[Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl

[Hilmar Lapp]

This has nothing to do with the input file but everything with run-time
loading of modules in perl on Windows. The error you get is generated by the
following line of code:

    $self->debug("attempting to load driver for adaptor class $class\n");

The class Bio::DB::BioSQL::BasePersistenceAdaptor.pm has a 'use
Bio::Root::Root' statement, it inherits directly from Bio::Root::Root, and
Bio::Root::Root does have a debug() method as you can (and should) easily
convince yourself of.

Have you run the bioperl-db test suite? If so, what was the result? If not,
run it.

So, I'm copying the bioperl list here in case somebody has more clues as to
why you might be seeing this error on WinXP. We've had a case before on the
list where it turned out eventually that there had been a version mix-up on
the machine and everything worked fine after re-installing from scratch.

    -hilmar

On 10/8/03 4:24 AM, "Robert Roth" <robert.roth at home.se> wrote:

> 
> Hello,
> 
> I'm using Mysql 4.0.15, Bioperl 1.2.3, bioperl-db from the cvs and perl
> 5.6.1 on WinXP.
> After installation I pre-loaded the the biosql database with the NCBI taxon
> database using
> load_ncbi_taxonomy.pl. Now when I try to load sequence data with
> load_seqdatabase.pl I get
> the following error,
> 
> perl load_seqdatabase.pl --host localhost --dbname biosql --dbus
> er root --namespace bioperl --debug --safe --testonly --format
> genbank test.genbank
> Loading test.genbank ...
> attempting to load adaptor class for Bio::Seq::RichSeq
>       attempting to load module Bio::DB::BioSQL::RichSeqAdaptor
> attempting to load adaptor class for Bio::Seq
>       attempting to load module Bio::DB::BioSQL::SeqAdaptor
> instantiating adaptor class Bio::DB::BioSQL::SeqAdaptor
> attempting to load adaptor class for Bio::SeqFeature::Generic
>       attempting to load module Bio::DB::BioSQL::GenericAdaptor
> attempting to load adaptor class for Bio::Root::Root
>       attempting to load module Bio::DB::BioSQL::RootAdaptor
> Undefined subroutine &Bio::Root::Root::debug called at
> E:/Perl/site/lib/Bio/DB/B
> ioSQL/BasePersistenceAdaptor.pm line 1502, <GEN0> line 41.
> 
> I've tried different formats (swiss and genbank) and different files with
> the same
> result. The line number given in the error always correspond to the end of
> the first
> record (and it doesn't matter if the file contains one or more records).
> Any ideas?
> 
> Many thanks in advance,
> 
> Robert
> 
> 
> _______________________________________________
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> BioSQL-l at open-bio.org
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> 

-- 
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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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