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From: Chetna D. W. <ch...@ug...> - 2003-04-18 16:12:02
|
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
>>
>>
>>
>>
>> -------------------------------------------------------
>> This sf.net email is sponsored by:ThinkGeek
>> Welcome to geek heaven.
>> http://thinkgeek.com/sf
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>
>
---------End of Included Message----------
|
|
From: Chetna D. W. <ch...@ug...> - 2003-04-18 17:44:55
|
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
>>>>
>>>>
>>>>
>>>>
>>>>-------------------------------------------------------
>>>>This sf.net email is sponsored by:ThinkGeek
>>>>Welcome to geek heaven.
>>>>http://thinkgeek.com/sf
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>
>>>>
>>>
>>>
>>---------End of Included Message----------
>>
>>
>>
>>
>>-------------------------------------------------------
>>This sf.net email is sponsored by:ThinkGeek
>>Welcome to geek heaven.
>>http://thinkgeek.com/sf
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>>
>
>
>
---------End of Included Message----------
|
|
From: Steve F. <st...@pc...> - 2003-04-18 16:32:16
|
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
>>>
>>>
>>>
>>>
>>>-------------------------------------------------------
>>>This sf.net email is sponsored by:ThinkGeek
>>>Welcome to geek heaven.
>>>http://thinkgeek.com/sf
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>>
>>
>>
>---------End of Included Message----------
>
>
>
>
>-------------------------------------------------------
>This sf.net email is sponsored by:ThinkGeek
>Welcome to geek heaven.
>http://thinkgeek.com/sf
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>
|
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