I have no access to 10.6, and am unable to test this as the maintainer. Feel free to update the package as suited. Note that many of the dependencies are optional, they add functionality to bioperl, but their absense doesn't break anything, AFAIK.
- Koen. On Thu, Nov 12, 2009 at 1:05 PM, David R. Morrison <[email protected]> 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 > ------------------------------------------------------------------------------ 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
