Hi,

Maybe bioperl is not meant to work on 10.6, but I tried a completely fresh fink installation on 10.6 (32-bit fink), and then:

fink install bioperl-pm588

however, when I try to use a program that uses a bioperl module, it does:

Can't locate Bio/SeqIO.pm in @INC (@INC contains: /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at gatherMitochondrialReads.pl line 25.

The libraries themselves are in:

/sw/lib/perl5/5.8.8

but if I add that to the PERL5LIB environmental variable, I now get:

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

Is there anyway to get bioperl working on 10.6 within fink, or is it not currently supported?

Many thanks in advance (and thanks for fink - I use it all the time).
Cheers,
Gavin
________________________________________________________

Gavin Sherlock
Assistant Professor, Research
Dept. of Genetics
S201A, Grant Building,
Stanford University Medical School,
Stanford,
CA 94305-5120
Tel: 650 498 6012
Fax: 650 724 3701

http://genome-www.stanford.edu/~sherlock




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