Bio-NEXUS 0.77

Released by
ARLIN
Version
Release Date
2012-02-09
Kwalitee
121.88
Core Kwalitee
84.38
LINKS

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(0x5609d5bbd4e8)
  • lib/Bio/NEXUS/Block.pm: HASH(0x5609d6d8f3a0)
  • lib/Bio/NEXUS/CharactersBlock.pm: HASH(0x5609d6d482a0)
  • lib/Bio/NEXUS/CodonsBlock.pm: HASH(0x5609d6d70b00)
  • lib/Bio/NEXUS/DataBlock.pm: HASH(0x5609d5c46b58)
  • lib/Bio/NEXUS/DistancesBlock.pm: HASH(0x5609d5bbc6f0)
  • lib/Bio/NEXUS/Functions.pm: HASH(0x5609d6de21e8)
  • lib/Bio/NEXUS/HistoryBlock.pm: HASH(0x5609d6da8f70)
  • lib/Bio/NEXUS/Matrix.pm: HASH(0x5609d5838a68)
  • lib/Bio/NEXUS/NHXCmd.pm: HASH(0x5609d60601f8)
  • lib/Bio/NEXUS/Node.pm: HASH(0x5609d6d691b0)
  • lib/Bio/NEXUS/NotesBlock.pm: HASH(0x5609d5c522f0)
  • lib/Bio/NEXUS/SetsBlock.pm: HASH(0x5609d5837dc8)
  • lib/Bio/NEXUS/SpanBlock.pm: HASH(0x5609d6df3bb8)
  • lib/Bio/NEXUS/TaxUnit.pm: HASH(0x5609d6060300)
  • lib/Bio/NEXUS/TaxUnitSet.pm: HASH(0x5609d6060318)
  • lib/Bio/NEXUS/TaxaBlock.pm: HASH(0x5609d605f060)
  • lib/Bio/NEXUS/Tools/GraphicsParams.pm: HASH(0x5609d6c8e7c0)
  • lib/Bio/NEXUS/Tools/NexModifier.pm: HASH(0x5609d6d8bae0)
  • lib/Bio/NEXUS/Tools/NexPlotter.pm: HASH(0x5609d6df40c8)
  • lib/Bio/NEXUS/Tree.pm: HASH(0x5609d5f63f48)
  • lib/Bio/NEXUS/TreesBlock.pm: HASH(0x5609d6728e40)
  • lib/Bio/NEXUS/UnalignedBlock.pm: HASH(0x5609d6d4b7b8)
  • lib/Bio/NEXUS/UnknownBlock.pm: HASH(0x5609d6d85118)
  • lib/Bio/NEXUS/WeightSet.pm: HASH(0x5609d5ef3c30)

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

Provides

Name File View
Bio::NEXUS::Util::StackTrace lib/Bio/NEXUS/Util/Exceptions.pm metacpan
MyData lib/Bio/NEXUS/Tools/NexPlotter.pm metacpan

Other Files
Build.PL metacpan
MANIFEST metacpan
META.yml metacpan
Makefile.PL metacpan
README metacpan
README_admin metacpan