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

Mark A. Jensen maj at fortinbras.us
Fri Feb 27 08:59:02 EST 2009


Hi Koen-
If the user can find the directory containing the file Bio/SeqIO/genbank.pm,
he can force the script to find it. Example: if the full path of the module is

/sw/lib/perl5/5.8.8/site/Bio/SeqIO/genbank.pm

then he should add the line

use lib '/sw/lib/perl5/5.8.8/site';

to the top of his script.

(I don't see any ../site or ../vendor paths in the @INC. I don't know about 
darwin,
but frequently externally installed modules will be installed in site or vendor 
paths
beneath a trunk directory like ../lib/perl5/5.8.8 in other systems.)
Mark

----- Original Message ----- 
From: "Koen van der Drift" <kvddrift at earthlink.net>
To: "Dave Messina" <David.Messina at sbc.su.se>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Friday, February 27, 2009 8:37 AM
Subject: Re: [Bioperl-l] Fw: broken Bio::SeqIO in bioperl on OS X (fink)


> 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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> 



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