[Bioperl-l] recursion issues with bioperl-db

Chris Fields cjfields at uiuc.edu
Sun Sep 2 21:40:48 EDT 2007


Okay, we can the previous posts!  Odd, but I started from scratch and  
can't reproduce the issue; there may have been some cross-talk with  
different bioperl installations on my laptop.  Anyway, everything  
passes now w/o recursion so I'll mark the bug as invalid.

chris

On Sep 2, 2007, at 6:57 PM, Chris Fields wrote:

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





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