[Bioperl-l] BioPerl - ext - Installation Problem

Shameer Khadar shameer at ncbs.res.in
Mon Sep 25 14:45:04 UTC 2006

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 :
make[1]: Entering directory `/software/bioperl-ext-1.4/Bio/Ext/Align'
-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
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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