[Bioperl-l] Trouble installing bioperl-db on MacOS X... Help?

Hilmar Lapp hlapp at gmx.net
Sat Jul 11 07:32:11 EDT 2009


Hi Cody,

it seems like bioperl-db fails to connect to your database, or it  
connects but doesn't have a database selected (in MySQL connecting  
without setting the database is legitimate) and so as soon as it wants  
to execute a statement it fails. Have you set your connection  
parameters in t/DBTestHarness.conf?

	-hilmar

On Jul 10, 2009, at 7:33 PM, cody h wrote:

> 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 by 15/16 test files)
>
> I am new to Perl and would really appreciate any help or guidance at  
> all!
> Thanks!
>
> Cody
>
> 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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-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================





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