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

[Chris Fields]

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
> Bio::DB::SeqFeature::Store                0.0000  1.0060
> Bio::DB::SeqFeature::Store::DBI::Iterator  0.0000  1.0060
> Bio::DB::SeqFeature::Store::DBI::Pg       0.0000  1.0060
> Bio::DB::SeqFeature::Store::DBI::SQLite   0.0000  1.0060
> Bio::DB::SeqFeature::Store::DBI::mysql    0.0000  1.0060
> Bio::DB::SeqFeature::Store::FeatureFileLoader  0.0000  1.0060
> Bio::DB::SeqFeature::Store::GFF2Loader    0.0000  1.0060
> Bio::DB::SeqFeature::Store::GFF3Loader    0.0000  1.0060
> Bio::DB::SeqFeature::Store::LoadHelper    0.0000  1.0060
> Bio::DB::SeqFeature::Store::Loader        0.0000  1.0060
> Bio::DB::SeqFeature::Store::bdb           0.0000  1.0060
> Bio::DB::SeqFeature::Store::berkeleydb    0.0000  1.0060
> Bio::DB::SeqFeature::Store::berkeleydb3   0.0000  1.0060
> Bio::DB::SeqFeature::Store::memory        0.0000  1.0060
> --------
> However, when I test the module in perl debugger it finds this:
> ---------
> DB<11> use Bio::DB::SeqFeature::Store print $Bio::DB::SeqFeature::Store::VERSION                                                                               
> 1.006001
> ---------
> I assume that something in the environment is not set up right and in general I have had a good deal of problems that might relate to this. If anyone have some pointers to what it could be I'd be grateful. 

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.

> On a side note: Is there a way to search bioperl mailing list archives? I might be retarded and I couldn't figure out how. 
> 
> Happy New Year,
> Darwin

http://www.bioperl.org/wiki/Mailing_lists

Look under 'Search the Mailing Lists' (only the main one is searchable).

chris