[Bioperl-l] Install help errors

[snoze pa]

Thanks Chris and all bioperl developers

On Fri, Jul 11, 2008 at 7:40 AM, Chris Fields <cjfields at uiuc.edu> wrote:
> 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
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> 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
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> 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
>
>
>
>
>