[Bioperl-l] Bio::Ext::Align build problems

Antonio Fernandez Guerra afernandez at ceab.csic.es
Sat Jan 31 11:40:33 EST 2009


Hi all,
finally I was able to build Bio::Ext::Align and avoid the relocation  
R_X86_64_32  error. I've added the -fPIC to the DEFINE hash attribute  
found at the WriteMakefile function of the Bio::Ext::Align Makefile.PL  
and the libraries where compiled with the -fPIC.

This is the original WriteMakefile function:

WriteMakefile(
     'NAME'	=> 'Bio::Ext::Align',
     'VERSION'   => '1.6.0',
     'LIBS'	=> ['-lm'],   # e.g., '-lm'
     'DEFINE'    => ' -DPOSIX -DNOERROR',     # e.g., '-DHAVE_SOMETHING'
     'INC'	=> '-I./libs',     # e.g., '-I/usr/include/other'
     'MYEXTLIB'  => 'libs/libsw$(LIB_EXT)',
     'clean'     => { 'FILES' => 'libs/*.o libs/*.a' }
);

And the one that worked for me:

WriteMakefile(
     'NAME'	=> 'Bio::Ext::Align',
     'VERSION'   => '1.6.0',
     'LIBS'	=> ['-lm'],   # e.g., '-lm'
     'DEFINE'    => ' -DPOSIX -DNOERROR -fPIC',     # e.g., '- 
DHAVE_SOMETHING'
     'INC'	=> '-I./libs',     # e.g., '-I/usr/include/other'
     'MYEXTLIB'  => 'libs/libsw$(LIB_EXT)',
     'clean'     => { 'FILES' => 'libs/*.o libs/*.a' }
);

I really don't know if it the good way to do that, I haven't played  
with the MakeMaker before. But before I've modified the Makefile.PL I  
could build it compiling by hand the libraries alone, and after  
running the Makefile.PL without adding the -fPIC flag.

I hope it helps,
Antoni.


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