Re: [GUSDEV] GUS 3.5 plugin registration error

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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.
>
>
>
>
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