Re: [GUSDEV] GUS 3.5 plugin registration error

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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.
>>
>>
>>
>>
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>
>  
>