[Bioperl-l] Install help errors

snoze pa snoze.pa at gmail.com
Thu Jul 10 18:46:05 UTC 2008


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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