[Gmod-help] Re: [Gmod-gbrowse] Can't locate object method "parse_types"

[Scott Cain]

Hi Alessandra,

Is it possible that you have more than one version of bioperl on your
server (or, if you have just one, is it too old)?  I'm not sure that you
need to do the update to gbrowse cvs, but you should make sure that you
don't have old bioperl libraries around messing things up.

Scott


On Tue, 2008-05-20 at 10:37 -0700, Dave Clements, GMOD Help Desk wrote:
> Alessandra,
> 
> The parse_types method was moved from GFF.pm to DasI.pm between
> BioPerl 1.40 and 1.5.0, which is relatively recently.  My guess is
> that you have incompatible versions of BioPerl and GBrowse.
> 
> Running the net installer with the -d option should install the latest
> of both GBrowse (the "stable" branch)  and the latest bioperl-live).
> Try:
> 
>   sudo perl gbrowse-netinstall.pl -d
> 
> Dave C.
> GMOD Help Desk
> 
> 
> On Mon, May 19, 2008 at 10:55 PM, Alessandra Bilardi
> <bilardi at cribi.unipd.it> wrote:
> > Hi all,
> > I use gbrowse 1.68 release. I install it with with
> > gbrowse_netinstall.pl without error. I obtain right gbrowse page but
> > without genome image and in /var/log/apache2/error.log there
> > are one error:
> >
> > Can't locate object method "parse_types" via package "Bio::DB::GFF::Adaptor::memory" at /usr/lib/perl/5.8.8/Bio/DB/GFF.pm line 3306.
> > Use of uninitialized value in print at gbrowse line 439.
> >
> > I don't understand this error because method "parse_types" is into Bio::DasI.pm
> >
> > Can you help me?
> >
> > Alessandra
> > =-=-=-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=
> >  CRIBI, University of Padova, Italy
> >  http://www.linkedin.com/in/bilardi
> > =-=-=-=-=-=-=-=-=-==-=-=-=-=-=-=-=-=-=
> >
> > -------------------------------------------------------------------------
> > This SF.net email is sponsored by: Microsoft
> > Defy all challenges. Microsoft(R) Visual Studio 2008.
> > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> > _______________________________________________
> > Gmod-gbrowse mailing list
> > Gmod-gbrowse at lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> >
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft 
> Defy all challenges. Microsoft(R) Visual Studio 2008. 
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory