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

Hilmar Lapp hlapp at gmx.net
Thu Feb 26 23:58:44 EST 2009

The problem isn't that the Bio::SeqIO::genbank module can't be found  
but what is indicated by the nested error message (i.e., the error  
that caused loading the module to fail): "Weak references are not  
implemented in the version of perl".

Bio::Species imports the weaken() and isweak() functions from  
Scalar::Util (and Bio::SeqIO::genbank requires Bio::Species).  
Apparently the perl installed in that system has been compiled such  
that it won't support weak references.


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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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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