[Bioperl-l] load_seqdatabase won't

[Mike Muratet]

Hilmar

Problem solved. Turned out to be a missing dependancy.

> 
> did you run the test suite that comes with bioperl-db? Every test  
> should pass or there is a problem.
> 

All tests on Bio::Ontology::Ontology failed for the original reason.

> Bio::Ontology::Ontology->new does take arguments, they are apparently  
> just not documented. I fixed this (in bioperl). At any rate, arguments  
> have no role in locating a method in perl. The use statement should be  
> present thoughi in the adaptor, I fixed this as well (in bioperl-db).
> 
> If you add the following line
> 
> use Bio::Ontology::Ontology;
> 
> after the end of the top introductory documentation, where the other  
> 'use' statements are, will that make your problem go away?
> 
> If it doesn't, what happens if you issue
> 
> 	$ perl -MBio::Ontology::Ontology -e '$obj =  
> Bio::Ontology::Ontology->new(-name=>"blah");'
> 
> (one single line despite any linebreaks your email reader may pretend  
> to you)
> 

I added the line, and perl -MBio::Ontology revealed that Graph/Directed
was missing. It used to be there. Strange. Reinstalled this module and
everything works. 

Thanks

Mike

> 
> On Wednesday, February 9, 2005, at 02:30  PM, Mike Muratet wrote:
> 
> > Hilmar
> >
> > I got the latest bioperl-db from the cvs server, and the latest biosql
> > from the openbio-org cvs server, and things were going swell. I was  
> > trying
> > to load some swissprot files and got the message:
> >
> > Could not store P97718: Can't locate object method "new" via package
> > "Bio::Ontology::Ontology" at
> > /usr/local/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> > SimpleValueAdaptor.pm
> > line 613, <GEN65> line 88
> >
> > I looked at SimpleValueAdaptor.pm and it's calling the 'new' method  
> > with
> > an argument,i.e., new(-name=>"Annotation Tags"). The perldoc for
> > Bio::Ontology::Ontology shows a new constructor that doesn't take any
> > arguments. I'm not experienced enough with OO perl to tell from the  
> > code
> > whether it does or not. SimpleValueAdaptor.pm _did_not_ define
> > Bio::Ontology::Ontology at the top of the file, but adding it doesn't  
> > fix
> > the problem.
> >
> > There must be a simple answer, but it's beyond me. Any ideas?
> >
> > Thanks
> >
> > Mike
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> 
> 
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