[Bioperl-l] test suite failing on mac os x 10.5

cody h plantboy at gmail.com
Fri Jun 26 14:46:35 EDT 2009


Hi,

I'm trying to install bioperl-db 1.5.2 on an intel mac running os 10.5.7.
The Build.PL file executes fine, but the test suite fails dramatically,
returning the error "No database selected" for many of the tests. All the
error calls seem to be originating from line 852 in
BasePersistenceAdaptor.pm. I took a look at the code but I could not figure
out why it wasn't working.

I have bioperl 1.5.2 installed and the biosql schema loaded into my mysql
server. The dependencies all seem to be working, but I haven't used them
enough to completely verify this, so that could be part of the problem. I
don't know which ones to check though. Does anyone have any idea why I might
be getting these "No database selected" errors? Here is a sample of the
error messages given by the ./Build test command (note, this same error is
generated byt 15/16 test files)

t/12ontology.t .... 1/738
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: error while executing statement in
Bio::DB::BioSQL::OntologyAdaptor::find_by_unique_key: No database selected
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
/Users/cody/Desktop/bioperl-db-1.5.2_100/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:948
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
/Users/cody/Desktop/bioperl-db-1.5.2_100/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:852
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
/Users/cody/Desktop/bioperl-db-1.5.2_100/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:182
STACK: Bio::DB::Persistent::PersistentObject::create
/Users/cody/Desktop/bioperl-db-1.5.2_100/blib/lib/Bio/DB/Persistent/PersistentObject.pm:244
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
/Users/cody/Desktop/bioperl-db-1.5.2_100/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:169
STACK: Bio::DB::Persistent::PersistentObject::create
/Users/cody/Desktop/bioperl-db-1.5.2_100/blib/lib/Bio/DB/Persistent/PersistentObject.pm:244
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
/Users/cody/Desktop/bioperl-db-1.5.2_100/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:169
STACK: Bio::DB::Persistent::PersistentObject::create
/Users/cody/Desktop/bioperl-db-1.5.2_100/blib/lib/Bio/DB/Persistent/PersistentObject.pm:244
STACK: t/12ontology.t:44
-----------------------------------------------------------
t/12ontology.t .... Dubious, test returned 255 (wstat 65280, 0xff00)


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