[Bioperl-l] Fw: broken Bio::SeqIO in bioperl on OS X (fink)

Koen van der Drift kvddrift at earthlink.net
Fri Feb 27 08:37:41 EST 2009


Hi Dave,

This is the output from the user:

$ perl -e 'print (join "\n", @INC, "\n")'
/sw/lib/perl5/5.8.8/darwin-thread-multi-2level
/sw/lib/perl5/5.8.8
/sw/lib/perl5/darwin-thread-multi-2level
/sw/lib/perl5
/sw/lib/perl5/darwin
/System/Library/Perl/5.8.8/darwin-thread-multi-2level
/System/Library/Perl/5.8.8
/Library/Perl/5.8.8/darwin-thread-multi-2level
/Library/Perl/5.8.8
/Library/Perl
/Network/Library/Perl/5.8.8/darwin-thread-multi-2level
/Network/Library/Perl/5.8.8
/Network/Library/Perl
/System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level
/System/Library/Perl/Extras/5.8.8
/Library/Perl/5.8.6
/Library/Perl/5.8.1


Additionally, he uses an Intel-Mac, I still have an older PPC-Mac. Maybe perl is compiled differently on both systems?

And to answer your other question, the bioperl package in fink does not do any testing, since that assumes the user to be online. If the user happens not to be online, the build will fail. So it's just a practical reason.

cheers,

- Koen.


-----Original Message-----
>From: Dave Messina <David.Messina at sbc.su.se>
>Sent: Feb 26, 2009 4:02 PM
>To: Koen van der Drift <kvddrift at earthlink.net>
>Cc: bioperl-l at lists.open-bio.org
>Subject: Re: [Bioperl-l] Fw: broken Bio::SeqIO in bioperl on OS X (fink)
>
>Hi Koen,
>
>I'm not very experienced with fink -- does it run the test suite as part of
>its install process?
>
>The error seems pretty straightforward:
>
>
>> >Bio::SeqIO: genbank cannot be found
>>
>
>
>> >MSG: Failed to load module Bio::SeqIO::genbank.
>
>
>
>Namely, that the module is either not present or not in perl's list of
>library directories (@INC).
>
>This doesn't seem like a BioPerl error to me, but without knowing more about
>fink I'm reluctant to assume it's a fink errror either.
>
>I would recommend the user first look where fink is supposed to install the
>BioPerl modules and verify that the modules are there.
>
>Then I would have him type
>
>perl -e 'print (join "\n", @INC, "\n")'
>
>on the command line and verify that the directory where he found the BioPerl
>modules is in that list.
>
>
>Dave





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