Many thanks for such a quick response - changing the script to use #!/sw/bin/perl5.8.8 makes it work perfectly.
Cheers, Gavin On Nov 12, 2009, at 10:05 AM, David R. Morrison wrote: > 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 >> [email protected] >> 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 [email protected] http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
