gmod_make_cvtermpath.pl

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gmod_make_cvtermpath.pl

Andrew McArthur
Colleagues,

We use Chado's cvtermpath table extensively in our work but have hit a hitch with the upgrade to Chado 1.1.  It may relate to a Perl version issue.  Here is what we have so far, any ideas?

root@arpcard-server:/usr/share/perl5/Bio/Chado# /usr/local/bin/gmod_make_cvtermpath.pl 
Base class package "DBIx::Class::Schema" is empty.
    (Perhaps you need to 'use' the module which defines that package first,
    or make that module available in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .).
 at /usr/share/perl5/Bio/Chado/Schema.pm line 9
BEGIN failed--compilation aborted at /usr/share/perl5/Bio/Chado/Schema.pm line 9.
Compilation failed in require at /usr/local/bin/gmod_make_cvtermpath.pl line 91.
BEGIN failed--compilation aborted at /usr/local/bin/gmod_make_cvtermpath.pl line 91.

root@arpcard-server:/usr/share/perl5/Bio/Chado# which perl
/usr/local/bin/perl

root@arpcard-server:/usr/share/perl5/Bio/Chado# perl /usr/local/bin/gmod_make_cvtermpath.pl 
Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: /usr/local/lib/perl5/site_perl/5.12.1/x86_64-linux /usr/local/lib/perl5/site_perl/5.12.1 /usr/local/lib/perl5/5.12.1/x86_64-linux /usr/local/lib/perl5/5.12.1 .) at /usr/local/bin/gmod_make_cvtermpath.pl line 93.
BEGIN failed--compilation aborted at /usr/local/bin/gmod_make_cvtermpath.pl line 93.


Much thanks,
Andrew McArthur

------
Andrew G. McArthur, Ph.D.
Bioinformatics Consulting Services
Phone: 905.296.3252, Mobile: 905.745.2794, Fax: 647.439.0829
AIM: [hidden email], Skype: agmcarthur




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Re: gmod_make_cvtermpath.pl

Scott Cain
Hi Andrew,

It looks to me like you have a few problems, stemming from the first.
First, you appear to have two perls installed: one at
/usr/local/bin/perl and one at /usr/bin/perl.  The script is using
/usr/bin/perl by default (you could edit it in place to point to the
other one if you prefer that one).  Each of your perls are missing
modules; my guess is that some of the time when you install modules,
you're using one perl and sometimes the other, and as a result,
neither has all of the modules needed.

Scott


On Wed, Jul 14, 2010 at 3:11 PM, Andrew McArthur <[hidden email]> wrote:

> Colleagues,
> We use Chado's cvtermpath table extensively in our work but have hit a hitch
> with the upgrade to Chado 1.1.  It may relate to a Perl version issue.  Here
> is what we have so far, any ideas?
>
> root@arpcard-server:/usr/share/perl5/Bio/Chado#
> /usr/local/bin/gmod_make_cvtermpath.pl
> Base class package "DBIx::Class::Schema" is empty.
>     (Perhaps you need to 'use' the module which defines that package first,
>     or make that module available in @INC (@INC contains: /etc/perl
> /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1 /usr/lib/perl5
> /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
> /usr/local/lib/site_perl .).
>  at /usr/share/perl5/Bio/Chado/Schema.pm line 9
> BEGIN failed--compilation aborted at /usr/share/perl5/Bio/Chado/Schema.pm
> line 9.
> Compilation failed in require at /usr/local/bin/gmod_make_cvtermpath.pl line
> 91.
> BEGIN failed--compilation aborted at /usr/local/bin/gmod_make_cvtermpath.pl
> line 91.
> root@arpcard-server:/usr/share/perl5/Bio/Chado# which perl
> /usr/local/bin/perl
> root@arpcard-server:/usr/share/perl5/Bio/Chado# perl
> /usr/local/bin/gmod_make_cvtermpath.pl
> Can't locate Bio/GMOD/Config.pm in @INC (@INC contains:
> /usr/local/lib/perl5/site_perl/5.12.1/x86_64-linux
> /usr/local/lib/perl5/site_perl/5.12.1
> /usr/local/lib/perl5/5.12.1/x86_64-linux /usr/local/lib/perl5/5.12.1 .) at
> /usr/local/bin/gmod_make_cvtermpath.pl line 93.
> BEGIN failed--compilation aborted at /usr/local/bin/gmod_make_cvtermpath.pl
> line 93.
>
> Much thanks,
> Andrew McArthur
> ------
> Andrew G. McArthur, Ph.D.
> Bioinformatics Consulting Services
> Email: [hidden email], Web: http://mcarthurlab.blogspot.com
> Phone: 905.296.3252, Mobile: 905.745.2794, Fax: 647.439.0829
> AIM: [hidden email], Skype: agmcarthur
>
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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