[Bioperl-l] Added 'Installing bioperl-db in Windows' to wiki, problems with bioperl-db

Chris Fields cjfields at uiuc.edu
Tue Feb 14 15:32:42 EST 2006


Hilmar, 

Good News: I've added a section to the bioperl wiki on installing bioperl-db
in Windows:

http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows#Installing_bioperl
-db

Bad News:  There's a new problem now. I updated from CVS yesterday; I walked
through the steps and ran 'nmake test', with everything passing fine.
However, load_seqdatabase.pl is extremely slow; it's loading a sequence
every 5 minutes or so.  I noticed (when using '-debug') that it is hanging
up in Bio::DB::BioSQL::SpeciesAdaptor each time.  If I create a database,
load the biosql schema, and load sequences w/o loading taxonomy, the problem
goes away.

Here's the debugging output (I cut it off at the point it hangs up):
----------------------------------------------------------------------------
-------------------------
C:\Perl\src\bioperl\bioperl-db\scripts\biosql>load_seqdatabase.pl -driver
mysql -namespace test -dbname biosql -dbuser root -dbpass ********** -format
genbank  -debug NP_252217.gpt
Loading NP_252217.gpt ...
attempting to load adaptor class for Bio::Seq::RichSeq
        attempting to load module Bio::DB::BioSQL::RichSeqAdaptor
attempting to load adaptor class for Bio::Seq
        attempting to load module Bio::DB::BioSQL::SeqAdaptor
instantiating adaptor class Bio::DB::BioSQL::SeqAdaptor
attempting to load adaptor class for Bio::Species
        attempting to load module Bio::DB::BioSQL::SpeciesAdaptor
instantiating adaptor class Bio::DB::BioSQL::SpeciesAdaptor
attempting to load adaptor class for Bio::Annotation::Collection
        attempting to load module Bio::DB::BioSQL::CollectionAdaptor
attempting to load adaptor class for Bio::Root::Root
        attempting to load module Bio::DB::BioSQL::RootAdaptor
attempting to load adaptor class for Bio::Root::RootI
        attempting to load module Bio::DB::BioSQL::RootIAdaptor
        attempting to load module Bio::DB::BioSQL::RootAdaptor
attempting to load adaptor class for Bio::AnnotationCollectionI
        attempting to load module
Bio::DB::BioSQL::AnnotationCollectionIAdaptor
        attempting to load module
Bio::DB::BioSQL::AnnotationCollectionAdaptor
instantiating adaptor class Bio::DB::BioSQL::AnnotationCollectionAdaptor
attempting to load adaptor class for Bio::Annotation::TypeManager
        attempting to load module Bio::DB::BioSQL::TypeManagerAdaptor
no adaptor found for class Bio::Annotation::TypeManager
attempting to load adaptor class for Bio::Annotation::SimpleValue
        attempting to load module Bio::DB::BioSQL::SimpleValueAdaptor
instantiating adaptor class Bio::DB::BioSQL::SimpleValueAdaptor
attempting to load adaptor class for Bio::Annotation::Reference
        attempting to load module Bio::DB::BioSQL::ReferenceAdaptor
instantiating adaptor class Bio::DB::BioSQL::ReferenceAdaptor
attempting to load adaptor class for Bio::Annotation::Comment
        attempting to load module Bio::DB::BioSQL::CommentAdaptor
instantiating adaptor class Bio::DB::BioSQL::CommentAdaptor
attempting to load adaptor class for Bio::Annotation::DBLink
        attempting to load module Bio::DB::BioSQL::DBLinkAdaptor
instantiating adaptor class Bio::DB::BioSQL::DBLinkAdaptor
attempting to load adaptor class for Bio::PrimarySeq
        attempting to load module Bio::DB::BioSQL::PrimarySeqAdaptor
instantiating adaptor class Bio::DB::BioSQL::PrimarySeqAdaptor
attempting to load adaptor class for Bio::SeqFeature::Generic
        attempting to load module Bio::DB::BioSQL::GenericAdaptor
attempting to load adaptor class for Bio::SeqFeatureI
        attempting to load module Bio::DB::BioSQL::SeqFeatureIAdaptor
        attempting to load module Bio::DB::BioSQL::SeqFeatureAdaptor
instantiating adaptor class Bio::DB::BioSQL::SeqFeatureAdaptor
attempting to load adaptor class for Bio::Location::Simple
        attempting to load module Bio::DB::BioSQL::SimpleAdaptor
attempting to load adaptor class for Bio::Location::Atomic
        attempting to load module Bio::DB::BioSQL::AtomicAdaptor
attempting to load adaptor class for Bio::LocationI
        attempting to load module Bio::DB::BioSQL::LocationIAdaptor
        attempting to load module Bio::DB::BioSQL::LocationAdaptor
instantiating adaptor class Bio::DB::BioSQL::LocationAdaptor
no adaptor found for class Bio::Annotation::TypeManager
no adaptor found for class Bio::Annotation::TypeManager
no adaptor found for class Bio::Annotation::TypeManager
no adaptor found for class Bio::Annotation::TypeManager
no adaptor found for class Bio::Annotation::TypeManager
no adaptor found for class Bio::Annotation::TypeManager
no adaptor found for class Bio::Annotation::TypeManager
attempting to load adaptor class for BioNamespace
        attempting to load module Bio::DB::BioSQL::BioNamespaceAdaptor
instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor
no adaptor found for class Bio::Annotation::TypeManager
no adaptor found for class Bio::Annotation::TypeManager
no adaptor found for class Bio::Annotation::TypeManager
no adaptor found for class Bio::Annotation::TypeManager
attempting to load driver for adaptor class
Bio::DB::BioSQL::BioNamespaceAdaptor
attempting to load driver for adaptor class
Bio::DB::BioSQL::BasePersistenceAdaptor
Using Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver peer
for Bio::DB::BioSQL::BioNamespaceAdaptor
preparing UK select statement: SELECT biodatabase.biodatabase_id,
biodatabase.name, biodatabase.authority FROM biodatabase WHERE name = ?
BioNamespaceAdaptor: binding UK column 1 to "test" (namespace)
preparing INSERT statement: INSERT INTO biodatabase (name, authority) VALUES
(?, ?)
BioNamespaceAdaptor::insert: binding column 1 to "test" (namespace)
BioNamespaceAdaptor::insert: binding column 2 to "" (authority)
attempting to load driver for adaptor class Bio::DB::BioSQL::SpeciesAdaptor
Using Bio::DB::BioSQL::mysql::SpeciesAdaptorDriver as driver peer for
Bio::DB::BioSQL::SpeciesAdaptor
preparing UK select statement: SELECT taxon_name.taxon_id, NULL, NULL,
taxon.ncbi_taxon_id, taxon_name.name, NULL FROM taxon, taxon_name WHERE
taxon.taxon_id = taxon_name.taxon_id AND name_class = ? AND ncbi_taxon_id =
?
SpeciesAdaptor: binding UK column 1 to "scientific name" (name_class)
SpeciesAdaptor: binding UK column 2 to "208964" (ncbi_taxid)  
----------------------------------------------------------------------------
-------------------------

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 





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