Kwalitee Issues

no_pod_errors

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

Error: GBrowse-2.55/contrib/install_macosx/BuildConfig.pm -- Around line 24: Unknown directive: =over4Around line 26: '=item' outside of any '=over' GBrowse-2.55/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 ISO8859-1 GBrowse-2.55/docs/pod/FAQ.pod -- Around line 48: Unknown E content in E<gmod-gbrowse@lists.sourceforge.net> GBrowse-2.55/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm -- Around line 26: =over is the last thing in the document?! GBrowse-2.55/lib/Bio/Graphics/Browser2/DataBase.pm -- Around line 69: '=item' outside of any '=over' =over without closing =back GBrowse-2.55/lib/Bio/Graphics/Browser2/DataSource.pm -- Around line 153: You forgot a '=back' before '=head2'Around line 874: '=item' outside of any '=over'Around line 1118: You forgot a '=back' before '=head2'

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::Tagger::Tag, Bio::Graphics::Browser2::Shellwords

consistent_version

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

Error: 0.01,0.10,0.20,0.30,0.5,1.00,1.01,1.10,1.17,2.55

no_unauthorized_packages

Ask the owner of the distribution (the one who released it first, or the one who is designated in x_authority) to give you a (co-)maintainer's permission.

Error:

  • Bio::DB::SeqFeature::Store::LoadHelper

use_warnings

Add 'use warnings' (or its equivalents) to all modules (this will require perl > 5.6), 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::GFF::Aggregator::match_gap, Bio::DB::GFF::Aggregator::reftranscript, Bio::DB::GFF::Aggregator::waba_alignment, Bio::DB::GFF::Aggregator::wormbase_gene, Bio::DB::SeqFeature::Store::Alias::Segment, Bio::DB::SeqFeature::Store::BedLoader, Bio::DB::SeqFeature::Store::LoadHelper, Bio::DB::Tagger::Tag, Bio::Graphics::Browser2::Action, Bio::Graphics::Browser2::CAlign, Bio::Graphics::Browser2::DataLoader, Bio::Graphics::Browser2::DataLoader::archive, Bio::Graphics::Browser2::DataLoader::bam, Bio::Graphics::Browser2::DataLoader::bed, Bio::Graphics::Browser2::DataLoader::bigbed, Bio::Graphics::Browser2::DataLoader::bigwig, Bio::Graphics::Browser2::DataLoader::generic, Bio::Graphics::Browser2::DataLoader::gff, Bio::Graphics::Browser2::DataLoader::gff3, Bio::Graphics::Browser2::DataLoader::sam, Bio::Graphics::Browser2::DataLoader::useq, Bio::Graphics::Browser2::DataLoader::wig2bigwig, Bio::Graphics::Browser2::ExternalData, Bio::Graphics::Browser2::GFFhelper, Bio::Graphics::Browser2::I18n, Bio::Graphics::Browser2::Markup, Bio::Graphics::Browser2::OptionPick, Bio::Graphics::Browser2::PadAlignment, Bio::Graphics::Browser2::Plugin, Bio::Graphics::Browser2::Plugin::AuthPlugin, Bio::Graphics::Browser2::PluginSet, Bio::Graphics::Browser2::Realign, Bio::Graphics::Browser2::RemoteSet, Bio::Graphics::Browser2::Render::Slave, Bio::Graphics::Browser2::Render::Slave::StagingServer, Bio::Graphics::Browser2::SendMail, Bio::Graphics::Browser2::Shellwords, Bio::Graphics::Browser2::TrackDumper, Bio::Graphics::Browser2::TrackDumper::RichSeqMaker, Bio::Graphics::Browser2::UserDB, Bio::Graphics::Browser2::UserTracks, Bio::Graphics::Browser2::UserTracks::Database, Bio::Graphics::Browser2::UserTracks::Filesystem, Bio::Graphics::Browser2::Util, Bio::Graphics::Karyotype, Bio::Graphics::Wiggle::Loader::Nosample, CGI::Toggle, Legacy::DB::SyntenyBlock, Legacy::DB::SyntenyIO, Legacy::Graphics::Browser, Legacy::Graphics::Browser::I18n, Legacy::Graphics::Browser::PageSettings, Legacy::Graphics::Browser::Synteny, Legacy::Graphics::Browser::Util, MyFeatureFileLoader

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).

Modules

Name Abstract Version View
Bio::DB::GFF::Aggregator::match_gap GFF3 match aggregator 0 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::SeqFeature::Store::Alias 0 metacpan
Bio::DB::SeqFeature::Store::Alias::Iterator 0 metacpan
Bio::DB::SeqFeature::Store::Alias::Segment 0 metacpan
Bio::DB::SeqFeature::Store::BedLoader 0 metacpan
Bio::DB::SeqFeature::Store::LoadHelper Internal utility for Bio::DB::SeqFeature::Store 1.10 metacpan
Bio::DB::Tagger Simple object tagging system 1.00 metacpan
Bio::DB::Tagger::Iterator 0 metacpan
Bio::DB::Tagger::Tag Authored tags 0 metacpan
Bio::DB::Tagger::mysql 0 metacpan
Bio::Graphics::Browser2 2.55 metacpan
Bio::Graphics::Browser2::Action 0 metacpan
Bio::Graphics::Browser2::AdminTracks 0 metacpan
Bio::Graphics::Browser2::AuthorizedFeatureFile Add HTTP authorization features to FeatureFile 0 metacpan
Bio::Graphics::Browser2::CAlign Compiled helper for Bio::Graphics::Browser::Realign 0 metacpan
Bio::Graphics::Browser2::CachedTrack 0 metacpan
Bio::Graphics::Browser2::DataBase A simple cache for database handles 0 metacpan
Bio::Graphics::Browser2::DataLoader 0 metacpan
Bio::Graphics::Browser2::DataLoader::archive 0 metacpan
Bio::Graphics::Browser2::DataLoader::bam 0 metacpan
Bio::Graphics::Browser2::DataLoader::bed 0 metacpan
Bio::Graphics::Browser2::DataLoader::bigbed 0 metacpan
Bio::Graphics::Browser2::DataLoader::bigwig 0 metacpan
Bio::Graphics::Browser2::DataLoader::featurefile 0 metacpan
Bio::Graphics::Browser2::DataLoader::generic 0 metacpan
Bio::Graphics::Browser2::DataLoader::gff 0 metacpan
Bio::Graphics::Browser2::DataLoader::gff3 0 metacpan
Bio::Graphics::Browser2::DataLoader::sam 0 metacpan
Bio::Graphics::Browser2::DataLoader::useq 0 metacpan
Bio::Graphics::Browser2::DataLoader::wig2bigwig 0 metacpan
Bio::Graphics::Browser2::DataLoader::wiggle 0 metacpan
Bio::Graphics::Browser2::DataSource 0 metacpan
Bio::Graphics::Browser2::ExternalData 0 metacpan
Bio::Graphics::Browser2::GFFhelper Helps gbrowse plugins handle GFF 0 metacpan
Bio::Graphics::Browser2::I18n 0 metacpan
Bio::Graphics::Browser2::Markup Markup routines for sequences in text form 0 metacpan
Bio::Graphics::Browser2::MetaDB 0 metacpan
Bio::Graphics::Browser2::MetaSegment 0 metacpan
Bio::Graphics::Browser2::MetaSegment::Iterator 0 metacpan
Bio::Graphics::Browser2::OptionPick Pick options 0 metacpan
Bio::Graphics::Browser2::PadAlignment Insert pads into a multiple alignment 0 metacpan
Bio::Graphics::Browser2::Plugin Base class for gbrowse plugins. 0.30 metacpan
Bio::Graphics::Browser2::Plugin::AuthPlugin Base class for authentication plugins 0 metacpan
Bio::Graphics::Browser2::PluginSet A set of plugins 0 metacpan
Bio::Graphics::Browser2::Realign Perl extension for Smith-Waterman alignments 0 metacpan
Bio::Graphics::Browser2::Region 0 metacpan
Bio::Graphics::Browser2::RegionSearch Search through multiple databases for feature matches. 0 metacpan
Bio::Graphics::Browser2::RemoteSet 0 metacpan
Bio::Graphics::Browser2::Render 0 metacpan
Bio::Graphics::Browser2::Render::HTML 0 metacpan
Bio::Graphics::Browser2::Render::HTML::TrackListing 0 metacpan
Bio::Graphics::Browser2::Render::HTML::TrackListing::Categories 0 metacpan
Bio::Graphics::Browser2::Render::Login 0 metacpan
Bio::Graphics::Browser2::Render::Slave 0 metacpan
Bio::Graphics::Browser2::Render::Slave::AWS_Balancer 0 metacpan
Bio::Graphics::Browser2::Render::Slave::StagingServer 0 metacpan
Bio::Graphics::Browser2::Render::Slave::Status 0 metacpan
Bio::Graphics::Browser2::Render::SnapshotManager 0 metacpan
Bio::Graphics::Browser2::Render::TrackConfig 0 metacpan
Bio::Graphics::Browser2::RenderPanels 0 metacpan
Bio::Graphics::Browser2::SendMail 0 metacpan
Bio::Graphics::Browser2::Session 0 metacpan
Bio::Graphics::Browser2::Shellwords 0 metacpan
Bio::Graphics::Browser2::SubtrackTable 0 metacpan
Bio::Graphics::Browser2::TrackDumper 0 metacpan
Bio::Graphics::Browser2::TrackDumper::RichSeqMaker 0 metacpan
Bio::Graphics::Browser2::UserConf 0 metacpan
Bio::Graphics::Browser2::UserDB 0.5 metacpan
Bio::Graphics::Browser2::UserTracks 0 metacpan
Bio::Graphics::Browser2::UserTracks::Database 0 metacpan
Bio::Graphics::Browser2::UserTracks::Filesystem 0 metacpan
Bio::Graphics::Browser2::Util Exported utilities 0 metacpan
Bio::Graphics::GBrowseFeature 0 metacpan
Bio::Graphics::Karyotype 0 metacpan
Bio::Graphics::Wiggle::Loader::Nosample 0 metacpan
CGI::Toggle Utility methods for collapsible sections 0 metacpan
FakeHomol 0 metacpan
LRUCache 0 metacpan
Legacy::DB::SyntenyBlock 0 metacpan
Legacy::DB::SyntenyIO 0 metacpan
Legacy::Graphics::Browser 1.17 metacpan
Legacy::Graphics::Browser::I18n 1.01 metacpan
Legacy::Graphics::Browser::PageSettings 0 metacpan
Legacy::Graphics::Browser::Synteny 0.01 metacpan
Legacy::Graphics::Browser::Util 0 metacpan
Legacy::Graphics::BrowserConfig 0 metacpan
MyFeatureFileLoader 0 metacpan

Other Files

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