gusdev-gusdev

[Gusdev-gusdev] LoadGoOntology

[Chetna D. W. <ch...@ug...>]

Hi,

I am trying to:
ga GUS::GOPredict::Plugin::LoadGoOntology --usage and I am getting @INC 
error whereas when I run:
ga GUS::GOPredict::Plugin::LoadGoAssoc --usage <--- runs fine!

Following is the error:

[chetna@mango Plugin]$ ga GUS::GOPredict::Plugin::LoadGoOntology 
--usage
Reading properties from /home/gus_home/config/GUS-PluginMgr.prop

ERROR: Can't locate CBIL/Bio/GeneOntologyParser/Parser.pm in @INC (@INC 
contains: /home/gus_home/lib/perl /usr/lib/perl5/5.6.1/i386-linux 
/usr/lib/perl5/5.6.1 /usr/lib/perl5/site_perl/5.6.1/i386-linux 
/usr/lib/perl5/site_perl/5.6.1 /usr/lib/perl5/site_perl/5.6.0/i386-linux 
/usr/lib/perl5/site_perl/5.6.0 /usr/lib/perl5/site_perl 
/usr/lib/perl5/vendor_perl/5.6.1/i386-linux 
/usr/lib/perl5/vendor_perl/5.6.1 /usr/lib/perl5/vendor_perl .) at 
/home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 3.
BEGIN failed--compilation aborted at 
/home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 3.
Compilation failed in require at (eval 1) line 1.


--------------------------- STACK TRACE -------------------------
        
GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
'Can\'t locate CBIL/Bio/GeneOntologyParser/Parser.pm in @INC (@IN...') 
called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 
248
        
GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
'GUS::GOPredict::Plugin::LoadGoOntology') called at 
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 361
        
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
'GUS::GOPredict::Plugin::LoadGoOntology') called at 
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
        
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
'GUS::GOPredict::Plugin::LoadGoOntology') called at 
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
        
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11

Both LoadGoAssoc and LoadGoOntology need 
CBIL/Bio/GeneOntologyParser/Parser.pm but I am wondering why would it 
fail for one and run for other.

Thanks and hope to hear from you'll,
Chetna

[Gusdev-gusdev] LoadGoOntology

[Paul M. <pj...@sa...>]

Hi,

I get an error when running the LoadGoOntology plugin.
It is up-to-date WRT cvs.
I have the CBIL_v1-4-0.tar.gz file, the Store.pm being identical to the 
one in my $GUS_HOME directory path.
Do I need a newer CBIL utilities ?

Wed Jun  9 14:00:09 2004        loading all .ontology files in 
/nfs/team81/pjm/temp/GUS_installation/GO/ in preparation for parsing
Wed Jun  9 14:00:10 2004        parsing all .ontology files in 
preparation for inserting into database
Wed Jun  9 14:00:39 2004        parsing finished; loading ontology into 
database
Can't locate object method "getDescription" via package 
"CBIL::Bio::GeneOntologyParser::Store" (perhaps you forgot to load 
"CBIL::Bio::GeneOntologyParser::Store"?) at 
/nfs/team81/pjm/GUS/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm 
line 452.

Paul.

Re: [Gusdev-gusdev] LoadGoOntology

[Steve F. <st...@pc...>]

paul-

it looks like Dave did not commit his latest changes to cvs.

he'll be in later tofday.

sorry about that,
steve

Paul Mooney wrote:

> Hi,
>
> I get an error when running the LoadGoOntology plugin.
> It is up-to-date WRT cvs.
> I have the CBIL_v1-4-0.tar.gz file, the Store.pm being identical to 
> the one in my $GUS_HOME directory path.
> Do I need a newer CBIL utilities ?
>
> Wed Jun  9 14:00:09 2004        loading all .ontology files in 
> /nfs/team81/pjm/temp/GUS_installation/GO/ in preparation for parsing
> Wed Jun  9 14:00:10 2004        parsing all .ontology files in 
> preparation for inserting into database
> Wed Jun  9 14:00:39 2004        parsing finished; loading ontology 
> into database
> Can't locate object method "getDescription" via package 
> "CBIL::Bio::GeneOntologyParser::Store" (perhaps you forgot to load 
> "CBIL::Bio::GeneOntologyParser::Store"?) at 
> /nfs/team81/pjm/GUS/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm 
> line 452.
>
> Paul.
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: GNOME Foundation
> Hackers Unite!  GUADEC: The world's #1 Open Source Desktop Event.
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Re: [Gusdev-gusdev] LoadGoOntology

[Dave B. <db...@pc...>]

Hey Paul,

I recommitted the relevant files; Steve is in the process of creating the 
new CBIL release.  When he is done, everything should work fine.

Let me know how the LoadGoOntology plugin runs; it is newly refactored.  
It works fine for me but I think you are the first to use it since, so 
good luck ;-)  (There shouldn't be any problems).

Dave

On Wed, 9 Jun 2004, Paul Mooney wrote:

> Hi,
> 
> I get an error when running the LoadGoOntology plugin.
> It is up-to-date WRT cvs.
> I have the CBIL_v1-4-0.tar.gz file, the Store.pm being identical to the 
> one in my $GUS_HOME directory path.
> Do I need a newer CBIL utilities ?
> 
> Wed Jun  9 14:00:09 2004        loading all .ontology files in 
> /nfs/team81/pjm/temp/GUS_installation/GO/ in preparation for parsing
> Wed Jun  9 14:00:10 2004        parsing all .ontology files in 
> preparation for inserting into database
> Wed Jun  9 14:00:39 2004        parsing finished; loading ontology into 
> database
> Can't locate object method "getDescription" via package 
> "CBIL::Bio::GeneOntologyParser::Store" (perhaps you forgot to load 
> "CBIL::Bio::GeneOntologyParser::Store"?) at 
> /nfs/team81/pjm/GUS/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm 
> line 452.
> 
> Paul.
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: GNOME Foundation
> Hackers Unite!  GUADEC: The world's #1 Open Source Desktop Event.
> GNOME Users and Developers European Conference, 28-30th June in Norway
> http://2004/guadec.org
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 

Re: [Gusdev-gusdev] LoadGoOntology

[Steve F. <st...@pc...>]

paul-   i have put version 1.5.0 on the download site  
http://www.cbil.upenn.edu/downloads/CBIL/releases/

dave-  i have added instructions to the cbil wiki.

steve

Dave Barkan wrote:

>Hey Paul,
>
>I recommitted the relevant files; Steve is in the process of creating the 
>new CBIL release.  When he is done, everything should work fine.
>
>Let me know how the LoadGoOntology plugin runs; it is newly refactored.  
>It works fine for me but I think you are the first to use it since, so 
>good luck ;-)  (There shouldn't be any problems).
>
>Dave
>
>On Wed, 9 Jun 2004, Paul Mooney wrote:
>
>  
>
>>Hi,
>>
>>I get an error when running the LoadGoOntology plugin.
>>It is up-to-date WRT cvs.
>>I have the CBIL_v1-4-0.tar.gz file, the Store.pm being identical to the 
>>one in my $GUS_HOME directory path.
>>Do I need a newer CBIL utilities ?
>>
>>Wed Jun  9 14:00:09 2004        loading all .ontology files in 
>>/nfs/team81/pjm/temp/GUS_installation/GO/ in preparation for parsing
>>Wed Jun  9 14:00:10 2004        parsing all .ontology files in 
>>preparation for inserting into database
>>Wed Jun  9 14:00:39 2004        parsing finished; loading ontology into 
>>database
>>Can't locate object method "getDescription" via package 
>>"CBIL::Bio::GeneOntologyParser::Store" (perhaps you forgot to load 
>>"CBIL::Bio::GeneOntologyParser::Store"?) at 
>>/nfs/team81/pjm/GUS/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm 
>>line 452.
>>
>>Paul.
>>
>>
>>
>>-------------------------------------------------------
>>This SF.Net email is sponsored by: GNOME Foundation
>>Hackers Unite!  GUADEC: The world's #1 Open Source Desktop Event.
>>GNOME Users and Developers European Conference, 28-30th June in Norway
>>http://2004/guadec.org
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>    
>>
>
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by: GNOME Foundation
>Hackers Unite!  GUADEC: The world's #1 Open Source Desktop Event.
>GNOME Users and Developers European Conference, 28-30th June in Norway
>http://2004/guadec.org
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

Re: [Gusdev-gusdev] LoadGoOntology

[Jonathan C. <cra...@pc...>]

Hi Chetna-

Chetna D. Warade wrote:
> I am trying to:
> ga GUS::GOPredict::Plugin::LoadGoOntology --usage and I am getting @INC 
> error whereas when I run:
> ga GUS::GOPredict::Plugin::LoadGoAssoc --usage <--- runs fine!
> 
> Following is the error:
> 
> [chetna@mango Plugin]$ ga GUS::GOPredict::Plugin::LoadGoOntology 
> --usage
> Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> 
> ERROR: Can't locate CBIL/Bio/GeneOntologyParser/Parser.pm in @INC (@INC 

I don't know the answer to this, but Dave Barkan has been working actively
on the GO-related plugins, and should be able to shed some light on the
problem.

> Both LoadGoAssoc and LoadGoOntology need 
> CBIL/Bio/GeneOntologyParser/Parser.pm but I am wondering why would it 
> fail for one and run for other.

Are you sure about that?  I just checked what's currently in CVS and
while LoadGoOntology.pm does "use" CBIL::Bio::GeneOntologyParser::Parser,
it looks like LoadGoAssoc uses CBIL::Bio::GeneAssocParser::Parser instead,
which would account for the difference in behavior you're seeing.  Perhaps
you have to download a new version of the CBIL tar file (and perhaps we
first need to generate one!)

Jonathan

-- 
Jonathan Crabtree
Senior Programmer Analyst
CBIL, Center for Bioinformatics
University of Pennsylvania, Philadelphia, PA

Re: [Gusdev-gusdev] LoadGoOntology

[Dave B. <db...@pc...>]

Hi Chetna,

I'm not sure why it's failing on your particular run, but I think the 
first thing to try is downloading a new release of the CBIL project.  The 
GeneOntologyParser has undergone some minor changes recently so it 
definitely couldn't hurt.

Before you do that, we should definitely create a new release.  I will 
talk to Steve about it and let you know when it is safe to proceed.

Thanks,
Dave


On Thu, 17 Apr 2003, Chetna D. Warade wrote:

> Hi,
> 
> I am trying to:
> ga GUS::GOPredict::Plugin::LoadGoOntology --usage and I am getting @INC 
> error whereas when I run:
> ga GUS::GOPredict::Plugin::LoadGoAssoc --usage <--- runs fine!
> 
> Following is the error:
> 
> [chetna@mango Plugin]$ ga GUS::GOPredict::Plugin::LoadGoOntology 
> --usage
> Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> 
> ERROR: Can't locate CBIL/Bio/GeneOntologyParser/Parser.pm in @INC (@INC 
> contains: /home/gus_home/lib/perl /usr/lib/perl5/5.6.1/i386-linux 
> /usr/lib/perl5/5.6.1 /usr/lib/perl5/site_perl/5.6.1/i386-linux 
> /usr/lib/perl5/site_perl/5.6.1 /usr/lib/perl5/site_perl/5.6.0/i386-linux 
> /usr/lib/perl5/site_perl/5.6.0 /usr/lib/perl5/site_perl 
> /usr/lib/perl5/vendor_perl/5.6.1/i386-linux 
> /usr/lib/perl5/vendor_perl/5.6.1 /usr/lib/perl5/vendor_perl .) at 
> /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 3.
> BEGIN failed--compilation aborted at 
> /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 3.
> Compilation failed in require at (eval 1) line 1.
> 
> 
> --------------------------- STACK TRACE -------------------------
>         
> GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
> 'Can\'t locate CBIL/Bio/GeneOntologyParser/Parser.pm in @INC (@IN...') 
> called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 
> 248
>         
> GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
> 'GUS::GOPredict::Plugin::LoadGoOntology') called at 
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 361
>         
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
> 'GUS::GOPredict::Plugin::LoadGoOntology') called at 
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
>         
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
> 'GUS::GOPredict::Plugin::LoadGoOntology') called at 
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
>         
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)', 
> 'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11
> 
> Both LoadGoAssoc and LoadGoOntology need 
> CBIL/Bio/GeneOntologyParser/Parser.pm but I am wondering why would it 
> fail for one and run for other.
> 
> Thanks and hope to hear from you'll,
> Chetna
> 
> 
> 
> 
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