[Rd] problems (seg-faults) while trying to compile for older suse versions
peter dalgaard
pdalgd at gmail.com
Wed Oct 5 12:00:21 CEST 2011
On Oct 5, 2011, at 11:04 , Detlef Steuer wrote:
>
>
>>
>> On Wed, 5 Oct 2011, Detlef Steuer wrote:
>>
>>> Hi!
>>>
>>> While preparing 2.13.2 in the build service I get stuck for some older
>>> releases of openSUSE / SLED.
>>>
>>> While it built fine for 2.13.1 now I get segfaults in 'make docs' and
>>> do so only for 32-bit architectures. This is not urgent, because only
>>> older releases are affected, nevertheless I would like to understand
>>> the cause.
>>>
>>> Attached are what I think the relevant parts of a build-log, including
>>> tracebacks of some segfaults.
>>
>> Nothing came through. But it seems specific to your system (and no
>> one reported anything in the run up to 2.13.2, including the RC test
>> period nor with 2.13.1 patched).
>
> Thank you for the answer.
>
> Yes.
>
> 2.13.1 patched worked fine till the moment 2.13.2 was released.
> Shouldn't these be more or less identical? Anything changed?
PCRE got updated at some point, last change Sep 16 AFAICT (based on the NEWS file in R-devel -- I'd rather not check out R-2-13-branch again). Since you are getting trouble from grep() and friends, this could be the root of the issue.
But doesn't SUSE have its own PCRE?
-pd
>
> It may very well be some defect in the build service, but it is reproducible.
>
> Here, this time inlined, the buildlog with traceback.
>
> ---
> Using BUILD_ROOT=/var/cache/obs/worker/root_8/.mount
> Using BUILD_ARCH=i586:i486:i386
> Doing kvm build in /var/cache/obs/worker/root_8/root
>
> build09 started "build R-base.spec" at Wed Oct 5 07:15:50 UTC 2011.
>
> Building R for project 'devel:languages:R:base' repository 'openSUSE_11.1' arch 'i586' srcmd5 '851a0904debdcf2f239e357a2e6ccb00'
>
> processing specfile /var/cache/obs/worker/root_8/.build-srcdir/R-base.spec ...
> running changelog2spec --target rpm --file /var/cache/obs/worker/root_8/.build-srcdir/R-base.spec
> init_buildsystem --cachedir /var/cache/build --prepare --clean --rpmlist /var/cache/obs/worker/root_8/.build.rpmlist /var/cache/obs/worker/root_8/.build-srcdir/R-base.spec build rpmlint-Factory ...
>
> --- snip --- setting up build environment
>
> installing libgcc43-4.3.3_20081022-9.5
> installing libgfortran43-4.3.3_20081022-9.5
>
> installing gcc43-c++-4.3.3_20081022-9.5
> installing gcc43-fortran-4.3.3_20081022-9.5
>
> installing gcc-c++-4.3-34.168
> installing gcc-fortran-4.3-34.168
>
> --- begin configure ---
>
> + cd R-2.13.2
> + export R_BROWSER=xdg-open
> + R_BROWSER=xdg-open
> + export R_PDFVIEWER=xdg-open
> + R_PDFVIEWER=xdg-open
> + CFLAGS='-march=i586 -mtune=i686 -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables'
> + export CFLAGS
> + CXXFLAGS='-march=i586 -mtune=i686 -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables'
> + export CXXFLAGS
> + FFLAGS='-march=i586 -mtune=i686 -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables'
> + export FFLAGS
> + ./configure --host=i686-suse-linux-gnu --build=i686-suse-linux-gnu --target=i586-suse-linux --program-prefix= --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib --libexecdir=/usr/lib --localstatedir=/var --sharedstatedir=/usr/com --mandir=/usr/share/man --infodir=/usr/share/info --enable-R-shlib
> checking build system type... i686-suse-linux-gnu
> checking host system type... i686-suse-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 whether ln -s works... yes
> checking for bison... no
> checking for byacc... no
> checking for ar... ar
> checking for a BSD-compatible install... /usr/bin/install -c
> checking for sed... /usr/bin/sed
> checking for which... /usr/bin/which
> checking for less... /usr/bin/less
> checking for gtar... no
> checking for gnutar... no
> checking for tar... /bin/tar
> checking for tex... /usr/bin/tex
> checking for latex... /usr/bin/latex
> checking for pdftex... /usr/bin/pdftex
> checking for pdflatex... /usr/bin/pdflatex
> checking for makeindex... /usr/bin/makeindex
> checking for makeinfo... /usr/bin/makeinfo
> checking whether makeinfo version is at least 4.7... yes
> checking for install-info... /usr/bin/install-info
> checking for texi2dvi... /usr/bin/texi2dvi
> checking for unzip... no
> checking for zip... no
> checking for gzip... /usr/bin/gzip
> checking for bzip2... /usr/bin/bzip2
> using default browser ... xdg-open
> checking for xdg-open... no
> checking for acroread... no
> checking for acroread4... no
> checking for xdg-open... no
> checking for evince... no
> checking for xpdf... no
> checking for gv... no
> checking for gnome-gv... no
> checking for ggv... no
> checking for okular... no
> checking for kpdf... no
> checking for open... no
> checking for gpdf... no
> checking for kghostview... no
> configure: WARNING: I could not determine a PDF viewer
> checking for notangle... false
> checking for pkg-config... /usr/bin/pkg-config
> checking for i686-suse-linux-gnu-gcc... no
> checking for gcc... gcc
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking how to run the C preprocessor... gcc -E
> checking for grep that handles long lines and -e... /usr/bin/grep
> checking for egrep... /usr/bin/grep -E
> checking whether gcc needs -traditional... no
> checking how to run the C preprocessor... gcc -E
> checking for gfortran... gfortran
> checking for i686-suse-linux-gnu-g77... (cached) gfortran
> checking whether we are using the GNU Fortran 77 compiler... yes
> checking whether gfortran accepts -g... yes
> checking for i686-suse-linux-gnu-g++... no
> checking for i686-suse-linux-gnu-c++... no
> checking for i686-suse-linux-gnu-gpp... no
> checking for i686-suse-linux-gnu-aCC... no
> checking for i686-suse-linux-gnu-CC... no
> checking for i686-suse-linux-gnu-cxx... no
> checking for i686-suse-linux-gnu-cc++... no
> checking for i686-suse-linux-gnu-cl.exe... no
> checking for i686-suse-linux-gnu-FCC... no
> checking for i686-suse-linux-gnu-KCC... no
> checking for i686-suse-linux-gnu-RCC... no
> checking for i686-suse-linux-gnu-xlC_r... no
> checking for i686-suse-linux-gnu-xlC... no
> checking for g++... g++
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> checking how to run the C++ preprocessor... g++ -E
> checking whether __attribute__((visibility())) is supported... yes
> checking whether gcc accepts -fvisibility... yes
> checking whether gfortran accepts -fvisibility... yes
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking minix/config.h usability... no
> checking minix/config.h presence... no
> checking for minix/config.h... no
> checking whether it is safe to define __EXTENSIONS__... yes
> checking for i686-suse-linux-gnu-gcc... no
> checking for i686-suse-linux-gnu-objcc... no
> checking for i686-suse-linux-gnu-objc... no
> checking for i686-suse-linux-gnu-cc... no
> checking for i686-suse-linux-gnu-CC... no
> 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 compiler found
> checking for a sed that does not truncate output... (cached) /usr/bin/sed
> checking for fgrep... /usr/bin/grep -F
> checking for ld used by gcc... /usr/i586-suse-linux/bin/ld
> checking if the linker (/usr/i586-suse-linux/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/i586-suse-linux/bin/ld option to reload object files... -r
> checking for i686-suse-linux-gnu-objdump... no
> checking for objdump... objdump
> checking how to recognize dependent libraries... pass_all
> checking for i686-suse-linux-gnu-ar... (cached) ar
> checking for i686-suse-linux-gnu-strip... no
> checking for strip... strip
> checking for i686-suse-linux-gnu-ranlib... no
> checking for ranlib... ranlib
> checking command to parse /usr/bin/nm -B output from gcc object... ok
> checking for dlfcn.h... yes
> checking whether we are using the GNU C++ compiler... (cached) yes
> checking whether g++ accepts -g... (cached) yes
> checking how to run the C++ preprocessor... g++ -E
> checking for i686-suse-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 gcc supports -fno-rtti -fno-exceptions... no
> checking for gcc option to produce PIC... -fPIC -DPIC
> checking if gcc PIC flag -fPIC -DPIC works... yes
> checking if gcc static flag -static works... yes
> checking if gcc supports -c -o file.o... yes
> checking if gcc supports -c -o file.o... (cached) yes
> checking whether the gcc linker (/usr/i586-suse-linux/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 for ld used by g++... /usr/i586-suse-linux/bin/ld
> checking if the linker (/usr/i586-suse-linux/bin/ld) is GNU ld... yes
> checking whether the g++ linker (/usr/i586-suse-linux/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/i586-suse-linux/bin/ld) 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/i586-suse-linux/bin/ld) 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 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 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 limits.h usability... yes
> checking limits.h presence... yes
> checking for limits.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 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 option to accept ISO C99... -std=gnu99
> checking for gcc -std=gnu99 option to accept ISO Standard C... (cached) -std=gnu99
> 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 long double... 12
> checking size of size_t... 4
> checking whether we can compute C Make dependencies... yes, using gcc -std=gnu99 -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/local/lib -L/usr/lib/gcc/i586-suse-linux/4.3 -L/usr/lib/gcc/i586-suse-linux/4.3/../../../../i586-suse-linux/lib -L/usr/lib/gcc/i586-suse-linux/4.3/../../.. -lgfortranbegin -lgfortran -lm
> checking how to get verbose linking output from gcc -std=gnu99... -v
> checking for C libraries of gcc -std=gnu99... -L/usr/local/lib -L/usr/lib/gcc/i586-suse-linux/4.3 -L/usr/lib/gcc/i586-suse-linux/4.3/../../../../i586-suse-linux/lib -L/usr/lib/gcc/i586-suse-linux/4.3/../../.. -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
> 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 nearbyint exists and is declared... yes
> checking whether nearbyintl exists and is declared... yes
> checking whether powl exists and is declared... yes
> checking whether rint 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 whether time exists and is declared... yes
> 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 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 setenv exists and is declared... yes
> checking whether unsetenv 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 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 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 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
> 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 cblas_cdotu_sub in vecLib framework... no
> 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 for iconvlist... no
> checking for iconv... yes
> checking for iconv declaration... install-shextern 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... no
> 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... yes
> checking X11/Xmu/Atoms.h presence... yes
> checking for X11/Xmu/Atoms.h... yes
> checking for XmuInternAtom in -lXmu... yes
> checking whether pkg-config knows about cairo and pango... yes
> checking whether cairo including pango is >= 1.2 and works... yes
> checking for tclConfig.sh... no
> checking for tclConfig.sh in library (sub)directories... /usr/lib/tclConfig.sh
> checking for tkConfig.sh... no
> checking for tkConfig.sh in library (sub)directories... /usr/lib/tkConfig.sh
> checking tcl.h usability... yes
> checking tcl.h presence... yes
> checking for tcl.h... yes
> checking tk.h usability... yes
> checking tk.h presence... yes
> checking for tk.h... yes
> checking whether compiling/linking Tcl/Tk code works... yes
> checking for BSD networking... yes
> checking if jpeglib version >= 6b... yes
> checking for jpeg_destroy_compress in -ljpeg... yes
> checking for main in -lz... 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 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 whether zlib support needs to be compiled... yes
> checking mmap support for zlib... yes
> checking whether bzip2 support needs to be compiled... yes
> checking for lzma_version_number in -llzma... no
> checking whether PCRE support needs to be compiled... 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... 64
> checking for _LARGEFILE_SOURCE value needed for large files... no
> checking whether KERN_USRSTACK sysctl is supported... no
> checking for visible __lib_stack_end... yes
> checking for lpr... no
> checking for lp... no
> checking for paperconf... false
> checking for java... no
> checking for javac... no
> checking for javah... no
> checking for jar... no
> checking whether Java compiler works... no
> checking whether Java compiler works for version 1.4... no
> checking whether Java interpreter works... no
> checking for i686-suse-linux-gnu-gfortran... no
> checking for i686-suse-linux-gnu-g95... no
> checking for i686-suse-linux-gnu-xlf95... no
> checking for i686-suse-linux-gnu-f95... no
> checking for i686-suse-linux-gnu-fort... no
> checking for i686-suse-linux-gnu-ifort... no
> checking for i686-suse-linux-gnu-ifc... no
> checking for i686-suse-linux-gnu-efc... no
> checking for i686-suse-linux-gnu-pgf95... no
> checking for i686-suse-linux-gnu-lf95... no
> checking for i686-suse-linux-gnu-ftn... no
> checking for i686-suse-linux-gnu-xlf90... no
> checking for i686-suse-linux-gnu-f90... no
> checking for i686-suse-linux-gnu-pgf90... no
> checking for i686-suse-linux-gnu-pghpf... no
> checking for i686-suse-linux-gnu-epcf90... no
> checking for i686-suse-linux-gnu-g77... no
> checking for i686-suse-linux-gnu-xlf... no
> checking for i686-suse-linux-gnu-f77... no
> checking for i686-suse-linux-gnu-frt... no
> checking for i686-suse-linux-gnu-pgf77... no
> checking for i686-suse-linux-gnu-cf77... no
> checking for i686-suse-linux-gnu-fort77... no
> checking for i686-suse-linux-gnu-fl32... no
> checking for i686-suse-linux-gnu-af77... no
> checking for gfortran... gfortran
> checking whether we are using the GNU Fortran compiler... yes
> checking whether gfortran accepts -g... yes
> checking for i686-suse-linux-gnu-gfortran... gfortran
> checking whether we are using the GNU Fortran compiler... (cached) yes
> checking whether 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 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/i586-suse-linux/bin/ld) 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 gfortran option to support OpenMP... -fopenmp
> checking for recommended packages... yes
> checking whether NLS is requested... yes
>
> Configuring src/extra/intl directory
> 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/msgfmt
> 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 i686-suse-linux-gnu-ranlib... 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 sys/param.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 whether imported symbols can be declared weak... yes
> checking for multithread API to use... none
> checking argz.h usability... yes
> checking argz.h presence... yes
> checking for argz.h... yes
> checking for inttypes.h... (cached) yes
> checking for limits.h... (cached) yes
> checking for unistd.h... (cached) yes
> checking for sys/param.h... (cached) yes
> checking for getcwd... yes
> checking for getegid... yes
> checking for geteuid... yes
> checking for getgid... yes
> checking for getuid... yes
> checking for mempcpy... (cached) yes
> checking for munmap... yes
> checking for stpcpy... yes
> checking for strcasecmp... yes
> checking for strdup... (cached) yes
> checking for strtoul... yes
> checking for tsearch... yes
> checking for argz_count... yes
> checking for argz_stringify... yes
> checking for argz_next... yes
> checking for __fsetlocking... yes
> checking whether feof_unlocked is declared... yes
> checking whether fgets_unlocked is declared... yes
> checking for iconv... (cached) yes
> checking for iconv declaration... (cached) install-shextern 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... no
> 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 shared library run path origin... done
> checking for CFPreferencesCopyAppValue... (cached) no
> checking for CFLocaleCopyCurrent... (cached) no
> checking whether included gettext is requested... no
> checking for GNU gettext in libc... yes
> checking whether to use NLS... yes
> checking where the gettext function comes from... libc
> Finished configuring src/extra/intl directory
>
> using as R_SHELL for scripts ... /bin/sh
> configure: creating ./config.status
> config.status: creating Makeconf
> config.status: creating Makefile
> config.status: creating doc/Makefile
> config.status: creating doc/html/Makefile
> config.status: creating doc/manual/Makefile
> config.status: creating etc/Makefile
> config.status: creating etc/Makeconf
> config.status: creating etc/Renviron
> config.status: creating etc/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/tre/Makefile
> config.status: creating src/extra/xdr/Makefile
> config.status: creating src/extra/xz/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/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/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/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 i686-suse-linux-gnu
>
> Source directory: .
> Installation directory: /usr
>
> C compiler: gcc -std=gnu99 -march=i586 -mtune=i686 -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables
> Fortran 77 compiler: gfortran -march=i586 -mtune=i686 -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables
>
> C++ compiler: g++ -march=i586 -mtune=i686 -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables
> Fortran 90/95 compiler: gfortran -g -O2
> Obj-C compiler:
>
> Interfaces supported: X11, tcltk
> External libraries: readline
> Additional capabilities: PNG, JPEG, TIFF, NLS, cairo
> Options enabled: shared R library, shared BLAS, R profiling
>
> Recommended packages: yes
>
> configure: WARNING: I could not determine a PDF viewer
> --- should use xdg-utils, but indeed no PDF viewer is installed. should I? ---
>
>
>
> --- snipped lots of compilation ---
>
> building package 'base'
> make[4]: Entering directory `/usr/src/packages/BUILD/R-2.13.2/src/library/base'
> mkdir -p -- ../../../library/base/demo
> mkdir -p -- ../../../library/base/po
> make[4]: Leaving directory `/usr/src/packages/BUILD/R-2.13.2/src/library/base'
> make[3]: Leaving directory `/usr/src/packages/BUILD/R-2.13.2/src/library/base'
> make[3]: Entering directory `/usr/src/packages/BUILD/R-2.13.2/src/library/tools'
> building package 'tools'
>
> -- builds fine ---
>
> make[3]: Leaving directory `/usr/src/packages/BUILD/R-2.13.2/src/library/tools'
> make[3]: Entering directory `/usr/src/packages/BUILD/R-2.13.2/src/library/utils'
> building package 'utils'
>
> -- builds fine ---
>
> make[3]: Leaving directory `/usr/src/packages/BUILD/R-2.13.2/src/library/utils'
> make[3]: Entering directory `/usr/src/packages/BUILD/R-2.13.2/src/library/grDevices'
> building package 'grDevices'
>
> ---builds fine --
>
> make[3]: Leaving directory `/usr/src/packages/BUILD/R-2.13.2/src/library/grDevices'
> make[3]: Entering directory `/usr/src/packages/BUILD/R-2.13.2/src/library/graphics'
> building package 'graphics'
>
> ...----everythings looks ok, but now:
>
> make[1]: Leaving directory `/usr/src/packages/BUILD/R-2.13.2/tests'
> make[1]: Entering directory `/usr/src/packages/BUILD/R-2.13.2/po'
> make[2]: Entering directory `/usr/src/packages/BUILD/R-2.13.2/po'
> 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/nn/LC_MESSAGES
> nn
> mkdir -p -- ../share/locale/pt_BR/LC_MESSAGES
> pt_BR
> mkdir -p -- ../share/locale/ru/LC_MESSAGES
> ru
> mkdir -p -- ../share/locale/tr/LC_MESSAGES
> tr
> mkdir -p -- ../share/locale/zh_CN/LC_MESSAGES
> zh_CN
> mkdir -p -- ../share/locale/zh_TW/LC_MESSAGES
> zh_TW
> mkdir -p -- ../share/locale/en at quot/LC_MESSAGES
> en at quot
> make[2]: Leaving directory `/usr/src/packages/BUILD/R-2.13.2/po'
> make[1]: Leaving directory `/usr/src/packages/BUILD/R-2.13.2/po'
>
> --- make docs gives seg-fault ?!
>
> you should 'make docs' now ...
> make[1]: Entering directory `/usr/src/packages/BUILD/R-2.13.2/doc'
>
> *** caught segfault ***
> address 0xffffffe3, cause 'memory not mapped'
>
> Traceback:
> 1: grep("[^[:blank:][:cntrl:]]", unlist(Rd[sections == "TEXT"]), perl = TRUE, useBytes = TRUE)
> 2: prepare2_Rd(Rd, Rdfile)
> 3: tools:::prepare_Rd(tools::parse_Rd("./NEWS.Rd"), stages = "install")
> 4: saveRDS(tools:::prepare_Rd(tools::parse_Rd("./NEWS.Rd"), stages = "install"), "NEWS.rds")
> aborting ...
> /bin/sh: line 1: 19586 Done echo "options(warn=1);saveRDS(tools:::prepare_Rd(tools::parse_Rd(\"./NEWS.Rd\"), stages = 'install'), 'NEWS.rds')"
> 19587 Segmentation fault | ../bin/R --vanilla --slave
> make[1]: *** [NEWS.rds] Error 139
> make[1]: Leaving directory `/usr/src/packages/BUILD/R-2.13.2/doc'
> make: [docs] Error 2 (ignored)
> make[1]: Entering directory `/usr/src/packages/BUILD/R-2.13.2/src/library'
> make[2]: Entering directory `/usr/src/packages/BUILD/R-2.13.2/src/library'
> installing parsed Rd
> make[3]: Entering directory `/usr/src/packages/BUILD/R-2.13.2/src/library'
>
> *** caught segfault ***
> address 0xffffffe3, cause 'memory not mapped'
>
> Traceback:
> 1: grep("[^[:blank:][:cntrl:]]", unlist(Rd[sections == "TEXT"]), perl = TRUE, useBytes = TRUE)
> 2: prepare2_Rd(Rd, Rdfile)
> 3: prepare_Rd(f, encoding = encoding, defines = os, stages = stages, warningCalls = FALSE, stage2 = step > 1L, stage3 = step > 2L)
> 4:
> FUN(c("/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/AIC.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/ARMAacf.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/ARMAtoMA.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/Beta.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/Binomial.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/Cauchy.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/Chisquare.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/Distributions.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/Exponential.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/Fdist.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/GammaDist.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/Geometric.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/HoltWinters.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/Hypergeometric.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/IQR.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/KalmanLike.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/Logistic.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/Lognormal.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/Multinom.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/NLSstAsymptotic.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/NLSstClosestX.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/NLSstLfAsymptote.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/NLSstRtAsymptote.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/NegBinomial.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/Normal.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/Poisson.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/SSD.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/SSasymp.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/SSasympOff.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/SSasympOrig.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/SSbiexp.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/SSfol.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/SSfpl.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/SSgompertz.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/SSlogis.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/SSmicmen.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/SSweibull.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/SignRank.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/StructTS.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/TDist.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/Tukey.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/TukeyHSD.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/Uniform.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/Weibull.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/Wilcoxon.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/acf.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/acf2AR.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/add1.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/addmargins.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/aggregate.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/alias.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/anova.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/anova.glm.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/anova.lm.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/anova.mlm.Rd",
> "/usr/src/packages/BUILD/
> R-2.13.2/src/library/stats/man/ansari.test.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/aov.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/approxfun.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/ar.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/ar.ols.Rd",
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> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/tsSmooth.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/tsdiag.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/tsp.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/uniroot.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/update.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/update.formula.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/var.test.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/varimax.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/vcov.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/weighted.mean.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/weighted.residuals.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/weights.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/wilcox.test.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/window.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/xtabs.Rd",
> "/usr/src/packages/BUILD/R-2.13.2/src/library/stats/man/zC.Rd")[[1L]], ...)
> 5: lapply(files, .fetch_Rd_object) 6: .build_Rd_db(dir, manfiles,
> db_file = db_file, encoding = encoding, built_file = built_file)
> 7: tools:::.install_package_Rd_objects("./stats",
> "../../library/stats") aborting ... /bin/sh: line 2: 19617
> Done echo
> "options(warn=1);tools:::.install_package_Rd_objects('./stats',
> '../../library/stats')" 19618 Segmentation fault |
> R_DEFAULT_PACKAGES=NULL ../../bin/R --vanilla --slave make[3]: ***
> [stats.Rdts] Error 1 make[3]: *** Waiting for unfinished jobs....
>
> *** caught segfault ***
> address 0xffffffe3, cause 'memory not mapped'
>
>
> --- and so on for each package
> --- snipped a lot --
>
> make[3]: Leaving directory `/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/src'
> installing to /usr/src/packages/BUILD/R-2.13.2/library/survival/libs
> ** R
> ** data
> ** moving datasets to lazyload DB
> ** inst
> ** preparing package for lazy loading
> ** help
>
> *** caught segfault ***
> address 0xffffffe3, cause 'memory not mapped'
>
> Traceback:
> 1: grep("[^[:blank:][:cntrl:]]", unlist(Rd[sections == "TEXT"]), perl = TRUE, useBytes = TRUE)
> 2: prepare2_Rd(Rd, Rdfile)
> 3: prepare_Rd(f, encoding = encoding, defines = os, stages = stages, warningCalls = FALSE, stage2 = step > 1L, stage3 = step > 2L)
> 4: FUN(c("/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/S[ 407.724261] serial8250: too much work for irq4
> urv.Rd", "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/aareg.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/aml.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/anova.coxph.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/attrassign.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/basehaz.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/bladder.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/cch.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/cgd.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/clogit.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/cluster.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/colon.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/cox.zph.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/coxph.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/coxph.control.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/coxph.detail.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/coxph.object.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/dsurvreg.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/frailty.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/heart.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/is.ratetable.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/kidney.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/lines.survfit.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/lung.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/mgus.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/model.frame.coxph.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/model.matrix.coxph.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/nwtco.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/ovarian.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/pbc.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/pbcseq.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/plot.aareg.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/plot.cox.zph.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/plot.survfit.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/predict.coxph.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/predict.survreg.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/print.aareg.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/print.summary.coxph.Rd",
> "/tmp/RtmpNIJVkk/
> R.INSTALL14eab96c/survival/man/print.summary.survexp.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/print.summary.survfit.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/print.survfit.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/pspline.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/pyears.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/ratetable.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/ratetableDate.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/rats.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/residuals.coxph.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/residuals.survreg.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/ridge.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/stanford2.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/strata.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/summary.aareg.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/summary.coxph.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/summary.survexp.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/summary.survfit.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/survConcordance.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/survSplit.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/survdiff.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/survexp.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/survexp.fit.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/survexp.us.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/survfit.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/survfit.coxph.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/survfit.formula.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/survfit.object.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/survfitcoxph.fit.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/survival-internal.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/survobrien.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/survreg.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/survreg.control.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/survreg.distributions.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/survreg.object.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/survregDtest.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/tcut.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/tobin.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/tt.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/untangle.specials.Rd",
> "/tmp/RtmpNIJVkk/R.INSTALL14eab96c/survival/man/veteran.Rd")[[1L]], ...)
> 5: lapply(files, .fetch_Rd_object) 6: .build_Rd_db(dir, manfiles,
> db_file = db_file, encoding = encoding, built_file = built_file)
> 7: .install_package_Rd_objects(".", instdir, encoding) 8:
> doTryCatch(return(expr), name, parentenv, handler) 9: tryCatchOne(expr,
> names, parentenv, handlers[[1L]]) 10: tryCatchList(expr, classes,
> parentenv, handlers) 11: tryCatch(expr, error = function(e) { call
> <- conditionCall(e) if (!is.null(call)) { if
> (identical(call[[1L]], quote(doTryCatch))) call <-
> sys.call(-4L) dcall <- deparse(call)[1L] prefix <-
> paste("Error in", dcall, ": ") LONG <- 75L msg <-
> conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <-
> 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if
> (is.na(w)) w <- 14L + nchar(dcall, type = "b") +
> nchar(sm[1L], type = "b") if (w >
> LONG) prefix <- paste(prefix, "\n ", sep = "") }
> else prefix <- "Error : " msg <- paste(prefix, conditionMessage(e),
> "\n", sep = "") .Internal(seterrmessage(msg[1L])) if (!silent &&
> identical(getOption("show.error.messages"), TRUE))
> { cat(msg, file =
> stderr()) .Internal(printDeferredWarnings()) }
> invisible(structure(msg, class = "try-error"))}) 12:
> try(.install_package_Rd_objects(".", instdir, encoding)) 13:
> do_install_source(pkg_name, instdir, pkg, desc) 14: do_install(pkg) 15:
> tools:::.install_packages()
> aborting ... /usr/src/packages/BUILD/R-2.13.2/bin/INSTALL: line 34:
> 19667 Done echo 'tools:::.install_packages()' 19668
> Segmentation fault | R_DEFAULT_PACKAGES= LC_COLLATE=C
> "${R_HOME}/bin/R" $myArgs --slave --args ${args} make[2]: ***
> [survival.ts] Error 1 make[2]: Leaving directory
> `/usr/src/packages/BUILD/R-2.13.2/src/library/Recommended' make[1]: ***
> [recommended-packages] Error 2 make[1]: Leaving directory
> `/usr/src/packages/BUILD/R-2.13.2/src/library/Recommended' make: ***
> [stamp-recommended] Error 2 error: Bad exit status
> from /var/tmp/rpm-tmp.54603 (%build)
>
>
> RPM build errors:
> cannot open Pubkeys index using db3 - No such file or directory (2)
> Bad exit status from /var/tmp/rpm-tmp.54603 (%build)
> [ 414.685190] Power down.
>
> ---
>
>>
>> There is no problem with e.g. i686 Fedora 14.
>>
>
> Detlef
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
--
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
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