[R] R-2.3.1 --enable-R-shlib

From: Francis De Brabandere <francis.debrabandere_at_cropdesign.com>
Date: Fri 14 Jul 2006 - 02:58:09 EST


Hi,

I've upgraded our server to the latest R version, everything went ok until I wanted to install RServe for our java clients.

RServe needs the shared library which can be compiled using configure --enable-R-shlib. All went ok but after running make I got this error:

gcc -shared -L/usr/local/lib64 -o libR.so Rembedded.o CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o apply.o arithmetic.o apse.o array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o eval.o format.o fourier.o gevents.o gram.o gram-ex.o graphics.o identical.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o model.o names.o objects.o optim.o optimize.o options.o par.o paste.o pcre.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o regex.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o `ls ../appl/*.o
../nmath/*.o ../unix/*.o 2>/dev/null` -lg2c -lm -lgcc_s
../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a
-lreadline -ldl -lm
/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.4/../../../../x86_64-suse-linux/bin/ld: CConverters.o: relocation R_X86_64_32S against `R_FunTab' can not be used when making a shared object; recompile with -fPIC CConverters.o: could not read symbols: Bad value collect2: ld returned 1 exit status

we tried setting the -fPIC using the export CFLAGS=-fPIC but that didn't help (more output but same bug later on)

Thanks in advance,

Francis

here is the full log + more info:

uname -a
Linux stat 2.6.8-24-smp #1 SMP Wed Oct 6 09:16:23 UTC 2004 x86_64 x86_64 x86_64 GNU/Linux

.......(last part of configure)....

R is now configured for x86_64-unknown-linux-gnu

  Source directory: .
  Installation directory: /usr/local

  C compiler:                gcc  -g -O2 -std=gnu99
  Fortran 77 compiler:       g77  -g -O2

  C++ compiler:              g++  -g -O2
  Fortran 90/95 compiler: g77 -g -O2
  Interfaces supported:      X11
  External libraries:        readline
  Additional capabilities:   iconv, MBCS, NLS
  Options enabled:           shared library, R profiling

  Recommended packages:      yes

configure: WARNING: you cannot build PDF versions of all the help pages
configure: WARNING: I could not determine a browser configure: WARNING: I could not determine a PDF viewer

[1806][root@stat:/opt/R]$ make

make[1]: Entering directory `/opt/R-2.3.1/m4'
make[1]: Nothing to be done for `R'.
make[1]: Leaving directory `/opt/R-2.3.1/m4'
make[1]: Entering directory `/opt/R-2.3.1/tools'
make[1]: Nothing to be done for `R'.
make[1]: Leaving directory `/opt/R-2.3.1/tools'
make[1]: Entering directory `/opt/R-2.3.1/doc'
make[2]: Entering directory `/opt/R-2.3.1/doc/html'
make[3]: Entering directory `/opt/R-2.3.1/doc/html/search'
make[3]: Leaving directory `/opt/R-2.3.1/doc/html/search'
make[2]: Leaving directory `/opt/R-2.3.1/doc/html'
make[2]: Entering directory `/opt/R-2.3.1/doc/manual'
make[2]: Nothing to be done for `R'.
make[2]: Leaving directory `/opt/R-2.3.1/doc/manual'
make[1]: Leaving directory `/opt/R-2.3.1/doc'
make[1]: Entering directory `/opt/R-2.3.1/etc'
make[1]: Leaving directory `/opt/R-2.3.1/etc'
make[1]: Entering directory `/opt/R-2.3.1/share'
make[1]: Leaving directory `/opt/R-2.3.1/share'
make[1]: Entering directory `/opt/R-2.3.1/src'
make[2]: Entering directory `/opt/R-2.3.1/src/scripts'
creating src/scripts/R.fe
make[3]: Entering directory `/opt/R-2.3.1/src/scripts'
make[3]: Leaving directory `/opt/R-2.3.1/src/scripts'
make[2]: Leaving directory `/opt/R-2.3.1/src/scripts'
make[2]: Entering directory `/opt/R-2.3.1/src/include'
config.status: creating src/include/config.h config.status: src/include/config.h is unchanged Rmath.h is unchanged
make[3]: Entering directory `/opt/R-2.3.1/src/include/R_ext'
make[3]: Nothing to be done for `R'.
make[3]: Leaving directory `/opt/R-2.3.1/src/include/R_ext'
make[2]: Leaving directory `/opt/R-2.3.1/src/include'
make[2]: Entering directory `/opt/R-2.3.1/src/extra'
make[3]: Entering directory `/opt/R-2.3.1/src/extra/bzip2'
make[4]: Entering directory `/opt/R-2.3.1/src/extra/bzip2'
make[4]: Leaving directory `/opt/R-2.3.1/src/extra/bzip2'
make[4]: Entering directory `/opt/R-2.3.1/src/extra/bzip2'
make[4]: `libbz2.a' is up to date.
make[4]: Leaving directory `/opt/R-2.3.1/src/extra/bzip2'
make[3]: Leaving directory `/opt/R-2.3.1/src/extra/bzip2'
make[3]: Entering directory `/opt/R-2.3.1/src/extra/pcre'
make[4]: Entering directory `/opt/R-2.3.1/src/extra/pcre'
make[4]: Leaving directory `/opt/R-2.3.1/src/extra/pcre'
make[4]: Entering directory `/opt/R-2.3.1/src/extra/pcre'
make[4]: `libpcre.a' is up to date.
make[4]: Leaving directory `/opt/R-2.3.1/src/extra/pcre'
make[3]: Leaving directory `/opt/R-2.3.1/src/extra/pcre'
make[3]: Entering directory `/opt/R-2.3.1/src/extra/zlib'
make[4]: Entering directory `/opt/R-2.3.1/src/extra/zlib'
make[4]: Leaving directory `/opt/R-2.3.1/src/extra/zlib'
make[4]: Entering directory `/opt/R-2.3.1/src/extra/zlib'
make[4]: `libz.a' is up to date.
make[4]: Leaving directory `/opt/R-2.3.1/src/extra/zlib'
make[3]: Leaving directory `/opt/R-2.3.1/src/extra/zlib'
make[2]: Leaving directory `/opt/R-2.3.1/src/extra'
make[2]: Entering directory `/opt/R-2.3.1/src/appl'
make[3]: Entering directory `/opt/R-2.3.1/src/appl'
make[3]: Leaving directory `/opt/R-2.3.1/src/appl'
make[3]: Entering directory `/opt/R-2.3.1/src/appl'
make[3]: `stamp-lo' is up to date.
make[3]: Leaving directory `/opt/R-2.3.1/src/appl'
make[2]: Leaving directory `/opt/R-2.3.1/src/appl'
make[2]: Entering directory `/opt/R-2.3.1/src/nmath'
make[3]: Entering directory `/opt/R-2.3.1/src/nmath'
make[3]: Leaving directory `/opt/R-2.3.1/src/nmath'
make[3]: Entering directory `/opt/R-2.3.1/src/nmath'
make[3]: `stamp-lo' is up to date.
make[3]: Leaving directory `/opt/R-2.3.1/src/nmath'
make[2]: Leaving directory `/opt/R-2.3.1/src/nmath'
make[2]: Entering directory `/opt/R-2.3.1/src/unix'
make[3]: Entering directory `/opt/R-2.3.1/src/unix'
make[3]: Leaving directory `/opt/R-2.3.1/src/unix'
make[3]: Entering directory `/opt/R-2.3.1/src/unix'
make[3]: `stamp-lo' is up to date.
make[3]: Leaving directory `/opt/R-2.3.1/src/unix'
make[2]: Leaving directory `/opt/R-2.3.1/src/unix'
make[2]: Entering directory `/opt/R-2.3.1/src/main'
make[3]: Entering directory `/opt/R-2.3.1/src/main'
make[3]: Leaving directory `/opt/R-2.3.1/src/main'
make[3]: Entering directory `/opt/R-2.3.1/src/main'
gcc -shared -L/usr/local/lib64 -o libR.so Rembedded.o CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o apply.o arithmetic.o apse.o array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o eval.o format.o fourier.o gevents.o gram.o gram-ex.o graphics.o identical.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o model.o names.o objects.o optim.o optimize.o options.o par.o paste.o pcre.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o regex.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o `ls ../appl/*.o
../nmath/*.o ../unix/*.o 2>/dev/null` -lg2c -lm -lgcc_s
../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a
-lreadline -ldl -lm
/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.4/../../../../x86_64-suse-linux/bin/ld: CConverters.o: relocation R_X86_64_32S against `R_FunTab' can not be used when making a shared object; recompile with -fPIC CConverters.o: could not read symbols: Bad value collect2: ld returned 1 exit status
make[3]: *** [libR.so] Error 1
make[3]: Leaving directory `/opt/R-2.3.1/src/main'
make[2]: *** [R] Error 2
make[2]: Leaving directory `/opt/R-2.3.1/src/main'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/opt/R-2.3.1/src'
make: *** [R] Error 1

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