[R] errors with compilation
Jason Tan
jason.tan at uwa.edu.au
Tue Dec 9 08:53:31 CET 2008
thanks. i noticed a syntax error. a missing semi colon.
any idea about the error below?
cc -I. -I../../../src/include -I../../../src/include -I/usr/local/
include -DHAVE_CONFIG_H -fPIC -g -O2 -c Rsock.c -o Rsock.o
/opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
cc -I. -I../../../src/include -I../../../src/include -I/usr/local/
include -DHAVE_CONFIG_H -fPIC -g -O2 -c internet.c -o internet.o
/opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
cc -I. -I../../../src/include -I../../../src/include -I/usr/local/
include -DHAVE_CONFIG_H -fPIC -g -O2 -c nanoftp.c -o nanoftp.o
/opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
cc -I. -I../../../src/include -I../../../src/include -I/usr/local/
include -DHAVE_CONFIG_H -fPIC -g -O2 -c nanohttp.c -o nanohttp.o
/opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
cc -I. -I../../../src/include -I../../../src/include -I/usr/local/
include -DHAVE_CONFIG_H -fPIC -g -O2 -c sock.c -o sock.o
/opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
cc -I. -I../../../src/include -I../../../src/include -I/usr/local/
include -DHAVE_CONFIG_H -fPIC -g -O2 -c sockconn.c -o sockconn.o
/opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
cc -shared -fPIC -L/usr/local/lib64 -o internet.so Rsock.o internet.o
nanoftp.o nanohttp.o sock.o sockconn.o
/opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
/usr/bin/ld: /usr/lib64/libpthread.a(ptw-fcntl.o): relocation
R_X86_64_32 against `a local symbol' can not be used when making a
shared object; recompile with -fPIC
/usr/lib64/libpthread.a: could not read symbols: Bad value
make[4]: *** [internet.so] Error 2
jason
On 09/12/2008, at 4:50 PM, Prof Brian Ripley wrote:
> Please try the R-patched.version of R (see the posting guide or the
> FAQ).
>
> That seems to be about an error in the R 2.8.0 sources that was
> corrected in October, and only happens if you do not ask for X11
> support (which most R users need, including it seems all the pre-
> release testers).
>
> On Tue, 9 Dec 2008, Jason Tan wrote:
>
>> Hi,
>>
>> i'm trying to compile R on a Cray XT3 using pgi/7.2.1 - CNL
>> (compute node linux)
>> The R version is 2.8.0
>>
>> this is the option
>> -enable-R-static-lib=yes
>> --disable-R-shlib
> /* The latter is the default */
>
>> CPICFLAGS=fpic
>> FPICFLAGS=fpic
>> CXXPICFLAGS=fpic
>> SHLIB_LDFLAGS=shared
>> --with-x=no
>> SHLIB_CXXLDFLAGS=shared
>> --disable-BLAS-shlib
>
> Do you really need to set all these? And are you sure you know the
> correct values? ('-shared' is standard on Linux.)
>
>> CFLAGS="-g -O2 -Kieee"
>> FFLAGS="-g -O2 -Kieee"
>> CXXFLAGS="-g -O2 -Kieee"
>> FCFLAGS="-g -O2 -Kieee"
>> CC=cc
>> F77=ftn
>> CXX=CC
>> FC=ftn
>>
>> R is now configured for x86_64-unknown-linux-gnu
>>
>> Source directory: .
>> Installation directory: /lus/nid00036/jasont/R
>>
>> C compiler: cc -g -O2 -Kieee
>> Fortran 77 compiler: ftn -g -O2 -Kieee
>>
>> C++ compiler: CC -g -O2 -Kieee
>> Fortran 90/95 compiler: ftn -g -O2 -Kieee
>> Obj-C compiler: gcc -g -O2
>>
>> Interfaces supported:
>> External libraries: readline
>> Additional capabilities: PNG, JPEG, iconv, MBCS, NLS
>> Options enabled: static R library, R profiling, Java
>>
>> Recommended packages: yes
>>
>> The error is :
>>
>> cc -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/
>> pcre -I. -I../../src/include -I../../src/include -I/usr/local/
>> include -DHAVE_CONFIG_H -g -O2 -Kieee -c pcre.c -o pcre.o
>> /opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
>> PGC-W-0155-64-bit integral value truncated (/usr/include/wctype.h:
>> 108)
>> PGC-W-0155-64-bit integral value truncated (/usr/include/wctype.h:
>> 109)
>> PGC-W-0155-64-bit integral value truncated (/usr/include/wctype.h:
>> 110)
>> PGC-W-0155-64-bit integral value truncated (/usr/include/wctype.h:
>> 111)
>> PGC/x86-64 Linux 7.2-1: compilation completed with warnings
>> cc -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/
>> pcre -I. -I../../src/include -I../../src/include -I/usr/local/
>> include -DHAVE_CONFIG_H -g -O2 -Kieee -c platform.c -o platform.o
>> /opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
>> PGC-S-0037-Syntax error: Recovery attempted by deleting identifier
>> FALSE (platform.c: 1657)
>> PGC-S-0094-Illegal type conversion required (platform.c: 1661)
>> PGC/x86-64 Linux 7.2-1: compilation completed with severe errors
>> make[3]: *** [platform.o] Error 2
>> make[3]: Leaving directory `/lus/nid00036/jasont/R-2.8.0/src/main'
>> make[2]: *** [R] Error 2
>> make[2]: Leaving directory `/lus/nid00036/jasont/R-2.8.0/src/main'
>> make[1]: *** [R] Error 1
>> make[1]: Leaving directory `/lus/nid00036/jasont/R-2.8.0/src'
>> make: *** [R] Error 1
>>
>>
>> Jason Tan
>> Senior Computer Support Officer
>> Western Australian Supercomputer Program (WASP)
>> The University of Western Australia
>> M024
>> 35 Stirling Highway
>> CRAWLEY WA 6009
>> Ph: +618 64888742
>> Fax: +618 6488 8088
>> Email: jason.tan at uwa.edu.au
>> Web: www.wasp.uwa.edu.au
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> --
> Brian D. Ripley, ripley at 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
>
Jason Tan
Senior Computer Support Officer
Western Australian Supercomputer Program (WASP)
The University of Western Australia
M024
35 Stirling Highway
CRAWLEY WA 6009
Ph: +618 64888742
Fax: +618 6488 8088
Email: jason.tan at uwa.edu.au
Web: www.wasp.uwa.edu.au
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