[GUSDEV] GUS 3.5 plugin registration error

[Jian Lu <jl...@vb...>]

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.