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

[Daniel Lang]

Hi Hilmar,
Yes, I have installed the latest bioperl-db:
lang at frontend-0-0:~/bioperl> perldoc -m Bio::DB::SimpleDBContext.pm |
grep '$Id'
# $Id: SimpleDBContext.pm,v 1.5 2005/08/26 19:34:14 lapp Exp $
lang at frontend-0-0:~/bioperl> perldoc -m Bio::DB::DBI::Pg.pm | grep '$Id'
# $Id: Pg.pm,v 1.2 2005/08/26 19:34:14 lapp Exp $

But your guess was right, I had a stone-age version in my @INC :(

Now everything works fine...

Thanks!

Regards,
Daniel:)


Hilmar Lapp wrote:
> 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.
> 
>     -hilmar
> 
> On Oct 18, 2005, at 2:31 AM, Daniel Lang wrote:
>