Re: [Gusdev-gusdev] LoadGoOntology

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

chetna-

which version of CBIL do you have?  (ie, which .tar file did you download?)

can you do this, and send the results.
 ls $PROJECT_HOME/CBIL/Bio/lib/perl/GeneOntologyParser/

steve

Chetna D. Warade wrote:

>Hi Dave,
>
>Thanks for looking into it. As Jonathan said in the previous email, he 
>is right about the fact that LoadGoAssoc uses GeneAssocParser/Parser 
>whereas LoadGoOntology uses GeneOntologyParser/Parser. 
>
>I really appreciate your help. Please do let me know when could I 
>download the new release of CBIL project.
>
>Thanks,
>Chetna
>
>---------Included Message----------
>  
>
>>Date: Fri, 18 Apr 2003 10:51:11 -0400 (EDT)
>>From: "Dave Barkan" <db...@pc...>
>>To: "Chetna D. Warade" <ch...@ug...>
>>Cc: <gus...@li...>
>>Subject: Re: [Gusdev-gusdev] LoadGoOntology
>>
>>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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>>    
>>
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