Kwalitee Issues

has_meta_yml

Add a META.yml to the distribution. Your buildtool should be able to autogenerate it.

main_module_version_matches_dist_version

Make sure that the main module name and version are the same of the distribution.

manifest_matches_dist

Run a proper command ("make manifest" or "./Build manifest", maybe with a force option), or use a distribution builder to generate the MANIFEST. Or update MANIFEST manually.

Error:

  • MANIFEST (203) does not match dist (206):
  • Missing in MANIFEST: MANIFEST.SKIP, bioperl.lisp, t/Species.t

no_files_to_be_skipped

Fix MANIFEST.SKIP or use an authoring tool which respects MANIFEST.SKIP. Note that each entry in MANIFEST.SKIP is a regular expression. You may need to add appropriate meta characters not to ignore necessary stuff.

Error: MANIFEST.SKIP,bioperl.lisp

no_pod_errors

Remove the POD errors. You can check for POD errors automatically by including Test::Pod to your test suite.

Error: bioperl-0.6.1/Bio/Root/Er r.pm -- Around line 987: Unterminated B<...> sequence bioperl-0.6.1/Bio/Root/Ob ject.pm -- Around line 336: Can't have a 0 in =over 0 bioperl-0.6.1/Bio/Tools/B last/HSP.pm -- Around line 83: Can't have a 0 in =over 0 bioperl-0.6.1/Bio/Tools/B last/Run/Webblast.pm -- Around line 344: Can't have a 0 in =over 0 bioperl-0.6.1/Bio/Tools/B last.pm -- Around line 339: Unterminated B<...> sequence

prereq_matches_use

List all used modules in META.yml requires

Error:

  • IO::Scalar

use_strict

Add 'use strict' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules are strictly written.

Error: Bio::Root::Xref

consistent_version

Split the distribution, or fix the version numbers to make them consistent (use the highest version number to avoid version downgrade).

Error: 0.01,0.011,0.014,0.04,0.041,0.043,0.05,0.076,0.09,0.091,0.1,0.2,1.01,1.24

has_meta_json

Add a META.json to the distribution. Your buildtool should be able to autogenerate it.

meta_yml_has_license

Define the license if you are using in Build.PL. If you are using MakeMaker (Makefile.PL) you should upgrade to ExtUtils::MakeMaker version 6.31.

proper_libs

Move your *.pm files in a directory named 'lib'. The directory structure should look like 'lib/Your/Module.pm' for a module named 'Your::Module'. If you need to provide additional files, e.g. for testing, that should not be considered for Kwalitee, then you should look at the 'provides' map in META.yml to limit the files scanned; or use the 'no_index' map to exclude parts of the distribution.

Error: Bio/Annotation.pm, Bio/Annotation/Comment.pm, Bio/Annotation/DBLink.pm, Bio/Annotation/Reference.pm, Bio/DB/Ace.pm, Bio/DB/GenBank.pm, Bio/DB/GenPept.pm, Bio/DB/RandomAccessI.pm, Bio/DB/SeqI.pm, Bio/Index/Abstract.pm, Bio/Index/AbstractSeq.pm, Bio/Index/EMBL.pm, Bio/Index/Fasta.pm, Bio/Index/SwissPfam.pm, Bio/LocatableSeq.pm, Bio/PrimarySeq.pm, Bio/PrimarySeqI.pm, Bio/Range.pm, Bio/RangeI.pm, Bio/Root/Err.pm, Bio/Root/Global.pm, Bio/Root/IOManager.pm, Bio/Root/Object.pm, Bio/Root/RootI.pm, Bio/Root/Utilities.pm, Bio/Root/Vector.pm, Bio/Root/Xref.pm, Bio/Search/Hit/Fasta.pm, Bio/Search/Hit/HitI.pm, Bio/Search/Processor.pm, Bio/Search/Processor/Fasta.pm, Bio/Search/Processor/ProcessorI.pm, Bio/Search/Result/Fasta.pm, Bio/Search/Result/ResultI.pm, Bio/SearchDist.pm, Bio/Seq.pm, Bio/SeqFeature/FeaturePair.pm, Bio/SeqFeature/Generic.pm, Bio/SeqFeatureI.pm, Bio/SeqI.pm, Bio/SeqIO.pm, Bio/SeqIO/FTHelper.pm, Bio/SeqIO/MultiFile.pm, Bio/SeqIO/embl.pm, Bio/SeqIO/fasta.pm, Bio/SeqIO/gcg.pm, Bio/SeqIO/genbank.pm, Bio/SeqIO/pir.pm, Bio/SeqIO/raw.pm, Bio/SeqIO/scf.pm, Bio/SeqIO/swiss.pm, Bio/SimpleAlign.pm, Bio/Species.pm, Bio/Tools/AlignFactory.pm, Bio/Tools/Blast.pm, Bio/Tools/Blast/HSP.pm, Bio/Tools/Blast/HTML.pm, Bio/Tools/Blast/Run/LocalBlast.pm, Bio/Tools/Blast/Run/Webblast.pm, Bio/Tools/Blast/Sbjct.pm, Bio/Tools/CodonTable.pm, Bio/Tools/Fasta.pm, Bio/Tools/HMMER/Domain.pm, Bio/Tools/HMMER/Results.pm, Bio/Tools/HMMER/Set.pm, Bio/Tools/IUPAC.pm, Bio/Tools/RestrictionEnzyme.pm, Bio/Tools/SeqAnal.pm, Bio/Tools/SeqPattern.pm, Bio/Tools/SeqStats.pm, Bio/Tools/SeqWords.pm, Bio/Tools/Sigcleave.pm, Bio/Tools/Sim4/Exon.pm, Bio/Tools/Sim4/Results.pm, Bio/Tools/WWW.pm, Bio/Tools/pSW.pm, Bio/UnivAln.pm

use_warnings

Add 'use warnings' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.

Error: Bio::Annotation, Bio::Annotation::Comment, Bio::Annotation::DBLink, Bio::Annotation::Reference, Bio::DB::Ace, Bio::DB::GenBank, Bio::DB::GenPept, Bio::DB::RandomAccessI, Bio::DB::SeqI, Bio::Index::Abstract, Bio::Index::AbstractSeq, Bio::Index::EMBL, Bio::Index::Fasta, Bio::Index::SwissPfam, Bio::LocatableSeq, Bio::PrimarySeq, Bio::PrimarySeqI, Bio::Range, Bio::RangeI, Bio::Root::Err, Bio::Root::Global, Bio::Root::IOManager, Bio::Root::Object, Bio::Root::RootI, Bio::Root::Utilities, Bio::Root::Vector, Bio::Root::Xref, Bio::Search::Hit::Fasta, Bio::Search::Hit::HitI, Bio::Search::Processor, Bio::Search::Processor::Fasta, Bio::Search::Processor::ProcessorI, Bio::Search::Result::Fasta, Bio::Search::Result::ResultI, Bio::SearchDist, Bio::Seq, Bio::SeqFeature::FeaturePair, Bio::SeqFeature::Generic, Bio::SeqFeatureI, Bio::SeqI, Bio::SeqIO, Bio::SeqIO::FTHelper, Bio::SeqIO::MultiFile, Bio::SeqIO::embl, Bio::SeqIO::fasta, Bio::SeqIO::gcg, Bio::SeqIO::genbank, Bio::SeqIO::pir, Bio::SeqIO::raw, Bio::SeqIO::scf, Bio::SeqIO::swiss, Bio::SimpleAlign, Bio::Species, Bio::Tools::AlignFactory, Bio::Tools::Blast, Bio::Tools::Blast::HSP, Bio::Tools::Blast::HTML, Bio::Tools::Blast::Run::LocalBlast, Bio::Tools::Blast::Run::Webblast, Bio::Tools::Blast::Sbjct, Bio::Tools::CodonTable, Bio::Tools::Fasta, Bio::Tools::HMMER::Domain, Bio::Tools::HMMER::Results, Bio::Tools::HMMER::Set, Bio::Tools::IUPAC, Bio::Tools::RestrictionEnzyme, Bio::Tools::SeqAnal, Bio::Tools::SeqPattern, Bio::Tools::SeqStats, Bio::Tools::SeqWords, Bio::Tools::Sigcleave, Bio::Tools::Sim4::Exon, Bio::Tools::Sim4::Results, Bio::Tools::WWW, Bio::Tools::pSW, Bio::UnivAln

has_separate_license_file

This is not a critical issue. Currently mainly informative for the CPANTS authors. It might be removed later.

Modules

Name Abstract Version View
Bio::Annotation A generic object for annotations metacpan
Bio::Annotation::Comment A Comment on an Annotation metacpan
Bio::Annotation::DBLink Database Link metacpan
Bio::Annotation::Reference Literature Reference Block metacpan
Bio::DB::Ace Database object interface to ACeDB servers metacpan
Bio::DB::GenBank Database object interface to GenBank metacpan
Bio::DB::GenPept Database object interface to GenPept metacpan
Bio::DB::RandomAccessI Abstract interface for a sequence database metacpan
Bio::DB::SeqI Abstract Interface for Sequence databases metacpan
Bio::Index::Abstract Abstract interface for indexing a flat file metacpan
Bio::Index::AbstractSeq Base class for AbstractSeq's metacpan
Bio::Index::EMBL Interface for indexing (multiple) EMBL/Swissprot .dat files (ie flat file embl/swissprot format). 0.1 metacpan
Bio::Index::Fasta Interface for indexing (multiple) fasta files 0.2 metacpan
Bio::Index::SwissPfam Interface for indexing swisspfam files 0.1 metacpan
Bio::LocatableSeq A Sequence object with start/end points on it metacpan
Bio::PrimarySeq Bioperl lightweight Sequence Object metacpan
Bio::PrimarySeqI Interface definition for a Bio::PrimarySeq metacpan
Bio::Range Pure perl RangeI implementation metacpan
Bio::RangeI Range interface metacpan
Bio::Root::Err 0.041 metacpan
Bio::Root::Global Global variables and utility functions metacpan
Bio::Root::IOManager Input and output manager for Perl5 objects. 0.043 metacpan
Bio::Root::Object A core Perl 5 object. 0.041 metacpan
Bio::Root::RootI Abstract interface to root object code metacpan
Bio::Root::Utilities General-purpose utility module 0.05 metacpan
Bio::Root::Vector Interface for managing linked lists of Perl5 objects. 0.04 metacpan
Bio::Root::Xref A generic cross-reference object. 0.01 metacpan
Bio::Search::Hit::Fasta Hit object specific for Fasta-generated hits metacpan
Bio::Search::Hit::HitI Abstract interface for Hit objects metacpan
Bio::Search::Processor DESCRIPTION of Object metacpan
Bio::Search::Processor::Fasta Processor of Fasta-generated data streams metacpan
Bio::Search::Processor::ProcessorI Abstract Interface for Processor Objects metacpan
Bio::Search::Result::Fasta Result object for FASTA-generated data sources metacpan
Bio::Search::Result::ResultI metacpan
Bio::SearchDist A perl wrapper around Sean Eddy's histogram object metacpan
Bio::Seq Sequence object, with features metacpan
Bio::SeqFeature::FeaturePair hold pair feature information e.g. blast hits metacpan
Bio::SeqFeature::Generic Generic SeqFeature metacpan
Bio::SeqFeatureI Abstract interface of a Sequence Feature metacpan
Bio::SeqI Abstract Interface of Sequence (with features) metacpan
Bio::SeqIO Handler for SeqIO Formats metacpan
Bio::SeqIO::FTHelper Helper class for Embl/Genbank feature tables metacpan
Bio::SeqIO::MultiFile Treating a set of files as a single input stream metacpan
Bio::SeqIO::embl EMBL sequence input/output stream metacpan
Bio::SeqIO::fasta fasta sequence input/output stream metacpan
Bio::SeqIO::gcg GCG sequence input/output stream metacpan
Bio::SeqIO::genbank metacpan
Bio::SeqIO::pir PIR sequence input/output stream metacpan
Bio::SeqIO::raw raw sequence file input/output stream metacpan
Bio::SeqIO::scf SCF sequence input/output stream metacpan
Bio::SeqIO::swiss metacpan
Bio::SimpleAlign metacpan
Bio::Species Generic species object metacpan
Bio::Tools::AlignFactory Base object for alignment factories metacpan
Bio::Tools::Blast 0.09 metacpan
Bio::Tools::Blast::HSP 0.09 metacpan
Bio::Tools::Blast::HTML 0.076 metacpan
Bio::Tools::Blast::Run::LocalBlast 0.01 metacpan
Bio::Tools::Blast::Run::Webblast 1.24 metacpan
Bio::Tools::Blast::Sbjct 0.091 metacpan
Bio::Tools::CodonTable Bioperl codon table object metacpan
Bio::Tools::Fasta 0.014 metacpan
Bio::Tools::HMMER::Domain One particular domain hit from HMMER metacpan
Bio::Tools::HMMER::Results Object representing HMMER output results metacpan
Bio::Tools::HMMER::Set Set of identical domains from HMMER matches metacpan
Bio::Tools::IUPAC metacpan
Bio::Tools::RestrictionEnzyme 0.04 metacpan
Bio::Tools::SeqAnal 0.011 metacpan
Bio::Tools::SeqPattern 0.011 metacpan
Bio::Tools::SeqStats Object holding statistics for one particular sequence metacpan
Bio::Tools::SeqWords Object holding n-mer statistics for one sequence metacpan
Bio::Tools::Sigcleave 0.01 metacpan
Bio::Tools::Sim4::Exon A single metacpan
Bio::Tools::Sim4::Results Results of one Sim4 run metacpan
Bio::Tools::WWW 0.014 metacpan
Bio::Tools::pSW DESCRIPTION of Object metacpan
Bio::UnivAln Bioperl alignment object 1.01 metacpan

Other Files

Bio/Tools/Blast/Run/Makefile.PL metacpan
Changes metacpan
MANIFEST metacpan
Makefile.PL metacpan
README metacpan