Dear All,
we're trying to implement R on the IBM p690 cluster "Jump" at the
research centre in J?lich, Germany (c.f.
http://www.fz-juelich.de/nic/Supercomputer/computer-e.html)
using the most recent version of R (2.1.0) and precisly following the
installation instructions.
After ./configure we get the final message:
----------------
R is now configured for powerpc-ibm-aix5.2.0.0
Source directory: .
Installation directory: /usr/local
C compiler: gcc -mno-fp-in-toc -g -O2
C++ compiler: g++ -g -O2
Fortran compiler: f77 -g
Interfaces supported: X11, tcltk
External libraries: readline, BLAS(ESSL)
Additional capabilities: PNG, JPEG, MBCS, NLS
Options enabled: R profiling
Recommended packages: yes
configure: WARNING: you cannot build info or html versions of the R manuals
configure: WARNING: I could not determine a browser
--------------
After make we get
ufzaloe@j36.!:
ufzaloe@j36.!: make
...
gcc -Wl,-bM:SRE -Wl,-H512 -Wl,-T512 -Wl,-bnoentry -Wl,-bexpall
-Wl,-bI:../../../etc/R.exp -L/usr/local/lib -o R_X11.so dataentry.lo
devX11.lo rotated.lo rbitmap.lo -lSM -lICE -lX11 -ljpeg -lpng -lz
ld: 0711-317 ERROR: Undefined symbol: .log10
ld: 0711-317 ERROR: Undefined symbol: .floor
ld: 0711-317 ERROR: Undefined symbol: .libintl_gettext
ld: 0711-317 ERROR: Undefined symbol: .pow
ld: 0711-317 ERROR: Undefined symbol: .sin
ld: 0711-317 ERROR: Undefined symbol: .cos
ld: 0711-317 ERROR: Undefined symbol: .tan
ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more
information.
collect2: ld returned 8 exit status
make: 1254-004 The error code from the last command is 1.
Stop.
make: 1254-004 The error code from the last command is 2.
Stop.
make: 1254-004 The error code from the last command is 1.
Stop.
make: 1254-004 The error code from the last command is 1.
Stop.
make: 1254-004 The error code from the last command is 1.
---------------
Before bugging the administiors in J?lich, we would like to ask the R
consortium: Are there any related experiences from people who worked on
the implementation of R on different platforms?
Thanks for help
Ralf Seppelt & Carsten Dormann
PS: the configure log-file is attached to this mail.
--
Dr. Ralf Seppelt
Professor at Martin-Luther Universit?t Halle-Wittenberg
Head of Dept. for Applied Landscape Ecology
Environmental Reasearch Centre (UFZ) Leipzig Halle
fon: +49 341 235 2021, fax: -2511, url: www.ufz.de
news: www.wiley-vch.de/publish/dt/books/ISBN3-527-30732-X/
-------------- next part --------------
./configure
checking build system type... powerpc-ibm-aix5.2.0.0
checking host system type... powerpc-ibm-aix5.2.0.0
loading site script './config.site'
loading build specific script './config.site'
checking for pwd... /usr/bin/pwd
checking whether builddir is srcdir... yes
checking for working aclocal... missing
checking for working autoconf... missing
checking for working automake... missing
checking for working autoheader... missing
checking for working makeinfo... found
checking for gawk... no
checking for mawk... no
checking for nawk... nawk
checking for egrep... grep -E
checking whether ln -s works... yes
checking for ranlib... ranlib
checking for bison... bison -y
checking for ar... ar
checking for a BSD-compatible install... /usr/opt/freeware/bin/install -c
checking for javac... /usr/java14/bin/javac
checking for sed... /usr/bin/sed
checking for less... /usr/bin/less
checking for perl... /usr/bin/perl
checking whether perl version is at least 5.004... yes
checking for dvips... /usr/local/bin/dvips
checking for tex... /usr/local/bin/tex
checking for latex... /usr/local/bin/latex
checking for makeindex... /usr/local/bin/makeindex
checking for pdftex... /usr/local/bin/pdftex
checking for pdflatex... /usr/local/bin/pdflatex
checking for makeinfo... /usr/local/bin/makeinfo
checking for unzip... /usr/local/bin/unzip
checking for zip... no
checking for gzip... /usr/bin/gzip
checking for firefox... no
checking for mozilla... no
checking for netscape... no
checking for galeon... no
checking for kfmclient... no
checking for opera... no
checking for gnome-moz-remote... no
checking for open... no
configure: WARNING: I could not determine a browser
checking for acroread... /usr/local/bin/acroread
checking for gcc... 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 gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -E
checking whether gcc needs -traditional... no
checking how to run the C preprocessor... gcc -E
checking for g77... no
checking for f77... f77
checking whether we are using the GNU Fortran 77 compiler... no
checking whether f77 accepts -g... yes
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 for a sed that does not truncate output... /usr/bin/sed
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking how to recognise dependent libraries... pass_all
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 dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking the maximum length of command line arguments... 8192
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for objdir... .libs
checking for ranlib... (cached) ranlib
checking for strip... strip
checking if gcc static flag works... yes
checking if gcc supports -fno-rtti -fno-exceptions... yes
checking for gcc option to produce PIC...
checking if gcc supports -c -o file.o... yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... aix5.2.0.0 ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... no
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC...
checking if g++ supports -c -o file.o... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... aix5.2.0.0 ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... no
appending configuration tag "F77" to libtool
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for f77 option to produce PIC...
checking if f77 supports -c -o file.o... no
checking whether the f77 linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... aix5.2.0.0 ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... no
checking whether makeinfo version is at least 4.7... no
configure: WARNING: you cannot build info or html versions of the R manuals
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking readline/history.h usability... no
checking readline/history.h presence... no
checking for readline/history.h... no
checking readline/readline.h usability... no
checking readline/readline.h presence... no
checking for readline/readline.h... no
checking for rl_callback_read_char in -lreadline... yes
checking for history_truncate_file... 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... no
checking elf.h presence... no
checking for elf.h... no
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... no
checking fpu_control.h presence... no
checking for fpu_control.h... no
checking grp.h usability... yes
checking grp.h presence... yes
checking for grp.h... yes
checking ieee754.h usability... no
checking ieee754.h presence... no
checking for ieee754.h... no
checking ieeefp.h usability... no
checking ieeefp.h presence... no
checking for ieeefp.h... no
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 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/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking sys/utsname.h usability... yes
checking sys/utsname.h presence... yes
checking for sys/utsname.h... yes
checking for unistd.h... (cached) yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking for string.h... (cached) yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking for GNU C library with version >= 2... no
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 whether byte ordering is bigendian... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for int... yes
checking size of int... 4
checking for long... yes
checking size of long... 4
checking for long long... yes
checking size of long long... 8
checking for long double... yes
checking size of long double... 8
checking whether we can compute C Make dependencies... no
checking whether gcc supports -c -o FILE.lo... yes
checking how to get verbose linking output from f77... -v
checking for Fortran libraries of f77... -L/usr/local/lib -lg -lxlf90
-L/usr/lpp/xlf/lib -lxlopt -lxlf -lxlomp_ser -lm
checking how to get verbose linking output from gcc... -v
checking for C libraries of gcc... -L/usr/local/lib
-L/usr/bin/../lib/gcc-lib/powerpc-ibm-aix5.1.0.0/2.9-aix51-020209
-L/usr/bin/../lib/gcc-lib -L/usr/opt/freeware/lib
-L/opt/freeware/GNUPro/lib/gcc-lib/powerpc-ibm-aix5.1.0.0/2.9-aix51-020209
-L/usr/bin/../lib/gcc-lib/powerpc-ibm-aix5.1.0.0/2.9-aix51-020209/../../..
-L/opt/freeware/GNUPro/lib/gcc-lib/powerpc-ibm-aix5.1.0.0/2.9-aix51-020209/../../..
/usr/bin/../lib/gcc-lib/powerpc-ibm-aix5.1.0.0/2.9-aix51-020209/libgcc.a -lg
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, no underscore, no extra
underscore
checking whether f77 appends underscores to external names... no
checking whether mixed C/Fortran code can be run... yes
checking whether f77 and gcc agree on int and double... yes
checking whether f77 and gcc agree on double complex... yes
checking whether f77 supports -c -o FILE.lo... yes
checking whether g++ accepts -M for generating dependencies... yes
checking whether g++ supports -c -o FILE.lo... yes
checking whether gcc accepts -mno-fp-in-toc... yes
checking for xmkmf... /usr/bin/X11/xmkmf
checking for off_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking whether alloca is declared... yes
checking for access... yes
checking for chdir... yes
checking for expm1... yes
checking for fcntl... yes
checking for finite... yes
checking for fseeko... yes
checking for ftello... yes
checking for ftruncate... yes
checking for getcwd... yes
checking for getgrgid... yes
checking for getpwuid... yes
checking for getuid... yes
checking for hypot... yes
checking for isascii... yes
checking for log1p... yes
checking for matherr... no
checking for mkdtemp... no
checking for mkfifo... yes
checking for popen... yes
checking for putenv... yes
checking for realpath... yes
checking for rint... yes
checking for setenv... yes
checking for strcoll... yes
checking for stat... yes
checking for strptime... yes
checking for symlink... yes
checking for system... yes
checking for times... yes
checking for unsetenv... yes
checking whether isfinite is declared... no
checking whether isnan is declared... yes
checking for finite... (cached) yes
checking for isnan... yes
checking whether isfinite is declared... (cached) no
checking whether isnan is declared... (cached) yes
checking whether you have IEEE 754 floating-point arithmetic... yes
checking for nl_langinfo and CODESET... yes
checking for acosh... yes
checking for asinh... yes
checking for atanh... 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 snprintf is declared... no
checking whether strdup is declared... yes
checking whether strncasecmp is declared... yes
checking whether vsnprintf is declared... no
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... no
checking for working finite... yes
checking for working log... yes
checking for working log1p... yes
checking for working strptime... yes
checking whether ftell works correctly on files opened for append... yes
checking for sgemm... no
checking for ATL_xerbla in -latlas... no
checking for sgemm in -lblas... yes
checking for dgemm in -ldgemm... no
checking for sgemm in -lblas... (cached) yes
checking for sgemm in -lessl... yes
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 for mbrtowc... yes
checking for mbstowcs... yes
checking for wcrtomb... yes
checking for wcscoll... yes
checking for wcsftime... yes
checking for wcstombs... yes
checking for wcswidth... yes
checking for wctrans... yes
checking for wcwidth... yes
checking whether wcwidth is declared... yes
checking whether wcswidth is declared... yes
checking iconv.h usability... yes
checking iconv.h presence... yes
checking for iconv.h... yes
checking for iconv... in libiconv
checking whether iconv() accepts "UTF-8" and "latin1"... no
checking for iconvlist... 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
using X11 ... yes
checking for KeySym... yes
checking for tclConfig.sh... no
checking for tclConfig.sh in library (sub)directories...
/usr/local/lib/tclConfig.sh
checking for tkConfig.sh... no
checking for tkConfig.sh in library (sub)directories...
/usr/local/lib/tkConfig.sh
checking /usr/local/tcl8.4.2/include/tcl8.4/generic/tcl.h usability... no
checking /usr/local/tcl8.4.2/include/tcl8.4/generic/tcl.h presence... no
checking for /usr/local/tcl8.4.2/include/tcl8.4/generic/tcl.h... no
checking /usr/local/tcl8.4.2/include/tcl8.4/tcl.h usability... no
checking /usr/local/tcl8.4.2/include/tcl8.4/tcl.h presence... no
checking for /usr/local/tcl8.4.2/include/tcl8.4/tcl.h... no
checking /usr/local/tcl8.4.2/include/tcl.h usability... yes
checking /usr/local/tcl8.4.2/include/tcl.h presence... yes
checking for /usr/local/tcl8.4.2/include/tcl.h... yes
checking /usr/local/tcl8.4.2/include/tk8.4/generic/tk.h usability... no
checking /usr/local/tcl8.4.2/include/tk8.4/generic/tk.h presence... no
checking for /usr/local/tcl8.4.2/include/tk8.4/generic/tk.h... no
checking /usr/local/tcl8.4.2/include/tk8.4/tk.h usability... no
checking /usr/local/tcl8.4.2/include/tk8.4/tk.h presence... no
checking for /usr/local/tcl8.4.2/include/tk8.4/tk.h... no
checking /usr/local/tcl8.4.2/include/tcl8.4/tk.h usability... no
checking /usr/local/tcl8.4.2/include/tcl8.4/tk.h presence... no
checking for /usr/local/tcl8.4.2/include/tcl8.4/tk.h... no
checking /usr/local/tcl8.4.2/include/tk.h usability... yes
checking /usr/local/tcl8.4.2/include/tk.h presence... yes
checking for /usr/local/tcl8.4.2/include/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 >= 1.0.5... 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 whether zlib support needs to be compiled... yes
checking mmap support for zlib... yes
checking whether bzip2 support needs to be compiled... yes
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 lpr... lpr
checking for paperconf... false
checking for recommended packages... yes
checking whether make sets $(MAKE)... yes
checking whether NLS is requested... yes
checking for msgfmt... no
checking for gmsgfmt... :
checking for xgettext... no
checking for msgmerge... no
checking for strerror in -lcposix... no
checking for signed... yes
checking for inline... inline
checking for off_t... (cached) yes
checking for long long... (cached) yes
checking for long double... yes
checking for wchar_t... yes
checking for wint_t... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for intmax_t... yes
checking whether printf() supports POSIX/XSI format strings... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for getpagesize... yes
checking for working mmap... no
checking whether we are using the GNU C Library 2.1 or newer... no
checking whether integer division by zero raises SIGFPE... no
checking for unsigned long long... yes
checking for inttypes.h... yes
checking whether the inttypes.h PRIxNN macros are broken... no
checking for stdint.h... (cached) yes
checking for SIZE_MAX... yes
checking for stdint.h... (cached) yes
checking for ld used by GCC... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking for shared library run path origin... done
checking for ptrdiff_t... yes
checking argz.h usability... no
checking argz.h presence... no
checking for argz.h... no
checking for limits.h... (cached) yes
checking for locale.h... (cached) yes
checking nl_types.h usability... yes
checking nl_types.h presence... yes
checking for nl_types.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... 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 unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for asprintf... no
checking for fwprintf... yes
checking for getcwd... (cached) yes
checking for getegid... yes
checking for geteuid... yes
checking for getgid... yes
checking for getuid... (cached) yes
checking for mempcpy... no
checking for munmap... yes
checking for putenv... (cached) yes
checking for setenv... (cached) yes
checking for setlocale... yes
checking for snprintf... (cached) yes
checking for stpcpy... yes
checking for strcasecmp... yes
checking for strdup... (cached) yes
checking for strtoul... yes
checking for tsearch... yes
checking for wcslen... yes
checking for __argz_count... no
checking for __argz_stringify... no
checking for __argz_next... no
checking for __fsetlocking... no
checking whether _snprintf is declared... no
checking whether _snwprintf is declared... no
checking whether feof_unlocked is declared... no
checking whether fgets_unlocked is declared... no
checking whether getc_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_langinfo and CODESET... (cached) yes
checking for LC_MESSAGES... yes
checking for bison... bison
checking version of bison... 1.34, ok
checking whether NLS is requested... yes
checking whether included gettext is requested... no
checking for GNU gettext in libc... no
checking for GNU gettext in libintl... no
checking whether to use NLS... yes
checking where the gettext function comes from... included intl directory
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
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config.status: creating etc/Makeconf
config.status: creating etc/Renviron
config.status: creating m4/Makefile
config.status: creating po/Makefile.in
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config.status: creating src/extra/Makefile
config.status: creating src/extra/bzip2/Makefile
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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
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config.status: creating src/library/datasets/DESCRIPTION
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config.status: creating src/library/grDevices/DESCRIPTION
config.status: creating src/library/grDevices/Makefile
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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
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config.status: creating src/library/profile/Makefile
config.status: creating src/library/stats/DESCRIPTION
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config.status: creating src/library/utils/Makefile
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R is now configured for powerpc-ibm-aix5.2.0.0
Source directory: .
Installation directory: /usr/local
C compiler: gcc -mno-fp-in-toc -g -O2
C++ compiler: g++ -g -O2
Fortran compiler: f77 -g
Interfaces supported: X11, tcltk
External libraries: readline, BLAS(ESSL)
Additional capabilities: PNG, JPEG, MBCS, NLS
Options enabled: R profiling
Recommended packages: yes
configure: WARNING: you cannot build info or html versions of the R manuals
configure: WARNING: I could not determine a browser
Ralf Seppelt wrote:> Dear All, > > we're trying to implement R on the IBM p690 cluster "Jump" at the > research centre in J?lich, Germany (c.f. > http://www.fz-juelich.de/nic/Supercomputer/computer-e.html) > using the most recent version of R (2.1.0) and precisly following the > installation instructions.How much cpu time for further R development do we get on that machine if we can help? ;-) Uwe Ligges> After ./configure we get the final message: > ---------------- > R is now configured for powerpc-ibm-aix5.2.0.0 > > Source directory: . > Installation directory: /usr/local > > C compiler: gcc -mno-fp-in-toc -g -O2 > C++ compiler: g++ -g -O2 > Fortran compiler: f77 -g > > Interfaces supported: X11, tcltk > External libraries: readline, BLAS(ESSL) > Additional capabilities: PNG, JPEG, MBCS, NLS > Options enabled: R profiling > > Recommended packages: yes > > configure: WARNING: you cannot build info or html versions of the R manuals > configure: WARNING: I could not determine a browser > > -------------- > After make we get > > ufzaloe@j36.!: > ufzaloe@j36.!: make > ... > gcc -Wl,-bM:SRE -Wl,-H512 -Wl,-T512 -Wl,-bnoentry -Wl,-bexpall > -Wl,-bI:../../../etc/R.exp -L/usr/local/lib -o R_X11.so dataentry.lo > devX11.lo rotated.lo rbitmap.lo -lSM -lICE -lX11 -ljpeg -lpng -lz > ld: 0711-317 ERROR: Undefined symbol: .log10 > ld: 0711-317 ERROR: Undefined symbol: .floor > ld: 0711-317 ERROR: Undefined symbol: .libintl_gettext > ld: 0711-317 ERROR: Undefined symbol: .pow > ld: 0711-317 ERROR: Undefined symbol: .sin > ld: 0711-317 ERROR: Undefined symbol: .cos > ld: 0711-317 ERROR: Undefined symbol: .tan > ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more > information. > collect2: ld returned 8 exit status > make: 1254-004 The error code from the last command is 1. > Stop. > make: 1254-004 The error code from the last command is 2. > Stop. > make: 1254-004 The error code from the last command is 1. > Stop. > make: 1254-004 The error code from the last command is 1. > Stop. > make: 1254-004 The error code from the last command is 1. > --------------- > > Before bugging the administiors in J?lich, we would like to ask the R > consortium: Are there any related experiences from people who worked on > the implementation of R on different platforms? > > Thanks for help > > Ralf Seppelt & Carsten Dormann > > PS: the configure log-file is attached to this mail. > > > > ------------------------------------------------------------------------ > > ./configure > checking build system type... powerpc-ibm-aix5.2.0.0 > checking host system type... powerpc-ibm-aix5.2.0.0 > loading site script './config.site' > loading build specific script './config.site' > checking for pwd... /usr/bin/pwd > checking whether builddir is srcdir... yes > checking for working aclocal... missing > checking for working autoconf... missing > checking for working automake... missing > checking for working autoheader... missing > checking for working makeinfo... found > checking for gawk... no > checking for mawk... no > checking for nawk... nawk > checking for egrep... grep -E > checking whether ln -s works... yes > checking for ranlib... ranlib > checking for bison... bison -y > checking for ar... ar > checking for a BSD-compatible install... /usr/opt/freeware/bin/install -c > checking for javac... /usr/java14/bin/javac > checking for sed... /usr/bin/sed > checking for less... /usr/bin/less > checking for perl... /usr/bin/perl > checking whether perl version is at least 5.004... yes > checking for dvips... /usr/local/bin/dvips > checking for tex... /usr/local/bin/tex > checking for latex... /usr/local/bin/latex > checking for makeindex... /usr/local/bin/makeindex > checking for pdftex... /usr/local/bin/pdftex > checking for pdflatex... /usr/local/bin/pdflatex > checking for makeinfo... /usr/local/bin/makeinfo > checking for unzip... /usr/local/bin/unzip > checking for zip... no > checking for gzip... /usr/bin/gzip > checking for firefox... no > checking for mozilla... no > checking for netscape... no > checking for galeon... no > checking for kfmclient... no > checking for opera... no > checking for gnome-moz-remote... no > checking for open... no > configure: WARNING: I could not determine a browser > checking for acroread... /usr/local/bin/acroread > checking for gcc... 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 gcc accepts -g... yes > checking for gcc option to accept ANSI C... none needed > checking how to run the C preprocessor... gcc -E > checking whether gcc needs -traditional... no > checking how to run the C preprocessor... gcc -E > checking for g77... no > checking for f77... f77 > checking whether we are using the GNU Fortran 77 compiler... no > checking whether f77 accepts -g... yes > 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 for a sed that does not truncate output... /usr/bin/sed > checking for ld used by gcc... /usr/bin/ld > checking if the linker (/usr/bin/ld) is GNU ld... no > checking for /usr/bin/ld option to reload object files... -r > checking for BSD-compatible nm... /usr/bin/nm -B > checking how to recognise dependent libraries... pass_all > 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 dlfcn.h usability... yes > checking dlfcn.h presence... yes > checking for dlfcn.h... yes > checking the maximum length of command line arguments... 8192 > checking command to parse /usr/bin/nm -B output from gcc object... ok > checking for objdir... .libs > checking for ranlib... 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(cached) yes > checking elf.h usability... no > checking elf.h presence... no > checking for elf.h... no > 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... no > checking fpu_control.h presence... no > checking for fpu_control.h... no > checking grp.h usability... yes > checking grp.h presence... yes > checking for grp.h... yes > checking ieee754.h usability... no > checking ieee754.h presence... no > checking for ieee754.h... no > checking ieeefp.h usability... no > checking ieeefp.h presence... no > checking for ieeefp.h... no > 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 for strings.h... 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src/scripts/R.sh > config.status: creating src/scripts/Rdconv > config.status: creating src/scripts/Rprof > config.status: creating src/scripts/SHLIB > config.status: creating src/scripts/Sd2Rd > config.status: creating src/scripts/build > config.status: creating src/scripts/check > config.status: creating src/scripts/f77 > 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: src/include/config.h is unchanged > config.status: executing default-1 commands > config.status: creating po/POTFILES > config.status: creating po/Makefile > config.status: executing stamp-h commands > > R is now configured for powerpc-ibm-aix5.2.0.0 > > Source directory: . > Installation directory: /usr/local > > C compiler: gcc -mno-fp-in-toc -g -O2 > C++ compiler: g++ -g -O2 > Fortran compiler: f77 -g > > Interfaces supported: X11, tcltk > External libraries: readline, BLAS(ESSL) > Additional capabilities: PNG, JPEG, MBCS, NLS > Options enabled: R profiling > > Recommended packages: yes > > configure: WARNING: you cannot build info or html versions of the R manuals > configure: WARNING: I could not determine a browser > > > ------------------------------------------------------------------------ > > ______________________________________________ > R-devel@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel
On Wed, 11 May 2005, Ralf Seppelt wrote:> Dear All, > > we're trying to implement R on the IBM p690 cluster "Jump" at the research > centre in J?lich, Germany (c.f. > http://www.fz-juelich.de/nic/Supercomputer/computer-e.html) > using the most recent version of R (2.1.0) and precisly following the > installation instructions.I don't think there are precise installation instructions for AIX 5.2.0. You should be aware that AIX is a very peculiar OS, and only experience with it is relevant. You seem to be missing a library containing those .foo entry points, but this is a module and modern OSes do not require all symbols to satisfied in a module (nor do they require import lists). You should also be aware that R has beta-test periods for new versions, and nothing was heard from any AIX user during that for 2.1.0. So it must have worked smoothly for all of them (if there are any left).> > After ./configure we get the final message: > ---------------- > R is now configured for powerpc-ibm-aix5.2.0.0 > > Source directory: . > Installation directory: /usr/local > > C compiler: gcc -mno-fp-in-toc -g -O2 > C++ compiler: g++ -g -O2 > Fortran compiler: f77 -g > > Interfaces supported: X11, tcltk > External libraries: readline, BLAS(ESSL) > Additional capabilities: PNG, JPEG, MBCS, NLS > Options enabled: R profiling > > Recommended packages: yes > > configure: WARNING: you cannot build info or html versions of the R manuals > configure: WARNING: I could not determine a browser > > -------------- > After make we get > > ufzaloe@j36.!: > ufzaloe@j36.!: make > ... > gcc -Wl,-bM:SRE -Wl,-H512 -Wl,-T512 -Wl,-bnoentry -Wl,-bexpall > -Wl,-bI:../../../etc/R.exp -L/usr/local/lib -o R_X11.so dataentry.lo > devX11.lo rotated.lo rbitmap.lo -lSM -lICE -lX11 -ljpeg -lpng -lz > ld: 0711-317 ERROR: Undefined symbol: .log10 > ld: 0711-317 ERROR: Undefined symbol: .floor > ld: 0711-317 ERROR: Undefined symbol: .libintl_gettext > ld: 0711-317 ERROR: Undefined symbol: .pow > ld: 0711-317 ERROR: Undefined symbol: .sin > ld: 0711-317 ERROR: Undefined symbol: .cos > ld: 0711-317 ERROR: Undefined symbol: .tan > ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more > information. > collect2: ld returned 8 exit status > make: 1254-004 The error code from the last command is 1. > Stop. > make: 1254-004 The error code from the last command is 2. > Stop. > make: 1254-004 The error code from the last command is 1. > Stop. > make: 1254-004 The error code from the last command is 1. > Stop. > make: 1254-004 The error code from the last command is 1. > --------------- > > Before bugging the administiors in J?lich, we would like to ask the R > consortium: Are there any related experiences from people who worked on the > implementation of R on different platforms? > > Thanks for help > > Ralf Seppelt & Carsten Dormann > > PS: the configure log-file is attached to this mail. > > > -- > Dr. Ralf Seppelt > Professor at Martin-Luther Universit?t Halle-Wittenberg > Head of Dept. for Applied Landscape Ecology > Environmental Reasearch Centre (UFZ) Leipzig Halle > fon: +49 341 235 2021, fax: -2511, url: www.ufz.de > news: www.wiley-vch.de/publish/dt/books/ISBN3-527-30732-X/ > > >-- Brian D. Ripley, ripley@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
On 11/05/2005, at 8:04 PM, Ralf Seppel wrote:> we're trying to implement R on the IBM p690 cluster "Jump" at the > research centre in J?lich, Germany (c.f. > http://www.fz-juelich.de/nic/Supercomputer/computer-e.html) > using the most recent version of R (2.1.0) and precisly following the > installation instructions. > > ............. > checking for cos in -lm... yes > checking for sin in -lm... yes > ............. > checking for GNU gettext in libc... no > checking for GNU gettext in libintl... no > checking whether to use NLS... yes > checking where the gettext function comes from... included intl > directory > ............... > gcc -Wl,-bM:SRE -Wl,-H512 -Wl,-T512 -Wl,-bnoentry -Wl,- > bexpall > -Wl,-bI:../../../etc/R.exp -L/usr/local/lib -o R_X11.so dataentry.lo > devX11.lo rotated.lo rbitmap.lo -lSM -lICE -lX11 -ljpeg -lpng -lz > ld: 0711-317 ERROR: Undefined symbol: .log10 > ld: 0711-317 ERROR: Undefined symbol: .floor > ld: 0711-317 ERROR: Undefined symbol: .libintl_gettext > ld: 0711-317 ERROR: Undefined symbol: .pow > ld: 0711-317 ERROR: Undefined symbol: .sin > ld: 0711-317 ERROR: Undefined symbol: .cos > ld: 0711-317 ERROR: Undefined symbol: .tan > ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more > information. > collect2: ld returned 8 exit statusThere seem to be problems in the autoconf stuff. cos and sin are being located in libm but the link line you show has no '-lm' which accounts for 6 of the 7 missing symbols. Also gettext seems to have been located by the configure script, but there is no option on the link line to include it in the link. Also search configure.in for strings like powerpc-ibm-aix to see what stuff is being done specifically for AIX. It may be out of date in relation to your system. If it was my problem, I would have look at those bits of the configure script and the sections of configure.in that generated them. Then I would compare the AC_SUBST variables with the makefile.in that generated the link. It seems there is some non- communication there. Bill Northcott
> From: Kurt Hornik > > >>>>> Brian D Ripley writes: > > > As far as I know R 2.0.1 was built on AIX. A quick diff > > gannet% diff ~/R/R-2.0.1/src/modules/X11/Makefile > > ~/R/R-2.1.0/src/modules/X11/Makefile > > 54c54 > > < $(SHLIB_LINK) -o $@ $(R_X11_la_LDFLAGS) $(R_X11_la_OBJECTS) > > $(R_X11_la_LIBADD) $(LIBS) > > --- > >> $(SHLIB_LINK) -o $@ $(R_X11_la_LDFLAGS) $(R_X11_la_OBJECTS) > > $(R_X11_la_LIBADD) > > 128c128,129 > > < ../../../src/include/Rmodules/RX11.h > > --- > >> ../../../src/include/Rmodules/RX11.h \ > >> ../../../src/include/Rconnections.h > > > suggests that AIX (alone) required $(LIBS) there. As it is > harmful on > > some other platforms (the intention is to pick up entry points in > > R.bin/libR rather than duplicate copies of static > libraries) I suspect we > > need an AIX-specific workaround (in particular the libintl > library is not > > going to be in LIBS). > > > This probably applies to other modules and even shared objects in > > packages. > > Yes. It would still be good if someone on AIX could provide > us with the > output of BUILDDIR/libtool --config. > > -k > > > Is there anyone with an AIX machine who is able to work through this > > and provide appropriate diffs?Sorry for being dense: could you explain what diff is needed? I unpacked R-patched_2005-05-12, and set: OBJECT_MODE=64 CC=xlc_r F77=xlf_r CXX=xlC_r CFLAGS/FLAGS/CXXFLAGS="-O -qstrict" Running make gave similar error, namely symbols that should be in libm not found. Below is output from BUILDDIR/libtool --config: --------------------------------- # Libtool was configured on host hpc2b.merck.com: # Shell to use when invoking shell scripts. SHELL="/bin/sh" # Whether or not to build shared libraries. build_libtool_libs=yes # Whether or not to build static libraries. build_old_libs=no # Whether or not to add -lc for building shared libraries. build_libtool_need_lc=yes # Whether or not to disallow shared libs when runtime libs are static allow_libtool_libs_with_static_runtimes=no # Whether or not to optimize for fast installation. fast_install=yes # The host system. host_aliashost=powerpc-ibm-aix5.1.0.0 # An echo program that does not interpret backslashes. echo="print -r" # The archiver. AR="ar" AR_FLAGS="cru" # A C compiler. LTCC="xlc_r" # A language-specific compiler. CC="xlc_r" # Is the compiler the GNU C compiler? with_gcc # An ERE matcher. EGREP="grep -E" # The linker used to build libraries. LD="/bin/ld" # Whether we need hard or soft links. LN_S="ln -s" # A BSD-compatible nm program. NM="/bin/nm -B" # A symbol stripping program STRIP="strip" # Used to examine libraries when file_magic_cmd begins "file" MAGIC_CMD=file # Used on cygwin: DLL creation program. DLLTOOL="dlltool" # Used on cygwin: object dumper. OBJDUMP="objdump" # Used on cygwin: assembler. AS="as" # The name of the directory that contains temporary libtool files. objdir=.libs # How to create reloadable object files. reload_flag=" -r" reload_cmds="\$LD\$reload_flag -o \$output\$reload_objs" # How to pass a linker flag through the compiler. wl="-Wl," # Object file suffix (normally "o"). objext="o" # Old archive suffix (normally "a"). libext="a" # Shared library suffix (normally ".so"). shrext_cmds='.so' # Executable file suffix (normally ""). exeext="" # Additional compiler flags for building library objects. pic_flag=" -DPIC" pic_mode=default # What is the maximum length of a command? max_cmd_len=8192 # Does compiler simultaneously support -c and -o options? compiler_c_o="yes" # Must we lock files when doing compilation ? need_locks="no" # Do we need the lib prefix for modules? need_lib_prefix=no # Do we need a version for libraries? need_version=no # Whether dlopen is supported. dlopen_support=unknown # Whether dlopen of programs is supported. dlopen_self=unknown # Whether dlopen of statically linked programs is supported. dlopen_self_static=unknown # Compiler flag to prevent dynamic linking. link_static_flag="-bnso -bI:/lib/syscalls.exp" # Compiler flag to turn off builtin functions. no_builtin_flag="" # Compiler flag to allow reflexive dlopens. export_dynamic_flag_spec="" # Compiler flag to generate shared objects directly from archives. whole_archive_flag_spec=" " # Compiler flag to generate thread-safe objects. thread_safe_flag_spec="" # Library versioning type. version_type=linux # Format of library name prefix. libname_spec="lib\$name" # List of archive names. First name is the real one, the rest are links. # The last name is the one that the linker finds with -lNAME. library_names_spec="\${libname}\${release}.a \$libname.a" # The coded name of the library, if different from the real name. soname_spec="\${libname}\${release}\${shared_ext}\$major" # Commands used to build and install an old-style archive. RANLIB="ranlib" old_archive_cmds="\$AR \$AR_FLAGS \$oldlib\$oldobjs\$old_deplibs~\$RANLIB \$oldlib" old_postinstall_cmds="\$RANLIB \$oldlib~chmod 644 \$oldlib" old_postuninstall_cmds="" # Create an old-style archive from a shared archive. old_archive_from_new_cmds="" # Create a temporary old-style archive to link instead of a shared archive. old_archive_from_expsyms_cmds="" # Commands used to build and install a shared archive. archive_cmds="" archive_expsym_cmds="\$CC \${wl}-bM:SRE -o \$output_objdir/\$soname \$libobjs \$deplibs \$compiler_flags \${wl}-bE:\$export_symbols \${wl}-bnoentry\${allow_undefined_flag}~\$AR \$AR_FLAGS \$output_objdir/\$libname\$release.a \$output_objdir/\$soname" postinstall_cmds="" postuninstall_cmds="" # Commands used to build a loadable module (assumed same as above if empty) module_cmds="" module_expsym_cmds="" # Commands to strip libraries. old_striplib="" striplib="" # Dependencies to place before the objects being linked to create a # shared library. predep_objects="" # Dependencies to place after the objects being linked to create a # shared library. postdep_objects="" # Dependencies to place before the objects being linked to create a # shared library. predeps="" # Dependencies to place after the objects being linked to create a # shared library. postdeps="" # The library search path used internally by the compiler when linking # a shared library. compiler_lib_search_path="" # Method to check whether dependent libraries are shared objects. deplibs_check_method="pass_all" # Command to use when deplibs_check_method == file_magic. file_magic_cmd="\$MAGIC_CMD" # Flag that allows shared libraries with undefined symbols to be built. allow_undefined_flag=" \${wl}-berok" # Flag that forces no undefined symbols. no_undefined_flag=" \${wl}-bernotok" # Commands used to finish a libtool library installation in a directory. finish_cmds="" # Same as above, but a single script fragment to be evaled but not shown. finish_eval="" # Take the output of nm and produce a listing of raw symbols and C names. global_symbol_pipe="sed -n -e 's/^.*[ ]\\([BCDT][BCDT]*\\)[ ][ ]*\\(\\)\\([_A-Za-z][_A-Za-z0-9]*\\)\$/\\1 \\2\\3 \\3/p'" # Transform the output of nm in a proper C declaration global_symbol_to_cdecl="sed -n -e 's/^. .* \\(.*\\)\$/extern int \\1;/p'" # Transform the output of nm in a C name address pair global_symbol_to_c_name_address="sed -n -e 's/^: \\([^ ]*\\) \$/ {\\\"\\1\\\", (lt_ptr) 0},/p' -e 's/^[BCDEGRST] \\([^ ]*\\) \\([^ ]*\\)\$/ {\"\\2\", (lt_ptr) \\&\\2},/p'" # This is the shared library runtime path variable. runpath_var # This is the shared library path variable. shlibpath_var=LIBPATH # Is shlibpath searched before the hard-coded library search path? shlibpath_overrides_runpath=unknown # How to hardcode a shared library path into an executable. hardcode_action=immediate # Whether we should hardcode library paths into libraries. hardcode_into_libs=yes # Flag to hardcode $libdir into a binary during linking. # This must work even if $libdir does not exist. hardcode_libdir_flag_spec="\${wl}-blibpath:\$libdir:/usr/local/lib:/usr/lpp/ xlopt:/usr/lib/threads:/usr/lib:/lib " # If ld is used when linking, flag to hardcode $libdir into # a binary during linking. This must work even if $libdir does # not exist. hardcode_libdir_flag_spec_ld="" # Whether we need a single -rpath flag with a separated argument. hardcode_libdir_separator=":" # Set to yes if using DIR/libNAME during linking hardcodes DIR into the # resulting binary. hardcode_direct=yes # Set to yes if using the -LDIR flag during linking hardcodes DIR into the # resulting binary. hardcode_minus_L=no # Set to yes if using SHLIBPATH_VAR=DIR during linking hardcodes DIR into # the resulting binary. hardcode_shlibpath_var=unsupported # Set to yes if building a shared library automatically hardcodes DIR into the library # and all subsequent libraries and executables linked against it. hardcode_automatic=no # Variables whose values should be saved in libtool wrapper scripts and # restored at relink time. variables_saved_for_relink="PATH " # Whether libtool must link a program against all its dependency libraries. link_all_deplibs=yes # Compile-time system search path for libraries sys_lib_search_path_spec="/lib /usr/lib /usr/local/lib" # Run-time system search path for libraries sys_lib_dlsearch_path_spec="/lib /usr/lib" # Fix the shell variable $srcfile for the compiler. fix_srcfile_path="" # Set to yes if exported symbols are required. always_export_symbols=yes # The commands to list exported symbols. export_symbols_cmds="\$NM -BCpg \$libobjs \$convenience | awk '{ if (((\\\$2 == \\\"T\\\") || (\\\$2 == \\\"D\\\") || (\\\$2 == \\\"B\\\")) && (substr(\\\$3,1,1) != \\\".\\\")) { print \\\$3 } }' | sort -u > \$export_symbols" # The commands to extract the exported symbol list from a shared archive. extract_expsyms_cmds="" # Symbols that should not be listed in the preloaded symbols. exclude_expsyms="_GLOBAL_OFFSET_TABLE_" # Symbols that must always be exported. include_expsyms="" -------------------------------> > > On Thu, 12 May 2005, Bill Northcott wrote: > > >> On 11/05/2005, at 11:26 PM, Kurt Hornik wrote: > >> >> There seem to be problems in the autoconf stuff. cos > and sin are > >> >> being located in libm but the link line you show has no > '-lm' which > >> >> accounts for 6 of the 7 missing symbols. Also gettext > seems to have > >> >> been located by the configure script, but there is no > option on the > >> >> link line to include it in the link. Also search > configure.in for > >> >> strings like powerpc-ibm-aix to see what stuff is being done > >> >> specifically for AIX. It may be out of date in relation to your > >> >> system. > >> >> > >> > > >> > > >> >> If it was my problem, I would have look at those bits of the > >> >> configure > >> >> script and the sections of configure.in that generated > them. Then I > >> >> would compare the AC_SUBST variables with the makefile.in that > >> >> generated the link. It seems there is some non- > communication there. > >> > >> > Yes most of the undefined symbols seem to come from > libm. But they > >> > would also be in libm on all other platforms which have such, and > >> > we do > >> > not include it there. On Linux I get > >> > >
Dear All, recently I posted a probably difficult question concerning the installation and implementation of R-2.1.0 on the IBM p690 cluster "Jump" at the research centre in J?lich, Germany. We identified several modifications for an installation such as: (i) the installation of the most recent iconflib in the local user directory (ii) the configuration command OBJECT_MODE=64 MAKE=gmake CC="cc -DSTDC" SHLIB_LDFLAGS="-Wl,-G" F77="xlf" PREFIX=/home3/zdvex/ufzaloe ./configure --without-x --without-blas --without-readline --with-libiconv-prefix=/home3/zdvex/ufzaloe/lib (iii) and the compilation command OBJECT_MODE=64 gmake (thanks to Christoph Pospiech for help). The really severe problem is, that the compilation now aboarts when making the survival R-library. This is what we get: gmake[3]: Leaving directory `/work/.j36/R.INSTALL.3207208/survival/src' ** R ** data ** moving datasets to lazyload DB ** inst ** preparing package for lazy loading /home3/zdvex/ufzaloe/R-2.1.0/bin/INSTALL[325]: 1364064 Illegal instruction(coredump) ERROR: lazy loading failed for package 'survival' ** Removing '/home3/zdvex/ufzaloe/R-2.1.0/library/survival' gmake[2]: *** [survival.ts] Error 1 gmake[2]: Leaving directory `/home3/zdvex/ufzaloe/R-2.1.0/src/library/Recommended' gmake[1]: *** [recommended-packages] Error 2 gmake[1]: Leaving directory `/home3/zdvex/ufzaloe/R-2.1.0/src/library/Recommended' gmake: *** [stamp-recommended] Error 2 ufzaloe@j36.!: (see attchment, zip archive of log-file). Besides the OS-problems (like missing readline implementation) it seems as if we need good help from the R developers community, as this most recent bug (compilation of survival) seems to an R problem. However, we are still strongly interested in getting this stuff running, any good suggestions very welcome! Cheers Ralf -------------- next part -------------- A non-text attachment was scrubbed... Name: putty.zip Type: application/x-tar Size: 25906 bytes Desc: not available Url : https://stat.ethz.ch/pipermail/r-devel/attachments/20050517/80fa4abf/putty.tar