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john paul | 25 Sep 17:23

Can't locate object method "get_dbxrefs"

Hello guys,

I need to pick your brain on this. I was trying to load some sequences in a
fresh RH build using bioperl-db and got the following error:

[tatedger <at> localhost biosql]$ perl load_seqdatabase.pl --host localhost
--dbuser root --dbname biosql --namespace swissprot --format swiss
/home/tatedger/tmp/uniprot_sprot.dat  --testonly
Loading /home/tatedger/tmp/uniprot_sprot.dat ...
Could not store Q4U9M9: Can't locate object method "get_dbxrefs" via package
"Bio::Ontology::Term" at
/usr/lib/perl5/site_perl/5.8.5/Bio/DB/Persistent/PersistentObject.pm line
552, <GEN0> line 70.

I have seen some posts on this regard (
http://bioperl.org/pipermail/bioperl-l/2008-April/027544.html) but it wasn't
clear to me what the solution would be.

My configuration:
- mysql version 4.1.7
- Red Hat Enterprise Linux ES release 4 (Nahant)

to install bioperl and bioperl-db I used the help found on the website
following
- cpan>install S/SE/SENDU/bioperl-1.5.2_102.tar.gz
- svn co svn://code.open-bio.org/bioperl/bioperl-db/trunk bioperl-db
- biosql schema is loaded and load_ncbi_taxonomy.pl worked fine.

bioperl-db  test 04 shows the same error.
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Brian Osborne | 25 Sep 17:40

Re: Can't locate object method "get_dbxrefs"

John,

What does:

 >locate Bio/Ontology/Term.pm

Say?

Brian O.

On Sep 25, 2008, at 11:23 AM, john paul wrote:

> Hello guys,
>
> I need to pick your brain on this. I was trying to load some  
> sequences in a
> fresh RH build using bioperl-db and got the following error:
>
> [tatedger <at> localhost biosql]$ perl load_seqdatabase.pl --host localhost
> --dbuser root --dbname biosql --namespace swissprot --format swiss
> /home/tatedger/tmp/uniprot_sprot.dat  --testonly
> Loading /home/tatedger/tmp/uniprot_sprot.dat ...
> Could not store Q4U9M9: Can't locate object method "get_dbxrefs" via  
> package
> "Bio::Ontology::Term" at
> /usr/lib/perl5/site_perl/5.8.5/Bio/DB/Persistent/PersistentObject.pm  
> line
> 552, <GEN0> line 70.
>
>
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john paul | 25 Sep 18:27

Re: Can't locate object method "get_dbxrefs"

On Thu, Sep 25, 2008 at 4:40 PM, Brian Osborne <bosborne11 <at> verizon.net>wrote:

> John,
>
> What does:
>
> >locate Bio/Ontology/Term.pm
>
> Say?
>

Silly me.

$ locate  Bio/Ontology/Term.pm
/usr/lib/perl5/site_perl/5.8.5/Bio/Ontology/Term.pm

and

 $ cat /usr/lib/perl5/site_perl/5.8.5/Bio/Ontology/Term.pm|grep get_dbxrefs
produced no answer

the latest version posted by Sendu on cpan says for that module

# $Id: Term.pm,v 1.31.4.1 2006/10/02 23:10:22 sendu Exp $
#
# BioPerl module for Bio::Ontology::Term
and the live version at (
http://code.open-bio.org/svnweb/index.cgi/bioperl/view/bioperl-live/trunk/Bio/Ontology/Term.pm
)
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Sendu Bala | 25 Sep 19:12
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Re: Can't locate object method "get_dbxrefs"

john paul wrote:
> - cpan>install S/SE/SENDU/bioperl-1.5.2_102.tar.gz
> - svn co svn://code.open-bio.org/bioperl/bioperl-db/trunk bioperl-db
[...]
> Can't locate object method "get_dbxrefs" via package "Bio::Ontology::Term"
[...]
> What am I doing wrong? Could you help?

You're using the svb versuib bioperl-db but the release version of core 
(aka live). Don't mix and match; use the same version of both. So either 
install bioperl-live from svn as well, or get rid of you svn bioperl-db 
and install bioperl-db 1.5.2: 
http://bioperl.org/DIST/bioperl-db-1.5.2_100.tar.gz

I'd recommend using svn for both.
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