[Bioperl-l] bioperl-db woes

Stefan Kirov stefan.kirov at bms.com
Thu Apr 17 09:40:29 EDT 2008


I'm having problems passing all the tests for bioperl-db. There are 2
distinct errors, first one:
Can't locate Bio/DB/BioSQL/RichSeqAdaptor.pm
   ***Which by the way is embed deep into several layers of eval, so I
am getting the actual error from the test:
    ***t/04swiss.........ok 3/52Can't locate object method "get_dbxrefs"
via package "Bio::Ontology::Term" at    
       
/home/kirovs/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm
line 552, <GEN0> line 78.
       or
       ------------- EXCEPTION: Bio::Root::Exception -------------

    MSG: Annotation of class Bio::Annotation::Collection not
    type-mapped. Internal error?
    STACK: Error::throw
    STACK: Bio::Root::Root::throw
    /home/kirovs/bioperl-live/Bio/Root/Root.pm:357
    STACK:
    Bio::DB::BioSQL::AnnotationCollectionAdaptor::_annotation_map_key
    Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:695
    STACK: Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children
    Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:204
    STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
    Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
    STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
    Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
    STACK: Bio::DB::Persistent::PersistentObject::store
    Bio/DB/Persistent/PersistentObject.pm:271
    STACK: Bio::DB::BioSQL::SeqAdaptor::store_children
    Bio/DB/BioSQL/SeqAdaptor.pm:224
    STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
    Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
    STACK: Bio::DB::Persistent::PersistentObject::create
    Bio/DB/Persistent/PersistentObject.pm:244
    STACK: t/04swiss.t:36
    -----------------------------------------------------------

It turns out the adaptor is really not there???
My bioperl-db is from
dev.open-bio.org/home/svn-repositories/bioperl/bioperl-db/trunk
bioperl-db (revision 14661)
Is this module being deprecated (I am sure it is not) my download
incomplete....?
The other problem was:
DBD::Oracle::st execute failed: ORA-02292: integrity constraint
(BIOSQL.FKTAX_ENT) violated - child record found (DBD ERROR:
OCIStmtExecute) [for Statement "DELETE FROM taxon WHERE oid = ?" with
ParamValues: :p1=9606] at
/home/kirovs/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm
line 320.
not ok 76
# Test 76 got: <UNDEF> (t/02species.t at line 71)
I have not tried to debug this one....
Thanks!
Stefan


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