[Bioperl-l] BioPerl - ext - Installation Problem

Shameer Khadar shameer at ncbs.res.in
Tue Sep 26 04:16:15 EDT 2006


Chris,
I will file do that. i am not so familiar with Bugzilla - any way I will
give it a try.
Thanks,
Shameer
> 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."
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


-- 
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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