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

[john paul]

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
)

says
# $Id: Term.pm 14708 2008-06-10 00:08:17Z heikki $
#
# BioPerl module for Bio::Ontology::Term
#
I was using an old distribution from CPAN.

reinstalling from the main trunk

svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk bioperl-live

solved the problem.

Thanks again

Tom


>
> 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
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
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