Security Advisories

Kwalitee Issues

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: *** ERROR: Unknown directive: =over4 at line 24 in file GBrowse-2.21/contrib/install_macosx/BuildConfig.pm *** ERROR: '=item' outside of any '=over' at line 26 in file GBrowse-2.21/contrib/install_macosx/BuildConfig.pm *** ERROR: Expected '=item *' at line 1185 in file GBrowse-2.21/docs/pod/CONFIGURE_HOWTO.pod *** ERROR: Expected '=item *' at line 1202 in file GBrowse-2.21/docs/pod/CONFIGURE_HOWTO.pod *** ERROR: Expected '=item *' at line 1212 in file GBrowse-2.21/docs/pod/CONFIGURE_HOWTO.pod *** ERROR: Non-ASCII character seen before =encoding in 'Gènes'. Assuming CP1252 at line 2352 in file GBrowse-2.21/docs/pod/CONFIGURE_HOWTO.pod *** ERROR: Unknown E content in E<gmod-gbrowse@lists.sourceforge.net> at line 48 in file GBrowse-2.21/docs/pod/FAQ.pod *** ERROR: =over is the last thing in the document?! at line 25 in file GBrowse-2.21/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm *** ERROR: '=item' outside of any '=over' at line 66 in file GBrowse-2.21/lib/Bio/Graphics/Browser2/DataBase.pm *** ERROR: =over without closing =back at line 66 in file GBrowse-2.21/lib/Bio/Graphics/Browser2/DataBase.pm *** ERROR: You forgot a '=back' before '=head2' at line 154 in file GBrowse-2.21/lib/Bio/Graphics/Browser2/DataSource.pm *** ERROR: '=item' outside of any '=over' at line 806 in file GBrowse-2.21/lib/Bio/Graphics/Browser2/DataSource.pm *** ERROR: You forgot a '=back' before '=head2' at line 1033 in file GBrowse-2.21/lib/Bio/Graphics/Browser2/DataSource.pm *** ERROR: empty =head2 at line 2947 in file GBrowse-2.21/lib/Legacy/Graphics/Browser.pm

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: 0.01,0.10,0.20,0.30,0.5,1.00,1.01,1.17,2.21

has_meta_json

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

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::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::BedLoader, Bio::DB::Tagger::Tag, Bio::Graphics::Browser2::Action, Bio::Graphics::Browser2::CAlign, Bio::Graphics::Browser2::DataLoader, Bio::Graphics::Browser2::DataLoader::bam, Bio::Graphics::Browser2::DataLoader::bed, Bio::Graphics::Browser2::DataLoader::bigwig, Bio::Graphics::Browser2::DataLoader::featurefile, Bio::Graphics::Browser2::DataLoader::generic, Bio::Graphics::Browser2::DataLoader::gff, Bio::Graphics::Browser2::DataLoader::gff3, Bio::Graphics::Browser2::DataLoader::sam, Bio::Graphics::Browser2::DataLoader::wiggle, 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::Shellwords, Bio::Graphics::Browser2::TrackDumper, 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, 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

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 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::BedLoader metacpan
Bio::DB::Tagger Simple object tagging system 1.00 metacpan
Bio::DB::Tagger::Iterator metacpan
Bio::DB::Tagger::Tag Authored tags metacpan
Bio::DB::Tagger::mysql metacpan
Bio::Graphics::Browser2 2.21 metacpan
Bio::Graphics::Browser2::Action metacpan
Bio::Graphics::Browser2::AdminTracks metacpan
Bio::Graphics::Browser2::AuthorizedFeatureFile Add HTTP authorization features to FeatureFile metacpan
Bio::Graphics::Browser2::CAlign Compiled helper for Bio::Graphics::Browser::Realign metacpan
Bio::Graphics::Browser2::CachedTrack metacpan
Bio::Graphics::Browser2::DataBase A simple cache for database handles metacpan
Bio::Graphics::Browser2::DataLoader metacpan
Bio::Graphics::Browser2::DataLoader::bam metacpan
Bio::Graphics::Browser2::DataLoader::bed metacpan
Bio::Graphics::Browser2::DataLoader::bigwig metacpan
Bio::Graphics::Browser2::DataLoader::featurefile metacpan
Bio::Graphics::Browser2::DataLoader::generic metacpan
Bio::Graphics::Browser2::DataLoader::gff metacpan
Bio::Graphics::Browser2::DataLoader::gff3 metacpan
Bio::Graphics::Browser2::DataLoader::sam metacpan
Bio::Graphics::Browser2::DataLoader::wiggle metacpan
Bio::Graphics::Browser2::DataSource metacpan
Bio::Graphics::Browser2::ExternalData metacpan
Bio::Graphics::Browser2::GFFhelper Helps gbrowse plugins handle GFF metacpan
Bio::Graphics::Browser2::I18n metacpan
Bio::Graphics::Browser2::Markup Markup routines for sequences in text form metacpan
Bio::Graphics::Browser2::MetaDB metacpan
Bio::Graphics::Browser2::MetaSegment metacpan
Bio::Graphics::Browser2::MetaSegment::Iterator metacpan
Bio::Graphics::Browser2::OptionPick Pick options metacpan
Bio::Graphics::Browser2::PadAlignment Insert pads into a multiple alignment metacpan
Bio::Graphics::Browser2::Plugin Base class for gbrowse plugins. 0.30 metacpan
Bio::Graphics::Browser2::Plugin::AuthPlugin Base class for authentication plugins metacpan
Bio::Graphics::Browser2::PluginSet A set of plugins metacpan
Bio::Graphics::Browser2::Realign Perl extension for Smith-Waterman alignments metacpan
Bio::Graphics::Browser2::Region metacpan
Bio::Graphics::Browser2::RegionSearch Search through multiple databases for feature matches. metacpan
Bio::Graphics::Browser2::RemoteSet metacpan
Bio::Graphics::Browser2::Render metacpan
Bio::Graphics::Browser2::Render::HTML metacpan
Bio::Graphics::Browser2::Render::Login metacpan
Bio::Graphics::Browser2::Render::Slave metacpan
Bio::Graphics::Browser2::Render::Slave::Status metacpan
Bio::Graphics::Browser2::RenderPanels metacpan
Bio::Graphics::Browser2::Session metacpan
Bio::Graphics::Browser2::Shellwords metacpan
Bio::Graphics::Browser2::SubtrackTable metacpan
Bio::Graphics::Browser2::TrackDumper metacpan
Bio::Graphics::Browser2::UserConf metacpan
Bio::Graphics::Browser2::UserDB 0.5 metacpan
Bio::Graphics::Browser2::UserTracks metacpan
Bio::Graphics::Browser2::UserTracks::Database metacpan
Bio::Graphics::Browser2::UserTracks::Filesystem metacpan
Bio::Graphics::Browser2::Util Exported utilities metacpan
Bio::Graphics::GBrowseFeature metacpan
Bio::Graphics::Karyotype metacpan
Bio::Graphics::Wiggle::Loader::Nosample metacpan
CGI::Toggle Utility methods for collapsible sections metacpan
FakeHomol metacpan
LRUCache metacpan
Legacy::DB::SyntenyBlock metacpan
Legacy::DB::SyntenyIO metacpan
Legacy::Graphics::Browser 1.17 metacpan
Legacy::Graphics::Browser::I18n 1.01 metacpan
Legacy::Graphics::Browser::PageSettings metacpan
Legacy::Graphics::Browser::Synteny 0.01 metacpan
Legacy::Graphics::Browser::Util metacpan
Legacy::Graphics::BrowserConfig metacpan
MyFeatureFileLoader 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