GBrowse 2.42
Security Advisories
An attacker is able to delete other users' accounts. No httponly cookie flag. Cross-site scripting vulnerability in generation of citation text.
Fixed version: >=2.56
Reported: 2017-01-15
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::Tagger::Tag, Bio::Graphics::Browser2::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-2.42/contrib/install_macosx/BuildConfig.pm -- Around line 24: Unknown directive: =over4 Around line 26: '=item' outside of any '=over' GBrowse-2.42/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-2.42/docs/pod/FAQ.pod -- Around line 48: Unknown E content in E<gmod-gbrowse@lists.sourceforge.net> GBrowse-2.42/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm -- Around line 26: =over is the last thing in the document?! GBrowse-2.42/lib/Bio/Graphics/Browser2/DataBase.pm -- Around line 66: '=item' outside of any '=over' =over without closing =back GBrowse-2.42/lib/Bio/Graphics/Browser2/DataSource.pm -- Around line 152: You forgot a '=back' before '=head2' Around line 855: '=item' outside of any '=over' Around line 1089: You forgot a '=back' before '=head2'
- 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::SendMail, 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
- consistent_version
-
Split the distribution, or fix the version numbers to make them consistent (use the highest version number to avoid version downgrade).
Error: 0.01,0.10,0.20,0.30,0.5,1.00,1.01,1.17,2.42
- 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::BedLoader | 0 | 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 | 2.42 | 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::bam | 0 | metacpan | |
Bio::Graphics::Browser2::DataLoader::bed | 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::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::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::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 |