[Bioperl-l] bioperl-db question

gang wu gwu at molbio.mgh.harvard.edu
Sat Nov 18 03:57:49 EST 2006


Hi everyone,

I used to use MySQL to host the BioSQL schema and load Genbank into it 
with the 'load_seqdatabase.pl' without problem(except extremely slow. It 
took about 12 hours to load Arabidopsis thaliana). I just loaded the 
BioSQL schema in Oracle 10g. I could load NCBI Taxonomy database without 
problem.

When I 'make test' with bioperl-db-1.5.2.R3, all tests can pass with 
MySQL while always saw an error with Oracle:
      Can't call method "bind_param" on an undefined value at 
/root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 939.

, where the code is $sth->bind_param();

Any idea what the problem is?

Gang


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