[Bioperl-l] bioperl-db woes

Chris Fields cjfields at uiuc.edu
Thu Apr 17 09:59:57 EDT 2008


The 'get_dbxrefs' problem looks related to recent changes I made when  
rolling back the significant feature/annotation changes introduced  
just prior to the 1.5 release, none which were fully implemented.  I  
can check that one out.  Odd though; these passed for me, but I'm  
using MySQL not oracle.

You may want to make sure you are using bioperl-live and that there  
isn't an older bioperl installation getting into the mix.

chris

On Apr 17, 2008, at 8:40 AM, Stefan Kirov wrote:

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





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