[Bioperl-l] Install help errors

[Chris Fields]

Okay, that's a bug related to some changes I made.  I can look into  
it; should be easy to fix.

chris

On Jul 10, 2008, at 1:46 PM, snoze pa wrote:

> With minor warning, It seems the nightly build pack of bioperl
> working. Atleast this time it is not crashing. I checked the sequence
> information in the DB, and all are there.
> Thanks a lot for your help.
> best s
>
> some warnings are
>
> MSG: The supplied lineage does not start near '
>
> and
>
> Use of get_dblinks is deprecated.  Note that prior use
> of this method could return either simple scalar values
> or Bio::Annotation::DBLink instances; only
> Bio::Annotation::DBLink is now supported.
> Use get_dbxrefs() instead
> STACK Bio::Ontology::Term::get_dblinks
> /usr/local/lib/perl5/site_perl/5.10.0/Bio/Ontology/Term.pm:437
> STACK Bio::DB::Persistent::PersistentObject::AUTOLOAD
> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/ 
> PersistentObject.pm:552
> STACK Bio::DB::BioSQL::TermAdaptor::store_children
> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/TermAdaptor.pm:280
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:214
> STACK Bio::DB::Persistent::PersistentObject::create
> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/ 
> PersistentObject.pm:244
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:169
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:251
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/ 
> PersistentObject.pm:271
> STACK Bio::DB::BioSQL::SeqAdaptor::store_children
> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/SeqAdaptor.pm:244
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:214
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:251
> STACK Bio::DB::Persistent::PersistentObject::store
> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/Persistent/ 
> PersistentObject.pm:271
> STACK (eval) /usr/local/bin/bp_load_seqdatabase.pl:623
> STACK toplevel /usr/local/bin/bp_load_seqdatabase.pl:605
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign