[Bioperl-l] CPAN/Bioperl can't find modules

[Mike Williams]

On Tue, Jan 4, 2011 at 11:16 PM, Chris Fields <cjfields at illinois.edu> wrote:
> On Jan 4, 2011, at 6:56 PM, Darwin Sorento Dichmann wrote:
>
>> Wet biologist here trying to get into NGS/bioperl/gbrowse. Something funky is going on in my gbrowse2 installation and in an attempt to fix it I reinstalled bioperl as well as other perl modules through CPAN (default settings, OSX 10.6).
>>
>> When I run CPAN -O to test if all modules are up to date I get a lot of errors like this (excerpt):
>>
>> ------
>> Macintosh:~ darwin$ cpan -O
>> CPAN: Storable loaded ok (v2.25)
>> Going to read '/Users/darwin/Library/Application Support/.cpan/Metadata'
>>  Database was generated on Tue, 04 Jan 2011 07:05:20 GMT
>> Module Name                                Local    CPAN
>>
>> Bio::DB::SeqFeature                       0.0000  1.0060
>> Bio::DB::SeqFeature::NormalizedFeature    0.0000  1.0060
>> Bio::DB::SeqFeature::NormalizedFeatureI   0.0000  1.0060
>> Bio::DB::SeqFeature::NormalizedTableFeatureI  0.0000  1.0060
>> Bio::DB::SeqFeature::Segment              0.0000  1.0060
> Might be, or it might be that BioPerl has a funky way of assigning the module version that's causing the noise; it's defined in Bio::Root::Version and exported to every module.  This isn't the only module that does this (I get the same problem for DateTime).  I have seen this in some instances; the best way to check for the version is Bio::Root::Version.
>
> Also, the version output here is chopped via printf (only reports to four decimal places).  Tell the truth, I wouldn't worry about it if the correct version is showing up via the debugger or command line.

I've seen the same thing with version numbers and CPAN.  This is a
snippet from a fedora 13 system that had Bio::Perl installed via CPAN.
  cpan -O reports:

Bio::Align::AlignI                        0.0000  1.0060
Bio::Align::DNAStatistics                 0.0000  1.0060
Bio::Align::PairwiseStatistics            0.0000  1.0060
Bio::Align::ProteinStatistics             0.0000  1.0060
Bio::Align::StatisticsI                   0.0000  1.0060
Bio::Align::Utilities                     0.0000  1.0060
Bio::AlignIO                              0.0000  1.0060

The same results are repeated for all Bio::Perl modules.

I usually use perl -MCPAN -e shell instead of using the cpan script.
With the CPAN module shell I get similar results:

cpan[1]> r /Bio::Perl/
Going to read '/root/.cpan/Metadata'
  Database was generated on Tue, 04 Jan 2011 07:05:20 GMT

Package namespace         installed    latest  in CPAN file
Bio::Perl                     undef  1.006001  CJFIELDS/BioPerl-1.6.1.tar.gz
1 installed module has no parsable version number

I once tried to use the upgrade command from the CPAN shell and it
re-installed all of Bio::Perl because of the version number issue.

Mike