[Bioperl-l] bioperl-live: audit of FIXME/???/TODO/etc and undef/die

Hilmar Lapp hlapp at gmx.net
Wed Sep 20 11:10:39 EDT 2006


I wasn't even aware that that was a 'requirement' <sigh> I'll see to  
fix the Ontology modules ...

On Sep 20, 2006, at 12:44 AM, Chris Fields wrote:

> Ouch!  That many?
>
> Chris
>
> On Sep 19, 2006, at 11:38 PM, Torsten Seemann wrote:
>
>> David,
>>
>>>  From running the deobfuscator on bioperl-live, I've found some
>>> formatting inconsistencies in the POD of some modules which are
>>> hard  for the deobfuscator to parse. I've corrected some of these
>>> in my  working (checked-out) copy of bioperl-live.
>>
>> Please check them in.
>>
>> I have written a script to audit all Perl modules to ensure the
>> NAME in the POD matches the Perl module and has the correct
>> capitilization.
>>
>> % cd bioperl-live/maintenance
>> % ./check_NAMEs.pl
>>
>> Here's the current buggy ones, before your commits AFAIK.
>>
>> Bio::IdCollectionI
>> Bio::Location::SplitLocationI
>> Bio::Search::Result::PullResultI
>> Bio::Search::HSP::HmmpfamHSP
>> Bio::Search::Hit::HmmpfamHit
>> Bio::Expression::FeatureGroup::FeatureGroupMas50
>> Bio::Expression::FeatureSet::FeatureSetMas50
>> Bio::DB::EUtilities::Cookie
>> Bio::DB::GFF::Adaptor::berkeleydb
>> Bio::DB::GFF::Adaptor::biofetch_oracle
>> Bio::DB::GFF::Adaptor::dbi::pg_fts
>> Bio::DB::GFF::Adaptor::memory::feature_serializer
>> Bio::DB::SeqFeature::Store::bdb
>> Bio::DB::SeqFeature::Store::DBI::Iterator
>> Bio::Matrix::PSM::SiteMatrixI
>> Bio::Matrix::PSM::ProtPsm
>> Bio::Matrix::PSM::IO::psiblast
>> Bio::Matrix::PSM::IO::transfac
>> Bio::Matrix::PSM::IO::meme
>> Bio::Graphics::Util
>> Bio::Graphics::Glyph::ex
>> Bio::Graphics::Glyph::three_letters
>> Bio::Graphics::Glyph::arrow
>> Bio::Graphics::Glyph::ruler_arrow
>> Bio::Graphics::Glyph::flag
>> Bio::Phenotype::Measure
>> Bio::Phenotype::PhenotypeI
>> Bio::Phenotype::Phenotype
>> Bio::Phenotype::Correlate
>> Bio::Phenotype::OMIM::MiniMIMentry
>> Bio::Phenotype::OMIM::OMIMparser
>> Bio::Phenotype::OMIM::OMIMentry
>> Bio::Phenotype::OMIM::OMIMentryAllelicVariant
>> Bio::SeqIO::qual
>> Bio::SeqIO::genbank
>> Bio::OntologyIO::simplehierarchy
>> Bio::OntologyIO::InterProParser
>> Bio::OntologyIO::soflat
>> Bio::OntologyIO::dagflat
>> Bio::OntologyIO::obo
>> Bio::OntologyIO::goflat
>> Bio::OntologyIO::Handlers::InterProHandler
>> Bio::Tools::pICalculator
>> Bio::Tools::ECnumber
>> Bio::SeqFeature::Gene::GeneStructureI
>> Bio::SeqFeature::Gene::Poly_A_site
>> Bio::Seq::SeqFastaSpeedFactory
>> Bio::Ontology::RelationshipI
>> Bio::Ontology::TermI
>> Bio::Ontology::InterProTerm
>> Bio::Ontology::RelationshipType
>> Bio::Ontology::OBOterm
>> Bio::Ontology::OBOEngine
>> Bio::Ontology::PathI
>> Bio::Ontology::OntologyEngineI
>> Bio::Ontology::Path
>> Bio::Ontology::GOterm
>> Bio::Ontology::Term
>> Bio::Ontology::SimpleGOEngine
>> Bio::Ontology::Relationship
>> Bio::Ontology::SimpleGOEngine::GraphAdaptor
>> Bio::Ontology::SimpleGOEngine::GraphAdaptor02
>>
>> -- 
>> Dr Torsten Seemann               http://www.vicbioinformatics.com
>> Victorian Bioinformatics Consortium, Monash University, Australia
>>
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
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> Bioperl-l at lists.open-bio.org
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>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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