Bio-NEXUS 0.77
Kwalitee Issues
- has_changelog
-
Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.
- has_license_in_source_file
-
Add =head1 LICENSE and the text of the license to the main module in your code.
- 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 (224) does not match dist (236):
- Missing in MANIFEST: doc/._Installation.pod, doc/._ToDo.txt, doc/._Tutorial.pod, doc/._changes.txt, exec/._tree_length.pl, lib/Bio/NEXUS/._UnalignedBlock.pm, t/._notesblock_methods.t, t/._tree_parsing.t, t/data/compliant/._02_character-polymorphic-uncertain.nex, t/data/compliant/._04_characterstatelabels_05.nex, t/data/compliant/._characters-block-interleave2.nex, t/data/compliant/._example1.nex
- 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::NEXUS::._UnalignedBlock
- no_pod_errors
-
Remove the POD errors. You can check for POD errors automatically by including Test::Pod to your test suite.
Error: Bio-NEXUS-0.77/exec/jags.pl -- Around line 68: Unknown directive: =ignore
- meta_yml_declares_perl_version
-
If you are using Build.PL define the {requires}{perl} = VERSION field. If you are using MakeMaker (Makefile.PL) you should upgrade ExtUtils::MakeMaker to 6.48 and use MIN_PERL_VERSION parameter. Perl::MinimumVersion can help you determine which version of Perl your module needs.
- has_meta_json
-
Add a META.json to the distribution. Your buildtool should be able to autogenerate it.
- no_dot_underscore_files
-
If you use Mac OS X, set COPYFILE_DISABLE (for OS 10.5 and better) or COPY_EXTENDED_ATTRIBUTES_DISABLE (for OS 10.4) environmental variable to true to exclude dot underscore files from a distribution.
Error:
- doc/._Installation.pod
- doc/._ToDo.txt
- doc/._Tutorial.pod
- doc/._changes.txt
- exec/._tree_length.pl
- lib/Bio/NEXUS/._UnalignedBlock.pm
- t/._notesblock_methods.t
- t/._tree_parsing.t
- t/data/compliant/._02_character-polymorphic-uncertain.nex
- t/data/compliant/._04_characterstatelabels_05.nex
- t/data/compliant/._characters-block-interleave2.nex
- t/data/compliant/._example1.nex
- 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.
- 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::NEXUS, Bio::NEXUS::._UnalignedBlock, Bio::NEXUS::AssumptionsBlock, Bio::NEXUS::Block, Bio::NEXUS::CharactersBlock, Bio::NEXUS::CodonsBlock, Bio::NEXUS::DataBlock, Bio::NEXUS::DistancesBlock, Bio::NEXUS::Functions, Bio::NEXUS::HistoryBlock, Bio::NEXUS::Matrix, Bio::NEXUS::NHXCmd, Bio::NEXUS::Node, Bio::NEXUS::NotesBlock, Bio::NEXUS::SetsBlock, Bio::NEXUS::SpanBlock, Bio::NEXUS::TaxUnit, Bio::NEXUS::TaxUnitSet, Bio::NEXUS::TaxaBlock, Bio::NEXUS::Tools::GraphicsParams, Bio::NEXUS::Tools::NexModifier, Bio::NEXUS::Tools::NexPlotter, Bio::NEXUS::Tree, Bio::NEXUS::TreesBlock, Bio::NEXUS::UnalignedBlock, Bio::NEXUS::UnknownBlock, Bio::NEXUS::Util::Exceptions, Bio::NEXUS::Util::Logger, Bio::NEXUS::WeightSet
- no_invalid_versions
-
Fix the version numbers so that version::is_lax($version) returns true.
Error:
- lib/Bio/NEXUS/AssumptionsBlock.pm: HASH(0x5609d33c93b8)
- lib/Bio/NEXUS/Block.pm: HASH(0x5609d48e9b90)
- lib/Bio/NEXUS/CharactersBlock.pm: HASH(0x5609d41250c0)
- lib/Bio/NEXUS/CodonsBlock.pm: HASH(0x5609d41cb908)
- lib/Bio/NEXUS/DataBlock.pm: HASH(0x5609d4a4e700)
- lib/Bio/NEXUS/DistancesBlock.pm: HASH(0x5609d4975980)
- lib/Bio/NEXUS/Functions.pm: HASH(0x5609d48cc150)
- lib/Bio/NEXUS/HistoryBlock.pm: HASH(0x5609d48850f8)
- lib/Bio/NEXUS/Matrix.pm: HASH(0x5609d488cec8)
- lib/Bio/NEXUS/NHXCmd.pm: HASH(0x5609d4984cc0)
- lib/Bio/NEXUS/Node.pm: HASH(0x5609d49dbc10)
- lib/Bio/NEXUS/NotesBlock.pm: HASH(0x5609d48cc390)
- lib/Bio/NEXUS/SetsBlock.pm: HASH(0x5609d488dac8)
- lib/Bio/NEXUS/SpanBlock.pm: HASH(0x5609d494aa70)
- lib/Bio/NEXUS/TaxUnit.pm: HASH(0x5609d4a40948)
- lib/Bio/NEXUS/TaxUnitSet.pm: HASH(0x5609d4a0aea8)
- lib/Bio/NEXUS/TaxaBlock.pm: HASH(0x5609d488d678)
- lib/Bio/NEXUS/Tools/GraphicsParams.pm: HASH(0x5609d48e4068)
- lib/Bio/NEXUS/Tools/NexModifier.pm: HASH(0x5609d4a375b0)
- lib/Bio/NEXUS/Tools/NexPlotter.pm: HASH(0x5609d4919950)
- lib/Bio/NEXUS/Tree.pm: HASH(0x5609d498d250)
- lib/Bio/NEXUS/TreesBlock.pm: HASH(0x5609d4a4df68)
- lib/Bio/NEXUS/UnalignedBlock.pm: HASH(0x5609d488d198)
- lib/Bio/NEXUS/UnknownBlock.pm: HASH(0x5609d48f24d0)
- lib/Bio/NEXUS/WeightSet.pm: HASH(0x5609d488dab0)
- meta_yml_has_provides
-
Add all modules contained in this distribution to the META.yml field 'provides'. Module::Build or Dist::Zilla::Plugin::MetaProvides do this automatically for you.
- 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_security_doc
-
Add SECURITY(.pod|md). See Software::Security::Policy.
- security_doc_contains_contact
-
Add SECURITY(.pod|md) and add a contact address. See Software::Security::Policy.
- has_contributing_doc
-
Add CONTRIBUTING(.pod|md). See https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/setting-guidelines-for-repository-contributors.
Modules
Name | Abstract | Version | View |
---|---|---|---|
Bio::NEXUS | An object-oriented Perl Applications Programming Interface (API) for the NEXUS file format | 0.77 | metacpan |
Bio::NEXUS::AssumptionsBlock | Represents ASSUMPTIONS block of a NEXUS file | metacpan | |
Bio::NEXUS::Block | Provides useful functions for blocks in NEXUS file (parent class). | metacpan | |
Bio::NEXUS::CharactersBlock | Represents a CHARACTERS Block (Data or Characters) of a NEXUS file | metacpan | |
Bio::NEXUS::CodonsBlock | Represents CODONS block in NEXUS file | metacpan | |
Bio::NEXUS::DataBlock | Represents the deprecated DATA Block in NEXUS file. | metacpan | |
Bio::NEXUS::DistancesBlock | Represents DISTANCES block in NEXUS file | metacpan | |
Bio::NEXUS::Functions | Provides private utiliy functions for the module | metacpan | |
Bio::NEXUS::HistoryBlock | Represents a HISTORY block of a NEXUS file | metacpan | |
Bio::NEXUS::Matrix | Provides functions for handling blocks that have matrices | metacpan | |
Bio::NEXUS::NHXCmd | Provides functions for manipulating nodes in trees | metacpan | |
Bio::NEXUS::Node | Provides functions for manipulating nodes in trees | metacpan | |
Bio::NEXUS::NotesBlock | Represents a NOTES block in a NEXUS file. | metacpan | |
Bio::NEXUS::SetsBlock | Represents SETS block of a NEXUS file | metacpan | |
Bio::NEXUS::SpanBlock | Represent SPAN block in a NEXUS file (contains meta data). | metacpan | |
Bio::NEXUS::TaxUnit | Represents a taxon unit in a NEXUS file | metacpan | |
Bio::NEXUS::TaxUnitSet | Represents a sets of OTUS (Bio::NEXUS::TaxUnits objects) in a NEXUS file | metacpan | |
Bio::NEXUS::TaxaBlock | Represents TAXA block of a NEXUS file | metacpan | |
Bio::NEXUS::Tools::GraphicsParams | metacpan | ||
Bio::NEXUS::Tools::NexModifier | metacpan | ||
Bio::NEXUS::Tools::NexPlotter | metacpan | ||
Bio::NEXUS::Tree | Provides functions for manipulating trees | metacpan | |
Bio::NEXUS::TreesBlock | Represents TREES block of a NEXUS file | metacpan | |
Bio::NEXUS::UnalignedBlock | Represents an UNALIGNED block of a NEXUS file | metacpan | |
Bio::NEXUS::UnknownBlock | Represents a simple object for storing information unrecognized blocks by the Bio::NEXUS module. | metacpan | |
Bio::NEXUS::Util::Exceptions | Exception classes for Bio::NEXUS. | metacpan | |
Bio::NEXUS::Util::Logger | Logging for Bio::NEXUS. | metacpan | |
Bio::NEXUS::WeightSet | Represents column weights in alignment ( for each character) | metacpan |