Bio-Mitomaster 0.10

Released by
MBRANDON
Version
Release Date
2010-04-20
Kwalitee
109.38
Core Kwalitee
68.75
LINKS

Kwalitee Issues

extracts_nicely

Pack the distribution with a proper command such as "make dist" and "./Build dist", or use a distribution builder such as Dist::Zilla, Dist::Milla, Minilla.

Error: More than one top directories are found: ._Bio_Mitomaster;Bio_Mitomaster

has_readme

Add a README to the distribution. It should contain a quick description of your module and how to install it.

has_manifest

Add a MANIFEST to the distribution. Your buildtool should be able to autogenerate it (eg "make manifest" or "./Build manifest")

has_meta_yml

Add a META.yml to the distribution. Your buildtool should be able to autogenerate it.

has_buildtool

Add a Makefile.PL (for ExtUtils::MakeMaker/Module::Install) or a Build.PL (for Module::Build and its friends), or use a distribution builder such as Dist::Zilla, Dist::Milla, Minilla.

has_changelog

Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.

has_tests

Add tests!

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: Cannot find MANIFEST in dist.

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_Mitomaster::lib::Bio::._Mitomaster, Bio_Mitomaster::lib::Bio::Mitomaster::._AASeq, Bio_Mitomaster::lib::Bio::Mitomaster::._FastaIO, Bio_Mitomaster::lib::Bio::Mitomaster::._GenbankIO, Bio_Mitomaster::lib::Bio::Mitomaster::._MitoSeq, Bio_Mitomaster::lib::Bio::Mitomaster::._RNASeq, Bio_Mitomaster::lib::Bio::Mitomaster::._Seq, Bio_Mitomaster::lib::Bio::Mitomaster::._SeqIO, Bio_Mitomaster::lib::Bio::Mitomaster::._SeqManipRole, Bio_Mitomaster::lib::Bio::Mitomaster::._SpeciesRef, Bio_Mitomaster::lib::Bio::Mitomaster::._Types, Bio_Mitomaster::lib::Bio::Mitomaster::._VariantsIO

prereq_matches_use

List all used modules in META.yml requires

Error:

  • Moose
  • Moose::Role
  • Moose::Util::TypeConstraints
  • Readonly

has_meta_json

Add a META.json to the distribution. Your buildtool should be able to autogenerate it.

has_tests_in_t_dir

Add tests or move tests.pl to the t/ directory!

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:

  • ._Bio_Mitomaster
  • Bio_Mitomaster/._Build.PL
  • Bio_Mitomaster/._Changes
  • Bio_Mitomaster/._MANIFEST
  • Bio_Mitomaster/._README
  • Bio_Mitomaster/._lib
  • Bio_Mitomaster/._t
  • Bio_Mitomaster/lib/._Bio
  • Bio_Mitomaster/lib/Bio/._Mitomaster
  • Bio_Mitomaster/lib/Bio/._Mitomaster.pm
  • Bio_Mitomaster/lib/Bio/Mitomaster/._AASeq.pm
  • Bio_Mitomaster/lib/Bio/Mitomaster/._FastaIO.pm
  • Bio_Mitomaster/lib/Bio/Mitomaster/._GenbankIO.pm
  • Bio_Mitomaster/lib/Bio/Mitomaster/._Manual.pod
  • Bio_Mitomaster/lib/Bio/Mitomaster/._MitoSeq.pm
  • Bio_Mitomaster/lib/Bio/Mitomaster/._RNASeq.pm
  • Bio_Mitomaster/lib/Bio/Mitomaster/._Seq.pm
  • Bio_Mitomaster/lib/Bio/Mitomaster/._SeqIO.pm
  • Bio_Mitomaster/lib/Bio/Mitomaster/._SeqManipRole.pm
  • Bio_Mitomaster/lib/Bio/Mitomaster/._SpeciesRef.pm
  • Bio_Mitomaster/lib/Bio/Mitomaster/._Types.pm
  • Bio_Mitomaster/lib/Bio/Mitomaster/._VariantsIO.pm
  • Bio_Mitomaster/t/._10-SpeciesRef.t
  • Bio_Mitomaster/t/._20-MitoSeq.t
  • Bio_Mitomaster/t/._30-Seq.t
  • Bio_Mitomaster/t/._40-RNASeq.t
  • Bio_Mitomaster/t/._50-AASeq.t
  • Bio_Mitomaster/t/._60-SeqIO.t
  • Bio_Mitomaster/t/._99-Mitomaster.t
  • Bio_Mitomaster/t/._boilerplate.t
  • Bio_Mitomaster/t/._pod-coverage.t
  • Bio_Mitomaster/t/._pod.t

proper_libs

Move your *.pm files in a directory named 'lib'. The directory structure should look like 'lib/Your/Module.pm' for a module named 'Your::Module'. If you need to provide additional files, e.g. for testing, that should not be considered for Kwalitee, then you should look at the 'provides' map in META.yml to limit the files scanned; or use the 'no_index' map to exclude parts of the distribution.

Error: Bio_Mitomaster/lib/Bio/Mitomaster.pm, Bio_Mitomaster/lib/Bio/Mitomaster/AASeq.pm, Bio_Mitomaster/lib/Bio/Mitomaster/FastaIO.pm, Bio_Mitomaster/lib/Bio/Mitomaster/GenbankIO.pm, Bio_Mitomaster/lib/Bio/Mitomaster/MitoSeq.pm, Bio_Mitomaster/lib/Bio/Mitomaster/RNASeq.pm, Bio_Mitomaster/lib/Bio/Mitomaster/Seq.pm, Bio_Mitomaster/lib/Bio/Mitomaster/SeqIO.pm, Bio_Mitomaster/lib/Bio/Mitomaster/SeqManipRole.pm, Bio_Mitomaster/lib/Bio/Mitomaster/SpeciesRef.pm, Bio_Mitomaster/lib/Bio/Mitomaster/Types.pm, Bio_Mitomaster/lib/Bio/Mitomaster/VariantsIO.pm, Bio_Mitomaster/lib/Bio/._Mitomaster.pm, Bio_Mitomaster/lib/Bio/Mitomaster/._AASeq.pm, Bio_Mitomaster/lib/Bio/Mitomaster/._FastaIO.pm, Bio_Mitomaster/lib/Bio/Mitomaster/._GenbankIO.pm, Bio_Mitomaster/lib/Bio/Mitomaster/._MitoSeq.pm, Bio_Mitomaster/lib/Bio/Mitomaster/._RNASeq.pm, Bio_Mitomaster/lib/Bio/Mitomaster/._Seq.pm, Bio_Mitomaster/lib/Bio/Mitomaster/._SeqIO.pm, Bio_Mitomaster/lib/Bio/Mitomaster/._SeqManipRole.pm, Bio_Mitomaster/lib/Bio/Mitomaster/._SpeciesRef.pm, Bio_Mitomaster/lib/Bio/Mitomaster/._Types.pm, Bio_Mitomaster/lib/Bio/Mitomaster/._VariantsIO.pm

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.

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_Mitomaster::lib::Bio::._Mitomaster, Bio_Mitomaster::lib::Bio::Mitomaster::._AASeq, Bio_Mitomaster::lib::Bio::Mitomaster::._FastaIO, Bio_Mitomaster::lib::Bio::Mitomaster::._GenbankIO, Bio_Mitomaster::lib::Bio::Mitomaster::._MitoSeq, Bio_Mitomaster::lib::Bio::Mitomaster::._RNASeq, Bio_Mitomaster::lib::Bio::Mitomaster::._Seq, Bio_Mitomaster::lib::Bio::Mitomaster::._SeqIO, Bio_Mitomaster::lib::Bio::Mitomaster::._SeqManipRole, Bio_Mitomaster::lib::Bio::Mitomaster::._SpeciesRef, Bio_Mitomaster::lib::Bio::Mitomaster::._Types, Bio_Mitomaster::lib::Bio::Mitomaster::._VariantsIO

has_separate_license_file

This is not a critical issue. Currently mainly informative for the CPANTS authors. It might be removed later.

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::Mitomaster Tool for mitochondrial DNA. 0.10 metacpan
Bio::Mitomaster::AASeq An mtDNA translation. 0.10 metacpan
Bio::Mitomaster::FastaIO Read and write fasta files. 0.10 metacpan
Bio::Mitomaster::GenbankIO Read and write fasta files. 0.10 metacpan
Bio::Mitomaster::MitoSeq Superclass for Mitomaster seq objects. 0.10 metacpan
Bio::Mitomaster::RNASeq An mtDNA transcript. 0.10 metacpan
Bio::Mitomaster::Seq An mtDNA sequence. 0.10 metacpan
Bio::Mitomaster::SeqIO Superclass for all file IO objects. 0.10 metacpan
Bio::Mitomaster::SeqManipRole A role for objects that manipulate indexed mitochondrial sequences. 0.10 metacpan
Bio::Mitomaster::SpeciesRef Reference object for species and ref sequence meta-data. 0.10 metacpan
Bio::Mitomaster::Types Just a package of type constraints. Not useful by itself 0.10 metacpan
Bio::Mitomaster::VariantsIO Read and write fasta files. 0.10 metacpan

Other Files
Bio_Mitomaster/Build.PL metacpan
Bio_Mitomaster/MANIFEST metacpan