Attachment 191008 Details for Bug 269511 – log

log

log.txt (text/plain), 220.32 KB, created by Joost Ruis on 2009-05-12 08:09:58 UTC

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Creator: Joost Ruis

Created: 2009-05-12 08:09:58 UTC

Size: 220.32 KB

patch

obsolete

> [32;01m*[0m You need one of these Fortran Compilers: gfortran ifc g77
> [32;01m*[0m Installed are:  gfortran ifort
>>>> Unpacking source...
>>>> Unpacking R-2.9.0.tar.gz to /var/tmp/portage/dev-lang/R-2.9.0/work
> [32;01m*[0m Applying patches for selected FORTRAN compiler: gfortran
>>>> Source unpacked in /var/tmp/portage/dev-lang/R-2.9.0/work
>>>> Preparing source in /var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0 ...
>>>> Source prepared.
>>>> Configuring source in /var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0 ...
> * econf: updating R-2.9.0/tools/config.guess with /usr/share/gnuconfig/config.guess
> * econf: updating R-2.9.0/tools/config.sub with /usr/share/gnuconfig/config.sub
>./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --disable-rpath --enable-R-profiling --enable-memory-profiling --enable-R-shlib --enable-linux-lfs --with-system-zlib --with-system-bzlib --with-system-pcre --with-blas=-lblas   --docdir=/usr/share/doc/R-2.9.0 rdocdir=/usr/share/doc/R-2.9.0 --enable-nls --disable-threads --without-lapack --without-tcltk --with-jpeglib --with-recommended-packages --with-libpng --with-readline --with-cairo --with-x
>checking build system type... x86_64-pc-linux-gnu
>checking host system type... x86_64-pc-linux-gnu
>loading site script './config.site'
>loading build specific script './config.site'
>checking for pwd... /bin/pwd
>checking whether builddir is srcdir... yes
>checking for working aclocal... found
>checking for working autoconf... found
>checking for working automake... found
>checking for working autoheader... found
>checking for gawk... gawk
>checking for grep that handles long lines and -e... /bin/grep
>checking for egrep... /bin/grep -E
>checking whether ln -s works... yes
>checking for bison... bison -y
>checking for ar... ar
>checking for a BSD-compatible install... /usr/bin/install -c
>checking for sed... /bin/sed
>checking for /usr/bin/less... /usr/bin/less
>checking for perl... /usr/bin/perl
>checking whether perl version is at least 5.8.0... yes
>checking for dvips... /usr/bin/dvips
>checking for tex... /usr/bin/tex
>checking for latex... /usr/bin/latex
>checking for makeindex... /usr/bin/makeindex
>checking for pdftex... /usr/bin/pdftex
>checking for pdflatex... /usr/bin/pdflatex
>checking for makeinfo... /usr/bin/makeinfo
>checking whether makeinfo version is at least 4.7... yes
>checking for texi2dvi... /usr/bin/texi2dvi
>checking for unzip... /usr/bin/unzip
>checking for zip... /usr/bin/zip
>checking for gzip... /bin/gzip
>using default browser ... /usr/bin/xdg-open
>checking for /usr/bin/xdg-open... /usr/bin/xdg-open
>checking for pkg-config... /usr/bin/pkg-config
>checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
>checking for C compiler default output file name... a.out
>checking whether the C compiler works... yes
>checking whether we are cross compiling... no
>checking for suffix of executables... 
>checking for suffix of object files... o
>checking whether we are using the GNU C compiler... yes
>checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
>checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
>checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
>checking whether x86_64-pc-linux-gnu-gcc needs -traditional... no
>checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
>checking for gfortran... gfortran
>checking for x86_64-pc-linux-gnu-g77... (cached) gfortran
>checking whether we are using the GNU Fortran 77 compiler... yes
>checking whether gfortran accepts -g... yes
>checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
>checking whether we are using the GNU C++ compiler... yes
>checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
>checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
>checking whether __attribute__((visibility())) is supported... yes
>checking whether x86_64-pc-linux-gnu-gcc accepts -fvisibility... yes
>checking whether gfortran accepts -fvisibility... yes
>checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
>checking whether we are using the GNU Objective C compiler... yes
>checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
>checking for Objective C++ compiler... trying some possibilities
>checking whether x86_64-pc-linux-gnu-g++ can compile ObjC++... yes
>x86_64-pc-linux-gnu-g++
>checking for a sed that does not truncate output... (cached) /bin/sed
>checking for fgrep... /bin/grep -F
>checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld
>checking if the linker (/usr/x86_64-pc-linux-gnu/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 whether the shell understands some XSI constructs... yes
>checking whether the shell understands "+="... yes
>checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r
>checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump
>checking how to recognize dependent libraries... pass_all
>checking for x86_64-pc-linux-gnu-ar... (cached) ar
>checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip
>checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
>checking command to parse /usr/bin/nm -B output from x86_64-pc-linux-gnu-gcc object... ok
>checking for ANSI C header files... yes
>checking for sys/types.h... yes
>checking for sys/stat.h... yes
>checking for stdlib.h... yes
>checking for string.h... yes
>checking for memory.h... yes
>checking for strings.h... yes
>checking for inttypes.h... yes
>checking for stdint.h... yes
>checking for unistd.h... yes
>checking for dlfcn.h... yes
>checking whether we are using the GNU C++ compiler... (cached) yes
>checking whether x86_64-pc-linux-gnu-g++ accepts -g... (cached) yes
>checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
>checking for x86_64-pc-linux-gnu-g77... (cached) gfortran
>checking whether we are using the GNU Fortran 77 compiler... (cached) yes
>checking whether gfortran accepts -g... (cached) yes
>checking for objdir... .libs
>checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no
>checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC
>checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes
>checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes
>checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes
>checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes
>checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
>checking whether -lc should be explicitly linked in... no
>checking dynamic linker characteristics... GNU/Linux ld.so
>checking how to hardcode library paths into programs... immediate
>checking whether stripping libraries is possible... yes
>checking if libtool supports shared libraries... yes
>checking whether to build shared libraries... yes
>checking whether to build static libraries... no
>checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64
>checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes
>checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
>checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC
>checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes
>checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes
>checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes
>checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes
>checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
>checking dynamic linker characteristics... 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/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
>checking dynamic linker characteristics... 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_completion_matches exists and is declared... yes
>checking for ANSI C header files... (cached) yes
>checking whether time.h and sys/time.h may both be included... 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 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 for dlfcn.h... (cached) yes
>checking elf.h usability... yes
>checking elf.h presence... yes
>checking for elf.h... yes
>checking fcntl.h usability... yes
>checking fcntl.h presence... yes
>checking for fcntl.h... yes
>checking floatingpoint.h usability... no
>checking floatingpoint.h presence... no
>checking for floatingpoint.h... no
>checking fpu_control.h usability... yes
>checking fpu_control.h presence... yes
>checking for fpu_control.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 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 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 pwd.h usability... yes
>checking pwd.h presence... yes
>checking for pwd.h... yes
>checking stdbool.h usability... yes
>checking stdbool.h presence... yes
>checking for stdbool.h... yes
>checking for strings.h... (cached) yes
>checking sys/param.h usability... yes
>checking sys/param.h presence... yes
>checking for sys/param.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/resource.h usability... yes
>checking sys/resource.h presence... yes
>checking for sys/resource.h... 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 time.h usability... yes
>checking time.h presence... yes
>checking for time.h... yes
>checking for unistd.h... (cached) yes
>checking errno.h usability... yes
>checking errno.h presence... yes
>checking for errno.h... yes
>checking for inttypes.h... (cached) yes
>checking stdarg.h usability... yes
>checking stdarg.h presence... yes
>checking for stdarg.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 pid_t... yes
>checking for size_t... yes
>checking whether SIZE_MAX is declared... yes
>checking for blkcnt_t... yes
>checking for type of socket length... socklen_t *
>checking for stack_t... yes
>checking for intptr_t... yes
>checking for uintptr_t... yes
>checking whether byte ordering is bigendian... no
>checking for an ANSI C-conforming const... yes
>checking for x86_64-pc-linux-gnu-gcc option to accept ISO C99... -std=gnu99
>checking for x86_64-pc-linux-gnu-gcc -std=gnu99 option to accept ISO Standard C... (cached) -std=gnu99
>checking for inline... inline
>checking for int... yes
>checking size of int... 4
>checking for long... yes
>checking size of long... 8
>checking for long long... yes
>checking size of long long... 8
>checking for double... yes
>checking size of double... 8
>checking for long double... yes
>checking size of long double... 16
>checking for size_t... (cached) yes
>checking size of size_t... 8
>checking whether we can compute C Make dependencies... yes, using x86_64-pc-linux-gnu-gcc -std=gnu99 -MM
>checking whether x86_64-pc-linux-gnu-gcc -std=gnu99 supports -c -o FILE.lo... yes
>checking how to get verbose linking output from gfortran... -v
>checking for Fortran 77 libraries of gfortran...  -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.2 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.2/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.2/../../.. -lgfortranbegin -lgfortran -lm
>checking how to get verbose linking output from x86_64-pc-linux-gnu-gcc -std=gnu99... -v
>checking for C libraries of x86_64-pc-linux-gnu-gcc -std=gnu99...  -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.2 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.2/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.3.2/../../.. -lgcc_s
>checking for dummy main to link with Fortran 77 libraries... none
>checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
>checking whether gfortran appends underscores to external names... yes
>checking whether gfortran appends extra underscores to external names... no
>checking whether mixed C/Fortran code can be run... yes
>checking whether gfortran and x86_64-pc-linux-gnu-gcc -std=gnu99 agree on int and double... yes
>checking whether gfortran and x86_64-pc-linux-gnu-gcc -std=gnu99 agree on double complex... yes
>checking whether x86_64-pc-linux-gnu-g++ accepts -M for generating dependencies... yes
>checking whether we can compute ObjC Make dependencies... yes, using x86_64-pc-linux-gnu-gcc -MM
>checking for ObjC runtime library... -lobjc
>checking for ObjC runtime style... gnu
>checking whether C runtime needs -D__NO_MATH_INLINES... no
>checking for xmkmf... /usr/bin/xmkmf
>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 log2 exists and is declared... yes
>checking whether log10 exists and is declared... yes
>checking whether rint exists and is declared... yes
>checking for fseeko... yes
>checking for ftello... yes
>checking for isblank... 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 sigaction exists and is declared... yes
>checking whether sigaltstack exists and is declared... yes
>checking whether sigemptyset exists and is declared... yes
>checking whether va_copy exists and is declared... yes
>checking whether __va_copy exists and is declared... yes
>checking whether fdopen exists and is declared... yes
>checking whether popen exists and is declared... yes
>checking whether setenv exists and is declared... yes
>checking whether system exists and is declared... yes
>checking whether unsetenv exists and is declared... yes
>checking whether strcoll exists and is declared... yes
>checking whether getrlimit exists and is declared... yes
>checking whether getrusage 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 times exists and is declared... yes
>checking whether time 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 getuid exists and is declared... yes
>checking whether symlink exists and is declared... yes
>checking whether sysconf 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 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 acosh... yes
>checking for asinh... yes
>checking for atanh... yes
>checking for mkdtemp... yes
>checking for snprintf... yes
>checking for strdup... yes
>checking for strncasecmp... yes
>checking for vsnprintf... yes
>checking whether acosh is declared... yes
>checking whether asinh is declared... yes
>checking whether atanh is declared... yes
>checking whether mkdtemp is declared... yes
>checking whether snprintf is declared... yes
>checking whether strdup is declared... yes
>checking whether strncasecmp is declared... yes
>checking whether vsnprintf 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 __setfpucw... no
>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 C99 double complex is supported... 
>checking complex.h usability... yes
>checking complex.h presence... yes
>checking for complex.h... yes
>checking for double complex... 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 whether cacosh exists and is declared... yes
>checking whether casinh exists and is declared... yes
>checking whether catanh exists and is declared... yes
>checking whether C99 double complex is compatible with Rcomplex... yes
>yes
>checking for cblas_cdotu_sub in vecLib framework... no
>checking for dgemm_ in -lblas  ... yes
>checking whether double complex BLAS can be used... yes
>checking whether the BLAS is complete... 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" and "UCS-*"... yes
>checking for iconvlist... no
>checking wchar.h usability... yes
>checking wchar.h presence... yes
>checking for wchar.h... yes
>checking wctype.h usability... yes
>checking wctype.h presence... yes
>checking for wctype.h... yes
>checking whether mbrtowc exists and is declared... yes
>checking whether wcrtomb exists and is declared... yes
>checking whether wcscoll exists and is declared... yes
>checking whether wcsftime exists and is declared... yes
>checking whether wcstod exists and is declared... yes
>checking whether mbstowcs exists and is declared... yes
>checking whether wcstombs exists and is declared... yes
>checking whether wctrans exists and is declared... yes
>checking whether iswblank exists and is declared... yes
>checking whether wctype exists and is declared... yes
>checking whether iswctype exists and is declared... yes
>checking for wctrans_t... yes
>checking for mbstate_t... yes
>checking for ICU... yes
>checking for X... libraries /usr/lib64, headers 
>checking whether -R must be followed by a space... neither works
>checking for gethostbyname... yes
>checking for connect... yes
>checking for remove... yes
>checking for shmat... yes
>checking for IceConnectionNumber in -lICE... yes
>checking X11/Intrinsic.h usability... yes
>checking X11/Intrinsic.h presence... yes
>checking for X11/Intrinsic.h... yes
>checking for XtToolkitInitialize in -lXt... yes
>using X11 ... yes
>checking for KeySym... yes
>checking X11/Xmu/Atoms.h usability... yes
>checking X11/Xmu/Atoms.h presence... yes
>checking for X11/Xmu/Atoms.h... yes
>checking for XmuInternAtom in -lXmu... yes
>checking whether pkg-config knows about cairo and pango... yes
>checking whether cairo including pango is >= 1.0 and works... yes
>checking for BSD networking... yes
>checking if jpeglib version >= 6b... yes
>checking for jpeg_destroy_compress in -ljpeg... yes
>checking for main in -lz... yes
>checking if libpng version >= 1.0.5... yes
>checking for png_create_write_struct in -lpng... 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 gzeof in -lz... yes
>checking zlib.h usability... yes
>checking zlib.h presence... yes
>checking for zlib.h... yes
>checking if zlib version >= 1.2.3... yes
>checking whether zlib support needs to be compiled... no
>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 >= 1.0.5... yes
>checking whether bzip2 support needs to be compiled... no
>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 >= 7.6... yes
>checking whether PCRE support needs to be compiled... no
>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 setitimer... yes
>checking for special C compiler options needed for large files... no
>checking for _FILE_OFFSET_BITS value needed for large files... no
>checking for _LARGEFILE_SOURCE value needed for large files... no
>checking whether KERN_USRSTACK sysctl is supported... no
>checking for visible __lib_stack_end... yes
>checking for lpr... lpr
>checking for paperconf... /usr/bin/paperconf
>checking for java... /etc/java-config-2/current-system-vm/jre/bin/java
>checking for javac... /etc/java-config-2/current-system-vm/bin/javac
>checking for javah... /etc/java-config-2/current-system-vm/bin/javah
>checking for jar... /etc/java-config-2/current-system-vm/bin/jar
>checking whether Java compiler works... yes
>checking whether Java compiler works for version 1.4... yes
>checking whether Java interpreter works... yes
>checking Java environment... /etc/java-config-2/current-system-vm
>checking for cached Java settings... no
>checking whether JNI programs can be compiled... yes
>checking for x86_64-pc-linux-gnu-gfortran... x86_64-pc-linux-gnu-gfortran
>checking whether we are using the GNU Fortran compiler... yes
>checking whether x86_64-pc-linux-gnu-gfortran accepts -g... yes
>checking for x86_64-pc-linux-gnu-gfortran... (cached) x86_64-pc-linux-gnu-gfortran
>checking whether we are using the GNU Fortran compiler... (cached) yes
>checking whether x86_64-pc-linux-gnu-gfortran accepts -g... (cached) yes
>checking if libtool supports shared libraries... yes
>checking whether to build shared libraries... yes
>checking whether to build static libraries... no
>checking for x86_64-pc-linux-gnu-gfortran option to produce PIC... -fPIC
>checking if x86_64-pc-linux-gnu-gfortran PIC flag -fPIC works... yes
>checking if x86_64-pc-linux-gnu-gfortran static flag -static works... no
>checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... yes
>checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... (cached) yes
>checking whether the x86_64-pc-linux-gnu-gfortran linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
>checking dynamic linker characteristics... 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 recommended packages... yes
>checking whether NLS is requested... yes
>checking whether make sets $(MAKE)... yes
>checking for a thread-safe mkdir -p... /bin/mkdir -p
>checking for msgfmt... /usr/bin/msgfmt
>checking for gmsgfmt... /usr/bin/gmsgfmt
>checking for xgettext... /usr/bin/xgettext
>checking for msgmerge... /usr/bin/msgmerge
>checking whether we are using the GNU C Library 2 or newer... yes
>checking for x86_64-pc-linux-gnu-ranlib... (cached) x86_64-pc-linux-gnu-ranlib
>checking for simple visibility declarations... yes
>checking for inline... inline
>checking for stdint.h... yes
>checking for stdlib.h... (cached) yes
>checking for unistd.h... (cached) yes
>checking for getpagesize... yes
>checking for working mmap... yes
>checking whether integer division by zero raises SIGFPE... yes
>checking for inttypes.h... yes
>checking for unsigned long long int... yes
>checking for inttypes.h... (cached) yes
>checking whether the inttypes.h PRIxNN macros are broken... no
>checking for ld used by GCC... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64
>checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes
>checking for shared library run path origin... done
>checking for multithread API to use... none
>checking argz.h usability... yes
>checking argz.h presence... yes
>checking for argz.h... yes
>checking for inttypes.h... (cached) yes
>checking for limits.h... (cached) yes
>checking for unistd.h... (cached) yes
>checking for sys/param.h... (cached) yes
>checking for getcwd... yes
>checking for getegid... yes
>checking for geteuid... yes
>checking for getgid... yes
>checking for getuid... yes
>checking for mempcpy... (cached) yes
>checking for munmap... yes
>checking for stpcpy... yes
>checking for strcasecmp... yes
>checking for strdup... (cached) yes
>checking for strtoul... yes
>checking for tsearch... yes
>checking for argz_count... yes
>checking for argz_stringify... yes
>checking for argz_next... yes
>checking for __fsetlocking... yes
>checking whether feof_unlocked is declared... yes
>checking whether fgets_unlocked is declared... yes
>checking for iconv... yes
>checking for iconv declaration... 
>         extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
>checking for NL_LOCALE_NAME macro... yes
>checking for bison... bison
>checking version of bison... 2.4, ok
>checking for long long int... yes
>checking for long double... yes
>checking for wchar_t... yes
>checking for wint_t... yes
>checking for intmax_t... yes
>checking whether printf() supports POSIX/XSI format strings... yes
>checking whether we are using the GNU C Library 2.1 or newer... yes
>checking for stdint.h... (cached) yes
>checking for SIZE_MAX... yes
>checking for stdint.h... (cached) yes
>checking for CFPreferencesCopyAppValue... no
>checking for CFLocaleCopyCurrent... no
>checking for ptrdiff_t... yes
>checking stddef.h usability... yes
>checking stddef.h presence... yes
>checking for stddef.h... yes
>checking for stdlib.h... (cached) yes
>checking for string.h... (cached) yes
>checking for asprintf... yes
>checking for fwprintf... yes
>checking for putenv... (cached) yes
>checking for setenv... yes
>checking for setlocale... yes
>checking for snprintf... (cached) yes
>checking for wcslen... yes
>checking whether _snprintf is declared... no
>checking whether _snwprintf is declared... no
>checking whether getc_unlocked is declared... yes
>checking for nl_langinfo and CODESET... (cached) yes
>checking for LC_MESSAGES... yes
>checking for CFPreferencesCopyAppValue... (cached) no
>checking for CFLocaleCopyCurrent... (cached) no
>checking whether included gettext is requested... no
>checking for GNU gettext in libc... yes
>checking whether to use NLS... yes
>checking where the gettext function comes from... libc
>using as R_SHELL for scripts ... /bin/sh
>configure: creating ./config.status
>config.status: creating Makeconf
>config.status: creating Makefile
>config.status: creating doc/Makefile
>config.status: creating doc/html/Makefile
>config.status: creating doc/html/search/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/ldpaths
>config.status: creating m4/Makefile
>config.status: creating po/Makefile.in
>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/bzip2/Makefile
>config.status: creating src/extra/intl/Makefile
>config.status: creating src/extra/pcre/Makefile
>config.status: creating src/extra/xdr/Makefile
>config.status: creating src/extra/zlib/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/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/grDevices/DESCRIPTION
>config.status: creating src/library/grDevices/Makefile
>config.status: creating src/library/grDevices/src/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/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/utils/DESCRIPTION
>config.status: creating src/library/utils/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/modules/vfonts/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/Rdconv
>config.status: creating src/scripts/Rdiff
>config.status: creating src/scripts/Rprof
>config.status: creating src/scripts/Sd2Rd
>config.status: creating src/scripts/build
>config.status: creating src/scripts/check
>config.status: creating src/scripts/f77_f2c
>config.status: creating src/scripts/mkinstalldirs
>config.status: creating src/scripts/pager
>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 tests/Native/Makefile
>config.status: creating tools/Makefile
>config.status: creating src/include/config.h
>config.status: executing libtool commands
>config.status: executing po-directories commands
>config.status: creating po/POTFILES
>config.status: creating po/Makefile
>config.status: executing stamp-h commands
> 
>R is now configured for x86_64-pc-linux-gnu
> 
>  Source directory:          .
>  Installation directory:    /usr
> 
>  C compiler:                x86_64-pc-linux-gnu-gcc -std=gnu99  -Os -march=x86-64 -pipe
>  Fortran 77 compiler:       gfortran  -O2
> 
>  C++ compiler:              x86_64-pc-linux-gnu-g++  -Os -march=x86-64 -pipe
>  Fortran 90/95 compiler:    x86_64-pc-linux-gnu-gfortran -O2
>  Obj-C compiler:	     x86_64-pc-linux-gnu-gcc -g -O2
> 
>  Interfaces supported:      X11
>  External libraries:        readline, BLAS(generic)
>  Additional capabilities:   PNG, JPEG, TIFF, iconv, MBCS, NLS, cairo, ICU
>  Options enabled:           shared R library, R profiling, memory profiling, Java
> 
>  Recommended packages:      yes
> 
>>>> Source configured.
>>>> Compiling source in /var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0 ...
>make -s -j3 
>creating src/scripts/R.fe
>mkdir -p -- ../../bin
>mkdir -p -- ../../include
>mkdir -p -- ../../../include/R_ext
>making bakslv.d from bakslv.c
>making binning.d from binning.c
>making cpoly.d from cpoly.c
>making fft.d from fft.c
>making cumsum.d from cumsum.c
>making fmin.d from fmin.c
>making integrate.d from integrate.c
>making interv.d from interv.c
>making lbfgsb.d from lbfgsb.c
>making machar.d from machar.c
>making maxcol.d from maxcol.c
>making pretty.d from pretty.c
>making rcont.d from rcont.c
>making rowsum.d from rowsum.c
>making stem.d from stem.c
>making strsignif.d from strsignif.c
>making tabulate.d from tabulate.c
>making zeroin.d from zeroin.c
>making uncmin.d from uncmin.c
>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 imax2.d from imax2.c
>making fsign.d from fsign.c
>making imin2.d from imin2.c
>making chebyshev.d from chebyshev.c
>making log1p.d from log1p.c
>making expm1.d from expm1.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 polygamma.d from polygamma.c
>making lbeta.d from lbeta.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 snorm.d from snorm.c
>making sexp.d from sexp.c
>making choose.d from choose.c
>making pgamma.d from pgamma.c
>making dgamma.d from dgamma.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 qunif.d from qunif.c
>making punif.d from punif.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 rt.d from rt.c
>making qt.d from qt.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 qweibull.d from qweibull.c
>making pweibull.d from pweibull.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
>config.status: creating src/unix/Makefile
>making dynload.d from dynload.c
>making edit.d from edit.c
>making stubs.d from stubs.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
>making aqua.d from aqua.c
>making Rembedded.d from Rembedded.c
>config.status: creating src/main/Makefile
>making CConverters.d from CConverters.c
>making CommandLineArgs.d from CommandLineArgs.c
>making Rdynload.d from Rdynload.c
>making Renviron.d from Renviron.c
>making apply.d from apply.c
>making RNG.d from RNG.c
>making apse.d from apse.c
>making arithmetic.d from arithmetic.c
>making array.d from array.c
>making attrib.d from attrib.c
>making base.d from base.c
>making bind.d from bind.c
>making character.d from character.c
>making builtin.d from builtin.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 cov.d from cov.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 deriv.d from deriv.c
>making devices.d from devices.c
>making dotcode.d from dotcode.c
>making dounzip.d from dounzip.c
>making duplicate.d from duplicate.c
>making dstruct.d from dstruct.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 fourier.d from fourier.c
>making gevents.d from gevents.c
>making gram.d from gram.c
>making gram-ex.d from gram-ex.c
>making gramRd.d from gramRd.c
>making graphics.d from graphics.c
>making identical.d from identical.c
>making inspect.d from inspect.c
>making internet.d from internet.c
>making inlined.d from inlined.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 model.d from model.c
>making names.d from names.c
>making objects.d from objects.c
>making optim.d from optim.c
>making optimize.d from optimize.c
>making options.d from options.c
>making par.d from par.c
>making paste.d from paste.c
>making pcre.d from pcre.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 random.d from random.c
>making regex.d from regex.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 size.d from size.c
>making sort.d from sort.c
>making split.d from split.c
>making source.d from source.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 unique.d from unique.c
>making util.d from util.c
>making version.d from version.c
>making vfonts.d from vfonts.c
>making Rmain.d from Rmain.c
>making alloca.d from alloca.c
>making acosh.d from acosh.c
>making asinh.d from asinh.c
>making atanh.d from atanh.c
>making mkdtemp.d from mkdtemp.c
>making snprintf.d from snprintf.c
>making strdup.d from strdup.c
>making vsnprintf.d from vsnprintf.c
>making strncasecmp.d from strncasecmp.c
>making xspline.d from xspline.c
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0/bin/exec
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0/lib
>making Rsock.d from Rsock.c
>making Lapack.d from Lapack.c
>making g_alab_her.d from g_alab_her.c
>making g_cntrlify.d from g_cntrlify.c
>making internet.d from internet.c
>making nanoftp.d from nanoftp.c
>making g_fontdb.d from g_fontdb.c
>making nanohttp.d from nanohttp.c
>making g_her_glyph.d from g_her_glyph.c
>making sock.d from sock.c
>making sockconn.d from sockconn.c
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0/modules
>/var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0/lib/libRlapack.so is unchanged
>making dataentry.d from dataentry.c
>making devX11.d from devX11.c
>making rotated.d from rotated.c
>making rbitmap.d from rbitmap.c
>mkdir -p -- ../../library
>building system startup profile
>mkdir -p -- ../../../library/base/R
>building package 'base'
>mkdir -p -- ../../../library/base/demo
>mkdir -p -- ../../../library/base/po
>mkdir -p -- ../../../library/base/man
>building package 'tools'
>mkdir -p -- ../../../library/tools
>mkdir -p -- ../../../library/tools/po
>mkdir -p -- ../../../library/tools/man
>mkdir -p -- ../../../library/tools/R
>making text.d from text.c
>making init.d from init.c
>making Rmd5.d from Rmd5.c
>making md5.d from md5.c
>x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -o tools.so text.o init.o Rmd5.o md5.o -L../../../../lib -lR
>mkdir -p -- ../../../../library/tools/libs
>building package 'utils'
>mkdir -p -- ../../../library/utils
>mkdir -p -- ../../../library/utils/R
>mkdir -p -- ../../../library/utils/po
>mkdir -p -- ../../../library/utils/man
>mkdir -p -- ../../../library/utils/Sweave
>mkdir -p -- ../../../library/utils/misc
>building package 'grDevices'
>mkdir -p -- ../../../library/grDevices
>mkdir -p -- ../../../library/grDevices/po
>mkdir -p -- ../../../library/grDevices/R
>mkdir -p -- ../../../library/grDevices/afm
>mkdir -p -- ../../../library/grDevices/man
>mkdir -p -- ../../../library/grDevices/enc
>making chull.d from chull.c
>making devNull.d from devNull.c
>making devPicTeX.d from devPicTeX.c
>making devPS.d from devPS.c
>making devQuartz.d from devQuartz.c
>making init.d from init.c
>x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -o grDevices.so chull.o devNull.o devPicTeX.o devPS.o devQuartz.o init.o -L../../../../lib -lR
>mkdir -p -- ../../../../library/grDevices/libs
>building package 'graphics'
>mkdir -p -- ../../../library/graphics
>mkdir -p -- ../../../library/graphics/R
>mkdir -p -- ../../../library/graphics/po
>mkdir -p -- ../../../library/graphics/man
>building package 'stats'
>mkdir -p -- ../../../library/stats
>mkdir -p -- ../../../library/stats/R
>mkdir -p -- ../../../library/stats/man
>mkdir -p -- ../../../library/stats/po
>making init.d from init.c
>making ansari.d from ansari.c
>making kmeans.d from kmeans.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 smooth.d from smooth.c
>making line.d from line.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 isoreg.d from isoreg.c
>making Srunmed.d from Srunmed.c
>making Trunmed.d from Trunmed.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 HoltWinters.d from HoltWinters.c
>making PPsum.d from PPsum.c
>making arima.d from arima.c
>making filter.d from filter.c
>making burg.d from burg.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
>x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -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 isoreg.o Srunmed.o Trunmed.o dblcen.o distance.o hclust-utils.o nls.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 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 -lblas -lgfortran -lm -L../../../../lib -lR
>mkdir -p -- ../../../../library/stats/libs
>building package 'datasets'
>mkdir -p -- ../../../library/datasets
>mkdir -p -- ../../../library/datasets/R
>mkdir -p -- ../../../library/datasets/man
>mkdir -p -- ../../../library/datasets/data
>building package 'methods'
>mkdir -p -- ../../../library/methods
>mkdir -p -- ../../../library/methods/R
>mkdir -p -- ../../../library/methods/po
>mkdir -p -- ../../../library/methods/man
>making do_substitute_direct.d from do_substitute_direct.c
>making methods_list_dispatch.d from methods_list_dispatch.c
>making init.d from init.c
>making slot.d from slot.c
>making class_support.d from class_support.c
>making tests.d from tests.c
>x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o -L../../../../lib -lR
>mkdir -p -- ../../../../library/methods/libs
>dumping R code in package 'methods'
>WARNING: ignoring environment value of R_HOME
>initializing class and method definitions ...done
>building package 'grid'
>mkdir -p -- ../../../library/grid
>mkdir -p -- ../../../library/grid/R
>mkdir -p -- ../../../library/grid/doc
>mkdir -p -- ../../../library/grid/po
>mkdir -p -- ../../../library/grid/man
>making gpar.d from gpar.c
>making just.d from just.c
>making grid.d from grid.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
>x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -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
>mkdir -p -- ../../../../library/grid/libs
>building package 'splines'
>mkdir -p -- ../../../library/splines
>mkdir -p -- ../../../library/splines/R
>mkdir -p -- ../../../library/splines/po
>mkdir -p -- ../../../library/splines/man
>making splines.d from splines.c
>x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -o splines.so splines.o -L../../../../lib -lR
>mkdir -p -- ../../../../library/splines/libs
>building package 'stats4'
>mkdir -p -- ../../../library/stats4
>mkdir -p -- ../../../library/stats4/R
>mkdir -p -- ../../../library/stats4/po
>mkdir -p -- ../../../library/stats4/man
>Creating a new generic function for "coef" in "stats4"
>Creating a new generic function for "summary" in "stats4"
>Creating a new generic function for "profile" in "stats4"
>Creating a new generic function for "plot" in "stats4"
>Creating a new generic function for "confint" in "stats4"
>Creating a new generic function for "logLik" in "stats4"
>Creating a new generic function for "vcov" in "stats4"
>Creating a new generic function for "update" in "stats4"
>building package 'tcltk'
>mkdir -p -- ../../../library/tcltk/R
>mkdir -p -- ../../../library/tcltk/exec
>mkdir -p -- ../../../library/tcltk/po
>mkdir -p -- ../../../library/tcltk/man
>installing parsed NAMESPACE files
>installing translations:
>mkdir -p -- ../share/locale/en/LC_MESSAGES
>  en
>mkdir -p -- ../share/locale/en_GB/LC_MESSAGES
>  en_GB
>mkdir -p -- ../share/locale/es/LC_MESSAGES
>  es
>mkdir -p -- ../share/locale/fr/LC_MESSAGES
>  fr
>mkdir -p -- ../share/locale/de/LC_MESSAGES
>  de
>mkdir -p -- ../share/locale/it/LC_MESSAGES
>  it
>mkdir -p -- ../share/locale/ja/LC_MESSAGES
>  ja
>mkdir -p -- ../share/locale/ko/LC_MESSAGES
>  ko
>mkdir -p -- ../share/locale/pt_BR/LC_MESSAGES
>  pt_BR
>mkdir -p -- ../share/locale/ru/LC_MESSAGES
>  ru
>mkdir -p -- ../share/locale/zh_CN/LC_MESSAGES
>  zh_CN
>mkdir -p -- ../share/locale/zh_TW/LC_MESSAGES
>  zh_TW
>you should 'make docs' now ...
>creating doc/manual/R-FAQ.html
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>building/updating package metadata ...
>building all R documentation indices
>WARNING: ignoring environment value of R_HOME
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>building all R object docs (text, HTML, LaTeX, examples)
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> >>> Building/Updating help pages for package 'base'
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>  Beta                              text    html    latex   example
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>WARNING: ignoring environment value of R_HOME
> >>> Building/Updating help pages for package 'datasets'
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>WARNING: ignoring environment value of R_HOME
> >>> Building/Updating help pages for package 'methods'
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>WARNING: ignoring environment value of R_HOME
> >>> Building/Updating help pages for package 'grid'
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>WARNING: ignoring environment value of R_HOME
> >>> Building/Updating help pages for package 'splines'
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>WARNING: ignoring environment value of R_HOME
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>WARNING: ignoring environment value of R_HOME
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>begin installing recommended package VR
>begin installing recommended package cluster
>begin installing recommended package boot
>WARNING: ignoring environment value of R_HOME
>* Installing *source* package 'cluster' ...
>** libs
>x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -o cluster.so clara.o daisy.o dysta.o fanny.o init.o meet.o mona.o pam.o sildist.o spannel.o twins.o -lgfortran -lm -L/var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0/lib -lR
>** R
>** data
>**  moving datasets to lazyload DB
>** inst
>** preparing package for lazy loading
>** help
>*** installing help indices
> >>> Building/Updating help pages for package 'cluster'
>     Formats: text html latex example 
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>** building package indices ...
>* DONE (cluster)
>begin installing recommended package codetools
>WARNING: ignoring environment value of R_HOME
>* Installing *source* package 'boot' ...
>** R
>** data
>**  moving datasets to lazyload DB
>** inst
>** preparing package for lazy loading
>** help
>*** installing help indices
> >>> Building/Updating help pages for package 'boot'
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>** building package indices ...
>* DONE (boot)
>begin installing recommended package foreign
>WARNING: ignoring environment value of R_HOME
>* Installing *source* package 'codetools' ...
>** R
>** preparing package for lazy loading
>** help
>*** installing help indices
> >>> Building/Updating help pages for package 'codetools'
>     Formats: text html latex example 
>  checkUsage                        text    html    latex   example
>  codetools                         text    html    latex
>  findGlobals                       text    html    latex   example
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>** building package indices ...
>* DONE (codetools)
>begin installing recommended package KernSmooth
>WARNING: ignoring environment value of R_HOME
>* Installing *source* package 'KernSmooth' ...
>** libs
>x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -lblas -lgfortran -lm -lgfortran -lm -L/var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0/lib -lR
>** R
>** inst
>** preparing package for lazy loading
>** help
>*** installing help indices
> >>> Building/Updating help pages for package 'KernSmooth'
>     Formats: text html latex example 
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>** building package indices ...
>* DONE (KernSmooth)
>begin installing recommended package lattice
>WARNING: ignoring environment value of R_HOME
>* Installing *source* package 'MASS' ...
>** libs
>x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -o MASS.so lqs.o MASS.o -L/var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0/lib -lR
>** R
>** data
>**  moving datasets to lazyload DB
>** inst
>** preparing package for lazy loading
>** help
>*** installing help indices
> >>> Building/Updating help pages for package 'MASS'
>     Formats: text html latex example 
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>** building package indices ...
>* DONE (MASS)
> 
>* Installing *source* package 'class' ...
>** libs
>x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -o class.so class.o -L/var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0/lib -lR
>** R
>** inst
>** preparing package for lazy loading
>** help
>*** installing help indices
> >>> Building/Updating help pages for package 'class'
>     Formats: text html latex example 
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>** building package indices ...
>* DONE (class)
> 
>* Installing *source* package 'nnet' ...
>** libs
>x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -o nnet.so nnet.o -L/var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0/lib -lR
>** R
>** inst
>** preparing package for lazy loading
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> >>> Building/Updating help pages for package 'nnet'
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>** building package indices ...
>* DONE (nnet)
> 
>* Installing *source* package 'spatial' ...
>** libs
>x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -o spatial.so init.o krc.o pps.o -L/var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0/lib -lR
>** R
>** inst
>** preparing package for lazy loading
>** help
>*** installing help indices
> >>> Building/Updating help pages for package 'spatial'
>     Formats: text html latex example 
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>** building package indices ...
>* DONE (spatial)
>* DONE (VR)
>begin installing recommended package rpart
>WARNING: ignoring environment value of R_HOME
>* Installing *source* package 'rpart' ...
>** libs
>x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -o rpart.so anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o rpart_callback.o rpart.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o s_to_rp.o s_xpred.o surrogate.o usersplit.o xval.o -L/var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0/lib -lR
>** R
>** data
>**  moving datasets to lazyload DB
>** inst
>** preparing package for lazy loading
>** help
>*** installing help indices
> >>> Building/Updating help pages for package 'rpart'
>     Formats: text html latex example 
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>** building package indices ...
>* DONE (rpart)
>begin installing recommended package survival
>WARNING: ignoring environment value of R_HOME
>* Installing *source* package 'lattice' ...
>** libs
>x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -o lattice.so init.o threeDplot.o -L/var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0/lib -lR
>** R
>** data
>**  moving datasets to lazyload DB
>** demo
>** preparing package for lazy loading
>** help
>*** installing help indices
> >>> Building/Updating help pages for package 'lattice'
>     Formats: text html latex example 
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>** building package indices ...
>* DONE (lattice)
>begin installing recommended package Matrix
>WARNING: ignoring environment value of R_HOME
>* Installing *source* package 'foreign' ...
>checking for gcc... x86_64-pc-linux-gnu-gcc -std=gnu99
>checking for C compiler default output file name... a.out
>checking whether the C compiler works... yes
>checking whether we are cross compiling... no
>checking for suffix of executables... 
>checking for suffix of object files... o
>checking whether we are using the GNU C compiler... yes
>checking whether x86_64-pc-linux-gnu-gcc -std=gnu99 accepts -g... yes
>checking for x86_64-pc-linux-gnu-gcc -std=gnu99 option to accept ANSI C... none needed
>checking whether x86_64-pc-linux-gnu-gcc -std=gnu99 accepts -Wno-long-long... yes
>checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -std=gnu99 -E
>checking for egrep... grep -E
>checking for ANSI C header files... yes
>checking for sys/types.h... yes
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>checking byteswap.h presence... yes
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>configure: creating ./config.status
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>** libs
>x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -o foreign.so avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o sfm-read.o spss.o stataread.o -L/var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0/lib -lR
>** R
>** inst
>** preparing package for lazy loading
>** help
>*** installing help indices
> >>> Building/Updating help pages for package 'foreign'
>     Formats: text html latex example 
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>** building package indices ...
>* DONE (foreign)
>begin installing recommended package nlme
>WARNING: ignoring environment value of R_HOME
>* Installing *source* package 'survival' ...
>** libs
>x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -o survival.so agexact.o agfit3.o agfit5.o agmart.o agmart2.o agscore.o agsurv1.o agsurv2.o agsurv3.o chinv2.o chinv3.o cholesky2.o cholesky3.o chsolve2.o chsolve3.o cox_Rcallback.o coxdetail.o coxfit2.o coxfit5.o coxmart.o coxph_wtest.o coxscho.o coxscore.o dmatrix.o doloop.o pyears1.o pyears2.o pyears3.o pystep.o survConcordance.o survdiff2.o survfit4.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o -L/var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0/lib -lR
>** R
>** data
>**  moving datasets to lazyload DB
>Read 200 items
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>** preparing package for lazy loading
>** help
>*** installing help indices
> >>> Building/Updating help pages for package 'survival'
>     Formats: text html latex example 
>  Surv                              text    html    latex   example
>  aareg                             text    html    latex   example
>  aml                               text    html    latex
>  anova.coxph                       text    html    latex   example
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>Note: removing empty section \examples in file 'survreg.control.Rd'
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>** building package indices ...
>* DONE (survival)
>WARNING: ignoring environment value of R_HOME
>* Installing *source* package 'nlme' ...
>** libs
>x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -o nlme.so corStruct.o gnls.o init.o matrix.o nlme.o nlmefit.o nlOptimizer.o nls.o pdMat.o -L/var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0/lib -lR
>** R
>** data
>**  moving datasets to lazyload DB
>** inst
>** preparing package for lazy loading
>** help
>*** installing help indices
> >>> Building/Updating help pages for package 'nlme'
>     Formats: text html latex example 
>  ACF                               text    html    latex   example
>  ACF.gls                           text    html    latex   example
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>  lmList                            text    html    latex   example
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>  logLik.reStruct                   text    html    latex
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>  model.matrix.reStruct             text    html    latex   example
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>** building package indices ...
>* DONE (nlme)
>begin installing recommended package mgcv
>WARNING: ignoring environment value of R_HOME
>* Installing *source* package 'mgcv' ...
>** libs
>x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -o mgcv.so gcv.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o qp.o tprs.o -L/var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0/lib -lRlapack -lblas -lgfortran -lm -L/var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0/lib -lR
>** R
>** inst
>** preparing package for lazy loading
>** help
>*** installing help indices
> >>> Building/Updating help pages for package 'mgcv'
>     Formats: text html latex example 
>  Predict.matrix                    text    html    latex   example
>  Predict.matrix.cr.smooth          text    html    latex   example
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>  sp.vcov                           text    html    latex   example
>  step.gam                          text    html    latex   example
>  summary.gam                       text    html    latex   example
>  te                                text    html    latex   example
>  tensor.prod.model.matrix          text    html    latex   example
>  uniquecombs                       text    html    latex   example
>  vcov.gam                          text    html    latex   example
>  vis.gam                           text    html    latex   example
>** building package indices ...
>* DONE (mgcv)
>WARNING: ignoring environment value of R_HOME
>* Installing *source* package 'Matrix' ...
>** libs
>x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o CHOLMOD.a COLAMD.a AMD.a -L/var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0/lib -lRlapack -lblas -lgfortran -lm -L/var/tmp/portage/dev-lang/R-2.9.0/work/R-2.9.0/lib -lR
>** R
>** data
>** inst
>** preparing package for lazy loading
>Creating a generic for "rcond" in package  "Matrix"
>    (the supplied definition differs from and overrides the implicit generic in package "base": Formal arguments differ: (x, norm, ...), (x, norm, triangular, ...))
>Creating a new generic function for "image" in "Matrix"
>Creating a new generic function for "solve" in "Matrix"
>Creating a new generic function for "determinant" in "Matrix"
>Creating a new generic function for "update" in "Matrix"
>Creating a new generic function for "colSums" in "Matrix"
>Creating a new generic function for "colMeans" in "Matrix"
>Creating a new generic function for "rowSums" in "Matrix"
>Creating a new generic function for "rowMeans" in "Matrix"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "colSums" no definition for class: "igCMatrix"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "rowSums" no definition for class: "igCMatrix"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "colMeans" no definition for class: "igCMatrix"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "rowMeans" no definition for class: "igCMatrix"
>Creating a new generic function for "crossprod" in "Matrix"
>Creating a new generic function for "tcrossprod" in "Matrix"
>Creating a new generic function for "t" in "Matrix"
>Creating a new generic function for "diag" in "Matrix"
>Creating a new generic function for "chol" in "Matrix"
>Creating a new generic function for "isSymmetric" in "Matrix"
>Creating a new generic function for "qr" in "Matrix"
>Creating a new generic function for "as.vector" in "Matrix"
>Creating a new generic function for "print" in "Matrix"
>Creating a new generic function for "zapsmall" in "Matrix"
>Creating a new generic function for "kronecker" in "Matrix"
>Creating a new generic function for "as.matrix" in "Matrix"
>Creating a new generic function for "as.array" in "Matrix"
>Creating a new generic function for "head" in "Matrix"
>Creating a new generic function for "tail" in "Matrix"
>Creating a new generic function for "drop" in "Matrix"
>Creating a new generic function for "mean" in "Matrix"
>Creating a new generic function for "cov2cor" in "Matrix"
>Creating a new generic function for "unname" in "Matrix"
>Creating a new generic function for "all.equal" in "Matrix"
>Creating a new generic function for "diff" in "Matrix"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.csr"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.csr"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.csc"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.csc"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.coo"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.coo"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.csr"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.csr"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.coo"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.csr"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.csc"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.coo"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.csr"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.coo"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.csc"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.csr"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.csr"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.coo"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.csc"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.csr"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.coo"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "matrix.csc"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "graphAM"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "graph"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "graphNEL"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "graphNEL"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "graph"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "graphNEL"
>Warning in matchSignature(signature, fdef, where) :
>  in the method signature for function "coerce" no definition for class: "graphNEL"
>Creating a new generic function for "summary" in "Matrix"
>Creating a new generic function for "qr.R" in "Matrix"
>Creating a new generic function for "qr.qy" in "Matrix"
>Creating a new generic function for "qr.qty" in "Matrix"
>Creating a new generic function for "qr.coef" in "Matrix"
>Creating a new generic function for "qr.resid" in "Matrix"
>Creating a new generic function for "qr.fitted" in "Matrix"
>** help
>*** installing help indices
> >>> Building/Updating help pages for package 'Matrix'
>     Formats: text html latex example 
>  BunchKaufman-methods              text    html    latex   example
>  CAex                              text    html    latex   example
>  CHMfactor-class                   text    html    latex   example
>  Cholesky-class                    text    html    latex   example
>  Cholesky                          text    html    latex   example
>  CsparseMatrix-class               text    html    latex   example
>  Diagonal                          text    html    latex   example
>  Hilbert                           text    html    latex   example
>  KNex                              text    html    latex   example
>  LU-class                          text    html    latex   example
>  Matrix-class                      text    html    latex   example
>  Matrix                            text    html    latex   example
>  MatrixFactorization-class         text    html    latex   example
>  RsparseMatrix-class               text    html    latex   example
>  Schur-class                       text    html    latex   example
>  Schur                             text    html    latex   example
>  SparseM-conv                      text    html    latex
>  Subassign-methods                 text    html    latex   example
>  TsparseMatrix-class               text    html    latex   example
>  USCounties                        text    html    latex   example
>  Xtrct-methods                     text    html    latex   example
>  all-methods                       text    html    latex   example
>  all.equal-methods                 text    html    latex   example
>  atomicVector-class                text    html    latex   example
>  band                              text    html    latex   example
>  bandSparse                        text    html    latex   example
>  bdiag                             text    html    latex   example
>  cBind                             text    html    latex   example
>  chol                              text    html    latex   example
>  colSums                           text    html    latex   example
>  compMatrix-class                  text    html    latex
>  dMatrix-class                     text    html    latex   example
>  ddenseMatrix-class                text    html    latex   example
>  ddiMatrix-class                   text    html    latex   example
>  denseMatrix-class                 text    html    latex   example
>  dgCMatrix-class                   text    html    latex   example
>  dgRMatrix-class                   text    html    latex
>  dgTMatrix-class                   text    html    latex   example
>  dgeMatrix-class                   text    html    latex
>  diagonalMatrix-class              text    html    latex   example
>  dpoMatrix-class                   text    html    latex   example
>  drop0                             text    html    latex   example
>  dsCMatrix-class                   text    html    latex   example
>  dsRMatrix-class                   text    html    latex   example
>  dsparseMatrix-class               text    html    latex   example
>  dsyMatrix-class                   text    html    latex   example
>  dtCMatrix-class                   text    html    latex   example
>  dtRMatrix-class-def               text    html    latex   example
>  dtpMatrix-class                   text    html    latex   example
>  dtrMatrix-class                   text    html    latex   example
>  expand                            text    html    latex   example
>  expm                              text    html    latex   example
>  externalFormats                   text    html    latex   example
>  facmul                            text    html    latex   example
>  forceSymmetric                    text    html    latex   example
>  generalMatrix-class               text    html    latex
>  image-methods                     text    html    latex   example
>  index-class                       text    html    latex   example
>  is.na-methods                     text    html    latex   example
>  isSymmetric-methods               text    html    latex
>  kronecker-methods                 text    html    latex   example
>  ldenseMatrix-class                text    html    latex   example
>  ldiMatrix-class                   text    html    latex   example
>  lgeMatrix-class                   text    html    latex   example
>  lsparseMatrix-classes             text    html    latex   example
>  lsyMatrix-class                   text    html    latex   example
>  ltrMatrix-class                   text    html    latex   example
>  lu                                text    html    latex   example
>  nMatrix-class                     text    html    latex   example
>  ndenseMatrix-class                text    html    latex   example
>  nearPD                            text    html    latex   example
>  ngeMatrix-class                   text    html    latex   example
>  nnzero                            text    html    latex   example
>  norm                              text    html    latex   example
>  nsparseMatrix-classes             text    html    latex   example
>  nsyMatrix-class                   text    html    latex   example
>  ntrMatrix-class                   text    html    latex   example
>  number-class                      text    html    latex   example
>  pMatrix-class                     text    html    latex   example
>  printSpMatrix                     text    html    latex   example
>  qr-methods                        text    html    latex
>  rcond                             text    html    latex   example
>  replValue-class                   text    html    latex   example
>  spMatrix                          text    html    latex   example
>  sparseLU-class                    text    html    latex   example
>  sparseMatrix-class                text    html    latex   example
>  sparseMatrix                      text    html    latex   example
>  sparseQR-class                    text    html    latex   example
>  sparseVector-class                text    html    latex   example
>  symmetricMatrix-class             text    html    latex   example
>  symmpart                          text    html    latex   example
>  tcrossprod                        text    html    latex   example
>  triangularMatrix-class            text    html    latex   example
>  unpack                            text    html    latex   example
>  unused-classes                    text    html    latex   example
>  xtabs                             text    html    latex   example
>** building package indices ...
>Loading required package: Matrix
> 
>Attaching package: 'Matrix'
> 
> 
>	The following object(s) are masked from package:stats :
> 
>	 xtabs 
> 
> 
>	The following object(s) are masked from package:base :
> 
>	 rcond 
> 
>* DONE (Matrix)
>make -s -j3 -j1 -C src/nmath/standalone libRmath_la_LDFLAGS=-Wl,-soname,libRmath.so.0.0.0 
>Copying source files
>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 expm1.d from expm1.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 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
>>>> Source compiled.
>>>> Test phase [not enabled]: dev-lang/R-2.9.0
> 
>>>> Install R-2.9.0 into /var/tmp/portage/dev-lang/R-2.9.0/image/ category dev-lang
>make -s -j3 DESTDIR=/var/tmp/portage/dev-lang/R-2.9.0/image/ install 
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R
>installing doc ...
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/share/doc/R-2.9.0
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/share/man/man1
>installing doc/html ...
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/share/doc/R-2.9.0/html
>installing doc/html/search ...
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/share/doc/R-2.9.0/html/search
>installing doc/manual ...
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/share/doc/R-2.9.0/manual
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/etc
>installing etc ...
>installing share ...
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/R
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/encodings
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/java
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/licenses
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/make
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/perl
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/perl/R
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/perl/File/Copy
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/perl/Text
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/sh
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/texmf
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/bin
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/bin
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/include
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/include/R_ext
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/pkgconfig
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/bin/exec
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/lib
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/modules
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/library
>installing packages ...
>  building HTML index ...
>installing translations:
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/locale/en/LC_MESSAGES
>  en
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/locale/en_GB/LC_MESSAGES
>  en_GB
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/locale/es/LC_MESSAGES
>  es
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/locale/fr/LC_MESSAGES
>  fr
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/locale/de/LC_MESSAGES
>  de
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/locale/it/LC_MESSAGES
>  it
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/locale/ja/LC_MESSAGES
>  ja
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/locale/ko/LC_MESSAGES
>  ko
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/locale/pt_BR/LC_MESSAGES
>  pt_BR
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/locale/ru/LC_MESSAGES
>  ru
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/locale/zh_CN/LC_MESSAGES
>  zh_CN
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/lib64/R/share/locale/zh_TW/LC_MESSAGES
>  zh_TW
>make -s -j3 -C src/nmath/standalone DESTDIR=/var/tmp/portage/dev-lang/R-2.9.0/image/ install 
>mkdir -p -- /var/tmp/portage/dev-lang/R-2.9.0/image//usr/include
>cp: cannot create regular file `/var/tmp/portage/dev-lang/R-2.9.0/image//usr/include/Rmath.h': No such file or directory
>make: *** [install-header] Error 1
>make: *** Waiting for unfinished jobs....
> [31;01m*[0m 
> [31;01m*[0m ERROR: dev-lang/R-2.9.0 failed.
> [31;01m*[0m Call stack:
> [31;01m*[0m               ebuild.sh, line   49:  Called src_install
> [31;01m*[0m             environment, line 3598:  Called die
> [31;01m*[0m The specific snippet of code:
> [31;01m*[0m       emake -C src/nmath/standalone DESTDIR="${D}" install || die "emake install math library failed";
> [31;01m*[0m  The die message:
> [31;01m*[0m   emake install math library failed
> [31;01m*[0m 
> [31;01m*[0m If you need support, post the topmost build error, and the call stack if relevant.
> [31;01m*[0m A complete build log is located at '/var/lib/entropy/logs/dev-lang:R-2.9.0:20090512-081330.log'.
> [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/dev-lang/R-2.9.0/temp/environment'.
> [31;01m*[0m
>

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Attachments on bug 269511: 191008