[BioSQL-l] [Bioperl-l] Can't locate object method "get_dbxrefs"

[Brian Osborne]

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.
>
>
> 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.
>
> [tatedger at localhost bioperl-db]$ perl t/04swiss.t
> 1..52
> ok 1
> ok 2
> ok 3
> ok 4
> ok 5
> 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 78.
>
>
> my @INC file looks like
> /usr/lib/perl5/5.8.5/i386-linux-thread-multi
> /usr/lib/perl5/5.8.5
> /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.5
> /usr/lib/perl5/site_perl/5.8.4
> /usr/lib/perl5/site_perl/5.8.3
> /usr/lib/perl5/site_perl/5.8.2
> /usr/lib/perl5/site_perl/5.8.1
> /usr/lib/perl5/site_perl/5.8.0
> /usr/lib/perl5/site_perl
> /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.5
> /usr/lib/perl5/vendor_perl/5.8.4
> /usr/lib/perl5/vendor_perl/5.8.3
> /usr/lib/perl5/vendor_perl/5.8.2
> /usr/lib/perl5/vendor_perl/5.8.1
> /usr/lib/perl5/vendor_perl/5.8.0
> /usr/lib/perl5/vendor_perl
>
> What am I doing wrong? Could you help?
>
> Thanks in advance for your help
> Tom
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