[R] errors with compilation

Prof Brian Ripley ripley at stats.ox.ac.uk
Tue Dec 9 09:22:46 CET 2008 

On Tue, 9 Dec 2008, Jason Tan wrote:

> thanks. i noticed a syntax error. a missing semi colon.

Which, as I said, was corrected weeks ago.

> any idea about the error below?

Yes: you need to ensure that dynamic libraries are used on x86_64 Linux. 
That's something specific to your setup: standard R does not use pthreads.

>
> 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
>
>
>
>

-- 
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

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