problem with make ontologies during setup

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

problem with make ontologies during setup

James Lewis
Hi,

Everything up to the make ontologies section of the install guide has worked fine,
and there didn't seem to be a problem with installing the relationship ontology. But
once I try the sequence ontology or the gene ontology, I get the following:

james@james-laptop:~/gmod-1.1$ make ontologies
./Build ontologies
Available ontologies:
[1] Relationship Ontology
[2] Sequence Ontology
[3] Gene Ontology
[4] Chado Feature Properties
[5] Cell Ontology
[6] Plant Ontology

Which ontologies would you like to load (Comma delimited)? [0]  3
fetching files for Gene Ontology
  +http://www.geneontology.org/ontology/gene_ontology.obo
    updated
    loading...Cannot quote a reference at /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 3736.
System call 'stag-storenode.pl -d 'dbi:Pg:dbname=chado;host=localhost;port=5432' --user james 
--password jjlewis  tmp/go/go.oboxml' failed: 256
Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
make: *** [ontologies] Error 2

The first thing I did was to check that all the files involved (that I was aware of) existed, which
they do, and none of them appear empty or something similarly odd.

Any ideas how to fix whatever isn't working here?

Thanks,

-James


------------------------------------------------------------------------------
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
Reply | Threaded
Open this post in threaded view
|

Re: problem with make ontologies during setup

Dave Clements, GMOD Help Desk-3
Hi James,

A few people were getting this error back in January when DBIx::Schema was updated to 0.38.  I think this should have been fixed in DBIx::DBStag 0.12.

Can you check which version of DBIx::DBStag you have installed?

Dave C

On Fri, Jul 2, 2010 at 2:42 PM, James Lewis <[hidden email]> wrote:
Hi,

Everything up to the make ontologies section of the install guide has worked fine,
and there didn't seem to be a problem with installing the relationship ontology. But
once I try the sequence ontology or the gene ontology, I get the following:

james@james-laptop:~/gmod-1.1$ make ontologies
./Build ontologies
Available ontologies:
[1] Relationship Ontology
[2] Sequence Ontology
[3] Gene Ontology
[4] Chado Feature Properties
[5] Cell Ontology
[6] Plant Ontology

Which ontologies would you like to load (Comma delimited)? [0]  3
fetching files for Gene Ontology
  +http://www.geneontology.org/ontology/gene_ontology.obo
    updated
    loading...Cannot quote a reference at /usr/local/share/perl/5.10.0/DBIx/DBStag.pm line 3736.
System call 'stag-storenode.pl -d 'dbi:Pg:dbname=chado;host=localhost;port=5432' --user james 
--password jjlewis  tmp/go/go.oboxml' failed: 256
Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
make: *** [ontologies] Error 2

The first thing I did was to check that all the files involved (that I was aware of) existed, which
they do, and none of them appear empty or something similarly odd.

Any ideas how to fix whatever isn't working here?

Thanks,

-James


------------------------------------------------------------------------------
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




--
===> PLEASE KEEP RESPONSES ON THE LIST <===
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/Calendar
http://gmod.org/wiki/Help_Desk_Feedback


------------------------------------------------------------------------------
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