[Bioperl-l] Fw: broken Bio::SeqIO in bioperl on OS X (fink)
cjfields at illinois.edu
Fri Feb 27 09:54:59 EST 2009
As Hilmar stated somewhere along this thread this is related to either
a lack of Scalar::Util or a bad/incomplete Scalar::Util installation
(maybe a pure perl only version).
> ------------- EXCEPTION -------------
> MSG: Failed to load module Bio::SeqIO::genbank. Weak references are
> not implemented in the version of perl at /sw/lib/perl5/5.8.8/Bio/
> Species.pm line 91
This can be rectified by installing/reinstalling Scalar::Util (it may
require a force install). See here for solutions:
As I see it there are two problems here. The first is with fink's
perl 5.8.8 package, which doesn't appear to have a weak-ref-enabled
Scalar::Util in core, causing the error. The second is with the
Build.PL in BioPerl 1.5.2 (which doesn't list Scalar::Util as a
required module). The latter may have rectified the former upon
installation if Scalar::Util wasn't present, but according to
perl -MModule::CoreList -e 'print Module::CoreList-
A full (weak-ref enabled) Scalar::Util should be present in the 5.8.8
core set of modules.
The Scalar::Util require issue has been rectified in the BioPerl 1.6
release, out now in CPAN, so I consider it fixed from our end.
On Feb 27, 2009, at 7:59 AM, Mark A. Jensen wrote:
> Hi Koen-
> If the user can find the directory containing the file Bio/SeqIO/
> he can force the script to find it. Example: if the full path of the
> module is
> 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.)
> ----- 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
>> Hi Dave,
>> This is the output from the user:
>> $ perl -e 'print (join "\n", @INC, "\n")'
>> 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.
>> - 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
>>> 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.
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