Bio-NEXUS 0.78
- Released by
- ARLIN
- Version
- Release Date
- 2012-02-10
- Kwalitee
- 121.88
- Core Kwalitee
- 84.38
- LINKS
Bio-NEXUS 0.78 Latest
Kwalitee Issues
- has_changelog
-
Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.
- buildtool_not_executable
-
Change the permissions of Build.PL/Makefile.PL to not-executable.
- 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 (225):
- Missing in MANIFEST: doc/._changes.txt
- 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-0.78/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/._changes.txt
- 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::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(0x55a43f956d50)
- lib/Bio/NEXUS/Block.pm: HASH(0x55a43faf7a30)
- lib/Bio/NEXUS/CharactersBlock.pm: HASH(0x55a43f96aa88)
- lib/Bio/NEXUS/CodonsBlock.pm: HASH(0x55a43fa74f78)
- lib/Bio/NEXUS/DataBlock.pm: HASH(0x55a43f97e6b8)
- lib/Bio/NEXUS/DistancesBlock.pm: HASH(0x55a43f9754a0)
- lib/Bio/NEXUS/Functions.pm: HASH(0x55a43f944f70)
- lib/Bio/NEXUS/HistoryBlock.pm: HASH(0x55a43f9838f8)
- lib/Bio/NEXUS/Matrix.pm: HASH(0x55a43f51f4f8)
- lib/Bio/NEXUS/NHXCmd.pm: HASH(0x55a43f9d0ec8)
- lib/Bio/NEXUS/Node.pm: HASH(0x55a43fa40ec0)
- lib/Bio/NEXUS/NotesBlock.pm: HASH(0x55a43fab96c0)
- lib/Bio/NEXUS/SetsBlock.pm: HASH(0x55a43fac2510)
- lib/Bio/NEXUS/SpanBlock.pm: HASH(0x55a43fae8d08)
- lib/Bio/NEXUS/TaxUnit.pm: HASH(0x55a43fa28228)
- lib/Bio/NEXUS/TaxUnitSet.pm: HASH(0x55a43fa6ad90)
- lib/Bio/NEXUS/TaxaBlock.pm: HASH(0x55a43fadf8e8)
- lib/Bio/NEXUS/Tools/GraphicsParams.pm: HASH(0x55a43fae8ed0)
- lib/Bio/NEXUS/Tools/NexModifier.pm: HASH(0x55a43fac1f58)
- lib/Bio/NEXUS/Tools/NexPlotter.pm: HASH(0x55a43e615318)
- lib/Bio/NEXUS/Tree.pm: HASH(0x55a43fa40818)
- lib/Bio/NEXUS/TreesBlock.pm: HASH(0x55a43f9f2f10)
- lib/Bio/NEXUS/UnalignedBlock.pm: HASH(0x55a43f512920)
- lib/Bio/NEXUS/UnknownBlock.pm: HASH(0x55a43fae85e8)
- lib/Bio/NEXUS/WeightSet.pm: HASH(0x55a43fa10108)
- 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).
Modules
| Name | Abstract | Version | View |
|---|---|---|---|
| Bio::NEXUS | An object-oriented Perl Applications Programming Interface (API) for the NEXUS file format | 0.78 | 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 |