[Bioperl-l] Re: Problem with Bio::DB::DBI::Pg after upgrading to core-1.5.1 and latest cvs

Hilmar Lapp hlapp at gnf.org
Tue Oct 18 12:55:56 EDT 2005

Bioperl-db required some changes to work fine with the 1.5.x releases, 
so it is critical that you upgrade bioperl-db as well if you upgrade 
Bioperl to 1.5. I believe the reason you're getting the error is a 
version incompatibility. SimpleDBContext does implement dsn(), and 
Pg.pm doesn't use SimpleDBContext as a literal anywhere.

However, you're saying that you are using the latest cvs update of 
bioperl-db, so maybe you haven't installed your upgraded bioperl-db 
version but did install the previous one?

You can check for individual versions of files by grep'ing for the $Id 
tag. Here's what you should see:

reigen: 9:49 19>perldoc -m Bio::DB::SimpleDBContext.pm | grep '$Id'
# $Id: SimpleDBContext.pm,v 1.5 2005/08/26 19:34:14 lapp Exp $
reigen: 9:51 20>perldoc -m Bio::DB::DBI::Pg.pm | grep '$Id'
# $Id: Pg.pm,v 1.2 2005/08/26 19:34:14 lapp Exp $
reigen: 9:52 21>

Did you run the tests? Was there a problem? If the tests run fine (they 
should) then it is almost certainly older modules installed somewhere 
else in your @INC that interfere with the new ones.


On Oct 18, 2005, at 2:31 AM, Daniel Lang wrote:

> Hi,
> I´ve just upgraded my bioperl-cvs-version(december 2004, the one right
> before 1.5 and the trouble with how Annotations were written out using
> Bio::Seq) to bioperl-1.5.1 in order to see if the features are now
> written out correctly. (See also "[BioSQL-l] strange error after
> changing to RC1.5" 09.03.2005)
> Seems like the core code is now working like it used to. But now the
> bioperl-db code for Pg has problems:(
> When I try to retrieve a sequence from a Pg-biosql db I receive the
> following error:
> Can't locate object method "dsn" via package "Bio::DB::SimpleDBContext"
> (perhaps you forgot to load "Bio::DB::SimpleDBContext"?) at
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/DBI/Pg.pm line 221.!
> I'm using the cvs-version (today) of bioperl-db with the 1.5.1 of core
> and run.
> I tried to use SimpleDBContext in Pg.pm - no effect.
> I don´t really get it what is happening there...
> Thanks in advance.
> Regards Daniel:)
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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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