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

Darwin Sorento Dichmann dichmann at berkeley.edu
Wed Jan 5 00:56:08 UTC 2011

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                                                                               
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. 

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,

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