[Bioperl-l] Install help errors

[Chris Fields]

Make sure you have an updated bioperl-db as well.  The call to  
get_dblinks() was changed to get_xrefs a while back and, IIRC, so was  
'The supplied lineage does not start near...' message, which is  
related to Bio::Species changes.

chris

On Jul 10, 2008, at 1:54 PM, Chris Fields wrote:

> 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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>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Marie-Claude Hofmann
> College of Veterinary Medicine
> University of Illinois Urbana-Champaign
>
>
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign