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From: Thiago S. <ma...@gm...> - 2005-07-22 18:03:14
|
Hello all, I have a simple question..... How can I load GenBank file using plugins ?=20 --=20 Thiago Seito Satake !! Tenha um bom dia !! Tel: (041) 990-55422 |
|
From: <fab...@de...> - 2005-07-21 14:17:36
|
Hello all, We're trying to load data into GUS 3.5 using those XML files in boostrap = data: http://www.gusdb.org/wiki/index.php/Bootstrap%20data We noticed that many of them are now incompatible with the new plugins ve= rsion and thus we had to make changes in some of those files.=20 We was wondering if you have a new compatible version of these XML files = to be able to make the load process without problems.=20 Some files that we would like to have is for: * ExternalDatabase * ExternalDatabaseRelease * ExternalDatabaseLink * and others too...=20 If someone has these new versions of XML files, is it possible to give us= an link to we get them? Thanks a lot, Fabr=EDcio. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. |
|
From: steve <sfi...@pc...> - 2005-07-20 21:04:55
|
junmin- please file this with the tracker. we don't handle bugs through email anymore. go to gusdb.org thanks, steve Junmin Liu wrote: > Hi, > looks like there is bug when you tried to build GUS/Model at the first > place. The build.xml doesn't declare the dependence of "Model" target > on "Supportted", however the bin/generateGusObjects use the > GUS::Supported::GusConfig. > > Here is the error message. > [junmin@hera rad]$ build GUS/Model install -append > [WritePropertyFiles] Jul 20, 2005 2:05:33 PM > org.gusdb.install.WritePropertyFileTask writeGusProp > [WritePropertyFiles] INFO: Skipping creation of GUS_CONFIG_FILE > /home/junmin/gus35/.gus.properties -- already exists > [WritePropertyFiles] Jul 20, 2005 2:05:33 PM > org.gusdb.install.WritePropertyFileTask writeInstallProp > [WritePropertyFiles] INFO: Recreating install.prop file > [WritePropertyFiles] Jul 20, 2005 2:05:33 PM > org.gusdb.install.WritePropertyFileTask writePluginProp > [WritePropertyFiles] INFO: Recreating GUS-PluginMgr.prop file > [copy] Copying 1 file to /www/rad/gushome/config > [copy] Copying 1 file to /www/rad/gushome/config > [echo] . > [echo] Installing GUS/ObjRelP > [mkdir] Created dir: /www/rad/gushome/bin > [copy] Copying 3 files to /www/rad/gushome/bin > [mkdir] Created dir: /www/rad/gushome/lib/perl/GUS/ObjRelP > [copy] Copying 18 files to /www/rad/gushome/lib/perl/GUS/ObjRelP > [mkdir] Created dir: /www/rad/gushome/doc/GUS/ObjRelP > [copy] Copying 3 files to /www/rad/gushome/doc/GUS/ObjRelP > [mkdir] Created dir: /www/rad/gushome/lib/perl/GUS/Model/Core > [mkdir] Created dir: /www/rad/gushome/lib/perl/GUS/Model/DoTS > [mkdir] Created dir: /www/rad/gushome/lib/perl/GUS/Model/RAD > [mkdir] Created dir: /www/rad/gushome/lib/perl/GUS/Model/SRes > [mkdir] Created dir: /www/rad/gushome/lib/perl/GUS/Model/TESS > [mkdir] Created dir: /www/rad/gushome/lib/perl/GUS/Model/PROT > [mkdir] Created dir: /www/rad/gushome/lib/perl/GUS/Model/Study > [echo] generating Perl Objects > [exec] Can't locate GUS/Supported/GusConfig.pm in @INC > ............. > > couple thoughts: > 1. One of obvious solution is to declare the dependence of "Model" on > "Supported", which I did and it runs OK. > > 2. While maybe it is bad idea, since "Model" should not depend on > "Supported". So maybe we should move the GusConfig.pm inside other > component like "ObjRelP". > > 3. Say in the documentation that we should not run "build GUS/Model > install" at first place. > > > I will file a bug in the tracker. > ---junmin > > > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Michael S. <msa...@pc...> - 2005-07-20 20:52:21
|
All, The attached preliminary report contains details about changes between 3.0 and 3.5. The next task for upgrading will be to validate the report, and to decided how to migrate data in dropped and/or changed tables. This is produced using the dbaCompareSchema utility that is on the trunk. CBIL Note: This is based on the 3.0 schema from the old CVS, not CBILBLD, so there are many changes here that have already been made in CBILBLD. I'll run a separate CBILBLD -> 3.5 change report soon. --Mike |
|
From: Thiago S. <ma...@gm...> - 2005-07-20 19:00:37
|
Hello all, we're trying to register some plugins into gus using the command: ga +create GUS::Community::Plugin::GBParser --commit We received some outputs: Database version does not match required version for Plugin. Database Version: 3.5 Plugin Version: HASH(0xa02ea20) - or -=20 ga +create GUS::Community::Plugin::LoadPfam --commit Database version does not match required version for Plugin. Database Version: 3.5 Plugin Version: HASH(0xa02ea20) Does anyone have already had a problem like this ?=20 Is it something wrong with our Plugin ? --=20 Thiago Seito Satake !! Tenha um bom dia !! Tel: (041) 990-55422 |
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From: Junmin L. <ju...@pc...> - 2005-07-20 18:32:45
|
Hi,
looks like there is bug when you tried to build GUS/Model at the first
place. The build.xml doesn't declare the dependence of "Model" target on
"Supportted", however the bin/generateGusObjects use the
GUS::Supported::GusConfig.
Here is the error message.
[junmin@hera rad]$ build GUS/Model install -append
[WritePropertyFiles] Jul 20, 2005 2:05:33 PM
org.gusdb.install.WritePropertyFileTask writeGusProp
[WritePropertyFiles] INFO: Skipping creation of GUS_CONFIG_FILE
/home/junmin/gus35/.gus.properties -- already exists
[WritePropertyFiles] Jul 20, 2005 2:05:33 PM
org.gusdb.install.WritePropertyFileTask writeInstallProp
[WritePropertyFiles] INFO: Recreating install.prop file
[WritePropertyFiles] Jul 20, 2005 2:05:33 PM
org.gusdb.install.WritePropertyFileTask writePluginProp
[WritePropertyFiles] INFO: Recreating GUS-PluginMgr.prop file
[copy] Copying 1 file to /www/rad/gushome/config
[copy] Copying 1 file to /www/rad/gushome/config
[echo] .
[echo] Installing GUS/ObjRelP
[mkdir] Created dir: /www/rad/gushome/bin
[copy] Copying 3 files to /www/rad/gushome/bin
[mkdir] Created dir: /www/rad/gushome/lib/perl/GUS/ObjRelP
[copy] Copying 18 files to /www/rad/gushome/lib/perl/GUS/ObjRelP
[mkdir] Created dir: /www/rad/gushome/doc/GUS/ObjRelP
[copy] Copying 3 files to /www/rad/gushome/doc/GUS/ObjRelP
[mkdir] Created dir: /www/rad/gushome/lib/perl/GUS/Model/Core
[mkdir] Created dir: /www/rad/gushome/lib/perl/GUS/Model/DoTS
[mkdir] Created dir: /www/rad/gushome/lib/perl/GUS/Model/RAD
[mkdir] Created dir: /www/rad/gushome/lib/perl/GUS/Model/SRes
[mkdir] Created dir: /www/rad/gushome/lib/perl/GUS/Model/TESS
[mkdir] Created dir: /www/rad/gushome/lib/perl/GUS/Model/PROT
[mkdir] Created dir: /www/rad/gushome/lib/perl/GUS/Model/Study
[echo] generating Perl Objects
[exec] Can't locate GUS/Supported/GusConfig.pm in @INC
.............
couple thoughts:
1. One of obvious solution is to declare the dependence of "Model" on
"Supported", which I did and it runs OK.
2. While maybe it is bad idea, since "Model" should not depend
on "Supported". So maybe we should move the GusConfig.pm inside other
component like "ObjRelP".
3. Say in the documentation that we should not run "build GUS/Model
install" at first place.
I will file a bug in the tracker.
---junmin
|
|
From: Michael S. <msa...@pc...> - 2005-07-20 12:08:17
|
Hi Fabricio, There is an bug for this when using it with Postgres: https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=3D41 It appears to be an issue at the database level-- Postgres doesn't seem to like some of the foreign key constraints. I'll reopen the bug since you've confirmed it as a second group. --Mike On 7/19/05 9:32 PM, "fab...@de..." <fab...@de...> wrote= : > Hello all,=20 >=20 > we're trying to load some data into gus using the several plugins. At the > moment > we're trying to insert the GeneOntology files: >=20 > * process.ontology > * component.ontology > * function.ontology > * GO.defs >=20 > To do this we're using the command: >=20 > ga GUS::Supported::Plugin::InsertGeneOntology --filePath > /usr/local/GUS/GUS35/gus_home/boostrap/gontology --functionExtDbName 'GO > Function' --processExtDbName 'GO Process' --componentExtDbName 'GO Compon= ent' > --createRelease --commit >=20 > and seems to be ok. We received some outputs from the execution process a= nd it > stops after "Loading sres.goterm"... something like this. >=20 > And remains at that point until now... The proccess is running for a many > times > and never finish (as we can see by the outputs). >=20 > Having seeing our machine load average it shows that the machine isn't > overloaded, but the ga process is still running. >=20 > Does anyone have already had a problem like this? Is it something wrong w= ith > our > Plugin command above? >=20 > Thanks a lot, >=20 > Fabr=EDcio. >=20 > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. >=20 >=20 > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Steve F. <sfi...@pc...> - 2005-07-20 05:36:36
|
folks- the GUS project, the WDK and others are now using Subversion (SVN) instead of CVS as its source code repository. it is very useful to be able to integrate repository commands into emacs, so you can commit the file you have just changed or compare versions. CVS offers a menu that makes this very easy. SVN has an emacs plugin that is not quite as elegant, but, offers the important tasks. i have put out a wiki page describing how to use it. it is available at http://www.gusdb.org/wiki/index.php/SubversionInEmacs steve |
|
From: Steve F. <sfi...@pc...> - 2005-07-20 02:09:29
|
gus folks- we at cbil have made a first pass at categorizing the tables of GUS (still waiting for the PROT schema, which will be soon). please take a look and send comments. its on the gus wiki: http://www.gusdb.org/wiki specifically: http://www.gusdb.org/wiki/index.php/TableCategories also, we are in the process of upgrading the schema browser so it can: - display categories - display the tables sorted by categories - allow gus users registered for the gus wiki to add and or edit table and row documentation steve |
|
From: <fab...@de...> - 2005-07-20 02:09:28
|
Hello all,=20 we're trying to load some data into gus using the several plugins. At the= moment we're trying to insert the GeneOntology files: * process.ontology=20 * component.ontology=20 * function.ontology=20 * GO.defs To do this we're using the command: ga GUS::Supported::Plugin::InsertGeneOntology --filePath /usr/local/GUS/GUS35/gus_home/boostrap/gontology --functionExtDbName 'GO Function' --processExtDbName 'GO Process' --componentExtDbName 'GO Compon= ent' --createRelease --commit and seems to be ok. We received some outputs from the execution process a= nd it stops after "Loading sres.goterm"... something like this. And remains at that point until now... The proccess is running for a many= times and never finish (as we can see by the outputs).=20 Having seeing our machine load average it shows that the machine isn't overloaded, but the ga process is still running. Does anyone have already had a problem like this? Is it something wrong w= ith our Plugin command above? Thanks a lot, Fabr=EDcio. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. |
|
From: Steve F. <sfi...@pc...> - 2005-07-19 21:30:46
|
yes, ed wrote the plugin and recently i did some refactoring.
the toxodb project will be deploying it soon in its new refactored
state. its one of there priorities.
so, we should be able to move it to Supported soon, and then the
GBParser can be considered retired.
steve
Chris Stoeckert wrote:
> Indeed, the plan is to replace with something based on BioPerl
> parsers and as we heard at the GUS workshop, Ed and Steve have been
> working on this. Any update from you guys?
>
> Chris
>
> On Jul 19, 2005, at 5:08 PM, an...@ma... wrote:
>
>> Yeah, that was me, but frankly I do not have the time to work on
>> this. I gave
>> ownership of this to Debbie Pinney a few years back, and she had put
>> in fixes
>> over time, but it is a known issues that we MUST replace this plugin
>> with
>> something based on BioPerl parsers.
>>
>> -angel
>> Quoting Jian Lu <jl...@vb...>:
>>
>>
>>> Mike,
>>>
>>> Thank you for response and suggestion. Since GBParser has been heavily
>>> used by community to load NCBI data, I think a high priority should be
>>> considered to support GBParser. Who is the original author?
>>>
>>> Jian
>>>
>>> Michael Saffitz wrote:
>>>
>>>
>>>> Hi Jian,
>>>>
>>>> Community plugins are provided as a point of reference, but are not
>>>> generally compatible with the current schema and app framework.
>>>> They are
>>>> not expected to work without (sometimes significant) modification.
>>>>
>>>> Be cautious for community plugins that do register-- they may have
>>>> runtime
>>>> errors or worse, run without error but improperly load data.
>>>>
>>>> If there is a specific community plugin you'd like to use, I suggest
>>>>
>>> working
>>>
>>>> with the original plugin author or other interested parties in the
>>>>
>>> community
>>>
>>>> to review, update, and fix the plugin to the Plugin standard, and
>>>> then it
>>>> can become a supported plugin!
>>>>
>>>> Thanks,
>>>>
>>>> Mike
>>>>
>>>>
>>>>
>>>>
>>>> On 7/19/05 4:08 PM, "Jian Lu" <jl...@vb...> wrote:
>>>>
>>>>
>>>>
>>>>
>>>>> I am trying to register GUS 3.5 plugins. The 'Supported' plugins are
>>>>> successful, but 'Community' plugins all failed to register at the
>>>>> first
>>>>> time run because most plugins have empty database versions like this
>>>>> requiredDbVersion => {}. After adding database version 3.5, some got
>>>>> registered, but majorities still failed (see below error log). I
>>>>> corrected some like GBParser and registered them.
>>>>>
>>>>> ###################### ERROR LOG ##############################
>>>>> GUS::Community::Plugin::AnnotatorsInterfaceSubmitter is already
>>>>>
>>> registered.
>>>
>>>>> Use '+update' if you need to register a new version.
>>>>> Tue Jul 19 08:48:29 2005 INFO Plugin
>>>>> GUS::Community::Plugin::AssembliesWithflCD registered with cvs
>>>>> revision
>>>>> '2924'
>>>>>
>>>>> Can't locate GUS/RAD/FileTranslator.pm in @INC (@INC contains:
>>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/
>>>>> site_perl/5.8.0
>>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> BatchArrayResultLoad
>>>>
>>>>> er.pm
>>>>> line 20.
>>>>> BEGIN failed--compilation aborted at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> BatchArrayResultLoad
>>>>
>>>>> er.pm
>>>>> line 20.
>>>>> Compilation failed in require at (eval 8) line 1.
>>>>>
>>>>> Tue Jul 19 08:48:31 2005 INFO Plugin
>>>>> GUS::Community::Plugin::DeleteFromTable registered with cvs revision
>>>>>
>>> '2924'
>>>
>>>>> Tue Jul 19 08:48:32 2005 INFO Plugin
>>>>> GUS::Community::Plugin::DeleteSimilarities registered with cvs
>>>>> revision
>>>>> '2924'
>>>>> Tue Jul 19 08:48:35 2005 INFO Plugin
>>>>> GUS::Community::Plugin::DupNRDBRows registered with cvs revision
>>>>> '2924'
>>>>>
>>>>> Can't locate GUS/Model/SRes/ExternalDatabaseKeyword.pm in @INC (@INC
>>>>> contains: /home/brcgusts/GUS/gus_home/lib/perl
>>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/
>>>>> site_perl/5.8.0
>>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>>> GBParser.pm
>>>>> line 43.
>>>>> BEGIN failed--compilation aborted at
>>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>>> GBParser.pm
>>>>> line 43.
>>>>> Compilation failed in require at (eval 8) line 1.
>>>>>
>>>>>
>>>>> Can't locate GUS/Model/RAD3/Study.pm in @INC (@INC contains:
>>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/
>>>>> site_perl/5.8.0
>>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> GenePixStudyModuleIL
>>>>
>>>>> oader.pm
>>>>> line 13.
>>>>> BEGIN failed--compilation aborted at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> GenePixStudyModuleIL
>>>>
>>>>> oader.pm
>>>>> line 13.
>>>>> Compilation failed in require at (eval 8) line 1.
>>>>>
>>>>> GUSLOGS ENV:
>>>>> Tue Jul 19 08:48:38 2005 INFO Plugin
>>>>> GUS::Community::Plugin::GenericParser2Gus registered with cvs
>>>>> revision
>>>>> '2924'
>>>>> Tue Jul 19 08:48:39 2005 INFO Plugin
>>>>> GUS::Community::Plugin::IdentifyAndLoadSnpsFromAssemblies registered
>>>>> with cvs revision '2924'
>>>>> String found where operator expected at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> ImportPlasmoDBAAFeat
>>>>
>>>>> ures.pm
>>>>> line 615, near "'prediction_algorithm_id'"
>>>>> (Missing semicolon on previous line?)
>>>>>
>>>>> syntax error at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> ImportPlasmoDBAAFeat
>>>>
>>>>> ures.pm
>>>>> line 615, near "'prediction_algorithm_id'"
>>>>> Global symbol "$motif_id" requires explicit package name at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> ImportPlasmoDBAAFeat
>>>>
>>>>> ures.pm
>>>>> line 616.
>>>>> Global symbol "$score" requires explicit package name at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> ImportPlasmoDBAAFeat
>>>>
>>>>> ures.pm
>>>>> line 618.
>>>>> Global symbol "%hash" requires explicit package name at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> ImportPlasmoDBAAFeat
>>>>
>>>>> ures.pm
>>>>> line 621.
>>>>> Global symbol "$start" requires explicit package name at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> ImportPlasmoDBAAFeat
>>>>
>>>>> ures.pm
>>>>> line 621.
>>>>> Global symbol "$stop" requires explicit package name at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> ImportPlasmoDBAAFeat
>>>>
>>>>> ures.pm
>>>>> line 621.
>>>>> Global symbol "$motif_id" requires explicit package name at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> ImportPlasmoDBAAFeat
>>>>
>>>>> ures.pm
>>>>> line 635.
>>>>> Global symbol "$score" requires explicit package name at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> ImportPlasmoDBAAFeat
>>>>
>>>>> ures.pm
>>>>> line 636.
>>>>> Global symbol "$motif_id" requires explicit package name at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> ImportPlasmoDBAAFeat
>>>>
>>>>> ures.pm
>>>>> line 637.
>>>>> Global symbol "$pf" requires explicit package name at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> ImportPlasmoDBAAFeat
>>>>
>>>>> ures.pm
>>>>> line 638.
>>>>> Global symbol "$info" requires explicit package name at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> ImportPlasmoDBAAFeat
>>>>
>>>>> ures.pm
>>>>> line 642.
>>>>> Global symbol "$score" requires explicit package name at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> ImportPlasmoDBAAFeat
>>>>
>>>>> ures.pm
>>>>> line 644.
>>>>> Global symbol "$start" requires explicit package name at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> ImportPlasmoDBAAFeat
>>>>
>>>>> ures.pm
>>>>> line 644.
>>>>> Global symbol "$stop" requires explicit package name at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> ImportPlasmoDBAAFeat
>>>>
>>>>> ures.pm
>>>>> line 644.
>>>>> Global symbol "$motif_id" requires explicit package name at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> ImportPlasmoDBAAFeat
>>>>
>>>>> ures.pm
>>>>> line 644.
>>>>> Global symbol "$pf" requires explicit package name at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> ImportPlasmoDBAAFeat
>>>>
>>>>> ures.pm
>>>>> line 648.
>>>>> syntax error at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> ImportPlasmoDBAAFeat
>>>>
>>>>> ures.pm
>>>>> line 656, near "}"
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> ImportPlasmoDBAAFeat
>>>>
>>>>> ures.pm
>>>>> has too many errors.
>>>>> Compilation failed in require at (eval 8) line 1.
>>>>>
>>>>> Tue Jul 19 08:48:42 2005 INFO Plugin
>>>>> GUS::Community::Plugin::ImportPlasmoDBPrediction registered with cvs
>>>>> revision '2924'
>>>>> Tue Jul 19 08:48:44 2005 INFO Plugin
>>>>> GUS::Community::Plugin::InsertDbRefAndDbRefNASequence registered
>>>>> with
>>>>> cvs revision '2924'
>>>>> Tue Jul 19 08:48:46 2005 INFO Plugin
>>>>> GUS::Community::Plugin::InsertDbRefAndDbRefNaSequenceGeneral
>>>>> registered
>>>>> with cvs revision '2924'
>>>>> Tue Jul 19 08:48:47 2005 INFO Plugin
>>>>> GUS::Community::Plugin::InsertNAFeatureComment registered with cvs
>>>>> revision '2924'
>>>>>
>>>>> Can't locate object method "new" via package
>>>>> "GUS::Community::Plugin::InsertOntologyEntry" at (eval 8) line 1.
>>>>>
>>>>>
>>>>> Can't locate object method "new" via package
>>>>> "GUS::Community::Plugin::InsertOntologyRelationshipType" at (eval
>>>>> 8) line
>>>>>
>>> 1.
>>>
>>>>>
>>>>>
>>>>> Can't locate object method "new" via package
>>>>> "GUS::Community::Plugin::InsertOntologyTermType" at (eval 8) line 1.
>>>>>
>>>>>
>>>>> Can't locate object method "new" via package
>>>>> "GUS::Community::Plugin::InsertPhylogeneticProfiles" at (eval 8)
>>>>> line 1.
>>>>>
>>>>>
>>>>> Can't locate XML/Simple.pm in @INC (@INC contains:
>>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/
>>>>> site_perl/5.8.0
>>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> InsertSeqsAndFeature
>>>>
>>>>> s.pm
>>>>> line 6.
>>>>> BEGIN failed--compilation aborted at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> InsertSeqsAndFeature
>>>>
>>>>> s.pm
>>>>> line 6.
>>>>> Compilation failed in require at (eval 8) line 1.
>>>>>
>>>>> Tue Jul 19 08:48:53 2005 INFO Plugin
>>>>> GUS::Community::Plugin::LoadBLATAlignments registered with cvs
>>>>> revision
>>>>> '2924'
>>>>> Tue Jul 19 08:48:54 2005 INFO Plugin
>>>>> GUS::Community::Plugin::LoadBlastSimilaritiesPK registered with cvs
>>>>> revision '2924'
>>>>> Tue Jul 19 08:48:56 2005 INFO Plugin
>>>>> GUS::Community::Plugin::LoadDocumentation registered with cvs
>>>>> revision
>>>>> '2924'
>>>>> Tue Jul 19 08:48:57 2005 INFO Plugin
>>>>> GUS::Community::Plugin::LoadEnzymeDatabase registered with cvs
>>>>> revision
>>>>> '2924'
>>>>>
>>>>> Can't locate object method "new" via package
>>>>> "GUS::Community::Plugin::LoadFromdbESTMirror" at (eval 8) line 1.
>>>>>
>>>>>
>>>>> Can't locate XML/Simple.pm in @INC (@INC contains:
>>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/
>>>>> site_perl/5.8.0
>>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> LoadGeneFeaturesFrom
>>>>
>>>>> XML.pm
>>>>> line 16.
>>>>> BEGIN failed--compilation aborted at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> LoadGeneFeaturesFrom
>>>>
>>>>> XML.pm
>>>>> line 16.
>>>>> Compilation failed in require at (eval 8) line 1.
>>>>>
>>>>> Tue Jul 19 08:49:00 2005 INFO Plugin
>>>>> GUS::Community::Plugin::LoadGenomeGaps registered with cvs
>>>>> revision '2924'
>>>>>
>>>>> Can't locate GUS/Model/RAD3/SAGETag.pm in @INC (@INC contains:
>>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/
>>>>> site_perl/5.8.0
>>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> LoadGenomicSageData.
>>>>
>>>>> pm
>>>>> line 11.
>>>>> BEGIN failed--compilation aborted at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> LoadGenomicSageData.
>>>>
>>>>> pm
>>>>> line 11.
>>>>> Compilation failed in require at (eval 8) line 1.
>>>>>
>>>>> Tue Jul 19 08:49:03 2005 INFO Plugin
>>>>> GUS::Community::Plugin::LoadHspsOnly registered with cvs revision
>>>>> '2924'
>>>>> Tue Jul 19 08:49:04 2005 INFO Plugin
>>>>> GUS::Community::Plugin::LoadMutualInformationScores registered
>>>>> with cvs
>>>>> revision '2924'
>>>>> Tue Jul 19 08:49:05 2005 INFO Plugin
>>>>> GUS::Community::Plugin::LoadPfam registered with cvs revision '2924'
>>>>> GUS::Community::Plugin::LoadSageResults is already registered.
>>>>> Use '+update' if you need to register a new version.
>>>>>
>>>>> Can't locate GUS/Model/RAD3/Study.pm in @INC (@INC contains:
>>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/
>>>>> site_perl/5.8.0
>>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> MAS5StudyModuleILoad
>>>>
>>>>> er.pm
>>>>> line 12.
>>>>> BEGIN failed--compilation aborted at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> MAS5StudyModuleILoad
>>>>
>>>>> er.pm
>>>>> line 12.
>>>>> Compilation failed in require at (eval 8) line 1.
>>>>>
>>>>> Tue Jul 19 08:49:09 2005 INFO Plugin
>>>>> GUS::Community::Plugin::MakeBestSimilarityPair registered with cvs
>>>>> revision '2924'
>>>>> Tue Jul 19 08:49:10 2005 INFO Plugin
>>>>> GUS::Community::Plugin::MakeDtd registered with cvs revision '2924'
>>>>> Tue Jul 19 08:49:11 2005 INFO Plugin
>>>>> GUS::Community::Plugin::MakeIndexWordLink registered with cvs
>>>>> revision
>>>>> '2924'
>>>>> Tue Jul 19 08:49:12 2005 INFO Plugin
>>>>> GUS::Community::Plugin::MakeIndexWordSimLink registered with cvs
>>>>> revision '2924'
>>>>> Tue Jul 19 08:49:13 2005 INFO Plugin
>>>>> GUS::Community::Plugin::OrthologGroupsMCL registered with cvs
>>>>> revision
>>>>> '2924'
>>>>>
>>>>> Can't locate GUS/Model/RAD3/Quantification.pm in @INC (@INC
>>>>> contains:
>>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/
>>>>> site_perl/5.8.0
>>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> SimpleArrayResultLoa
>>>>
>>>>> der.pm
>>>>> line 28.
>>>>> BEGIN failed--compilation aborted at
>>>>>
>>>
>>>
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> SimpleArrayResultLoa
>>>>
>>>>> der.pm
>>>>> line 28.
>>>>> Compilation failed in require at (eval 8) line 1.
>>>>>
>>>>> Tue Jul 19 08:49:15 2005 INFO Plugin
>>>>> GUS::Community::Plugin::UpdateNASequences registered with cvs
>>>>> revision
>>>>> '2924'
>>>>>
>>>>> Can't locate V.pm in @INC (@INC contains:
>>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/
>>>>> site_perl/5.8.0
>>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>>> XdbLister.pm
>>>>> line 10.
>>>>> BEGIN failed--compilation aborted at
>>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>>> XdbLister.pm
>>>>> line 10.
>>>>> Compilation failed in require at (eval 8) line 1.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -------------------------------------------------------
>>>>> SF.Net email is sponsored by: Discover Easy Linux Migration
>>>>> Strategies
>>>>> from IBM. Find simple to follow Roadmaps, straightforward articles,
>>>>> informative Webcasts and more! Get everything you need to get up to
>>>>> speed, fast. http://ads.osdn.com/? ad_id=7477&alloc_id=16492&op=click
>>>>> _______________________________________________
>>>>> Gusdev-gusdev mailing list
>>>>> Gus...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
>>> from IBM. Find simple to follow Roadmaps, straightforward articles,
>>> informative Webcasts and more! Get everything you need to get up to
>>> speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>
>>
>> --
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
>> from IBM. Find simple to follow Roadmaps, straightforward articles,
>> informative Webcasts and more! Get everything you need to get up to
>> speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
> speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
|
|
From: Chris S. <sto...@pc...> - 2005-07-19 21:17:32
|
Indeed, the plan is to replace with something based on BioPerl
parsers and as we heard at the GUS workshop, Ed and Steve have been
working on this. Any update from you guys?
Chris
On Jul 19, 2005, at 5:08 PM, an...@ma... wrote:
> Yeah, that was me, but frankly I do not have the time to work on
> this. I gave
> ownership of this to Debbie Pinney a few years back, and she had
> put in fixes
> over time, but it is a known issues that we MUST replace this
> plugin with
> something based on BioPerl parsers.
>
> -angel
> Quoting Jian Lu <jl...@vb...>:
>
>
>> Mike,
>>
>> Thank you for response and suggestion. Since GBParser has been
>> heavily
>> used by community to load NCBI data, I think a high priority
>> should be
>> considered to support GBParser. Who is the original author?
>>
>> Jian
>>
>> Michael Saffitz wrote:
>>
>>
>>> Hi Jian,
>>>
>>> Community plugins are provided as a point of reference, but are not
>>> generally compatible with the current schema and app framework.
>>> They are
>>> not expected to work without (sometimes significant) modification.
>>>
>>> Be cautious for community plugins that do register-- they may
>>> have runtime
>>> errors or worse, run without error but improperly load data.
>>>
>>> If there is a specific community plugin you'd like to use, I suggest
>>>
>> working
>>
>>> with the original plugin author or other interested parties in the
>>>
>> community
>>
>>> to review, update, and fix the plugin to the Plugin standard, and
>>> then it
>>> can become a supported plugin!
>>>
>>> Thanks,
>>>
>>> Mike
>>>
>>>
>>>
>>>
>>> On 7/19/05 4:08 PM, "Jian Lu" <jl...@vb...> wrote:
>>>
>>>
>>>
>>>
>>>> I am trying to register GUS 3.5 plugins. The 'Supported' plugins
>>>> are
>>>> successful, but 'Community' plugins all failed to register at
>>>> the first
>>>> time run because most plugins have empty database versions like
>>>> this
>>>> requiredDbVersion => {}. After adding database version 3.5, some
>>>> got
>>>> registered, but majorities still failed (see below error log). I
>>>> corrected some like GBParser and registered them.
>>>>
>>>> ###################### ERROR LOG ##############################
>>>> GUS::Community::Plugin::AnnotatorsInterfaceSubmitter is already
>>>>
>> registered.
>>
>>>> Use '+update' if you need to register a new version.
>>>> Tue Jul 19 08:48:29 2005 INFO Plugin
>>>> GUS::Community::Plugin::AssembliesWithflCD registered with cvs
>>>> revision
>>>> '2924'
>>>>
>>>> Can't locate GUS/RAD/FileTranslator.pm in @INC (@INC contains:
>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/
>>>> site_perl/5.8.0
>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> BatchArrayResultLoad
>>>
>>>> er.pm
>>>> line 20.
>>>> BEGIN failed--compilation aborted at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> BatchArrayResultLoad
>>>
>>>> er.pm
>>>> line 20.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>> Tue Jul 19 08:48:31 2005 INFO Plugin
>>>> GUS::Community::Plugin::DeleteFromTable registered with cvs
>>>> revision
>>>>
>> '2924'
>>
>>>> Tue Jul 19 08:48:32 2005 INFO Plugin
>>>> GUS::Community::Plugin::DeleteSimilarities registered with cvs
>>>> revision
>>>> '2924'
>>>> Tue Jul 19 08:48:35 2005 INFO Plugin
>>>> GUS::Community::Plugin::DupNRDBRows registered with cvs revision
>>>> '2924'
>>>>
>>>> Can't locate GUS/Model/SRes/ExternalDatabaseKeyword.pm in @INC
>>>> (@INC
>>>> contains: /home/brcgusts/GUS/gus_home/lib/perl
>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/
>>>> site_perl/5.8.0
>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> GBParser.pm
>>>> line 43.
>>>> BEGIN failed--compilation aborted at
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> GBParser.pm
>>>> line 43.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>>
>>>> Can't locate GUS/Model/RAD3/Study.pm in @INC (@INC contains:
>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/
>>>> site_perl/5.8.0
>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> GenePixStudyModuleIL
>>>
>>>> oader.pm
>>>> line 13.
>>>> BEGIN failed--compilation aborted at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> GenePixStudyModuleIL
>>>
>>>> oader.pm
>>>> line 13.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>> GUSLOGS ENV:
>>>> Tue Jul 19 08:48:38 2005 INFO Plugin
>>>> GUS::Community::Plugin::GenericParser2Gus registered with cvs
>>>> revision
>>>> '2924'
>>>> Tue Jul 19 08:48:39 2005 INFO Plugin
>>>> GUS::Community::Plugin::IdentifyAndLoadSnpsFromAssemblies
>>>> registered
>>>> with cvs revision '2924'
>>>> String found where operator expected at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 615, near "'prediction_algorithm_id'"
>>>> (Missing semicolon on previous line?)
>>>>
>>>> syntax error at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 615, near "'prediction_algorithm_id'"
>>>> Global symbol "$motif_id" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 616.
>>>> Global symbol "$score" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 618.
>>>> Global symbol "%hash" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 621.
>>>> Global symbol "$start" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 621.
>>>> Global symbol "$stop" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 621.
>>>> Global symbol "$motif_id" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 635.
>>>> Global symbol "$score" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 636.
>>>> Global symbol "$motif_id" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 637.
>>>> Global symbol "$pf" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 638.
>>>> Global symbol "$info" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 642.
>>>> Global symbol "$score" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 644.
>>>> Global symbol "$start" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 644.
>>>> Global symbol "$stop" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 644.
>>>> Global symbol "$motif_id" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 644.
>>>> Global symbol "$pf" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 648.
>>>> syntax error at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 656, near "}"
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> has too many errors.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>> Tue Jul 19 08:48:42 2005 INFO Plugin
>>>> GUS::Community::Plugin::ImportPlasmoDBPrediction registered with
>>>> cvs
>>>> revision '2924'
>>>> Tue Jul 19 08:48:44 2005 INFO Plugin
>>>> GUS::Community::Plugin::InsertDbRefAndDbRefNASequence registered
>>>> with
>>>> cvs revision '2924'
>>>> Tue Jul 19 08:48:46 2005 INFO Plugin
>>>> GUS::Community::Plugin::InsertDbRefAndDbRefNaSequenceGeneral
>>>> registered
>>>> with cvs revision '2924'
>>>> Tue Jul 19 08:48:47 2005 INFO Plugin
>>>> GUS::Community::Plugin::InsertNAFeatureComment registered with cvs
>>>> revision '2924'
>>>>
>>>> Can't locate object method "new" via package
>>>> "GUS::Community::Plugin::InsertOntologyEntry" at (eval 8) line 1.
>>>>
>>>>
>>>> Can't locate object method "new" via package
>>>> "GUS::Community::Plugin::InsertOntologyRelationshipType" at
>>>> (eval 8) line
>>>>
>> 1.
>>
>>>>
>>>>
>>>> Can't locate object method "new" via package
>>>> "GUS::Community::Plugin::InsertOntologyTermType" at (eval 8)
>>>> line 1.
>>>>
>>>>
>>>> Can't locate object method "new" via package
>>>> "GUS::Community::Plugin::InsertPhylogeneticProfiles" at (eval 8)
>>>> line 1.
>>>>
>>>>
>>>> Can't locate XML/Simple.pm in @INC (@INC contains:
>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/
>>>> site_perl/5.8.0
>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> InsertSeqsAndFeature
>>>
>>>> s.pm
>>>> line 6.
>>>> BEGIN failed--compilation aborted at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> InsertSeqsAndFeature
>>>
>>>> s.pm
>>>> line 6.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>> Tue Jul 19 08:48:53 2005 INFO Plugin
>>>> GUS::Community::Plugin::LoadBLATAlignments registered with cvs
>>>> revision
>>>> '2924'
>>>> Tue Jul 19 08:48:54 2005 INFO Plugin
>>>> GUS::Community::Plugin::LoadBlastSimilaritiesPK registered with cvs
>>>> revision '2924'
>>>> Tue Jul 19 08:48:56 2005 INFO Plugin
>>>> GUS::Community::Plugin::LoadDocumentation registered with cvs
>>>> revision
>>>> '2924'
>>>> Tue Jul 19 08:48:57 2005 INFO Plugin
>>>> GUS::Community::Plugin::LoadEnzymeDatabase registered with cvs
>>>> revision
>>>> '2924'
>>>>
>>>> Can't locate object method "new" via package
>>>> "GUS::Community::Plugin::LoadFromdbESTMirror" at (eval 8) line 1.
>>>>
>>>>
>>>> Can't locate XML/Simple.pm in @INC (@INC contains:
>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/
>>>> site_perl/5.8.0
>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> LoadGeneFeaturesFrom
>>>
>>>> XML.pm
>>>> line 16.
>>>> BEGIN failed--compilation aborted at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> LoadGeneFeaturesFrom
>>>
>>>> XML.pm
>>>> line 16.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>> Tue Jul 19 08:49:00 2005 INFO Plugin
>>>> GUS::Community::Plugin::LoadGenomeGaps registered with cvs
>>>> revision '2924'
>>>>
>>>> Can't locate GUS/Model/RAD3/SAGETag.pm in @INC (@INC contains:
>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/
>>>> site_perl/5.8.0
>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> LoadGenomicSageData.
>>>
>>>> pm
>>>> line 11.
>>>> BEGIN failed--compilation aborted at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> LoadGenomicSageData.
>>>
>>>> pm
>>>> line 11.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>> Tue Jul 19 08:49:03 2005 INFO Plugin
>>>> GUS::Community::Plugin::LoadHspsOnly registered with cvs
>>>> revision '2924'
>>>> Tue Jul 19 08:49:04 2005 INFO Plugin
>>>> GUS::Community::Plugin::LoadMutualInformationScores registered
>>>> with cvs
>>>> revision '2924'
>>>> Tue Jul 19 08:49:05 2005 INFO Plugin
>>>> GUS::Community::Plugin::LoadPfam registered with cvs revision
>>>> '2924'
>>>> GUS::Community::Plugin::LoadSageResults is already registered.
>>>> Use '+update' if you need to register a new version.
>>>>
>>>> Can't locate GUS/Model/RAD3/Study.pm in @INC (@INC contains:
>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/
>>>> site_perl/5.8.0
>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> MAS5StudyModuleILoad
>>>
>>>> er.pm
>>>> line 12.
>>>> BEGIN failed--compilation aborted at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> MAS5StudyModuleILoad
>>>
>>>> er.pm
>>>> line 12.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>> Tue Jul 19 08:49:09 2005 INFO Plugin
>>>> GUS::Community::Plugin::MakeBestSimilarityPair registered with cvs
>>>> revision '2924'
>>>> Tue Jul 19 08:49:10 2005 INFO Plugin
>>>> GUS::Community::Plugin::MakeDtd registered with cvs revision '2924'
>>>> Tue Jul 19 08:49:11 2005 INFO Plugin
>>>> GUS::Community::Plugin::MakeIndexWordLink registered with cvs
>>>> revision
>>>> '2924'
>>>> Tue Jul 19 08:49:12 2005 INFO Plugin
>>>> GUS::Community::Plugin::MakeIndexWordSimLink registered with cvs
>>>> revision '2924'
>>>> Tue Jul 19 08:49:13 2005 INFO Plugin
>>>> GUS::Community::Plugin::OrthologGroupsMCL registered with cvs
>>>> revision
>>>> '2924'
>>>>
>>>> Can't locate GUS/Model/RAD3/Quantification.pm in @INC (@INC
>>>> contains:
>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/
>>>> site_perl/5.8.0
>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> SimpleArrayResultLoa
>>>
>>>> der.pm
>>>> line 28.
>>>> BEGIN failed--compilation aborted at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>> SimpleArrayResultLoa
>>>
>>>> der.pm
>>>> line 28.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>> Tue Jul 19 08:49:15 2005 INFO Plugin
>>>> GUS::Community::Plugin::UpdateNASequences registered with cvs
>>>> revision
>>>> '2924'
>>>>
>>>> Can't locate V.pm in @INC (@INC contains:
>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/
>>>> site_perl/5.8.0
>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> XdbLister.pm
>>>> line 10.
>>>> BEGIN failed--compilation aborted at
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/
>>>> XdbLister.pm
>>>> line 10.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>>
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> SF.Net email is sponsored by: Discover Easy Linux Migration
>>>> Strategies
>>>> from IBM. Find simple to follow Roadmaps, straightforward articles,
>>>> informative Webcasts and more! Get everything you need to get up to
>>>> speed, fast. http://ads.osdn.com/?
>>>> ad_id=7477&alloc_id=16492&op=click
>>>> _______________________________________________
>>>> Gusdev-gusdev mailing list
>>>> Gus...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is sponsored by: Discover Easy Linux Migration
>> Strategies
>> from IBM. Find simple to follow Roadmaps, straightforward articles,
>> informative Webcasts and more! Get everything you need to get up to
>> speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>
>
> --
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
> speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: <an...@ma...> - 2005-07-19 21:09:00
|
Yeah, that was me, but frankly I do not have the time to work on this. I gave
ownership of this to Debbie Pinney a few years back, and she had put in fixes
over time, but it is a known issues that we MUST replace this plugin with
something based on BioPerl parsers.
-angel
Quoting Jian Lu <jl...@vb...>:
> Mike,
>
> Thank you for response and suggestion. Since GBParser has been heavily
> used by community to load NCBI data, I think a high priority should be
> considered to support GBParser. Who is the original author?
>
> Jian
>
> Michael Saffitz wrote:
>
> >Hi Jian,
> >
> >Community plugins are provided as a point of reference, but are not
> >generally compatible with the current schema and app framework. They are
> >not expected to work without (sometimes significant) modification.
> >
> >Be cautious for community plugins that do register-- they may have runtime
> >errors or worse, run without error but improperly load data.
> >
> >If there is a specific community plugin you'd like to use, I suggest
> working
> >with the original plugin author or other interested parties in the
> community
> >to review, update, and fix the plugin to the Plugin standard, and then it
> >can become a supported plugin!
> >
> >Thanks,
> >
> >Mike
> >
> >
> >
> >
> >On 7/19/05 4:08 PM, "Jian Lu" <jl...@vb...> wrote:
> >
> >
> >
> >>I am trying to register GUS 3.5 plugins. The 'Supported' plugins are
> >>successful, but 'Community' plugins all failed to register at the first
> >>time run because most plugins have empty database versions like this
> >>requiredDbVersion => {}. After adding database version 3.5, some got
> >>registered, but majorities still failed (see below error log). I
> >>corrected some like GBParser and registered them.
> >>
> >>###################### ERROR LOG ##############################
> >>GUS::Community::Plugin::AnnotatorsInterfaceSubmitter is already
> registered.
> >>Use '+update' if you need to register a new version.
> >>Tue Jul 19 08:48:29 2005 INFO Plugin
> >>GUS::Community::Plugin::AssembliesWithflCD registered with cvs revision
> >>'2924'
> >>
> >>Can't locate GUS/RAD/FileTranslator.pm in @INC (@INC contains:
> >>/home/brcgusts/GUS/gus_home/lib/perl
> >>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> >>/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> >>/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/BatchArrayResultLoad
> >>er.pm
> >>line 20.
> >>BEGIN failed--compilation aborted at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/BatchArrayResultLoad
> >>er.pm
> >>line 20.
> >>Compilation failed in require at (eval 8) line 1.
> >>
> >>Tue Jul 19 08:48:31 2005 INFO Plugin
> >>GUS::Community::Plugin::DeleteFromTable registered with cvs revision
> '2924'
> >>Tue Jul 19 08:48:32 2005 INFO Plugin
> >>GUS::Community::Plugin::DeleteSimilarities registered with cvs revision
> >>'2924'
> >>Tue Jul 19 08:48:35 2005 INFO Plugin
> >>GUS::Community::Plugin::DupNRDBRows registered with cvs revision '2924'
> >>
> >>Can't locate GUS/Model/SRes/ExternalDatabaseKeyword.pm in @INC (@INC
> >>contains: /home/brcgusts/GUS/gus_home/lib/perl
> >>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> >>/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> >>/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> >>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm
> >>line 43.
> >>BEGIN failed--compilation aborted at
> >>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm
> >>line 43.
> >>Compilation failed in require at (eval 8) line 1.
> >>
> >>
> >>Can't locate GUS/Model/RAD3/Study.pm in @INC (@INC contains:
> >>/home/brcgusts/GUS/gus_home/lib/perl
> >>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> >>/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> >>/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GenePixStudyModuleIL
> >>oader.pm
> >>line 13.
> >>BEGIN failed--compilation aborted at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GenePixStudyModuleIL
> >>oader.pm
> >>line 13.
> >>Compilation failed in require at (eval 8) line 1.
> >>
> >>GUSLOGS ENV:
> >>Tue Jul 19 08:48:38 2005 INFO Plugin
> >>GUS::Community::Plugin::GenericParser2Gus registered with cvs revision
> >>'2924'
> >>Tue Jul 19 08:48:39 2005 INFO Plugin
> >>GUS::Community::Plugin::IdentifyAndLoadSnpsFromAssemblies registered
> >>with cvs revision '2924'
> >>String found where operator expected at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> >>ures.pm
> >>line 615, near "'prediction_algorithm_id'"
> >> (Missing semicolon on previous line?)
> >>
> >>syntax error at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> >>ures.pm
> >>line 615, near "'prediction_algorithm_id'"
> >>Global symbol "$motif_id" requires explicit package name at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> >>ures.pm
> >>line 616.
> >>Global symbol "$score" requires explicit package name at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> >>ures.pm
> >>line 618.
> >>Global symbol "%hash" requires explicit package name at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> >>ures.pm
> >>line 621.
> >>Global symbol "$start" requires explicit package name at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> >>ures.pm
> >>line 621.
> >>Global symbol "$stop" requires explicit package name at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> >>ures.pm
> >>line 621.
> >>Global symbol "$motif_id" requires explicit package name at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> >>ures.pm
> >>line 635.
> >>Global symbol "$score" requires explicit package name at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> >>ures.pm
> >>line 636.
> >>Global symbol "$motif_id" requires explicit package name at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> >>ures.pm
> >>line 637.
> >>Global symbol "$pf" requires explicit package name at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> >>ures.pm
> >>line 638.
> >>Global symbol "$info" requires explicit package name at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> >>ures.pm
> >>line 642.
> >>Global symbol "$score" requires explicit package name at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> >>ures.pm
> >>line 644.
> >>Global symbol "$start" requires explicit package name at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> >>ures.pm
> >>line 644.
> >>Global symbol "$stop" requires explicit package name at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> >>ures.pm
> >>line 644.
> >>Global symbol "$motif_id" requires explicit package name at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> >>ures.pm
> >>line 644.
> >>Global symbol "$pf" requires explicit package name at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> >>ures.pm
> >>line 648.
> >>syntax error at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> >>ures.pm
> >>line 656, near "}"
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> >>ures.pm
> >>has too many errors.
> >>Compilation failed in require at (eval 8) line 1.
> >>
> >>Tue Jul 19 08:48:42 2005 INFO Plugin
> >>GUS::Community::Plugin::ImportPlasmoDBPrediction registered with cvs
> >>revision '2924'
> >>Tue Jul 19 08:48:44 2005 INFO Plugin
> >>GUS::Community::Plugin::InsertDbRefAndDbRefNASequence registered with
> >>cvs revision '2924'
> >>Tue Jul 19 08:48:46 2005 INFO Plugin
> >>GUS::Community::Plugin::InsertDbRefAndDbRefNaSequenceGeneral registered
> >>with cvs revision '2924'
> >>Tue Jul 19 08:48:47 2005 INFO Plugin
> >>GUS::Community::Plugin::InsertNAFeatureComment registered with cvs
> >>revision '2924'
> >>
> >>Can't locate object method "new" via package
> >>"GUS::Community::Plugin::InsertOntologyEntry" at (eval 8) line 1.
> >>
> >>
> >>Can't locate object method "new" via package
> >>"GUS::Community::Plugin::InsertOntologyRelationshipType" at (eval 8) line
> 1.
> >>
> >>
> >>Can't locate object method "new" via package
> >>"GUS::Community::Plugin::InsertOntologyTermType" at (eval 8) line 1.
> >>
> >>
> >>Can't locate object method "new" via package
> >>"GUS::Community::Plugin::InsertPhylogeneticProfiles" at (eval 8) line 1.
> >>
> >>
> >>Can't locate XML/Simple.pm in @INC (@INC contains:
> >>/home/brcgusts/GUS/gus_home/lib/perl
> >>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> >>/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> >>/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/InsertSeqsAndFeature
> >>s.pm
> >>line 6.
> >>BEGIN failed--compilation aborted at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/InsertSeqsAndFeature
> >>s.pm
> >>line 6.
> >>Compilation failed in require at (eval 8) line 1.
> >>
> >>Tue Jul 19 08:48:53 2005 INFO Plugin
> >>GUS::Community::Plugin::LoadBLATAlignments registered with cvs revision
> >>'2924'
> >>Tue Jul 19 08:48:54 2005 INFO Plugin
> >>GUS::Community::Plugin::LoadBlastSimilaritiesPK registered with cvs
> >>revision '2924'
> >>Tue Jul 19 08:48:56 2005 INFO Plugin
> >>GUS::Community::Plugin::LoadDocumentation registered with cvs revision
> >>'2924'
> >>Tue Jul 19 08:48:57 2005 INFO Plugin
> >>GUS::Community::Plugin::LoadEnzymeDatabase registered with cvs revision
> >>'2924'
> >>
> >>Can't locate object method "new" via package
> >>"GUS::Community::Plugin::LoadFromdbESTMirror" at (eval 8) line 1.
> >>
> >>
> >>Can't locate XML/Simple.pm in @INC (@INC contains:
> >>/home/brcgusts/GUS/gus_home/lib/perl
> >>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> >>/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> >>/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGeneFeaturesFrom
> >>XML.pm
> >>line 16.
> >>BEGIN failed--compilation aborted at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGeneFeaturesFrom
> >>XML.pm
> >>line 16.
> >>Compilation failed in require at (eval 8) line 1.
> >>
> >>Tue Jul 19 08:49:00 2005 INFO Plugin
> >>GUS::Community::Plugin::LoadGenomeGaps registered with cvs revision '2924'
> >>
> >>Can't locate GUS/Model/RAD3/SAGETag.pm in @INC (@INC contains:
> >>/home/brcgusts/GUS/gus_home/lib/perl
> >>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> >>/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> >>/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGenomicSageData.
> >>pm
> >>line 11.
> >>BEGIN failed--compilation aborted at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGenomicSageData.
> >>pm
> >>line 11.
> >>Compilation failed in require at (eval 8) line 1.
> >>
> >>Tue Jul 19 08:49:03 2005 INFO Plugin
> >>GUS::Community::Plugin::LoadHspsOnly registered with cvs revision '2924'
> >>Tue Jul 19 08:49:04 2005 INFO Plugin
> >>GUS::Community::Plugin::LoadMutualInformationScores registered with cvs
> >>revision '2924'
> >>Tue Jul 19 08:49:05 2005 INFO Plugin
> >>GUS::Community::Plugin::LoadPfam registered with cvs revision '2924'
> >>GUS::Community::Plugin::LoadSageResults is already registered.
> >>Use '+update' if you need to register a new version.
> >>
> >>Can't locate GUS/Model/RAD3/Study.pm in @INC (@INC contains:
> >>/home/brcgusts/GUS/gus_home/lib/perl
> >>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> >>/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> >>/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/MAS5StudyModuleILoad
> >>er.pm
> >>line 12.
> >>BEGIN failed--compilation aborted at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/MAS5StudyModuleILoad
> >>er.pm
> >>line 12.
> >>Compilation failed in require at (eval 8) line 1.
> >>
> >>Tue Jul 19 08:49:09 2005 INFO Plugin
> >>GUS::Community::Plugin::MakeBestSimilarityPair registered with cvs
> >>revision '2924'
> >>Tue Jul 19 08:49:10 2005 INFO Plugin
> >>GUS::Community::Plugin::MakeDtd registered with cvs revision '2924'
> >>Tue Jul 19 08:49:11 2005 INFO Plugin
> >>GUS::Community::Plugin::MakeIndexWordLink registered with cvs revision
> >>'2924'
> >>Tue Jul 19 08:49:12 2005 INFO Plugin
> >>GUS::Community::Plugin::MakeIndexWordSimLink registered with cvs
> >>revision '2924'
> >>Tue Jul 19 08:49:13 2005 INFO Plugin
> >>GUS::Community::Plugin::OrthologGroupsMCL registered with cvs revision
> >>'2924'
> >>
> >>Can't locate GUS/Model/RAD3/Quantification.pm in @INC (@INC contains:
> >>/home/brcgusts/GUS/gus_home/lib/perl
> >>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> >>/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> >>/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/SimpleArrayResultLoa
> >>der.pm
> >>line 28.
> >>BEGIN failed--compilation aborted at
>
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/SimpleArrayResultLoa
> >>der.pm
> >>line 28.
> >>Compilation failed in require at (eval 8) line 1.
> >>
> >>Tue Jul 19 08:49:15 2005 INFO Plugin
> >>GUS::Community::Plugin::UpdateNASequences registered with cvs revision
> >>'2924'
> >>
> >>Can't locate V.pm in @INC (@INC contains:
> >>/home/brcgusts/GUS/gus_home/lib/perl
> >>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> >>/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> >>/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> >>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/XdbLister.pm
> >>line 10.
> >>BEGIN failed--compilation aborted at
> >>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/XdbLister.pm
> >>line 10.
> >>Compilation failed in require at (eval 8) line 1.
> >>
> >>
> >>
> >>
> >>-------------------------------------------------------
> >>SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> >>from IBM. Find simple to follow Roadmaps, straightforward articles,
> >>informative Webcasts and more! Get everything you need to get up to
> >>speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click
> >>_______________________________________________
> >>Gusdev-gusdev mailing list
> >>Gus...@li...
> >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>
> >>
> >
> >
> >
>
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
> speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
--
|
|
From: Chris S. <sto...@pc...> - 2005-07-19 21:01:17
|
Hi, There has been some discussion as to the history, semantics, and usage of RNAType versus RNAFeature. After digging into old emails a bit more and with helpful prodding from Steve, I believe that I can define the usage of these NAFeature views. RNAFeature: This view is for mRNAs (protein coding RNAs). This is why it has attributes referring to translation. RNAType: This view is for non-coding RNAs. In the CBIL instance of GUS, we have rRNA, tRNA, snRNA, snoRNA, and scRNA. Chris |
|
From: Elisabetta M. <man...@pc...> - 2005-07-19 20:55:04
|
Jian,
I think this was announced at the recent GUS workshop, don't know if it
is mentioned also on the gusdb website. In any case, some of the
Community plugins released with GUS 3.5.0 had not undergone updates to
make them compliant with 3.5.0 yet.
For example, all Community plugins that have to do with RAD dataloading
were not upgraded yet, they were simply copied here from the GUS 3.0
repository. This explains some of the problems you copied below when
trying to use them. As far as these RAD plugins go, they have now been
assigned *to individuals at CBIL* who are currently working on updating
and testing those too so that they will all be 3.5 compatible. However you
should also remember that the Community plugins might be specific to a
particular instance of GUS and might not be usable by all other instances.
In essence Community plugin are to be taken as plugins that for a variety
of reasons (not yet upgraded or instance specific) might not necessarily
be usable by all. It's the Supported plugins that are meant to be
upgraded and of widespread use.
As far as RAD dataloading goes, the plugins in *Supported* that refer to
RAD are of course updated to 3.5 and have been tested.
Elisabetta
---
On Tue, 19 Jul 2005, Jian Lu wrote:
> I am trying to register GUS 3.5 plugins. The 'Supported' plugins are
> successful, but 'Community' plugins all failed to register at the first time
> run because most plugins have empty database versions like this
> requiredDbVersion => {}. After adding database version 3.5, some got
> registered, but majorities still failed (see below error log). I corrected
> some like GBParser and registered them.
>
> ###################### ERROR LOG ##############################
> GUS::Community::Plugin::AnnotatorsInterfaceSubmitter is already registered.
> Use '+update' if you need to register a new version.
> Tue Jul 19 08:48:29 2005 INFO Plugin
> GUS::Community::Plugin::AssembliesWithflCD registered with cvs revision
> '2924'
>
> Can't locate GUS/RAD/FileTranslator.pm in @INC (@INC contains:
> /home/brcgusts/GUS/gus_home/lib/perl
> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/BatchArrayResultLoader.pm
> line 20.
> BEGIN failed--compilation aborted at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/BatchArrayResultLoader.pm
> line 20.
> Compilation failed in require at (eval 8) line 1.
>
> Tue Jul 19 08:48:31 2005 INFO Plugin
> GUS::Community::Plugin::DeleteFromTable registered with cvs revision '2924'
> Tue Jul 19 08:48:32 2005 INFO Plugin
> GUS::Community::Plugin::DeleteSimilarities registered with cvs revision
> '2924'
> Tue Jul 19 08:48:35 2005 INFO Plugin
> GUS::Community::Plugin::DupNRDBRows registered with cvs revision '2924'
>
> Can't locate GUS/Model/SRes/ExternalDatabaseKeyword.pm in @INC (@INC
> contains: /home/brcgusts/GUS/gus_home/lib/perl
> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm line
> 43.
> BEGIN failed--compilation aborted at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm line
> 43.
> Compilation failed in require at (eval 8) line 1.
>
>
> Can't locate GUS/Model/RAD3/Study.pm in @INC (@INC contains:
> /home/brcgusts/GUS/gus_home/lib/perl
> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GenePixStudyModuleILoader.pm
> line 13.
> BEGIN failed--compilation aborted at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GenePixStudyModuleILoader.pm
> line 13.
> Compilation failed in require at (eval 8) line 1.
>
> GUSLOGS ENV:
> Tue Jul 19 08:48:38 2005 INFO Plugin
> GUS::Community::Plugin::GenericParser2Gus registered with cvs revision '2924'
> Tue Jul 19 08:48:39 2005 INFO Plugin
> GUS::Community::Plugin::IdentifyAndLoadSnpsFromAssemblies registered with cvs
> revision '2924'
> String found where operator expected at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
> line 615, near "'prediction_algorithm_id'"
> (Missing semicolon on previous line?)
>
> syntax error at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
> line 615, near "'prediction_algorithm_id'"
> Global symbol "$motif_id" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
> line 616.
> Global symbol "$score" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
> line 618.
> Global symbol "%hash" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
> line 621.
> Global symbol "$start" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
> line 621.
> Global symbol "$stop" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
> line 621.
> Global symbol "$motif_id" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
> line 635.
> Global symbol "$score" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
> line 636.
> Global symbol "$motif_id" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
> line 637.
> Global symbol "$pf" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
> line 638.
> Global symbol "$info" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
> line 642.
> Global symbol "$score" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
> line 644.
> Global symbol "$start" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
> line 644.
> Global symbol "$stop" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
> line 644.
> Global symbol "$motif_id" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
> line 644.
> Global symbol "$pf" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
> line 648.
> syntax error at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
> line 656, near "}"
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
> has too many errors.
> Compilation failed in require at (eval 8) line 1.
>
> Tue Jul 19 08:48:42 2005 INFO Plugin
> GUS::Community::Plugin::ImportPlasmoDBPrediction registered with cvs revision
> '2924'
> Tue Jul 19 08:48:44 2005 INFO Plugin
> GUS::Community::Plugin::InsertDbRefAndDbRefNASequence registered with cvs
> revision '2924'
> Tue Jul 19 08:48:46 2005 INFO Plugin
> GUS::Community::Plugin::InsertDbRefAndDbRefNaSequenceGeneral registered with
> cvs revision '2924'
> Tue Jul 19 08:48:47 2005 INFO Plugin
> GUS::Community::Plugin::InsertNAFeatureComment registered with cvs revision
> '2924'
>
> Can't locate object method "new" via package
> "GUS::Community::Plugin::InsertOntologyEntry" at (eval 8) line 1.
>
>
> Can't locate object method "new" via package
> "GUS::Community::Plugin::InsertOntologyRelationshipType" at (eval 8) line 1.
>
>
> Can't locate object method "new" via package
> "GUS::Community::Plugin::InsertOntologyTermType" at (eval 8) line 1.
>
>
> Can't locate object method "new" via package
> "GUS::Community::Plugin::InsertPhylogeneticProfiles" at (eval 8) line 1.
>
>
> Can't locate XML/Simple.pm in @INC (@INC contains:
> /home/brcgusts/GUS/gus_home/lib/perl
> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/InsertSeqsAndFeatures.pm
> line 6.
> BEGIN failed--compilation aborted at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/InsertSeqsAndFeatures.pm
> line 6.
> Compilation failed in require at (eval 8) line 1.
>
> Tue Jul 19 08:48:53 2005 INFO Plugin
> GUS::Community::Plugin::LoadBLATAlignments registered with cvs revision
> '2924'
> Tue Jul 19 08:48:54 2005 INFO Plugin
> GUS::Community::Plugin::LoadBlastSimilaritiesPK registered with cvs revision
> '2924'
> Tue Jul 19 08:48:56 2005 INFO Plugin
> GUS::Community::Plugin::LoadDocumentation registered with cvs revision '2924'
> Tue Jul 19 08:48:57 2005 INFO Plugin
> GUS::Community::Plugin::LoadEnzymeDatabase registered with cvs revision
> '2924'
>
> Can't locate object method "new" via package
> "GUS::Community::Plugin::LoadFromdbESTMirror" at (eval 8) line 1.
>
>
> Can't locate XML/Simple.pm in @INC (@INC contains:
> /home/brcgusts/GUS/gus_home/lib/perl
> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGeneFeaturesFromXML.pm
> line 16.
> BEGIN failed--compilation aborted at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGeneFeaturesFromXML.pm
> line 16.
> Compilation failed in require at (eval 8) line 1.
>
> Tue Jul 19 08:49:00 2005 INFO Plugin
> GUS::Community::Plugin::LoadGenomeGaps registered with cvs revision '2924'
>
> Can't locate GUS/Model/RAD3/SAGETag.pm in @INC (@INC contains:
> /home/brcgusts/GUS/gus_home/lib/perl
> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGenomicSageData.pm
> line 11.
> BEGIN failed--compilation aborted at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGenomicSageData.pm
> line 11.
> Compilation failed in require at (eval 8) line 1.
>
> Tue Jul 19 08:49:03 2005 INFO Plugin
> GUS::Community::Plugin::LoadHspsOnly registered with cvs revision '2924'
> Tue Jul 19 08:49:04 2005 INFO Plugin
> GUS::Community::Plugin::LoadMutualInformationScores registered with cvs
> revision '2924'
> Tue Jul 19 08:49:05 2005 INFO Plugin GUS::Community::Plugin::LoadPfam
> registered with cvs revision '2924'
> GUS::Community::Plugin::LoadSageResults is already registered.
> Use '+update' if you need to register a new version.
>
> Can't locate GUS/Model/RAD3/Study.pm in @INC (@INC contains:
> /home/brcgusts/GUS/gus_home/lib/perl
> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/MAS5StudyModuleILoader.pm
> line 12.
> BEGIN failed--compilation aborted at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/MAS5StudyModuleILoader.pm
> line 12.
> Compilation failed in require at (eval 8) line 1.
>
> Tue Jul 19 08:49:09 2005 INFO Plugin
> GUS::Community::Plugin::MakeBestSimilarityPair registered with cvs revision
> '2924'
> Tue Jul 19 08:49:10 2005 INFO Plugin GUS::Community::Plugin::MakeDtd
> registered with cvs revision '2924'
> Tue Jul 19 08:49:11 2005 INFO Plugin
> GUS::Community::Plugin::MakeIndexWordLink registered with cvs revision '2924'
> Tue Jul 19 08:49:12 2005 INFO Plugin
> GUS::Community::Plugin::MakeIndexWordSimLink registered with cvs revision
> '2924'
> Tue Jul 19 08:49:13 2005 INFO Plugin
> GUS::Community::Plugin::OrthologGroupsMCL registered with cvs revision '2924'
>
> Can't locate GUS/Model/RAD3/Quantification.pm in @INC (@INC contains:
> /home/brcgusts/GUS/gus_home/lib/perl
> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/SimpleArrayResultLoader.pm
> line 28.
> BEGIN failed--compilation aborted at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/SimpleArrayResultLoader.pm
> line 28.
> Compilation failed in require at (eval 8) line 1.
>
> Tue Jul 19 08:49:15 2005 INFO Plugin
> GUS::Community::Plugin::UpdateNASequences registered with cvs revision '2924'
>
> Can't locate V.pm in @INC (@INC contains:
> /home/brcgusts/GUS/gus_home/lib/perl
> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/XdbLister.pm line
> 10.
> BEGIN failed--compilation aborted at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/XdbLister.pm line
> 10.
> Compilation failed in require at (eval 8) line 1.
>
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
> speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: Jian Lu <jl...@vb...> - 2005-07-19 20:53:40
|
Mike,
Thank you for response and suggestion. Since GBParser has been heavily
used by community to load NCBI data, I think a high priority should be
considered to support GBParser. Who is the original author?
Jian
Michael Saffitz wrote:
>Hi Jian,
>
>Community plugins are provided as a point of reference, but are not
>generally compatible with the current schema and app framework. They are
>not expected to work without (sometimes significant) modification.
>
>Be cautious for community plugins that do register-- they may have runtime
>errors or worse, run without error but improperly load data.
>
>If there is a specific community plugin you'd like to use, I suggest working
>with the original plugin author or other interested parties in the community
>to review, update, and fix the plugin to the Plugin standard, and then it
>can become a supported plugin!
>
>Thanks,
>
>Mike
>
>
>
>
>On 7/19/05 4:08 PM, "Jian Lu" <jl...@vb...> wrote:
>
>
>
>>I am trying to register GUS 3.5 plugins. The 'Supported' plugins are
>>successful, but 'Community' plugins all failed to register at the first
>>time run because most plugins have empty database versions like this
>>requiredDbVersion => {}. After adding database version 3.5, some got
>>registered, but majorities still failed (see below error log). I
>>corrected some like GBParser and registered them.
>>
>>###################### ERROR LOG ##############################
>>GUS::Community::Plugin::AnnotatorsInterfaceSubmitter is already registered.
>>Use '+update' if you need to register a new version.
>>Tue Jul 19 08:48:29 2005 INFO Plugin
>>GUS::Community::Plugin::AssembliesWithflCD registered with cvs revision
>>'2924'
>>
>>Can't locate GUS/RAD/FileTranslator.pm in @INC (@INC contains:
>>/home/brcgusts/GUS/gus_home/lib/perl
>>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
>>/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/BatchArrayResultLoad
>>er.pm
>>line 20.
>>BEGIN failed--compilation aborted at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/BatchArrayResultLoad
>>er.pm
>>line 20.
>>Compilation failed in require at (eval 8) line 1.
>>
>>Tue Jul 19 08:48:31 2005 INFO Plugin
>>GUS::Community::Plugin::DeleteFromTable registered with cvs revision '2924'
>>Tue Jul 19 08:48:32 2005 INFO Plugin
>>GUS::Community::Plugin::DeleteSimilarities registered with cvs revision
>>'2924'
>>Tue Jul 19 08:48:35 2005 INFO Plugin
>>GUS::Community::Plugin::DupNRDBRows registered with cvs revision '2924'
>>
>>Can't locate GUS/Model/SRes/ExternalDatabaseKeyword.pm in @INC (@INC
>>contains: /home/brcgusts/GUS/gus_home/lib/perl
>>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
>>/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm
>>line 43.
>>BEGIN failed--compilation aborted at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm
>>line 43.
>>Compilation failed in require at (eval 8) line 1.
>>
>>
>>Can't locate GUS/Model/RAD3/Study.pm in @INC (@INC contains:
>>/home/brcgusts/GUS/gus_home/lib/perl
>>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
>>/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GenePixStudyModuleIL
>>oader.pm
>>line 13.
>>BEGIN failed--compilation aborted at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GenePixStudyModuleIL
>>oader.pm
>>line 13.
>>Compilation failed in require at (eval 8) line 1.
>>
>>GUSLOGS ENV:
>>Tue Jul 19 08:48:38 2005 INFO Plugin
>>GUS::Community::Plugin::GenericParser2Gus registered with cvs revision
>>'2924'
>>Tue Jul 19 08:48:39 2005 INFO Plugin
>>GUS::Community::Plugin::IdentifyAndLoadSnpsFromAssemblies registered
>>with cvs revision '2924'
>>String found where operator expected at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
>>ures.pm
>>line 615, near "'prediction_algorithm_id'"
>> (Missing semicolon on previous line?)
>>
>>syntax error at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
>>ures.pm
>>line 615, near "'prediction_algorithm_id'"
>>Global symbol "$motif_id" requires explicit package name at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
>>ures.pm
>>line 616.
>>Global symbol "$score" requires explicit package name at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
>>ures.pm
>>line 618.
>>Global symbol "%hash" requires explicit package name at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
>>ures.pm
>>line 621.
>>Global symbol "$start" requires explicit package name at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
>>ures.pm
>>line 621.
>>Global symbol "$stop" requires explicit package name at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
>>ures.pm
>>line 621.
>>Global symbol "$motif_id" requires explicit package name at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
>>ures.pm
>>line 635.
>>Global symbol "$score" requires explicit package name at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
>>ures.pm
>>line 636.
>>Global symbol "$motif_id" requires explicit package name at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
>>ures.pm
>>line 637.
>>Global symbol "$pf" requires explicit package name at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
>>ures.pm
>>line 638.
>>Global symbol "$info" requires explicit package name at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
>>ures.pm
>>line 642.
>>Global symbol "$score" requires explicit package name at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
>>ures.pm
>>line 644.
>>Global symbol "$start" requires explicit package name at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
>>ures.pm
>>line 644.
>>Global symbol "$stop" requires explicit package name at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
>>ures.pm
>>line 644.
>>Global symbol "$motif_id" requires explicit package name at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
>>ures.pm
>>line 644.
>>Global symbol "$pf" requires explicit package name at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
>>ures.pm
>>line 648.
>>syntax error at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
>>ures.pm
>>line 656, near "}"
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
>>ures.pm
>>has too many errors.
>>Compilation failed in require at (eval 8) line 1.
>>
>>Tue Jul 19 08:48:42 2005 INFO Plugin
>>GUS::Community::Plugin::ImportPlasmoDBPrediction registered with cvs
>>revision '2924'
>>Tue Jul 19 08:48:44 2005 INFO Plugin
>>GUS::Community::Plugin::InsertDbRefAndDbRefNASequence registered with
>>cvs revision '2924'
>>Tue Jul 19 08:48:46 2005 INFO Plugin
>>GUS::Community::Plugin::InsertDbRefAndDbRefNaSequenceGeneral registered
>>with cvs revision '2924'
>>Tue Jul 19 08:48:47 2005 INFO Plugin
>>GUS::Community::Plugin::InsertNAFeatureComment registered with cvs
>>revision '2924'
>>
>>Can't locate object method "new" via package
>>"GUS::Community::Plugin::InsertOntologyEntry" at (eval 8) line 1.
>>
>>
>>Can't locate object method "new" via package
>>"GUS::Community::Plugin::InsertOntologyRelationshipType" at (eval 8) line 1.
>>
>>
>>Can't locate object method "new" via package
>>"GUS::Community::Plugin::InsertOntologyTermType" at (eval 8) line 1.
>>
>>
>>Can't locate object method "new" via package
>>"GUS::Community::Plugin::InsertPhylogeneticProfiles" at (eval 8) line 1.
>>
>>
>>Can't locate XML/Simple.pm in @INC (@INC contains:
>>/home/brcgusts/GUS/gus_home/lib/perl
>>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
>>/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/InsertSeqsAndFeature
>>s.pm
>>line 6.
>>BEGIN failed--compilation aborted at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/InsertSeqsAndFeature
>>s.pm
>>line 6.
>>Compilation failed in require at (eval 8) line 1.
>>
>>Tue Jul 19 08:48:53 2005 INFO Plugin
>>GUS::Community::Plugin::LoadBLATAlignments registered with cvs revision
>>'2924'
>>Tue Jul 19 08:48:54 2005 INFO Plugin
>>GUS::Community::Plugin::LoadBlastSimilaritiesPK registered with cvs
>>revision '2924'
>>Tue Jul 19 08:48:56 2005 INFO Plugin
>>GUS::Community::Plugin::LoadDocumentation registered with cvs revision
>>'2924'
>>Tue Jul 19 08:48:57 2005 INFO Plugin
>>GUS::Community::Plugin::LoadEnzymeDatabase registered with cvs revision
>>'2924'
>>
>>Can't locate object method "new" via package
>>"GUS::Community::Plugin::LoadFromdbESTMirror" at (eval 8) line 1.
>>
>>
>>Can't locate XML/Simple.pm in @INC (@INC contains:
>>/home/brcgusts/GUS/gus_home/lib/perl
>>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
>>/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGeneFeaturesFrom
>>XML.pm
>>line 16.
>>BEGIN failed--compilation aborted at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGeneFeaturesFrom
>>XML.pm
>>line 16.
>>Compilation failed in require at (eval 8) line 1.
>>
>>Tue Jul 19 08:49:00 2005 INFO Plugin
>>GUS::Community::Plugin::LoadGenomeGaps registered with cvs revision '2924'
>>
>>Can't locate GUS/Model/RAD3/SAGETag.pm in @INC (@INC contains:
>>/home/brcgusts/GUS/gus_home/lib/perl
>>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
>>/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGenomicSageData.
>>pm
>>line 11.
>>BEGIN failed--compilation aborted at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGenomicSageData.
>>pm
>>line 11.
>>Compilation failed in require at (eval 8) line 1.
>>
>>Tue Jul 19 08:49:03 2005 INFO Plugin
>>GUS::Community::Plugin::LoadHspsOnly registered with cvs revision '2924'
>>Tue Jul 19 08:49:04 2005 INFO Plugin
>>GUS::Community::Plugin::LoadMutualInformationScores registered with cvs
>>revision '2924'
>>Tue Jul 19 08:49:05 2005 INFO Plugin
>>GUS::Community::Plugin::LoadPfam registered with cvs revision '2924'
>>GUS::Community::Plugin::LoadSageResults is already registered.
>>Use '+update' if you need to register a new version.
>>
>>Can't locate GUS/Model/RAD3/Study.pm in @INC (@INC contains:
>>/home/brcgusts/GUS/gus_home/lib/perl
>>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
>>/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/MAS5StudyModuleILoad
>>er.pm
>>line 12.
>>BEGIN failed--compilation aborted at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/MAS5StudyModuleILoad
>>er.pm
>>line 12.
>>Compilation failed in require at (eval 8) line 1.
>>
>>Tue Jul 19 08:49:09 2005 INFO Plugin
>>GUS::Community::Plugin::MakeBestSimilarityPair registered with cvs
>>revision '2924'
>>Tue Jul 19 08:49:10 2005 INFO Plugin
>>GUS::Community::Plugin::MakeDtd registered with cvs revision '2924'
>>Tue Jul 19 08:49:11 2005 INFO Plugin
>>GUS::Community::Plugin::MakeIndexWordLink registered with cvs revision
>>'2924'
>>Tue Jul 19 08:49:12 2005 INFO Plugin
>>GUS::Community::Plugin::MakeIndexWordSimLink registered with cvs
>>revision '2924'
>>Tue Jul 19 08:49:13 2005 INFO Plugin
>>GUS::Community::Plugin::OrthologGroupsMCL registered with cvs revision
>>'2924'
>>
>>Can't locate GUS/Model/RAD3/Quantification.pm in @INC (@INC contains:
>>/home/brcgusts/GUS/gus_home/lib/perl
>>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
>>/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/SimpleArrayResultLoa
>>der.pm
>>line 28.
>>BEGIN failed--compilation aborted at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/SimpleArrayResultLoa
>>der.pm
>>line 28.
>>Compilation failed in require at (eval 8) line 1.
>>
>>Tue Jul 19 08:49:15 2005 INFO Plugin
>>GUS::Community::Plugin::UpdateNASequences registered with cvs revision
>>'2924'
>>
>>Can't locate V.pm in @INC (@INC contains:
>>/home/brcgusts/GUS/gus_home/lib/perl
>>/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
>>/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/XdbLister.pm
>>line 10.
>>BEGIN failed--compilation aborted at
>>/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/XdbLister.pm
>>line 10.
>>Compilation failed in require at (eval 8) line 1.
>>
>>
>>
>>
>>-------------------------------------------------------
>>SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
>>from IBM. Find simple to follow Roadmaps, straightforward articles,
>>informative Webcasts and more! Get everything you need to get up to
>>speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click
>>_______________________________________________
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>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>
>
>
|
|
From: Michael S. <msa...@pc...> - 2005-07-19 20:24:53
|
Hi Jian,
Community plugins are provided as a point of reference, but are not
generally compatible with the current schema and app framework. They are
not expected to work without (sometimes significant) modification.
Be cautious for community plugins that do register-- they may have runtime
errors or worse, run without error but improperly load data.
If there is a specific community plugin you'd like to use, I suggest working
with the original plugin author or other interested parties in the community
to review, update, and fix the plugin to the Plugin standard, and then it
can become a supported plugin!
Thanks,
Mike
On 7/19/05 4:08 PM, "Jian Lu" <jl...@vb...> wrote:
> I am trying to register GUS 3.5 plugins. The 'Supported' plugins are
> successful, but 'Community' plugins all failed to register at the first
> time run because most plugins have empty database versions like this
> requiredDbVersion => {}. After adding database version 3.5, some got
> registered, but majorities still failed (see below error log). I
> corrected some like GBParser and registered them.
>
> ###################### ERROR LOG ##############################
> GUS::Community::Plugin::AnnotatorsInterfaceSubmitter is already registered.
> Use '+update' if you need to register a new version.
> Tue Jul 19 08:48:29 2005 INFO Plugin
> GUS::Community::Plugin::AssembliesWithflCD registered with cvs revision
> '2924'
>
> Can't locate GUS/RAD/FileTranslator.pm in @INC (@INC contains:
> /home/brcgusts/GUS/gus_home/lib/perl
> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/BatchArrayResultLoad
> er.pm
> line 20.
> BEGIN failed--compilation aborted at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/BatchArrayResultLoad
> er.pm
> line 20.
> Compilation failed in require at (eval 8) line 1.
>
> Tue Jul 19 08:48:31 2005 INFO Plugin
> GUS::Community::Plugin::DeleteFromTable registered with cvs revision '2924'
> Tue Jul 19 08:48:32 2005 INFO Plugin
> GUS::Community::Plugin::DeleteSimilarities registered with cvs revision
> '2924'
> Tue Jul 19 08:48:35 2005 INFO Plugin
> GUS::Community::Plugin::DupNRDBRows registered with cvs revision '2924'
>
> Can't locate GUS/Model/SRes/ExternalDatabaseKeyword.pm in @INC (@INC
> contains: /home/brcgusts/GUS/gus_home/lib/perl
> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm
> line 43.
> BEGIN failed--compilation aborted at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm
> line 43.
> Compilation failed in require at (eval 8) line 1.
>
>
> Can't locate GUS/Model/RAD3/Study.pm in @INC (@INC contains:
> /home/brcgusts/GUS/gus_home/lib/perl
> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GenePixStudyModuleIL
> oader.pm
> line 13.
> BEGIN failed--compilation aborted at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GenePixStudyModuleIL
> oader.pm
> line 13.
> Compilation failed in require at (eval 8) line 1.
>
> GUSLOGS ENV:
> Tue Jul 19 08:48:38 2005 INFO Plugin
> GUS::Community::Plugin::GenericParser2Gus registered with cvs revision
> '2924'
> Tue Jul 19 08:48:39 2005 INFO Plugin
> GUS::Community::Plugin::IdentifyAndLoadSnpsFromAssemblies registered
> with cvs revision '2924'
> String found where operator expected at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> ures.pm
> line 615, near "'prediction_algorithm_id'"
> (Missing semicolon on previous line?)
>
> syntax error at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> ures.pm
> line 615, near "'prediction_algorithm_id'"
> Global symbol "$motif_id" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> ures.pm
> line 616.
> Global symbol "$score" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> ures.pm
> line 618.
> Global symbol "%hash" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> ures.pm
> line 621.
> Global symbol "$start" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> ures.pm
> line 621.
> Global symbol "$stop" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> ures.pm
> line 621.
> Global symbol "$motif_id" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> ures.pm
> line 635.
> Global symbol "$score" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> ures.pm
> line 636.
> Global symbol "$motif_id" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> ures.pm
> line 637.
> Global symbol "$pf" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> ures.pm
> line 638.
> Global symbol "$info" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> ures.pm
> line 642.
> Global symbol "$score" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> ures.pm
> line 644.
> Global symbol "$start" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> ures.pm
> line 644.
> Global symbol "$stop" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> ures.pm
> line 644.
> Global symbol "$motif_id" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> ures.pm
> line 644.
> Global symbol "$pf" requires explicit package name at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> ures.pm
> line 648.
> syntax error at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> ures.pm
> line 656, near "}"
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeat
> ures.pm
> has too many errors.
> Compilation failed in require at (eval 8) line 1.
>
> Tue Jul 19 08:48:42 2005 INFO Plugin
> GUS::Community::Plugin::ImportPlasmoDBPrediction registered with cvs
> revision '2924'
> Tue Jul 19 08:48:44 2005 INFO Plugin
> GUS::Community::Plugin::InsertDbRefAndDbRefNASequence registered with
> cvs revision '2924'
> Tue Jul 19 08:48:46 2005 INFO Plugin
> GUS::Community::Plugin::InsertDbRefAndDbRefNaSequenceGeneral registered
> with cvs revision '2924'
> Tue Jul 19 08:48:47 2005 INFO Plugin
> GUS::Community::Plugin::InsertNAFeatureComment registered with cvs
> revision '2924'
>
> Can't locate object method "new" via package
> "GUS::Community::Plugin::InsertOntologyEntry" at (eval 8) line 1.
>
>
> Can't locate object method "new" via package
> "GUS::Community::Plugin::InsertOntologyRelationshipType" at (eval 8) line 1.
>
>
> Can't locate object method "new" via package
> "GUS::Community::Plugin::InsertOntologyTermType" at (eval 8) line 1.
>
>
> Can't locate object method "new" via package
> "GUS::Community::Plugin::InsertPhylogeneticProfiles" at (eval 8) line 1.
>
>
> Can't locate XML/Simple.pm in @INC (@INC contains:
> /home/brcgusts/GUS/gus_home/lib/perl
> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/InsertSeqsAndFeature
> s.pm
> line 6.
> BEGIN failed--compilation aborted at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/InsertSeqsAndFeature
> s.pm
> line 6.
> Compilation failed in require at (eval 8) line 1.
>
> Tue Jul 19 08:48:53 2005 INFO Plugin
> GUS::Community::Plugin::LoadBLATAlignments registered with cvs revision
> '2924'
> Tue Jul 19 08:48:54 2005 INFO Plugin
> GUS::Community::Plugin::LoadBlastSimilaritiesPK registered with cvs
> revision '2924'
> Tue Jul 19 08:48:56 2005 INFO Plugin
> GUS::Community::Plugin::LoadDocumentation registered with cvs revision
> '2924'
> Tue Jul 19 08:48:57 2005 INFO Plugin
> GUS::Community::Plugin::LoadEnzymeDatabase registered with cvs revision
> '2924'
>
> Can't locate object method "new" via package
> "GUS::Community::Plugin::LoadFromdbESTMirror" at (eval 8) line 1.
>
>
> Can't locate XML/Simple.pm in @INC (@INC contains:
> /home/brcgusts/GUS/gus_home/lib/perl
> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGeneFeaturesFrom
> XML.pm
> line 16.
> BEGIN failed--compilation aborted at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGeneFeaturesFrom
> XML.pm
> line 16.
> Compilation failed in require at (eval 8) line 1.
>
> Tue Jul 19 08:49:00 2005 INFO Plugin
> GUS::Community::Plugin::LoadGenomeGaps registered with cvs revision '2924'
>
> Can't locate GUS/Model/RAD3/SAGETag.pm in @INC (@INC contains:
> /home/brcgusts/GUS/gus_home/lib/perl
> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGenomicSageData.
> pm
> line 11.
> BEGIN failed--compilation aborted at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGenomicSageData.
> pm
> line 11.
> Compilation failed in require at (eval 8) line 1.
>
> Tue Jul 19 08:49:03 2005 INFO Plugin
> GUS::Community::Plugin::LoadHspsOnly registered with cvs revision '2924'
> Tue Jul 19 08:49:04 2005 INFO Plugin
> GUS::Community::Plugin::LoadMutualInformationScores registered with cvs
> revision '2924'
> Tue Jul 19 08:49:05 2005 INFO Plugin
> GUS::Community::Plugin::LoadPfam registered with cvs revision '2924'
> GUS::Community::Plugin::LoadSageResults is already registered.
> Use '+update' if you need to register a new version.
>
> Can't locate GUS/Model/RAD3/Study.pm in @INC (@INC contains:
> /home/brcgusts/GUS/gus_home/lib/perl
> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/MAS5StudyModuleILoad
> er.pm
> line 12.
> BEGIN failed--compilation aborted at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/MAS5StudyModuleILoad
> er.pm
> line 12.
> Compilation failed in require at (eval 8) line 1.
>
> Tue Jul 19 08:49:09 2005 INFO Plugin
> GUS::Community::Plugin::MakeBestSimilarityPair registered with cvs
> revision '2924'
> Tue Jul 19 08:49:10 2005 INFO Plugin
> GUS::Community::Plugin::MakeDtd registered with cvs revision '2924'
> Tue Jul 19 08:49:11 2005 INFO Plugin
> GUS::Community::Plugin::MakeIndexWordLink registered with cvs revision
> '2924'
> Tue Jul 19 08:49:12 2005 INFO Plugin
> GUS::Community::Plugin::MakeIndexWordSimLink registered with cvs
> revision '2924'
> Tue Jul 19 08:49:13 2005 INFO Plugin
> GUS::Community::Plugin::OrthologGroupsMCL registered with cvs revision
> '2924'
>
> Can't locate GUS/Model/RAD3/Quantification.pm in @INC (@INC contains:
> /home/brcgusts/GUS/gus_home/lib/perl
> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/SimpleArrayResultLoa
> der.pm
> line 28.
> BEGIN failed--compilation aborted at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/SimpleArrayResultLoa
> der.pm
> line 28.
> Compilation failed in require at (eval 8) line 1.
>
> Tue Jul 19 08:49:15 2005 INFO Plugin
> GUS::Community::Plugin::UpdateNASequences registered with cvs revision
> '2924'
>
> Can't locate V.pm in @INC (@INC contains:
> /home/brcgusts/GUS/gus_home/lib/perl
> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/XdbLister.pm
> line 10.
> BEGIN failed--compilation aborted at
> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/XdbLister.pm
> line 10.
> Compilation failed in require at (eval 8) line 1.
>
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
> speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
|
|
From: Jian Lu <jl...@vb...> - 2005-07-19 20:09:02
|
I am trying to register GUS 3.5 plugins. The 'Supported' plugins are
successful, but 'Community' plugins all failed to register at the first
time run because most plugins have empty database versions like this
requiredDbVersion => {}. After adding database version 3.5, some got
registered, but majorities still failed (see below error log). I
corrected some like GBParser and registered them.
###################### ERROR LOG ##############################
GUS::Community::Plugin::AnnotatorsInterfaceSubmitter is already registered.
Use '+update' if you need to register a new version.
Tue Jul 19 08:48:29 2005 INFO Plugin
GUS::Community::Plugin::AssembliesWithflCD registered with cvs revision
'2924'
Can't locate GUS/RAD/FileTranslator.pm in @INC (@INC contains:
/home/brcgusts/GUS/gus_home/lib/perl
/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/BatchArrayResultLoader.pm
line 20.
BEGIN failed--compilation aborted at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/BatchArrayResultLoader.pm
line 20.
Compilation failed in require at (eval 8) line 1.
Tue Jul 19 08:48:31 2005 INFO Plugin
GUS::Community::Plugin::DeleteFromTable registered with cvs revision '2924'
Tue Jul 19 08:48:32 2005 INFO Plugin
GUS::Community::Plugin::DeleteSimilarities registered with cvs revision
'2924'
Tue Jul 19 08:48:35 2005 INFO Plugin
GUS::Community::Plugin::DupNRDBRows registered with cvs revision '2924'
Can't locate GUS/Model/SRes/ExternalDatabaseKeyword.pm in @INC (@INC
contains: /home/brcgusts/GUS/gus_home/lib/perl
/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm
line 43.
BEGIN failed--compilation aborted at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GBParser.pm
line 43.
Compilation failed in require at (eval 8) line 1.
Can't locate GUS/Model/RAD3/Study.pm in @INC (@INC contains:
/home/brcgusts/GUS/gus_home/lib/perl
/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GenePixStudyModuleILoader.pm
line 13.
BEGIN failed--compilation aborted at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/GenePixStudyModuleILoader.pm
line 13.
Compilation failed in require at (eval 8) line 1.
GUSLOGS ENV:
Tue Jul 19 08:48:38 2005 INFO Plugin
GUS::Community::Plugin::GenericParser2Gus registered with cvs revision
'2924'
Tue Jul 19 08:48:39 2005 INFO Plugin
GUS::Community::Plugin::IdentifyAndLoadSnpsFromAssemblies registered
with cvs revision '2924'
String found where operator expected at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
line 615, near "'prediction_algorithm_id'"
(Missing semicolon on previous line?)
syntax error at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
line 615, near "'prediction_algorithm_id'"
Global symbol "$motif_id" requires explicit package name at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
line 616.
Global symbol "$score" requires explicit package name at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
line 618.
Global symbol "%hash" requires explicit package name at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
line 621.
Global symbol "$start" requires explicit package name at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
line 621.
Global symbol "$stop" requires explicit package name at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
line 621.
Global symbol "$motif_id" requires explicit package name at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
line 635.
Global symbol "$score" requires explicit package name at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
line 636.
Global symbol "$motif_id" requires explicit package name at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
line 637.
Global symbol "$pf" requires explicit package name at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
line 638.
Global symbol "$info" requires explicit package name at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
line 642.
Global symbol "$score" requires explicit package name at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
line 644.
Global symbol "$start" requires explicit package name at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
line 644.
Global symbol "$stop" requires explicit package name at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
line 644.
Global symbol "$motif_id" requires explicit package name at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
line 644.
Global symbol "$pf" requires explicit package name at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
line 648.
syntax error at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
line 656, near "}"
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ImportPlasmoDBAAFeatures.pm
has too many errors.
Compilation failed in require at (eval 8) line 1.
Tue Jul 19 08:48:42 2005 INFO Plugin
GUS::Community::Plugin::ImportPlasmoDBPrediction registered with cvs
revision '2924'
Tue Jul 19 08:48:44 2005 INFO Plugin
GUS::Community::Plugin::InsertDbRefAndDbRefNASequence registered with
cvs revision '2924'
Tue Jul 19 08:48:46 2005 INFO Plugin
GUS::Community::Plugin::InsertDbRefAndDbRefNaSequenceGeneral registered
with cvs revision '2924'
Tue Jul 19 08:48:47 2005 INFO Plugin
GUS::Community::Plugin::InsertNAFeatureComment registered with cvs
revision '2924'
Can't locate object method "new" via package
"GUS::Community::Plugin::InsertOntologyEntry" at (eval 8) line 1.
Can't locate object method "new" via package
"GUS::Community::Plugin::InsertOntologyRelationshipType" at (eval 8) line 1.
Can't locate object method "new" via package
"GUS::Community::Plugin::InsertOntologyTermType" at (eval 8) line 1.
Can't locate object method "new" via package
"GUS::Community::Plugin::InsertPhylogeneticProfiles" at (eval 8) line 1.
Can't locate XML/Simple.pm in @INC (@INC contains:
/home/brcgusts/GUS/gus_home/lib/perl
/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/InsertSeqsAndFeatures.pm
line 6.
BEGIN failed--compilation aborted at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/InsertSeqsAndFeatures.pm
line 6.
Compilation failed in require at (eval 8) line 1.
Tue Jul 19 08:48:53 2005 INFO Plugin
GUS::Community::Plugin::LoadBLATAlignments registered with cvs revision
'2924'
Tue Jul 19 08:48:54 2005 INFO Plugin
GUS::Community::Plugin::LoadBlastSimilaritiesPK registered with cvs
revision '2924'
Tue Jul 19 08:48:56 2005 INFO Plugin
GUS::Community::Plugin::LoadDocumentation registered with cvs revision
'2924'
Tue Jul 19 08:48:57 2005 INFO Plugin
GUS::Community::Plugin::LoadEnzymeDatabase registered with cvs revision
'2924'
Can't locate object method "new" via package
"GUS::Community::Plugin::LoadFromdbESTMirror" at (eval 8) line 1.
Can't locate XML/Simple.pm in @INC (@INC contains:
/home/brcgusts/GUS/gus_home/lib/perl
/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGeneFeaturesFromXML.pm
line 16.
BEGIN failed--compilation aborted at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGeneFeaturesFromXML.pm
line 16.
Compilation failed in require at (eval 8) line 1.
Tue Jul 19 08:49:00 2005 INFO Plugin
GUS::Community::Plugin::LoadGenomeGaps registered with cvs revision '2924'
Can't locate GUS/Model/RAD3/SAGETag.pm in @INC (@INC contains:
/home/brcgusts/GUS/gus_home/lib/perl
/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGenomicSageData.pm
line 11.
BEGIN failed--compilation aborted at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/LoadGenomicSageData.pm
line 11.
Compilation failed in require at (eval 8) line 1.
Tue Jul 19 08:49:03 2005 INFO Plugin
GUS::Community::Plugin::LoadHspsOnly registered with cvs revision '2924'
Tue Jul 19 08:49:04 2005 INFO Plugin
GUS::Community::Plugin::LoadMutualInformationScores registered with cvs
revision '2924'
Tue Jul 19 08:49:05 2005 INFO Plugin
GUS::Community::Plugin::LoadPfam registered with cvs revision '2924'
GUS::Community::Plugin::LoadSageResults is already registered.
Use '+update' if you need to register a new version.
Can't locate GUS/Model/RAD3/Study.pm in @INC (@INC contains:
/home/brcgusts/GUS/gus_home/lib/perl
/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/MAS5StudyModuleILoader.pm
line 12.
BEGIN failed--compilation aborted at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/MAS5StudyModuleILoader.pm
line 12.
Compilation failed in require at (eval 8) line 1.
Tue Jul 19 08:49:09 2005 INFO Plugin
GUS::Community::Plugin::MakeBestSimilarityPair registered with cvs
revision '2924'
Tue Jul 19 08:49:10 2005 INFO Plugin
GUS::Community::Plugin::MakeDtd registered with cvs revision '2924'
Tue Jul 19 08:49:11 2005 INFO Plugin
GUS::Community::Plugin::MakeIndexWordLink registered with cvs revision
'2924'
Tue Jul 19 08:49:12 2005 INFO Plugin
GUS::Community::Plugin::MakeIndexWordSimLink registered with cvs
revision '2924'
Tue Jul 19 08:49:13 2005 INFO Plugin
GUS::Community::Plugin::OrthologGroupsMCL registered with cvs revision
'2924'
Can't locate GUS/Model/RAD3/Quantification.pm in @INC (@INC contains:
/home/brcgusts/GUS/gus_home/lib/perl
/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/SimpleArrayResultLoader.pm
line 28.
BEGIN failed--compilation aborted at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/SimpleArrayResultLoader.pm
line 28.
Compilation failed in require at (eval 8) line 1.
Tue Jul 19 08:49:15 2005 INFO Plugin
GUS::Community::Plugin::UpdateNASequences registered with cvs revision
'2924'
Can't locate V.pm in @INC (@INC contains:
/home/brcgusts/GUS/gus_home/lib/perl
/usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/site_perl/5.8.0
/home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
/usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/XdbLister.pm
line 10.
BEGIN failed--compilation aborted at
/home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/XdbLister.pm
line 10.
Compilation failed in require at (eval 8) line 1.
|
|
From: Mark S. H. <mh...@ug...> - 2005-07-19 18:08:33
|
ok. I don't know if any other plugins rely on the schema setting
default values. In the interest of moving forward I will update the
dbEST plugin to set a value so there will be a workable solution
regardless of what's decided later. That seems to be the simplest
(trivial, now that I see how to do it) and most robust solution.
Thanks,
M
On Jul 19, 2005, at 11:42 AM, Michael Saffitz wrote:
>
> Hi Mark,
>
> The 3.5 schema installation doesn't set any default values. Please
> file
> this as a bug so we can review and decided whether to either:
>
> * fix the install to set default values
> * to make these columns nullable
> * to update plugins/code to set values
>
> --Mike
>
> On 7/19/05 12:24 AM, "Mark S. Heiges" <mh...@ug...> wrote:
>
>
>> ApiComplexa::DataLoad::Plugin::dbEST is the same as
>> GUS::Community::Plugin::dbEST (recently renamed to
>> LoadFromdbESTMirror.pm) except it reads from a remote database link
>> to Penn's dbEST mirror.
>>
>> With GUS 3.5 it throws the error
>> cannot insert NULL into
>> ("DOTS"."NASEQUENCEIMP"."SEQUENCE_VERSION")
>>
>> This error is clear enough but this was not a problem in GUS 3.0
>> where sequence_version would always get set to '1'.
>> Sequence_version doesn't seem to get set by dbEST so apparently there
>> is some default assignment elsewhere. Checking a GUS3.0 Oracle
>> instance, there appears to be a default value defined in the
>> NaSequenceImp table definition that I don't have in my 3.5 instance.
>>
>> Does sequence_version need to be explicitly set by plugins for 3.5 or
>> is my 3.5 NaSequenceImp table erroneously missing a default value
>> for that column?
>>
>>
>> -M
>>
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is sponsored by: Discover Easy Linux Migration
>> Strategies
>> from IBM. Find simple to follow Roadmaps, straightforward articles,
>> informative Webcasts and more! Get everything you need to get up to
>> speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>
>
>
|
|
From: Michael S. <msa...@pc...> - 2005-07-19 15:42:47
|
Hi Mark,
The 3.5 schema installation doesn't set any default values. Please file
this as a bug so we can review and decided whether to either:
* fix the install to set default values
* to make these columns nullable
* to update plugins/code to set values
--Mike
On 7/19/05 12:24 AM, "Mark S. Heiges" <mh...@ug...> wrote:
> ApiComplexa::DataLoad::Plugin::dbEST is the same as
> GUS::Community::Plugin::dbEST (recently renamed to
> LoadFromdbESTMirror.pm) except it reads from a remote database link
> to Penn's dbEST mirror.
>
> With GUS 3.5 it throws the error
> cannot insert NULL into ("DOTS"."NASEQUENCEIMP"."SEQUENCE_VERSION")
>
> This error is clear enough but this was not a problem in GUS 3.0
> where sequence_version would always get set to '1'.
> Sequence_version doesn't seem to get set by dbEST so apparently there
> is some default assignment elsewhere. Checking a GUS3.0 Oracle
> instance, there appears to be a default value defined in the
> NaSequenceImp table definition that I don't have in my 3.5 instance.
>
> Does sequence_version need to be explicitly set by plugins for 3.5 or
> is my 3.5 NaSequenceImp table erroneously missing a default value
> for that column?
>
>
> -M
>
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
> speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
|
|
From: Mark S. H. <mh...@ug...> - 2005-07-19 04:24:47
|
ApiComplexa::DataLoad::Plugin::dbEST is the same as
GUS::Community::Plugin::dbEST (recently renamed to
LoadFromdbESTMirror.pm) except it reads from a remote database link
to Penn's dbEST mirror.
With GUS 3.5 it throws the error
cannot insert NULL into ("DOTS"."NASEQUENCEIMP"."SEQUENCE_VERSION")
This error is clear enough but this was not a problem in GUS 3.0
where sequence_version would always get set to '1'.
Sequence_version doesn't seem to get set by dbEST so apparently there
is some default assignment elsewhere. Checking a GUS3.0 Oracle
instance, there appears to be a default value defined in the
NaSequenceImp table definition that I don't have in my 3.5 instance.
Does sequence_version need to be explicitly set by plugins for 3.5 or
is my 3.5 NaSequenceImp table erroneously missing a default value
for that column?
-M
|
|
From: Michael S. <msa...@pc...> - 2005-07-18 17:34:28
|
Yes, sorry for not being more clear. When I said that it should not affect any local code, I meant it should not affect any local (uncommitted) modifications. (Of course, you should always make a copy of your repository before running switch-- I have had issues with it). There are some codebase cleanup items that will need to be addressed. Also, for now, the GusAppFramework project will stay as GUS in the $PROJECT_HOME. In a future release, we'll be renaming this to comply with the standards (i.e. To GusAppFramework or something similar), but for the time being that would affect too much code and is being tabled. --Mike On 7/18/05 1:16 PM, "Junmin Liu" <ju...@pc...> wrote: > But I think the build process including the build.xml files have to be > changed to reflect this move. > > Currently the GUS's build.xml still use GUS as the project name and the > schema installation will fail since there is no GUS/Schema compoment. > > ---junmin > > > On Mon, 18 Jul 2005, Michael Saffitz wrote: > >> >> Please note the following repository changes, currently being made, which >> were discussed and approved at the Workshop. >> >> GUS/trunk/Schema has been promoted to it's own project, GusSchema >> >> GUS has been renamed to GusAppFramework >> >> It will most likely be necessary to recheckout/switch to the new >> directories. This should not affect any local code. >> >> In the GUS repository: >> >> svn switch https://www.cbil.upenn.edu/svn/gus/GusAppFramework/trunk >> >> --Mike >> >> >> >> >> ------------------------------------------------------- >> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies >> from IBM. Find simple to follow Roadmaps, straightforward articles, >> informative Webcasts and more! Get everything you need to get up to >> speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> |
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From: Junmin L. <ju...@pc...> - 2005-07-18 17:25:52
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Hi, Kumar, Most likely it is about the perl script: GUS_home/bin/generateGusObjects. You definitely can add some debug statements inside the file. --junmin On Mon, 18 Jul 2005, Kumar, Sanjeev (Contr) wrote: > Hi, > I am getting during GUS3.5 installation and the error message is not ver= y descriptive. > I am wondering if there is any log file is getting generated during GUS3= =2E5 installation > which can tell some more information regarding the error, for example li= ne number at which > error occured or statement which failed etc. > I am not able to find any such errorloog file. Do anyone know about it. > Also, is there any otherway to find the details regarding the error? > > Thanks > Sanjeev > > -----Original Message----- > From: Kumar, Sanjeev (Contr) > Sent: Tuesday, July 12, 2005 7:09 PM > To: 'gus...@li...' > Subject: FW: gus 3.5 installation error > > > > > -----Original Message----- > From: Kumar, Sanjeev (Contr) > Sent: Tuesday, July 12, 2005 7:08 PM > To: 'gus...@li...' > Subject: RE: gus 3.5 installation error > > > > Hi, > I am getting following error while doing the GUS3.5 installation. > It has created schema object successfully , but at the time of creation = of perl object it is throwing error message. > Can anyone help me ? > > Thanks > Sanjeev > > [oragus35@rdevse02 oragus35]$ build GUS install > -append > [WritePropertyFiles] Jul 12, 2005 7:10:43 PM > org.gusdb.install.WritePropertyFileTask writeGusProp > [WritePropertyFiles] INFO: Skipping creation of > GUS_CONFIG_FILE /home/oragus35/GUS/gus.properties -- > already exists > [WritePropertyFiles] Jul 12, 2005 7:10:43 PM > org.gusdb.install.WritePropertyFileTask > writeInstallProp > [WritePropertyFiles] INFO: Recreating install.prop > file > [WritePropertyFiles] Jul 12, 2005 7:10:43 PM > org.gusdb.install.WritePropertyFileTask > writePluginProp > [WritePropertyFiles] INFO: Recreating > GUS-PluginMgr.prop file > [copy] Copying 1 file to > /home/oragus35/GUS/gus_home/config > [copy] Copying 1 file to > /home/oragus35/GUS/gus_home/config > [echo] . > [echo] Installing CBIL/Bio > [echo] . > [echo] Installing CBIL/CSP > [echo] . > [echo] Installing CBIL/Util > [echo] . > [echo] Installing CBIL/HQ > [echo] . > [echo] Installing CBIL/ObjectMapper > [concat] No existing files and no nested text, > doing nothing > [echo] . > [echo] Installing GUS/Supported > [echo] . > [echo] Installing GUS/Community > [echo] . > [echo] Installing GUS/DBAdmin > [echo] . > [echo] Installing GUS/GOPredict > [echo] . > [echo] Installing GUS/ObjRelP > [echo] generating Perl Objects > > BUILD FAILED > /home/oragus35/GUS/project_home/install/build.xml:28: > The following error occurred while executing this > line: > /home/oragus35/GUS/project_home/GUS/build.xml:225: > exec returned: -1 > > Total time: 7 seconds > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: Junmin L. <ju...@pc...> - 2005-07-18 17:16:48
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But I think the build process including the build.xml files have to be changed to reflect this move. Currently the GUS's build.xml still use GUS as the project name and the schema installation will fail since there is no GUS/Schema compoment. ---junmin On Mon, 18 Jul 2005, Michael Saffitz wrote: > > Please note the following repository changes, currently being made, which > were discussed and approved at the Workshop. > > GUS/trunk/Schema has been promoted to it's own project, GusSchema > > GUS has been renamed to GusAppFramework > > It will most likely be necessary to recheckout/switch to the new > directories. This should not affect any local code. > > In the GUS repository: > > svn switch https://www.cbil.upenn.edu/svn/gus/GusAppFramework/trunk > > --Mike > > > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: Kumar, S. \(Contr\) <San...@ng...> - 2005-07-18 16:58:38
|
Hi,
I am getting during GUS3.5 installation and the error message is not =
very descriptive.
I am wondering if there is any log file is getting generated during =
GUS3.5 installation=20
which can tell some more information regarding the error, for example =
line number at which=20
error occured or statement which failed etc.
I am not able to find any such errorloog file. Do anyone know about =
it.
Also, is there any otherway to find the details regarding the error?
Thanks
Sanjeev
-----Original Message-----
From: Kumar, Sanjeev (Contr)=20
Sent: Tuesday, July 12, 2005 7:09 PM
To: 'gus...@li...'
Subject: FW: gus 3.5 installation error
-----Original Message-----
From: Kumar, Sanjeev (Contr)=20
Sent: Tuesday, July 12, 2005 7:08 PM
To: 'gus...@li...'
Subject: RE: gus 3.5 installation error
Hi,
I am getting following error while doing the GUS3.5 installation.
It has created schema object successfully , but at the time of =
creation of perl object it is throwing error message.
Can anyone help me ?
Thanks
Sanjeev
[oragus35@rdevse02 oragus35]$ build GUS install
-append=20
[WritePropertyFiles] Jul 12, 2005 7:10:43 PM
org.gusdb.install.WritePropertyFileTask writeGusProp
[WritePropertyFiles] INFO: Skipping creation of
GUS_CONFIG_FILE /home/oragus35/GUS/gus.properties --
already exists
[WritePropertyFiles] Jul 12, 2005 7:10:43 PM
org.gusdb.install.WritePropertyFileTask
writeInstallProp
[WritePropertyFiles] INFO: Recreating install.prop
file
[WritePropertyFiles] Jul 12, 2005 7:10:43 PM
org.gusdb.install.WritePropertyFileTask
writePluginProp
[WritePropertyFiles] INFO: Recreating
GUS-PluginMgr.prop file
[copy] Copying 1 file to
/home/oragus35/GUS/gus_home/config
[copy] Copying 1 file to
/home/oragus35/GUS/gus_home/config
[echo] .
[echo] Installing CBIL/Bio
[echo] .
[echo] Installing CBIL/CSP
[echo] .
[echo] Installing CBIL/Util
[echo] .
[echo] Installing CBIL/HQ
[echo] .
[echo] Installing CBIL/ObjectMapper
[concat] No existing files and no nested text,
doing nothing
[echo] .
[echo] Installing GUS/Supported
[echo] .
[echo] Installing GUS/Community
[echo] .
[echo] Installing GUS/DBAdmin
[echo] .
[echo] Installing GUS/GOPredict
[echo] .
[echo] Installing GUS/ObjRelP
[echo] generating Perl Objects
=20
BUILD FAILED
/home/oragus35/GUS/project_home/install/build.xml:28:
The following error occurred while executing this
line:
/home/oragus35/GUS/project_home/GUS/build.xml:225:
exec returned: -1
=20
Total time: 7 seconds
__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around=20
http://mail.yahoo.com=20
|
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