[Bioperl-l] Help:: running perlmod2www.pl

Sun, 23 Jun 2002 22:46:14 -0700 (PDT)

Dear Members,

I have problem running the script perlmod2www.pl:
OS:WinME
ActivePerl 5.6.1
BioPerl1.0

When I run the script,  like this....
C:\Pdoc-1.0pack\scripts>perl perlmod2www.pl -source
c:\Perl\lib\bioperl1.0\bioperl\bio
-target \pdoc1.0\pdoc -wroot C:\pdoc1.0\pdoc >pdoc.txt

The output is given below >>..which gives only the
half way documentation...passing through
only 5-6 subdirectories of
c:\Perl\lib\bioperl1.0\bioperl\bio...
Even it does not create the index.html file of 3
frames.

But when run through the individual subdirectories of
c:\Perl\lib\bioperl1.0\bioperl\bio, it creates the 
documentation with index file limited only to that
subdirectory modules.

>>Here is the Output: Please read the error message at
the end of this output:

Getting tree from
c:\Perl\lib\bioperl1.0\bioperl\bio...
Generating indexes...
Creating levels index file
\pdoc1.0\pdoc\all_packages.html
Creating global Perl modules index file
\pdoc1.0\pdoc\all_modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Variation\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Variation\IO\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\TreeIO\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Tree\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Tools\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Tools\StateMachine\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Tools\Sim4\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Tools\Prediction\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Tools\HMMER\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Tools\Blast\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Tools\BPlite\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Tools\Alignment\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Tools\Run\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Tools\Run\Alignment\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Symbol\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Structure\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Structure\SecStr\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Structure\SecStr\STRIDE\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Structure\SecStr\DSSP\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Structure\IO\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\SeqIO\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\SeqIO\game\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\SeqFeature\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\SeqFeature\Gene\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Seq\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\SearchIO\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\SearchIO\Writer\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Search\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Search\Result\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Search\Hit\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Search\HSP\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Root\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\MapIO\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Map\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Location\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\LiveSeq\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\LiveSeq\IO\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Index\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Graphics\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Graphics\Glyph\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Factory\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Event\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Biblio\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Biblio\IO\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Annotation\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\AlignIO\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\Align\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\DB\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\DB\GFF\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\DB\GFF\Aggregator\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\DB\GFF\Adaptor\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\DB\GFF\Adaptor\dbi\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\DB\GFF\Util\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\DB\Biblio\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\DB\Flat\modules.html
Creating Perl modules index file
\pdoc1.0\pdoc\DB\Flat\BDB\modules.html
Generating documentation from
c:\Perl\lib\bioperl1.0\bioperl\bio\
# File c:\Perl\lib\bioperl1.0\bioperl\bio\AlignIO.pm
-> Rendering Bio::AlignIO in
   \pdoc1.0\pdoc\AlignIO.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\AnalysisParserI.pm
-> Rendering Bio::AnalysisParserI in
   \pdoc1.0\pdoc\AnalysisParserI.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\AnalysisResultI.pm
-> Rendering Bio::AnalysisResultI in
   \pdoc1.0\pdoc\AnalysisResultI.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Annotation.pm
-> Rendering Bio::Annotation in
   \pdoc1.0\pdoc\Annotation.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\AnnotationCollectionI.pm
-> Rendering Bio::AnnotationCollectionI in
   \pdoc1.0\pdoc\AnnotationCollectionI.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\AnnotationI.pm
-> Rendering Bio::AnnotationI in
   \pdoc1.0\pdoc\AnnotationI.html
# File c:\Perl\lib\bioperl1.0\bioperl\bio\Biblio.pm
-> Rendering Bio::Biblio in
   \pdoc1.0\pdoc\Biblio.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\DBLinkContainerI.pm
-> Rendering Bio::DBLinkContainerI in
   \pdoc1.0\pdoc\DBLinkContainerI.html
# File c:\Perl\lib\bioperl1.0\bioperl\bio\DasI.pm
-> Rendering Bio::DasI in
   \pdoc1.0\pdoc\DasI.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\DasSegmentI.pm
Warning: failed to parse and/or convert file
c:\Perl\lib\bioperl1.0\bioperl\bio\DasSegmentI.pm!
Check if package name definition is correct ('package'
line)
File skipped.
# File c:\Perl\lib\bioperl1.0\bioperl\bio\Graphics.pm
-> Rendering Bio::Graphics in
   \pdoc1.0\pdoc\Graphics.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\LocatableSeq.pm
-> Rendering Bio::LocatableSeq in
   \pdoc1.0\pdoc\LocatableSeq.html
# File c:\Perl\lib\bioperl1.0\bioperl\bio\LocationI.pm
-> Rendering Bio::LocationI in
   \pdoc1.0\pdoc\LocationI.html
# File c:\Perl\lib\bioperl1.0\bioperl\bio\MapIO.pm
-> Rendering Bio::MapIO in
   \pdoc1.0\pdoc\MapIO.html
# File c:\Perl\lib\bioperl1.0\bioperl\bio\Perl.pm
-> Rendering Bio::Perl in
   \pdoc1.0\pdoc\Perl.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\PrimarySeq.pm
-> Rendering Bio::PrimarySeq in
   \pdoc1.0\pdoc\PrimarySeq.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\PrimarySeqI.pm
-> Rendering Bio::PrimarySeqI in
   \pdoc1.0\pdoc\PrimarySeqI.html
# File c:\Perl\lib\bioperl1.0\bioperl\bio\Range.pm
-> Rendering Bio::Range in
   \pdoc1.0\pdoc\Range.html
# File c:\Perl\lib\bioperl1.0\bioperl\bio\RangeI.pm
-> Rendering Bio::RangeI in
   \pdoc1.0\pdoc\RangeI.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\SearchDist.pm
-> Rendering Bio::SearchDist in
   \pdoc1.0\pdoc\SearchDist.html
# File c:\Perl\lib\bioperl1.0\bioperl\bio\SearchIO.pm
-> Rendering Bio::SearchIO in
   \pdoc1.0\pdoc\SearchIO.html
# File c:\Perl\lib\bioperl1.0\bioperl\bio\Seq.pm
-> Rendering Bio::Seq in
   \pdoc1.0\pdoc\Seq.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\SeqAnalysisParserI.pm
-> Rendering Bio::SeqAnalysisParserI in
   \pdoc1.0\pdoc\SeqAnalysisParserI.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\SeqFeatureI.pm
-> Rendering Bio::SeqFeatureI in
   \pdoc1.0\pdoc\SeqFeatureI.html
# File c:\Perl\lib\bioperl1.0\bioperl\bio\SeqI.pm
-> Rendering Bio::SeqI in
   \pdoc1.0\pdoc\SeqI.html
# File c:\Perl\lib\bioperl1.0\bioperl\bio\SeqIO.pm
-> Rendering Bio::SeqIO in
   \pdoc1.0\pdoc\SeqIO.html
# File c:\Perl\lib\bioperl1.0\bioperl\bio\SeqUtils.pm
-> Rendering Bio::SeqUtils in
   \pdoc1.0\pdoc\SeqUtils.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\SimpleAlign.pm
-> Rendering Bio::SimpleAlign in
   \pdoc1.0\pdoc\SimpleAlign.html
# File c:\Perl\lib\bioperl1.0\bioperl\bio\Species.pm
-> Rendering Bio::Species in
   \pdoc1.0\pdoc\Species.html
# File c:\Perl\lib\bioperl1.0\bioperl\bio\TreeIO.pm
-> Rendering Bio::TreeIO in
   \pdoc1.0\pdoc\TreeIO.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\UpdateableSeqI.pm
-> Rendering Bio::UpdateableSeqI in
   \pdoc1.0\pdoc\UpdateableSeqI.html
Generating documentation from
c:\Perl\lib\bioperl1.0\bioperl\bio\Variation\
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Variation\AAChange.pm
-> Rendering Bio::Variation::AAChange in
   \pdoc1.0\pdoc\Variation\AAChange.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Variation\AAReverseMutate.pm
-> Rendering Bio::Variation::AAReverseMutate in
   \pdoc1.0\pdoc\Variation\AAReverseMutate.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Variation\Allele.pm
-> Rendering Bio::Variation::Allele in
   \pdoc1.0\pdoc\Variation\Allele.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Variation\DNAMutation.pm
-> Rendering Bio::Variation::DNAMutation in
   \pdoc1.0\pdoc\Variation\DNAMutation.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Variation\IO.pm
-> Rendering Bio::Variation::IO in
   \pdoc1.0\pdoc\Variation\IO.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Variation\RNAChange.pm
-> Rendering Bio::Variation::RNAChange in
   \pdoc1.0\pdoc\Variation\RNAChange.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Variation\SeqDiff.pm
-> Rendering Bio::Variation::SeqDiff in
   \pdoc1.0\pdoc\Variation\SeqDiff.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Variation\VariantI.pm
-> Rendering Bio::Variation::VariantI in
   \pdoc1.0\pdoc\Variation\VariantI.html
Generating documentation from
c:\Perl\lib\bioperl1.0\bioperl\bio\Variation\IO\
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Variation\IO\flat.pm
-> Rendering Bio::Variation::IO::flat in
   \pdoc1.0\pdoc\Variation\IO\flat.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Variation\IO\xml.pm
-> Rendering Bio::Variation::IO::xml in
   \pdoc1.0\pdoc\Variation\IO\xml.html
Generating documentation from
c:\Perl\lib\bioperl1.0\bioperl\bio\TreeIO\
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\TreeIO\TreeEventBuilder.pm
-> Rendering Bio::TreeIO::TreeEventBuilder in
   \pdoc1.0\pdoc\TreeIO\TreeEventBuilder.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\TreeIO\newick.pm
-> Rendering Bio::TreeIO::newick in
   \pdoc1.0\pdoc\TreeIO\newick.html
Generating documentation from
c:\Perl\lib\bioperl1.0\bioperl\bio\Tree\
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Tree\AlleleNode.pm
-> Rendering Bio::Tree::AlleleNode in
   \pdoc1.0\pdoc\Tree\AlleleNode.html
# File c:\Perl\lib\bioperl1.0\bioperl\bio\Tree\Node.pm
-> Rendering Bio::Tree::Node in
   \pdoc1.0\pdoc\Tree\Node.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Tree\NodeI.pm
-> Rendering Bio::Tree::NodeI in
   \pdoc1.0\pdoc\Tree\NodeI.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Tree\RandomFactory.pm
-> Rendering Bio::Tree::RandomFactory in
   \pdoc1.0\pdoc\Tree\RandomFactory.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Tree\Statistics.pm
-> Rendering Bio::Tree::Statistics in
   \pdoc1.0\pdoc\Tree\Statistics.html
# File c:\Perl\lib\bioperl1.0\bioperl\bio\Tree\Tree.pm
-> Rendering Bio::Tree::Tree in
   \pdoc1.0\pdoc\Tree\Tree.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Tree\TreeI.pm
-> Rendering Bio::Tree::TreeI in
   \pdoc1.0\pdoc\Tree\TreeI.html
Generating documentation from
c:\Perl\lib\bioperl1.0\bioperl\bio\Tools\
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Tools\AlignFactory.pm
-> Rendering Bio::Tools::AlignFactory in
   \pdoc1.0\pdoc\Tools\AlignFactory.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Tools\AnalysisResult.pm
-> Rendering Bio::Tools::AnalysisResult in
   \pdoc1.0\pdoc\Tools\AnalysisResult.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Tools\BPbl2seq.pm
-> Rendering Bio::Tools::BPbl2seq in
   \pdoc1.0\pdoc\Tools\BPbl2seq.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Tools\BPlite.pm
-> Rendering Bio::Tools::BPlite in
   \pdoc1.0\pdoc\Tools\BPlite.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Tools\BPpsilite.pm
-> Rendering Bio::Tools::BPpsilite in
   \pdoc1.0\pdoc\Tools\BPpsilite.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Tools\Blast.pm
-> Rendering Bio::Tools::Blast in
   \pdoc1.0\pdoc\Tools\Blast.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Tools\CodonTable.pm
-> Rendering Bio::Tools::CodonTable in
   \pdoc1.0\pdoc\Tools\CodonTable.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Tools\EPCR.pm
-> Rendering Bio::Tools::EPCR in
   \pdoc1.0\pdoc\Tools\EPCR.html
# File
c:\Perl\lib\bioperl1.0\bioperl\bio\Tools\ESTScan.pm
-> Rendering Bio::Tools::ESTScan in
   \pdoc1.0\pdoc\Tools\ESTScan.html

The Output terminates with these lines>>
Can't find unicode character property definition via
main->r or r.pl at unicode/
Is/r.pl line 0

Any help would be highly appreciated.
Thanks..

-Viren

=====
Viren Konde
CNRS-Marseille 
FRANCE

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