[Bioperl-l] load_seqdatabase won't

Hilmar Lapp hlapp at gmx.net
Thu Feb 10 03:13:54 EST 2005


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

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 =  

(one single line despite any linebreaks your email reader may pretend  
to you)


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
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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