Bio-NEXUS 0.67

Released by
TJHLADISH
Version
Release Date
2006-09-12
Kwalitee
131.25
Core Kwalitee
90.62
LINKS

Kwalitee Issues

meta_yml_conforms_to_known_spec

Take a look at the META.yml Spec at https://metacpan.org/pod/CPAN::Meta::History::Meta_1_4 (for version 1.4) or https://metacpan.org/pod/CPAN::Meta::Spec (for version 2), and change your META.yml accordingly.

Error: Expected a map structure from string or file. (requires) [Validation: 1.0]

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.

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.

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::AssumptionsBlock, Bio::NEXUS::Block, Bio::NEXUS::CharactersBlock, Bio::NEXUS::CodonsBlock, Bio::NEXUS::DataBlock, Bio::NEXUS::DistancesBlock, Bio::NEXUS::Functions, Bio::NEXUS::HistoryBlock, Bio::NEXUS::MatrixBlock, Bio::NEXUS::Node, Bio::NEXUS::NotesBlock, Bio::NEXUS::SetsBlock, Bio::NEXUS::SpanBlock, Bio::NEXUS::TaxUnit, Bio::NEXUS::TaxUnitSet, Bio::NEXUS::TaxaBlock, Bio::NEXUS::Tree, Bio::NEXUS::TreesBlock, Bio::NEXUS::UnalignedBlock, Bio::NEXUS::UnknownBlock, 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(0x5609d4d357d0)
  • lib/Bio/NEXUS/Block.pm: HASH(0x5609d4d3eec0)
  • lib/Bio/NEXUS/CharactersBlock.pm: HASH(0x5609d4d4a9e8)
  • lib/Bio/NEXUS/CodonsBlock.pm: HASH(0x5609d4d18568)
  • lib/Bio/NEXUS/DataBlock.pm: HASH(0x5609d4d2fd20)
  • lib/Bio/NEXUS/DistancesBlock.pm: HASH(0x5609d4d1e0b0)
  • lib/Bio/NEXUS/Functions.pm: HASH(0x5609d4d4a418)
  • lib/Bio/NEXUS/HistoryBlock.pm: HASH(0x5609d4d2ac80)
  • lib/Bio/NEXUS/MatrixBlock.pm: HASH(0x5609d4d24cd8)
  • lib/Bio/NEXUS/Node.pm: HASH(0x5609d4d18868)
  • lib/Bio/NEXUS/NotesBlock.pm: HASH(0x5609d4d45c60)
  • lib/Bio/NEXUS/SetsBlock.pm: HASH(0x5609d4d18790)
  • lib/Bio/NEXUS/SpanBlock.pm: HASH(0x5609d4d44fd0)
  • lib/Bio/NEXUS/TaxUnit.pm: HASH(0x5609d4d30080)
  • lib/Bio/NEXUS/TaxUnitSet.pm: HASH(0x5609d4d186e8)
  • lib/Bio/NEXUS/TaxaBlock.pm: HASH(0x5609d4d17a58)
  • lib/Bio/NEXUS/Tree.pm: HASH(0x5609d4d180b8)
  • lib/Bio/NEXUS/TreesBlock.pm: HASH(0x5609d4d0ce58)
  • lib/Bio/NEXUS/UnalignedBlock.pm: HASH(0x5609d4d35fe0)
  • lib/Bio/NEXUS/UnknownBlock.pm: HASH(0x5609d4d90790)
  • lib/Bio/NEXUS/WeightSet.pm: HASH(0x5609d4d0cb88)

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 0.67 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::MatrixBlock Provides functions for handling blocks that have matrices 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::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::WeightSet Represents column weights in alignment ( for each character) metacpan

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