[Bioperl-l] recursion issues with bioperl-db

Chris Fields cjfields at uiuc.edu
Sun Sep 2 19:57:59 EDT 2007


Apologies if you get this more than once; the first post appeared to  
get sent w/o a proper subject line.  Posted this to biosql-l already  
but felt it needed posting here as well.

I noticed some critical recursion issues with bioperl-db when working  
in Bio::Ontology changes.  This was using bioperl-live (post-feature/ 
annotation fixes).  Bug report is here:

http://bugzilla.open-bio.org/show_bug.cgi?id=2355

It seems to be Bio:Taxon related; this is from 03swiss.t:

--------------------- WARNING ---------------------
MSG: recursion detected for Bio::Taxon object
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm:681
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm:630
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm:692
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm:630
...
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm:587
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm:253
STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
PrimarySeqAdaptor.pm:229
STACK Bio::DB::BioSQL::SeqAdaptor::store_children
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
SeqAdaptor.pm:217
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm:214
STACK Bio::DB::Persistent::PersistentObject::create
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/Persistent/ 
PersistentObject.pm:244
STACK toplevel t/04swiss.t:36
---------------------------------------------------

Also, seeing this with 13remove.t and 15.cluster.t, both of which  
appear to infinitely recurse:

Deep recursion on subroutine
"Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent" at
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm
line 587, <GEN0> line 1.
Deep recursion on subroutine
"Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child" at
/Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm
line 630, <GEN0> line 1.


chris



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