/zi4/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [1182] Overfull \hbox (16.41006pt too wide) in paragraph at lines 3846--3847 []\T1/zi4/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] Underfull \hbox (badness 1436) in paragraph at lines 4443--4446 []\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "SealedMethodDefinition" \T1/ptm/m/n/ 10 is cre-ated by a call to [][]\T1/zi4/m/n/10 setMethod[][][] \T1/ptm/m/n/10 w ith ar-gu-ment Underfull \hbox (badness 1769) in paragraph at lines 4472--4478 []\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4472--4478 \T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T 1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by [1193] Underfull \hbox (badness 1092) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 names cor-re-spond-ing to some or all of the for-mal ar-gu-ments . In the pre-vi-ous ex-am-ple, Underfull \hbox (badness 1117) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 if se-lect-ing class \T1/zi4/m/n/10 "track" \T1/ptm/m/n/10 for \ T1/zi4/m/n/10 x\T1/ptm/m/n/10 , find-ing that the se-lec-tion was an-other meth -ods list and [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] Underfull \vbox (badness 10000) has occurred while \output is active [1203] [1204] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/zi4/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1205] Underfull \hbox (badness 4036) in paragraph at lines 5437--5440 []\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10 the method to use in re-sponse to a [1206] 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 [1207] [1208] [1209] [1210] 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 [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] Underfull \hbox (badness 1675) in paragraph at lines 6451--6457 \T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1219] [1220] [1221] [1222] Underfull \vbox (badness 10000) has occurred while \output is active [1223] [1224] [1225] [1226]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1227] [1228] [1229]pdfTeX warning (ext4): desti nation with the same identifier (name{Rfn.Complex}) has been already used, dupl icate 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} [1230] 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 [1231] [1232] [1233] Underfull \hbox (badness 1286) in paragraph at lines 7484--7486 []\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal ly [1234] [1235] [1236] [1237] [1238] [1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] [1260] Underfull \vbox (badness 10000) has occurred while \output is active [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271] [1272] [1273] [1274] [1275] 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., [1276] [1277] [1278] [1279]) (./parallel-pkg.tex [1280] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4 /m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1281] [1282] [1283] [1284] [1285] [1286] [1287] [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] Underfull \hbox (badness 3386) in paragraph at lines 1339--1342 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the [1302] [1303] [1304]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319]) (./stats-pkg.tex [1320] Chapter 10. [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] Underfull \hbox (badness 1412) in paragraph at lines 847--849 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm \T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1334] [1335] [1336] [1337] [1338] [1339] [1340] [1341] Underfull \hbox (badness 2503) in paragraph at lines 1328--1331 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1342] [1343] [1344] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class [1345] [1346] [1347] [1348] 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 1546) in paragraph at lines 1773--1777 \T1/zi4/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can han-dle miss-ing [1349] [1350] [1351] [1352] [1353] [1354] [1355] 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 [1356] [1357] [1358] [1359] [1360] 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 [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] 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 [1373] [1374] Underfull \hbox (badness 2503) in paragraph at lines 3390--3393 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] 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 = [1395] [1396] Underfull \hbox (badness 3612) in paragraph at lines 4754--4756 []\T1/ptm/m/n/10 The \T1/zi4/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por t aliased co-ef-fi-cients (see [][]\T1/zi4/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b y de-fault where [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] Underfull \hbox (badness 2556) in paragraph at lines 5270--5273 []\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/ ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p tm/m/n/10 . For Underfull \hbox (badness 2932) 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/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is given by [1405] [1406] [1407] [1408] Underfull \hbox (badness 1142) in paragraph at lines 5527--5539 \T1/ptm/m/n/10 For \T1/zi4/m/n/10 cov()\T1/ptm/m/n/10 , a non-Pearson method is un-usual but avail-able for the sake of com-plete-ness. [1409] [1410] [1411] Underfull \hbox (badness 2503) in paragraph at lines 5679--5683 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1412] [1413] [1414] [1415] [1416] [1417] [1418] [1419] Underfull \hbox (badness 8132) in paragraph at lines 6183--6188 \T1/ptm/m/n/10 then \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is a den-dro-gram of the sa me graph struc-ture as \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and for each node, [1420] [1421] [1422] [1423] [1424] Underfull \hbox (badness 7081) in paragraph at lines 6461--6464 []\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 10000) in paragraph at lines 6465--6467 []\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also [1425] [1426] [1427] [1428] [1429] Underfull \vbox (badness 3803) has occurred while \output is active [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] Underfull \hbox (badness 10000) in paragraph at lines 7310--7313 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] Underfull \hbox (badness 2626) in paragraph at lines 8954--8957 []\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/ m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1465] Underfull \hbox (badness 2503) in paragraph at lines 9061--9065 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1466] Underfull \hbox (badness 2564) 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/zi4/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 [1467] [1468] [1469] [1470] [1471] Overfull \hbox (3.53955pt too wide) in paragraph at lines 9435--9437 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] 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 [1487] [1488] [1489] [1490] [1491] 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 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 10730--10733 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][ ]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it- er-a-tion. Hence, [1492] 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: [1493] [1494] [1495] [1496] [1497] [1498] 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 1867) in paragraph at lines 11209--11218 \T1/ptm/m/n/10 in the row case. If ei-ther is miss-ing, as by de-fault, then th e or-der-ing of the cor-re- [1499] [1500] [1501] [1502] [1503] Underfull \hbox (badness 10000) 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/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1504] [1505] [1506]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} [1507] [1508] Underfull \hbox (badness 1484) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 The func-tion \T1/zi4/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 [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] 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/zi4/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when [1519] [1520] [1521] [1522] [1523] [1524] 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 [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] 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 [1537] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] 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 [1547] [1548] Underfull \hbox (badness 10000) in paragraph at lines 14271--14275 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = Underfull \hbox (badness 1199) in paragraph at lines 14278--14280 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] Underfull \hbox (badness 2503) in paragraph at lines 15346--15350 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] Underfull \hbox (badness 1584) in paragraph at lines 15858--15864 []\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response \T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(, "offset") \T1 /ptm/m/n/10 and [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] 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 [1601] [1602] Underfull \vbox (badness 10000) has occurred while \output is active [1603] Underfull \vbox (badness 10000) has occurred while \output is active [1604] [1605] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] Underfull \hbox (badness 1377) in paragraph at lines 18445--18450 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) 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 1454) in paragraph at lines 18463--18467 \T1/ptm/m/n/10 value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 18471--18475 []\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \ T1/ptm/m/n/10 meth-ods if [1617] [1618] [1619] Underfull \vbox (badness 10000) has occurred while \output is active [1620] Overfull \hbox (15.73795pt too wide) in paragraph at lines 18695--18695 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 18698--18698 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1621] [1622] [1623] [1624] [1625] [1626] 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 [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] 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 [1636] [1637] [1638] [1639] [1640] Underfull \hbox (badness 5563) in paragraph at lines 19864--19866 []\T1/ptm/m/n/10 logical. If \T1/zi4/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 [1641] [1642] [1643] [1644] [1645] [1646] Underfull \hbox (badness 2503) in paragraph at lines 20242--20245 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of \T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 , [1647] Underfull \hbox (badness 10000) in paragraph at lines 20269--20271 []\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or [1648] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] [1663] [1664] Underfull \hbox (badness 10000) in paragraph at lines 21342--21348 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1665] [1666] [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] 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 [1688] [1689] [1690] [1691] [1692] [1693] [1694] [1695] Overfull \hbox (27.74408pt too wide) in paragraph at lines 23251--23251 [] \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1696] [1697] [1698] [1699] [1700] 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 [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] 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/zi4/m/n/10 y = run med(x, k) \T1/ptm/m/n/10 sim-ply has [1710] Underfull \hbox (badness 3690) in paragraph at lines 24139--24143 [][][]\T1/zi4/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 [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718] Underfull \hbox (badness 2165) in paragraph at lines 24616--24621 []\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm /m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1 0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 , [1719] [1720] [1721] [1722] 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/zi4/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/zi4/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 Underfull \hbox (badness 1132) in paragraph at lines 24834--24838 \T1/zi4/m/n/10 length(coef(object)) \T1/ptm/m/n/10 which is too large in case o f un-de-ter-mined co-ef-fi-cients, e.g., for [1723] [1724] [1725] [1726] [1727] [1728] [1729] Underfull \hbox (badness 10000) in paragraph at lines 25306--25311 []\T1/ptm/m/n/10 integer or [][]\T1/zi4/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when [1730] [1731] [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] Underfull \vbox (badness 10000) has occurred while \output is active [1746] Underfull \hbox (badness 3514) in paragraph at lines 26362--26367 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1747] [1748] Underfull \hbox (badness 3514) in paragraph at lines 26458--26463 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1749] Underfull \hbox (badness 3514) in paragraph at lines 26544--26549 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1750] Overfull \hbox (2.23795pt too wide) in paragraph at lines 26596--26596 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1751] Underfull \hbox (badness 3514) in paragraph at lines 26632--26638 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1752] [1753] [1754] [1755] Underfull \hbox (badness 3514) in paragraph at lines 26846--26851 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1756] [1757] Underfull \hbox (badness 3514) in paragraph at lines 26933--26938 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1758] Underfull \hbox (badness 3514) in paragraph at lines 26998--27003 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1759] [1760] Underfull \hbox (badness 3514) in paragraph at lines 27092--27097 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1761] Underfull \hbox (badness 6691) in paragraph at lines 27184--27189 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion [1762] [1763] [1764] [1765] [1766] [1767] [1768] [1769] [1770] 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/zi4/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] [1780] Underfull \hbox (badness 5431) 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/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1781] [1782] [1783] Underfull \hbox (badness 5431) 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/z i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1784] [1785] [1786] [1787] [1788] [1789] 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 [1790] [1791] 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/zi4/m/n/10 rt()\T1/ptm/m/n/10 , only for [1792] [1793] 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 [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809] [1810] [1811] [1812] Underfull \hbox (badness 10000) in paragraph at lines 30274--30278 []\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect [1813] [1814] [1815] Underfull \vbox (badness 10000) has occurred while \output is active [1816] [1817] [1818] 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 [1819] [1820] [1821] [1822] [1823] [1824] [1825] [1826] [1827] 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 [1828] Underfull \hbox (badness 2142) in paragraph at lines 31242--31247 []\T1/ptm/m/n/10 When \T1/zi4/m/n/10 x \T1/ptm/m/n/10 (and \T1/zi4/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 [1829] [1830] [1831] [1832] [1833] [1834] Underfull \hbox (badness 10000) in paragraph at lines 31647--31652 []\T1/ptm/m/n/10 There is a \T1/zi4/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/zi4/m/n/10 table \T1/ptm/m/n/10 or [1835] [1836] [1837]) (./stats4-pkg.tex [1838] Chapter 11. [1839] [1840] [1841] [1842] [1843] [1844]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup licate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1845] [1846] [1847] [1848]) (./tcltk-pkg.tex Chapter 12. [1849] [1850] [1851] [1852] [1853] [1854] [1855] Underfull \vbox (badness 10000) has occurred while \output is active [1856] Underfull \vbox (badness 10000) has occurred while \output is active [1857] Underfull \hbox (badness 1546) in paragraph at lines 664--671 []\T1/zi4/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 [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] [1868] Underfull \hbox (badness 3019) in paragraph at lines 1407--1410 [][][]\T1/zi4/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/zi4/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1869]) (./tools-pkg.tex [1870] Chapter 13. [1871] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [1872] Underfull \hbox (badness 3039) in paragraph at lines 164--167 []\T1/zi4/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 [1873] [1874] Underfull \hbox (badness 1308) 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 types Underfull \hbox (badness 4967) in paragraph at lines 285--298 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1 0 formatMastersthesis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 285--298 \T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm /m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma tTechreport \T1/ptm/m/n/10 and [1875] [1876] Underfull \hbox (badness 3039) in paragraph at lines 389--391 []\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine to use. Over-rides any [1877] [1878] [1879] [1880] [1881] [1882] [1883] Underfull \vbox (badness 10000) has occurred while \output is active [1884] [1885] [1886] [1887] 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 [1888] 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- [1889] 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-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1199--1202 \T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 , [1890] [1891] [1892] 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 [1893] [1894] [1895] Underfull \hbox (badness 2293) in paragraph at lines 1551--1553 []\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with its func-tion-al-ity in-te-grated into that of [1896] [1897] 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 Underfull \hbox (badness 1082) in paragraph at lines 1696--1698 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see [1898] [1899] [1900] [1901]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1893 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1902] [1903] [1904] [1905] [1906] Overfull \hbox (17.27782pt too wide) in paragraph at lines 2195--2195 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1907] [1908] [1909] 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 [1910] [1911] [1912] [1913] [1914] [1915] [1916] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 2829. [1917] [1918] [1919] [1920] Underfull \hbox (badness 1424) in paragraph at lines 3111--3113 []\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t or of links, as re-turned by [1921] [1922] [1923] [1924] [1925] [1926] [1927] [1928] [1929] [1930] [1931] [1932] 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 , [1933] [1934] Underfull \hbox (badness 10000) in paragraph at lines 3950--3953 []\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1935] [1936] 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 [1937] [1938] [1939] Underfull \hbox (badness 1838) in paragraph at lines 4257--4263 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4257--4263 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [1940] Underfull \hbox (badness 5726) in paragraph at lines 4337--4342 []\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 reduce \T1/ptm/m/n/10 is \T1/zi4/m/sl/10 TR UE\T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/zi4/m/sl/10 DependsList \T1/ptm/m/n/10 ob-ject Underfull \hbox (badness 7221) in paragraph at lines 4337--4342 \T1/ptm/m/n/10 such that a min-i-mal set of de-pen-den-cies are spec-i-fied (fo r in-stance if there was [1941] [1942] [1943] Underfull \hbox (badness 2197) in paragraph at lines 4486--4496 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4 /m/sl/10 available.packages[][][]\T1/ptm/m/n/10 : Underfull \hbox (badness 2229) in paragraph at lines 4486--4496 \T1/ptm/m/n/10 fields will al-ways be in-cluded, plus the file name in field \T 1/zi4/m/sl/10 "File" \T1/ptm/m/n/10 if [1944] 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 [1945] [1946] [1947]) (./utils-pkg.tex [1948] Chapter 14. [1949] Underfull \hbox (badness 2556) 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/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ', [1950] [1951] [1952] [1953] [1954] [1955] [1956] [1957] Underfull \hbox (badness 10000) in paragraph at lines 620--626 []\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1 0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 620--626 \T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the [1958] [1959] Underfull \hbox (badness 5847) in paragraph at lines 753--759 []\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to se-lect which of the pack-ages on the repos-i-to- Underfull \hbox (badness 4229) in paragraph at lines 753--759 \T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi 4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as [1960] Underfull \hbox (badness 3861) in paragraph at lines 821--826 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/ 10 "License_is_FOSS"\T1/ptm/m/n/10 , [1961] [1962] [1963] Underfull \hbox (badness 1430) in paragraph at lines 992--999 \T1/ptm/m/n/10 in-di-cat-ing that the bib-tex code should be given in ad-di-tio n to the for- Underfull \hbox (badness 1931) in paragraph at lines 992--999 \T1/ptm/m/n/10 mat-ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not mo re than $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is Underfull \hbox (badness 1038) in paragraph at lines 992--999 \T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma x", 1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally. 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 [1964] [1965] [1966] Underfull \vbox (badness 10000) has occurred while \output is active [1967] [1968] [1969] [1970] [1971] Underfull \hbox (badness 1371) in paragraph at lines 1482--1484 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [1972] [1973] [1974] [1975] [1976] [1977] [1978] Underfull \hbox (badness 2057) in paragraph at lines 1959--1961 []\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th is func-tion is in-voked for its side ef-fect of up-dat-ing [1979] [1980] 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/zi4/m/sl/10 CITATION\T1/ptm/m/n/10 ' file via [1981] 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 [1982] [1983] [1984] [1985] Underfull \hbox (badness 1661) in paragraph at lines 2374--2381 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sim-pli-fied to an [][]\T1/zi4/m/sl/10 array[][][] \T1/ptm/m/n/10 (typ-i- Underfull \hbox (badness 1748) in paragraph at lines 2390--2393 []\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4 /m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m /n/10 ar-gu-ment above. In the lat-ter case, the iden-tity [1986] [1987] [1988] [1989] [1990] [1991] [1992] Underfull \hbox (badness 10000) in paragraph at lines 2800--2804 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/ m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read us-ing Overfull \hbox (59.4187pt too wide) in paragraph at lines 2805--2808 []\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi 4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[] [][](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , [1993] [1994] [1995] [1996] [1997] [1998] [1999] [2000] [2001] [2002] Underfull \hbox (badness 1430) 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/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [2003] 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 [2004] [2005] Underfull \hbox (badness 10000) in paragraph at lines 3686--3688 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow nload.file[][][] \T1/ptm/m/n/10 and [2006] [2007] [2008] [2009] [2010] [2011] [2012] [2013] [2014] [2015] [2016]pdf TeX warning (ext4): destination with the same identifier (name{Rfn.format}) 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} [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] [2027] [2028] [2029] [2030] [2031] [2032] Underfull \hbox (badness 1371) in paragraph at lines 5377--5379 []\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T 1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to [2033] 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 [2034] [2035] [2036] 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, [2037] 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 [2038] [2039] 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 [2040] 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 [2041] Underfull \hbox (badness 1325) in paragraph at lines 5980--5984 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able [2042] 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/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pac k-age in-stall. E.g., [2043] Underfull \hbox (badness 3219) in paragraph at lines 6136--6143 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/ 10 "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 [2044] [2045] Underfull \hbox (badness 10000) in paragraph at lines 6236--6241 [][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages [][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/ 10 , [2046] [2047] [2048] [2049] [2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] Underfull \hbox (badness 10000) in paragraph at lines 7669--7671 []\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi 4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 7683--7685 []\T1/zi4/m/sl/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 2310) in paragraph at lines 7691--7696 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2070] [2071] [2072] [2073] [2074] [2075] [2076] [2077] [2078] 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 [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086] [2087] [2088] [2089] [2090] [2091] Underfull \hbox (badness 1097) in paragraph at lines 9118--9121 []\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b e used on Win-dows, in which case [2092] Underfull \hbox (badness 3000) in paragraph at lines 9254--9259 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t able[][][]\T1/ptm/m/n/10 ; [2093] [2094] [2095] [2096] [2097] [2098] [2099] [2100] [2101] Underfull \hbox (badness 2134) in paragraph at lines 9837--9842 [][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write. table[][][]\T1/ptm/m/n/10 ; [2102] [2103] [2104] [2105] [2106] [2107] [2108] Underfull \hbox (badness 5077) in paragraph at lines 10262--10266 []\T1/zi4/m/sl/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/zi4/m/ sl/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 2469) in paragraph at lines 10274--10278 []\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia , The Free En-cy-clo-pe-dia. Underfull \hbox (badness 3428) in paragraph at lines 10274--10278 [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac- [2109] [2110] [2111] [2112] [2113] Underfull \hbox (badness 4060) in paragraph at lines 10551--10554 []\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var i-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 10574--10574 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2114] Underfull \hbox (badness 10000) in paragraph at lines 10637--10639 []\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/zi4/m /sl/10 file.show[][][] \T1/ptm/m/n/10 is used. 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11665--11667 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends Overfull \hbox (5.8567pt too wide) in paragraph at lines 11667--11669 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_results [2231] Overfull \hbox (5.8567pt too wide) in paragraph at lines 11669--11671 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings [2232] [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240]) (./fullrefman.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.write.matrix} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.lmList} 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): 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Transcript written on fullrefman.log. make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' make[1]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2' /usr/bin/make -k vignettes make[1]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/m4' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/m4' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/tools' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/tools' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' make[3]: 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make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include/R_ext' make[4]: Nothing to be done for 'R'. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include/R_ext' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[5]: 'Makedeps' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[5]: 'libtre.a' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[4]: 'libappl.a' is up to date. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[4]: 'libnmath.a' is up to date. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[4]: 'libunix.a' is up to date. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-z,relro -DR_HOME='"/root/git/r-backports/stretch/r-base-3.5.2"' \ -o Rscript ./Rscript.c make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' /root/git/r-backports/stretch/r-base-3.5.2/lib/libR.so is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' /root/git/r-backports/stretch/r-base-3.5.2/bin/exec/R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[5]: 'internet.so' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[5]: 'lapack.so' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[5]: 'R_X11.so' is up to date. make[5]: 'R_de.so' is up to date. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' /root/git/r-backports/stretch/r-base-3.5.2/modules/R_X11.so is unchanged /root/git/r-backports/stretch/r-base-3.5.2/modules/R_de.so is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/profile' building system startup profile make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/profile' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' building package 'translations' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/translations' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' building package 'base' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' building package 'tools' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' ../../../../library/tools/libs/tools.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' installing 'sysdata.rda' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' building package 'compiler' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/compiler' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[4]: Nothing to be done for 'mklazycomp'. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tools' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' building package 'utils' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' all.R is unchanged make[5]: Nothing to be done for 'iconvlist'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' ../../../../library/utils/libs/utils.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' installing 'sysdata.rda' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/utils' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' building package 'grDevices' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' ../../../../library/grDevices/libs/grDevices.so is unchanged make[8]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[9]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[10]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[10]: 'cairo.so' is up to date. make[10]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[9]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[8]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src/cairo' make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grDevices' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' building package 'graphics' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' ../../../../library/graphics/libs/graphics.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/graphics' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' building package 'stats' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' ../../../../library/stats/libs/stats.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' building package 'datasets' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/datasets' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' building package 'methods' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' ../../../../library/methods/libs/methods.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[5]: Nothing to be done for 'RfilesLazy'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/methods' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' building package 'grid' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' ../../../../library/grid/libs/grid.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/grid' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' building package 'splines' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' ../../../../library/splines/libs/splines.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/splines' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' building package 'stats4' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/stats4' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' building package 'tcltk' all.R is unchanged make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' ../../../../library/tcltk/libs/tcltk.so is unchanged make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk/src' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/tcltk' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' building package 'parallel' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' all.R is unchanged make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[6]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' make[7]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' ../../../../library/parallel/libs/parallel.so is unchanged make[7]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' make[6]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel/src' make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[5]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[5]: Nothing to be done for 'mklazycomp'. make[5]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/parallel' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/base' installing parsed NAMESPACE files make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/tests' make[2]: Nothing to be done for 'R'. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/tests' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' installing parsed Rd make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 compiler parallel make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' building/updating package metadata ... make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' writing package indices make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/Recommended' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library/Recommended' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' building/updating vignettes for package 'grid' ... processing 'grid.Rnw' building/updating vignettes for package 'parallel' ... building/updating vignettes for package 'utils' ... make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[1]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2' touch make-indep-stamp *** check *** touch check-stamp fakeroot debian/rules binary-arch *** install-arch *** dh_testdir dh_testroot dh_prep -a dh_installdirs -A /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core /usr/bin/make DESTDIR=/root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core install make[1]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/m4' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/m4' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/tools' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/tools' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' installing doc ... mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/doc mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/man/man1 make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' installing doc/html ... mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/doc/html make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/html' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' installing doc/manual ... mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/doc/manual mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/doc/manual/images make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/etc' mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/lib/R/etc installing etc ... make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/etc' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/share' installing share ... mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/share mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/share/R mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/share/dictionaries mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/share/encodings mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/share/java mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/share/licenses mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/share/make mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/share/Rd mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/share/Rd/macros mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/share/sh mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/share/texmf mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/share/texmf/bibtex/bib mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/share/texmf/bibtex/bst mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/share/texmf/tex/latex make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/share' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/scripts' mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/lib/R/bin make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/scripts' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include/R_ext' mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/include/R_ext make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include/R_ext' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/blas' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/blas' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tre' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tzone' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/tzone' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/xdr' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/xdr' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/intl' make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra/intl' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/extra' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/appl' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[3]: Nothing to be done for 'install'. make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-z,relro -DR_HOME='"/usr/lib/R"' \ -o Rscript ./Rscript.c mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/lib/pkgconfig make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/lib/R/bin/exec make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/lib/R/lib make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/main' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/lib/R/modules make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/internet' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/lapack' make[4]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[4]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules/X11' make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/modules' make[3]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/lib/R/library installing packages ... building HTML index ... make[3]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/library' make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/tests' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/tests' make[1]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2' (cd src/unix; \ rm -vf Rscript /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/bin/Rscript; \ /usr/bin/make CFLAGS="-g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ CXXFLAGS="-g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT" \ FFLAGS="-g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -D_REENTRANT" \ CC="gcc -std=gnu99" \ CXX=g++ \ F77=gfortran \ RHOME=/usr/lib/R \ DESTDIR=/root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core \ install-Rscript ) removed 'Rscript' removed '/root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/bin/Rscript' make[1]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' gcc -std=gnu99 -I. -I../../src/include -I../../src/include -DHAVE_CONFIG_H -g -O2 -fdebug-prefix-map=/root/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -D_REENTRANT -Wl,-z,relro -DR_HOME='"/usr/lib/R"' \ -o Rscript ./Rscript.c make[1]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/unix' #ls -ltr /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/bin/ #strings src/unix/Rscript cp -vax src/unix/Rscript /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/bin/ 'src/unix/Rscript' -> '/root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/bin/Rscript' #ls -ltr /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/bin/ #strings /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/bin/Rscript (cd src/nmath/standalone; \ /usr/bin/make DESTDIR=/root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core install ) make[1]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath/standalone' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include' make[2]: 'Rmath.h' is up to date. make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/include' /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/include/Rmath.h is unchanged make[1]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/src/nmath/standalone' chmod a+x /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/share/sh/echo.sh rm -v /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/lib/R/COPYING removed '/root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/lib/R/COPYING' (cd /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/lib/R/; \ ln -s ../../share/common-licenses/GPL-2 COPYING) rm -v /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/doc/COPYING removed '/root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/doc/COPYING' (cd /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/doc; \ ln -s ../../../share/common-licenses/GPL-2 COPYING) (cd /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/texmf/tex/latex && \ ln -s ../../../R/share/texmf R) dh_movefiles --sourcedir=debian/r-base-core -pr-doc-html dh_movefiles --sourcedir=debian/r-base-core -pr-base-html make prefix=/root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr \ rdocdir=/root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/R/doc \ install-pdf make[1]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' installing R manuals in PDF format ... make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' make[1]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2' make prefix=/root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr \ infodir=/root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info install-info make[1]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2' make[2]: Entering directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' mkdir -p -- /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info /usr/bin/install -c -m 644 "./dir" "/root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info" installing R info pages ... updating '/root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/dir' ... you need to adjust /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/dir manually you need to adjust /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/dir manually you need to adjust /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/dir manually you need to adjust /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/dir manually you need to adjust /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/dir manually you need to adjust /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/dir manually you need to adjust /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/dir manually make[2]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2/doc/manual' make[1]: Leaving directory '/root/git/r-backports/stretch/r-base-3.5.2' dh_movefiles --sourcedir=debian/r-base-core -pr-doc-pdf dh_movefiles --sourcedir=debian/r-base-core -pr-doc-html touch install-indep-stamp gunzip -9v /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/*.gz /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-FAQ.info.gz: 67.0% -- replaced with /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-FAQ.info /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-admin.info.gz: 68.1% -- replaced with /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-admin.info /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-data.info.gz: 70.7% -- replaced with /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-data.info /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-exts.info-1.gz: 66.7% -- replaced with /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-exts.info-1 /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-exts.info-2.gz: 69.8% -- replaced with /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-exts.info-2 /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-exts.info-3.gz: 83.3% -- replaced with /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-exts.info-3 /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-exts.info.gz: 69.7% -- replaced with /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-exts.info /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-intro.info.gz: 70.0% -- replaced with /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-intro.info /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-ints.info.gz: 68.0% -- replaced with /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-ints.info /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-lang.info.gz: 71.7% -- replaced with /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/info/R-lang.info dh_movefiles --sourcedir=debian/r-base-core -pr-doc-info rm -vf /root/git/r-backports/stretch/r-base-3.5.2/debian/r-doc-info/usr/share/info/dir \ /root/git/r-backports/stretch/r-base-3.5.2/debian/r-doc-info/usr/share/info/dir.old removed '/root/git/r-backports/stretch/r-base-3.5.2/debian/r-doc-info/usr/share/info/dir' dh_installdirs -pr-mathlib usr/include usr/lib \ usr/share/lintian/overrides \ usr/lib/pkgconfig dh_movefiles --sourcedir=debian/r-base-core -pr-mathlib (cd /root/git/r-backports/stretch/r-base-3.5.2/debian/r-mathlib/usr/lib; \ ls -l ; \ mv -v libRmath.so libRmath.so.1.0.0; \ ln -sv libRmath.so.1.0.0 libRmath.so.1; \ ln -sv libRmath.so.1 libRmath.so) total 2024 -rw-r--r-- 1 root root 1274606 Dec 20 17:29 libRmath.a -rwxr-xr-x 1 root root 786496 Dec 20 17:29 libRmath.so drwxr-xr-x 2 root root 4096 Dec 20 17:29 pkgconfig 'libRmath.so' -> 'libRmath.so.1.0.0' 'libRmath.so.1' -> 'libRmath.so.1.0.0' 'libRmath.so' -> 'libRmath.so.1' install -m 0644 src/include/Rmath.h \ /root/git/r-backports/stretch/r-base-3.5.2/debian/r-mathlib/usr/include install -m 0644 debian/Rprofile.site /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/etc/R install -m 0644 debian/Renviron.site /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/etc/R (cd /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/lib/R/etc; \ cat /root/git/r-backports/stretch/r-base-3.5.2/debian/Renviron-R_LIBS.patch | patch --verbose; \ mv Makeconf repositories ldpaths ../../../../etc/R/; \ mv Renviron Renviron.ucf; \ ln -s /etc/R/Makeconf .; \ ln -s /etc/R/Renviron .; \ ln -s /etc/R/Renviron.site .; \ ln -s /etc/R/Rprofile.site .; \ ln -s /etc/R/ldpaths .; \ ln -s /etc/R/repositories . ) Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |--- Renviron.orig 2003-04-04 06:52:22.000000000 -0500 |+++ Renviron 2003-04-04 06:49:05.000000000 -0500 -------------------------- patching file Renviron Using Plan A... Hunk #1 succeeded at 42 with fuzz 2 (offset 9 lines). done dh_bash-completion # edd 12 Jan 2016 new location #install -m 0644 debian/R.bash-completion \ # debian/r-base-core/usr/share/bash-completion/completions/R (cd /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/lib/; \ ln -sv R/lib/libR.so . ) './libR.so' -> 'R/lib/libR.so' (cd debian/icon-class-patch && munpack rlogo_icon.png.mpack) rlogo_icon.png (application/octet-stream) install -m 0644 debian/icon-class-patch/rlogo_icon.png \ debian/r-base-core/usr/share/icons/hicolor/48x48/apps install -m 0644 debian/icon-class-patch/R.desktop \ debian/r-base-core/usr/share/applications rm debian/icon-class-patch/rlogo_icon.png touch install-arch-stamp *** binary-arch *** dh_testdir -a dh_testroot -a dh_installdocs -pr-base-core doc/NEWS.* README \ debian/README.Atlas \ debian/README.mathlib dh_installdocs -pr-mathlib doc/NEWS.* README \ debian/README.mathlib dh_installdocs -pr-base-core-dbg dh_installexamples -pr-mathlib src/nmath/standalone/test.c #dh_installmenu -a # (cd /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../../lib/R/doc .) (cd /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../R/doc .) (cd /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/doc/r-base-core && ln -s ../../../lib/R/library .) install -p -m 0644 debian/r-base-core.lintian \ /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/share/lintian/overrides/r-base-core install -p -m 0644 debian/r-recommended.lintian \ /root/git/r-backports/stretch/r-base-3.5.2/debian/r-recommended/usr/share/lintian/overrides/r-recommended install -p -m 0644 debian/r-mathlib.lintian \ /root/git/r-backports/stretch/r-base-3.5.2/debian/r-mathlib/usr/share/lintian/overrides/r-mathlib dh_installchangelogs -a -k doc/NEWS dh_strip --dbg-package=r-base-core-dbg dh_compress -a dh_fixperms -a dh_link -a dh_makeshlibs -a dh_installdeb -a dh_perl -a dh_shlibdeps -a -l /root/git/r-backports/stretch/r-base-3.5.2/debian/r-base-core/usr/lib/R/lib dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libtcl8.6.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libtk8.6.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libR.so' dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/modules/lapack.so debian/r-base-core/usr/lib/R/lib/libR.so debian/r-base-core/usr/lib/R/library/stats/libs/stats.so were not linked against libgfortran.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/modules/R_X11.so debian/r-base-core/usr/lib/R/library/tcltk/libs/tcltk.so debian/r-base-core/usr/lib/R/modules/R_de.so were not linked against libXext.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/modules/R_X11.so debian/r-base-core/usr/lib/R/modules/R_de.so were not linked against libICE.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/modules/R_X11.so debian/r-base-core/usr/lib/R/modules/R_de.so were not linked against libSM.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/modules/R_X11.so debian/r-base-core/usr/lib/R/library/grDevices/libs/cairo.so debian/r-base-core/usr/lib/R/modules/R_de.so were not linked against libglib-2.0.so.0 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-base-core/usr/lib/R/library/tcltk/libs/tcltk.so was not linked against libXss.so.1 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-mathlib/usr/lib/libRmath.so.1.0.0 was not linked against libgomp.so.1 (it uses none of the library's symbols) dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package r-base-core: unknown substitution variable ${perl:Depends} dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'r-base-core-dbg' in '../r-base-core-dbg_3.5.2-1~stretchcran.0_armhf.deb'. dpkg-deb: building package 'r-mathlib' in '../r-mathlib_3.5.2-1~stretchcran.0_armhf.deb'. dpkg-deb: building package 'r-base-core' in '../r-base-core_3.5.2-1~stretchcran.0_armhf.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../r-base_3.5.2-1~stretchcran.0_armhf.changes dpkg-genchanges: warning: the current version (3.5.2-1~stretchcran.0) is earlier than the previous one (3.5.2-1) dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build r-base-3.5.2 dpkg-buildpackage: info: binary-only upload (no source included)