[Bioperl-l] installation problems with bioperl-ext on x86_64 running SuSE linux

mailing lists simon.rayner.mlist at gmail.com
Mon May 29 03:37:24 EDT 2006


Hello,

i'm having a problem trying to install the bioperl-ext package on my
system.

biowiv:~/.cpan/build/bioperl-ext-1.4/Bio/Ext/Align # perl Makefile.PL
Writing Makefile for Bio::Ext::Align
biowiv:~/.cpan/build/bioperl-ext-1.4/Bio/Ext/Align # make
cc -c  -I./libs -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS
-DDEBUGGING -fno-strict-aliasing -pipe -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -fPIC -O2 -fmessage-length=0 -Wall
-D_FORTIFY_SOURCE=2 -g -Wall -pipe   -DVERSION=\"0.1\" -DXS_VERSION=
\"0.1\" -fPIC "-I/usr/lib/perl5/5.8.7/x86_64-linux-thread-multi/CORE"
-DPOSIX -DNOERROR Align.c
In file included from Align.xs:12:
./libs/sw.h:1360:1: warning: "/*" within comment
.
.
.
Running Mkbootstrap for Bio::Ext::Align ()
chmod 644 Align.bs
rm -f blib/arch/auto/Bio/Ext/Align/Align.so
LD_RUN_PATH="" cc  -shared -L/usr/local/lib64 Align.o  -o
blib/arch/auto/Bio/Ext/Align/Align.so libs/libsw.a  -lm
/usr/lib64/gcc/x86_64-suse-linux/4.0.2/../../../../x86_64-suse-linux/bin/ld:
libs/libsw.a(aln.o): relocation R_X86_64_32 against `a local symbol' can not
be used when making a shared object; recompile with -fPIC
libs/libsw.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make: *** [blib/arch/auto/Bio/Ext/Align/Align.so] Error 1
biowiv:~/.cpan/build/bioperl-ext-1.4/Bio/Ext/Align #
biowiv:~/.cpan/build/bioperl-ext-1.4/Bio/Ext/Align #
biowiv:~/.cpan/build/bioperl-ext-1.4/Bio/Ext/Align #

the -fPIC flag is already set in the makefile.

I found a similar problem in an earlier posting with the following
suggestions....


  From: Aaron J. Mackey <amackey <at> pcbi.upenn.edu>
  Subject: Re: compiling bioperl-ext
  Newsgroups: gmane.comp.lang.perl.bio.general
  Date: 2004-06-09 20:46:05 GMT (1 year, 50 weeks, 3 days, 3 hours and 50
  minutes ago)

  1) Are you starting with a clean build directory?

  2) Does installing other compiled Perl modules work for you (e.g.
  Data::Dumper or Storable)?

  That's a pretty arcane error, and if the answer to #2 is "no", then I
  don't think we can help you.

  -Aaron


....In my case, both 1) and 2) are true.  I installed Data::Dumper without
any problems.


I've found plenty of similar incidences for other sofware and it seems to
relate to
32/64bit issues.

Does anyone have any suggestions about how to get around this?

thanks

Simon Rayner



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