[Bioperl-guts-l] [Bug 2668] New: bioperl-ext fails to compile on x86_64

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Nov 17 20:15:15 EST 2008


           Summary: bioperl-ext fails to compile on x86_64
           Product: BioPerl
           Version: main-trunk
          Platform: Other
        OS/Version: Other
            Status: NEW
          Severity: normal
          Priority: P2
         Component: bioperl-ext
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: fmarass at uvic.ca

I downloaded bioperl-ext from the main trunk of svn. I tried to compile with
$ perl Makefile.PL
$ make
but make fails with

cc -c  -I./libs -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe
-I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g  
-DVERSION=\"1.5.3\" -DXS_VERSION=\"1.5.3\" -fPIC "-I/usr/lib/perl/5.10/CORE" 
Running Mkbootstrap for Bio::Ext::Align ()
chmod 644 Align.bs
rm -f blib/arch/auto/Bio/Ext/Align/Align.so
cc  -shared -O2 -g -L/usr/local/lib 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: *** [blib/arch/auto/Bio/Ext/Align/Align.so] Error 1

I'm running Debian testing on an amd64 architecture.

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