Re: [Gmod-schema] Error while trying to load data. (API in bioperl that required changes to GMOD?)

[Scott C. <cai...@gm...>]

Hi Andrew,

Thanks for trying the new bioperl.  I was going to work on this today
but ran into problems loading ontologies that I had to fix first.  I'll
take a look at this tomorrow.

Scott


On Fri, 2007-10-19 at 00:46 +0000, Andrew DRew wrote:
> Hi all,
> 
> I ran into a new error.  I loaded loaded my bioperl from cpan, and then a 
> read a message from 
> http://www.nabble.com/problem-with-gmod_bulk_load_gff3.pl-t4633426.html 
> saying that a perl version didn't work with gmod.   However, I followed the 
> directions and still get an error
> 
> So I downloaded the cvs from bioperl.org
> $ mkdir ~/src;
> $ mkdir ~/src/bioperl
> $ cd ~/src/bioperl
>     * Login to CVS (password is "cvs"):
> $ cvs -d :pserver:cv...@co...:/home/repository/bioperl login
>     * Checkout the BioPerl core module, only (the right thing to do for most 
> people):
> $ cvs -d :pserver:cv...@co...:/home/repository/bioperl checkout 
> bioperl-live
> 
> This is the error message I get.  While trying to install the yeast data
> 
> $ gmod_bulk_load_gff3.pl --organism yeast --gfffile 
> saccharomyces_cerevisiae.gff
> Preparing data for inserting into the FlyBase database
> (This may take a while ...)
> Can't locate object method "database" via package 
> "Bio::Annotation::SimpleValue" at 
> /usr/lib/perl5/site_perl/5.8.5/Bio/GMOD/DB/Adapter.pm line 3059, <GEN0> line 
> 20.
> Issuing rollback() for database handle being DESTROY'd without explicit 
> disconnect
> 
> My perl version
> perl -MBio::Perl -le 'print Bio::Perl->VERSION;'
> 1.005002102
> 
> 
> Any ideas or suggestions
> 
> TIA
> Drew
> 
> 
> 
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         ca...@cs...
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory