[Bioperl-l] BioPerl - ext - Installation Problem

Chris Fields cjfields at uiuc.edu
Mon Sep 25 11:39:12 EDT 2006


You may want to file this as a bug using Bugzilla.  I'm not sure if  
anyone else has tried to install bioperl-ext on 64 bit, but this  
seems to be part of the problem: "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."

Chris

On Sep 25, 2006, at 9:45 AM, Shameer Khadar wrote:

> Dear All,
> I have recently moved to my new system, now I am on a FC3, AMD 64 bit
> machine - I have installed Bioperl but I am not able to install  
> Bioper-ext
> Iam getting these error :
> ************************************************88
> make[1]: Entering directory `/software/bioperl-ext-1.4/Bio/Ext/Align'
> gcc -c  -I./libs -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS
> -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include
> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g
> -pipe -m64   -DVERSION=\"0.1\" -DXS_VERSION=\"0.1\" -fPIC
> "-I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/CORE"  -DPOSIX
> -DNOERROR Align.c
> Running Mkbootstrap for Bio::Ext::Align ()
> chmod 644 Align.bs
> rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so
> gcc  -shared Align.o  -o ../blib/arch/auto/Bio/Ext/Align/Align.so
> libs/libsw.a \   -lm          \
>
> /usr/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[1]: *** [../blib/arch/auto/Bio/Ext/Align/Align.so] Error 1
> make[1]: Leaving directory `/software/bioperl-ext-1.4/Bio/Ext/Align'
> make: *** [subdirs] Error 2
> **************************************************
> It will be great If I can get any help to get it installed on my  
> comp !!!
> Thanks in advance
>
>
> -- 
> Shameer Khadar
> Jr. Research Fellow
> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> National Centre for Biological Sciences (TIFR)
> UAS - GKVK Campus - Bellary Road Bangalore - 65 - Karnataka - India
> T - 91-080-23636420-32 EXT 4241 F - 91-080-23636662/23636675
> W - http://www.ncbs.res.in
> --------------------------------------------------
> "Refrain from illusions, insist on work and not words,
>  patiently seek divine and scientific truth."
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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