[Bioperl-l] Bioperl-db make test failures

[Hilmar Lapp]

This is strange, actually both of them. Did you run the tests against a 
database with content loaded prior to the tests, or was it a freshly 
created instance of the schema?

If the latter, which RDBMS, and version of bioperl are you using?

	-hilmar

On Tuesday, February 10, 2004, at 10:07  AM, Adam Witney wrote:

> Hi,
>
> I am trying out bioperl-db and biosql. I downloaded both from CVS and
> installed the biosql schema ok. However I have some test failures with
> bioperl-db:
>
> t/cluster.......ok 5/160Use of uninitialized value in join or string at
> blib/lib/Bio/DB/BioSQL/BaseDriver.pm line 1835, <GEN0> line 1.
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::BiosequenceAdaptor (driver) failed, 
> values
> were ("","0","dna","") FKs (2)
> ERROR:  invalid input syntax for integer: ""
>
> ... And
>
> t/species.......ok 68/65
> ------------- EXCEPTION  -------------
> MSG: create: object (Bio::Species) failed to insert or to be found by 
> unique
> key
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:207
> STACK Bio::DB::Persistent::PersistentObject::create
> blib/lib/Bio/DB/Persistent/PersistentObject.pm:243
> STACK toplevel t/species.t:76
>
> Are these known problems or have I missed something?
>
> Thanks
>
> Adam
>
>
> -- 
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------