There are incompatibilities between perl 5.10.0 (which is /usr/bin/ perl in 10.6) and perl 5.8.8. To call bioperl-pm588 in other scripts, you will have to modify their starting lines to #!/sw/bin/perl5.8.8
Better for you, probably, would be to have bioperl-pm updated to a 5.10.0 version (bioperl-pm5100). I don't know if anybody has tried doing that: bioperl-pm has a lot of dependencies so we will need to make sure that all of the dependent packages can be updated as well. -- Dave On Nov 12, 2009, at 9:22 AM, Gavin Sherlock wrote: > 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 > > > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > 30-Day > trial. Simplify your report design, integration and deployment - and > focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Fink-devel mailing list > Fink-devel@lists.sourceforge.net > http://news.gmane.org/gmane.os.apple.fink.devel > Subscription management: > https://lists.sourceforge.net/lists/listinfo/fink-devel ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
