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

[rbogard]

Thank you all for your help! I was able to get bioperl working via manual
download and install. It was a combination of permissions issues and X86_64
vs. X86_32 compatibility issues. Using fink to download and install seems to
have given me a combination of 32 and 64 associated files (I probably did
something wrong in config). 



rbogard wrote:
> 
> 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):
> PERL5LIB=/sw/lib/perl5/5.8.8:$PERL5LIB
> 
> 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:
> 
> MANPATH=/sw/share/man:/usr/share/man:/usr/X11/man:/sw/lib/perl5/5.10.0/man:/usr/X11R6/man:/sw/lib/perl5-core/5.8.8/man:/sw/lib/perl5/5.8.8/man
> PERL5LIB=/sw/lib/perl5/5.8.8:/sw/lib/perl5:/sw/lib/perl5/darwin:/sw/lib/perl5/5.8.8
> PATH=/sw/bin:/sw/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/X11R6/bin
> INFOPATH=/sw/share/info:/sw/info:/usr/share/info
> 
> 
> This is the perl script I'm attempting to run:
> #!/sw/bin/perl5.8.8
> use strict;
> use Bio::Perl;
> $seq_object = get_sequence('swiss',"ROA1_HUMAN");
> write_sequence(">roa1.fasta",'fasta',$seq_object);
> 
> Here is the error output:
> 
> dyld: lazy symbol binding failed: Symbol not found: _Perl_Tstack_sp_ptr
>   Referenced from:
> /sw/lib/perl5/5.8.8/darwin-thread-multi-2level/auto/IO/IO.bundle
>   Expected in: dynamic lookup
> 
> dyld: Symbol not found: _Perl_Tstack_sp_ptr
>   Referenced from:
> /sw/lib/perl5/5.8.8/darwin-thread-multi-2level/auto/IO/IO.bundle
>   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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