[Bioperl-l] error installing bioperl-db

[Hilmar Lapp]

Did you configure the name of your driver to be 'postgresql'? Is this a 
new DBD driver for PostgreSQL? The DBD driver used to be Pg (DBD::Pg), 
so bioperl-db just uses the same convention or name.

I.e., change postgresql to Pg in your configuration 
(t/DBHarness.biosql.conf), unless the DBD driver you are using is 
indeed DBD::postgresql.

If the DBD driver you are using is indeed DBD::postgresql and not 
DBD::Pg then copy Bio/DB/DBI/Pg.pm to Bio/DB/DBI/postgresql.pm and 
rename (or copy) the directory Bio/DB/BioSQL/Pg to 
Bio/DB/BioSQL/postgresql.

Hth,

	-hilmar

On Jul 19, 2005, at 3:03 PM, Andrew Stewart wrote:

> I'm having a problem while trying to install the bioperl-db modules.  
> While trying to run a make test, I get the following error:
>
> t/01dbadaptor.....ok 1/13                                              
>      ------------- EXCEPTION  -------------
> *MSG: Failed to load module Bio::DB::DBI::postgresql*. Can't locate 
> Bio/DB/DBI/postgresql.pm in @INC (@INC contains: t 
> /usr/local/bioperl-db/blib/lib /usr/local/bioperl-db/blib/arch 
> /sw/lib/perl5/5.8.1/darwin-thread-multi-2level /sw/lib/perl5/5.8.1 
> /sw/lib/perl5 /sw/lib/perl5/darwin /Users/astew/usr/lib 
> /System/Library/Perl/5.8.1/darwin-thread-multi-2level 
> /System/Library/Perl/5.8.1 
> /Library/Perl/5.8.1/darwin-thread-multi-2level /Library/Perl/5.8.1 
> /Library/Perl /Network/Library/Perl/5.8.1/darwin-thread-multi-2level 
> /Network/Library/Perl/5.8.1 /Network/Library/Perl .) at 
> /sw/lib/perl5/5.8.1/Bio/Root/Root.pm line 396.
>
> STACK Bio::Root::Root::_load_module 
> /sw/lib/perl5/5.8.1/Bio/Root/Root.pm:398
> STACK Bio::DB::SimpleDBContext::dbi 
> /usr/local/bioperl-db/blib/lib/Bio/DB/SimpleDBContext.pm:296
> STACK Bio::DB::BioSQL::DBAdaptor::new 
> /usr/local/bioperl-db/blib/lib/Bio/DB/BioSQL/DBAdaptor.pm:85
> STACK Bio::DB::BioDB::new 
> /usr/local/bioperl-db/blib/lib/Bio/DB/BioDB.pm:203
> STACK DBTestHarness::get_DBAdaptor t/DBTestHarness.pm:257
> STACK DBTestHarness::get_DBContext t/DBTestHarness.pm:272
> STACK toplevel t/01dbadaptor.t:23
>
> --------------------------------------
> t/01dbadaptor.....dubious
>        Test returned status 2 (wstat 512, 0x200)
> DIED. FAILED tests 2-13
>        Failed 12/13 tests, 7.69% okay
>
>
> Where am I supposed to find Bio::DB::DBI::postgresql ?
>
>
> -Andrew Stewart
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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