[Bioperl-l] Error in loading into biosql database

[Siddhartha Basu]

Hi,
Thanks for the information. I have tried the following combination

bioperl => 1.2.0
bioperl-db => branch before-singapore-change
biosql-schema => branch before-singapore-change

Unfortunately it did'nt work for me though. Now i am getting a different 
error message....

=========================================================================
DBD::mysql::st execute failed: Table 'biosql.taxon_name' doesn't exist 
at 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm 
line 791, <GEN0> line 111.

------------- EXCEPTION  -------------
MSG: Could not store P31946:
------------- EXCEPTION  -------------
MSG: error while executing statement in 
Bio::DB::BioSQL::SpeciesAdaptor::find_by_unique_key: Table 
'biosql.taxon_name' doesn't exist
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:797
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:182
STACK Bio::DB::Persistent::PersistentObject::create 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm:242
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:169
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:240
STACK Bio::DB::Persistent::PersistentObject::store 
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObject.pm:266
STACK (eval) load_seqdatabase.pl:424
STACK toplevel load_seqdatabase.pl:423

--------------------------------------


STACK toplevel load_seqdatabase.pl:433

--------------------------------------

===========================================================================

Am i using the right combination, or do i have to change something.


siddhartha

> 
> If you want a combination that works, and you want it right now, then  
> go for before-singapore-change tags on both biosql-schema and  
> bioperl-db, in combination with bioperl 1.2.0. (*not* the bioperl main  
> trunk, nor the upcoming 1.2.1.).
> 
> Otherwise, you need to be patient for 1 or more 2 weeks as things are  
> shaping up towards a schema freeze.
> 
>     -hilmar