[Gmod-help] problems with Gbrowse 1.69

[Scott Cain]

Hi Jason,

The "can't locate method" message makes me wonder if there is more
than one bioperl installed on the server, and so it's not using the
right Bio::Graphics::Browser.  Is that a possibility?

Scott


On Tue, Oct 7, 2008 at 1:57 PM, Jason Phillips <japhill at email.unc.edu> wrote:
> I'm beating my head against this problem that seems to have spontaneously
> appeared in my gbrowse configuration.  We are using 1.69 and have updated
> the bioperl to use the 'live' version straight from cvs.  It seemed like
> over night the browser stopped working correctly.  I looked in my httpd log
> and found these associated with requesting gbrowse data from firefox:
>
> [Tue Oct 07 11:37:41 2008] [error] [client 72.173.20.224]
> Bio::Graphics::BrowserConfig=HASH(0x3fcc050) at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
> line 587., referer:
> http://www.mimulusevolution.org/cgi-bin/gbrowse/Scaffolds_6x/
> [Tue Oct 07 11:37:41 2008] [error] [client 72.173.20.224]
> Bio::Graphics::BrowserConfig=HASH(0x3fcc050) at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
> line 587., referer:
> http://www.mimulusevolution.org/cgi-bin/gbrowse/Scaffolds_6x/
> [Tue Oct 07 11:37:41 2008] [error] [client 72.173.20.224] Use of
> uninitialized value in numeric gt (>) at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser/UploadSet.pm
> line 155., referer:
> http://www.mimulusevolution.org/cgi-bin/gbrowse/Scaffolds_6x/
> [Tue Oct 07 11:37:41 2008] [error] [client 72.173.20.224] Can't locate
> object method "overview" via package "Bio::Graphics::Browser" at
> /home/www/cgi-bin/gbrowse line 1925., referer:
> http://www.mimulusevolution.org/cgi-bin/gbrowse/Scaffolds_6x/
>
>
> Can you narrow down the possible problems that these log entries would
> indicate?
>
> Let me know if you need more information to diagnose the problem.
>
>
> Thanks
>
> Jason Phillips
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   cain.cshl at gmail.com
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research