Subject: Re: Install help errors
Newsgroups: gmane.comp.lang.perl.bio.general
Date: 2008-07-10 18:46:05 GMT (51 weeks, 3 days, 3 hours and 17 minutes ago)
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