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

[john paul]

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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