[Bioperl-l] Problems with bioperl in Mac OS X 10.6 (Perl 5.10.0)

rbogard ryan_bogard at hms.harvard.edu
Sun Nov 15 22:30:22 EST 2009

In advance, any advice would be grealy appreciated! I have installed
bioperl-588pm via fink but I am having difficulties calling the modules in
script. The following is added to .profile (bash):

If I change this to /sw/lib/perl5 then I get an @INC error, as use Bio::PERL
cannot be located.

The environment variables are as follows:


This is the perl script I'm attempting to run:
use strict;
use Bio::Perl;
$seq_object = get_sequence('swiss',"ROA1_HUMAN");

Here is the error output:

dyld: lazy symbol binding failed: Symbol not found: _Perl_Tstack_sp_ptr
  Referenced from:
  Expected in: dynamic lookup

dyld: Symbol not found: _Perl_Tstack_sp_ptr
  Referenced from:
  Expected in: dynamic lookup

Trace/BPT trap

I have looked through many forum postings and attempted the solutions
offered in those instances, but none seem to work in my case. I'm not sure
if it's because I have perl 5.10.0 installed while attempting to call
bioperl 5.8.8; however, others seem to have it working just fine.

Thank you, Ryan 
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