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

Dave Messina David.Messina at sbc.su.se
Thu Feb 26 16:02:14 EST 2009


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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