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Re: [Gusdev-gusdev] LoadGoOntology
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From: Chetna D. W. <ch...@ug...> - 2003-04-18 17:44:55
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Hi Steve,
1)
Here's the result:
[chetna@mango chetna]$ cd
/home/projects/CBIL/Bio/lib/perl/GeneOntolgyParser/
[chetna@mango GeneOntolgyParser]$ ls
ParseDemo.pm Parser.pm Store.pm Term.pm
[chetna@mango GeneOntolgyParser]$ env | grep PROJECT_HOME
PROJECT_HOME=/home/projects
[chetna@mango GeneOntolgyParser]$
2) I downloaded CBIL_v1-2-0.tar on Mar 12th.
Thanks,
Chetna
---------Included Message----------
>Date: Fri, 18 Apr 2003 12:37:14 -0400
>From: "Steve Fischer" <st...@pc...>
>Cc: "Dave Barkan" <db...@pc...>,
<gus...@li...>
>Subject: Re: [Gusdev-gusdev] LoadGoOntology
>
>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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>>>>
>>>>
>>>>
>>>
>>>
>>---------End of Included Message----------
>>
>>
>>
>>
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>>
>
>
>
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