Kwalitee Issues

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::DB::Das::BioSQL::Iterator, Bio::DB::Tagger::Tag, Bio::Graphics::Browser::Shellwords

main_module_version_matches_dist_version

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

no_pod_errors

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

Error: GBrowse-1.99/contrib/install_macosx/BuildConfig.pm -- Around line 24: Unknown directive: =over4 Around line 26: '=item' outside of any '=over' GBrowse-1.99/docs/pod/CONFIGURE_HOWTO.pod -- Around line 1185: Expected '=item *' Around line 1202: Expected '=item *' Around line 1212: Expected '=item *' Around line 2352: Non-ASCII character seen before =encoding in 'Gènes'. Assuming CP1252 GBrowse-1.99/docs/pod/FAQ.pod -- Around line 48: Unknown E content in E<gmod-gbrowse@lists.sourceforge.net> GBrowse-1.99/lib/Bio/DB/Das/Chado/Segment/Feature.pm -- Around line 1123: '=item' outside of any '=over' Around line 1144: You forgot a '=back' before '=head2' GBrowse-1.99/lib/Bio/Graphics/Browser/AuthorizedFeatureFile.pm -- Around line 25: =over is the last thing in the document?! GBrowse-1.99/lib/Bio/Graphics/Browser/DataBase.pm -- Around line 46: '=item' outside of any '=over' =over without closing =back GBrowse-1.99/lib/Bio/Graphics/Browser/DataSource.pm -- Around line 98: You forgot a '=back' before '=head2' Around line 539: '=item' outside of any '=over' Around line 714: You forgot a '=back' before '=head2'

has_meta_json

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

has_known_license_in_source_file

Add =head1 LICENSE and/or the proper text of the well-known license to the main module in your code.

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::DB::Das::BioSQL, Bio::DB::Das::BioSQL::BioDatabaseAdaptor, Bio::DB::Das::BioSQL::DBAdaptor, Bio::DB::Das::BioSQL::Iterator, Bio::DB::Das::BioSQL::PartialSeqAdaptor, Bio::DB::Das::BioSQL::Segment, Bio::DB::Das::Chado, Bio::DB::Das::Chado::Segment, Bio::DB::Das::Chado::Segment::Feature, Bio::DB::GFF::Aggregator::match_gap, Bio::DB::GFF::Aggregator::reftranscript, Bio::DB::GFF::Aggregator::waba_alignment, Bio::DB::GFF::Aggregator::wormbase_gene, Bio::DB::GFF::SyntenyBlock, Bio::DB::GFF::SyntenyIO, Bio::DB::Tagger::Tag, Bio::Graphics::Browser::GFFPrinter, Bio::Graphics::Browser::GFFhelper, Bio::Graphics::Browser::I18n, Bio::Graphics::Browser::Markup, Bio::Graphics::Browser::OptionPick, Bio::Graphics::Browser::PadAlignment, Bio::Graphics::Browser::Plugin, Bio::Graphics::Browser::PluginSet, Bio::Graphics::Browser::Realign, Bio::Graphics::Browser::RemoteSet, Bio::Graphics::Browser::Render::Slave, Bio::Graphics::Browser::Shellwords, Bio::Graphics::Browser::UploadSet, Bio::Graphics::Browser::UserData, Bio::Graphics::Browser::Util, Bio::Graphics::Karyotype, CGI::Toggle

consistent_version

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

Error: 0.02,0.10,0.11,0.12,0.20,0.30,1.99

meta_yml_has_repository_resource

Add a 'repository' resource to the META.yml via 'meta_add' accessor (for Module::Build) or META_ADD parameter (for ExtUtils::MakeMaker).

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::DB::Das::BioSQL DAS-style access to a BioSQL database 0.02 metacpan
Bio::DB::Das::BioSQL::BioDatabaseAdaptor metacpan
Bio::DB::Das::BioSQL::DBAdaptor class that helps to use custom object adaptors metacpan
Bio::DB::Das::BioSQL::Feature metacpan
Bio::DB::Das::BioSQL::Iterator metacpan
Bio::DB::Das::BioSQL::PartialSeqAdaptor class that helps to use custom object adaptors metacpan
Bio::DB::Das::BioSQL::Segment DAS-style access to a BioSQL database 0.02 metacpan
Bio::DB::Das::Chado DAS-style access to a chado database 0.11 metacpan
Bio::DB::Das::Chado::Segment DAS-style access to a chado database 0.11 metacpan
Bio::DB::Das::Chado::Segment::Feature 0.12 metacpan
Bio::DB::Das::ChadoIterator metacpan
Bio::DB::GFF::Aggregator::match_gap GFF3 match aggregator metacpan
Bio::DB::GFF::Aggregator::reftranscript 0.10 metacpan
Bio::DB::GFF::Aggregator::waba_alignment A WABA alignment 0.20 metacpan
Bio::DB::GFF::Aggregator::wormbase_gene Wormbase gene aggregator 0.30 metacpan
Bio::DB::GFF::SyntenyBlock metacpan
Bio::DB::GFF::SyntenyIO metacpan
Bio::DB::Tagger Simple object tagging system metacpan
Bio::DB::Tagger::Iterator metacpan
Bio::DB::Tagger::Tag Authored tags metacpan
Bio::DB::Tagger::mysql metacpan
Bio::Graphics::Browser 1.99 metacpan
Bio::Graphics::Browser::AuthorizedFeatureFile Add HTTP authorization features to FeatureFile metacpan
Bio::Graphics::Browser::CachedTrack metacpan
Bio::Graphics::Browser::DataBase A simple cache for database handles metacpan
Bio::Graphics::Browser::DataSource metacpan
Bio::Graphics::Browser::GFFPrinter metacpan
Bio::Graphics::Browser::GFFhelper Helps gbrowse plugins handle GFF metacpan
Bio::Graphics::Browser::I18n metacpan
Bio::Graphics::Browser::Markup Markup routines for sequences in text form metacpan
Bio::Graphics::Browser::MetaSegment metacpan
Bio::Graphics::Browser::MetaSegment::Iterator metacpan
Bio::Graphics::Browser::OptionPick Pick options metacpan
Bio::Graphics::Browser::PadAlignment Insert pads into a multiple alignment metacpan
Bio::Graphics::Browser::Plugin Base class for gbrowse plugins. 0.20 metacpan
Bio::Graphics::Browser::PluginSet A set of plugins metacpan
Bio::Graphics::Browser::Realign Perl extension for Smith-Waterman alignments metacpan
Bio::Graphics::Browser::Region metacpan
Bio::Graphics::Browser::RegionSearch Search through multiple databases for feature matches. metacpan
Bio::Graphics::Browser::RemoteSet metacpan
Bio::Graphics::Browser::Render metacpan
Bio::Graphics::Browser::Render::HTML metacpan
Bio::Graphics::Browser::Render::Slave metacpan
Bio::Graphics::Browser::Render::Slave::Status metacpan
Bio::Graphics::Browser::RenderPanels metacpan
Bio::Graphics::Browser::Session metacpan
Bio::Graphics::Browser::Shellwords metacpan
Bio::Graphics::Browser::UploadSet A set of uploaded feature files metacpan
Bio::Graphics::Browser::UserData metacpan
Bio::Graphics::Browser::Util Exported utilities metacpan
Bio::Graphics::GBrowseFeature metacpan
Bio::Graphics::Karyotype metacpan
CGI::Toggle Utility methods for collapsible sections metacpan
FakeHomol metacpan

Other Files

Build.PL metacpan
Changes metacpan
MANIFEST metacpan
META.yml metacpan
Makefile.PL metacpan
README metacpan
README.GBrowse-2.00 metacpan
README.IF.GBROWSE.ISNT.WORKING metacpan
README.fedora_and_selinux metacpan
README.gff3 metacpan