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

Koen van der Drift kvddrift at earthlink.net
Thu Feb 26 20:00:11 EST 2009


Hi Dave,

I forwarded him the command and will post back here when I get an  
answer. For what's it worth, I tested his script on my iMac with the  
same setup, and got no error at all.

- Koen.



On Feb 26, 2009, at 4:02 PM, Dave Messina wrote:

> 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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