Bio-Phylo 0.09

Released by
RVOSA
Version
Release Date
2006-05-18
Kwalitee
137.5
Core Kwalitee
93.75
LINKS

Kwalitee Issues

buildtool_not_executable

Change the permissions of Build.PL/Makefile.PL to not-executable.

no_pod_errors

Remove the POD errors. You can check for POD errors automatically by including Test::Pod to your test suite.

Error: Bio-Phylo-0.09/lib/Bio/Phylo/Manual.pod -- Around line 132: Non-ASCII character seen before =encoding in 'façade'. Assuming CP1252

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.

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::Phylo, Bio::Phylo::Forest, Bio::Phylo::Forest::Node, Bio::Phylo::Forest::Tree, Bio::Phylo::Generator, Bio::Phylo::Listable, Bio::Phylo::Matrices, Bio::Phylo::Matrices::Alignment, Bio::Phylo::Matrices::Datum, Bio::Phylo::Matrices::Matrix, Bio::Phylo::Matrices::Sequence, Bio::Phylo::Parsers::Fastnewick, Bio::Phylo::Parsers::Fastnexus, Bio::Phylo::Parsers::Newick, Bio::Phylo::Parsers::Nexus, Bio::Phylo::Parsers::Table, Bio::Phylo::Parsers::Taxlist, Bio::Phylo::Taxa, Bio::Phylo::Taxa::Taxon, Bio::Phylo::Unparsers::Mrp, Bio::Phylo::Unparsers::Nexus, Bio::Phylo::Unparsers::Pagel, Bio::Phylo::Util::CONSTANT, Bio::Phylo::Util::IDPool

no_invalid_versions

Fix the version numbers so that version::is_lax($version) returns true.

Error:

  • lib/Bio/Phylo/Forest.pm: HASH(0x5609d68e0160)
  • lib/Bio/Phylo/Forest/Node.pm: HASH(0x5609d678f6e0)
  • lib/Bio/Phylo/Forest/Tree.pm: HASH(0x5609d6807858)
  • lib/Bio/Phylo/Generator.pm: HASH(0x5609d67889c0)
  • lib/Bio/Phylo/IO.pm: HASH(0x5609d6a53b18)
  • lib/Bio/Phylo/Listable.pm: HASH(0x5609d67997e0)
  • lib/Bio/Phylo/Matrices.pm: HASH(0x5609d6b96570)
  • lib/Bio/Phylo/Matrices/Alignment.pm: HASH(0x5609d6783b80)
  • lib/Bio/Phylo/Matrices/Datum.pm: HASH(0x5609d655d758)
  • lib/Bio/Phylo/Matrices/Matrix.pm: HASH(0x5609d5f67c68)
  • lib/Bio/Phylo/Matrices/Sequence.pm: HASH(0x5609d32f2138)
  • lib/Bio/Phylo/Parsers/Fastnewick.pm: HASH(0x5609d6772ca0)
  • lib/Bio/Phylo/Parsers/Fastnexus.pm: HASH(0x5609d6891d88)
  • lib/Bio/Phylo/Parsers/Newick.pm: HASH(0x5609d688c838)
  • lib/Bio/Phylo/Parsers/Nexus.pm: HASH(0x5609d679d800)
  • lib/Bio/Phylo/Parsers/Table.pm: HASH(0x5609d6806f88)
  • lib/Bio/Phylo/Parsers/Taxlist.pm: HASH(0x5609d42052b8)
  • lib/Bio/Phylo/Taxa.pm: HASH(0x5609d68e07c0)
  • lib/Bio/Phylo/Taxa/Taxon.pm: HASH(0x5609d678f008)
  • lib/Bio/Phylo/Treedrawer.pm: HASH(0x5609d680baf8)
  • lib/Bio/Phylo/Treedrawer/Svg.pm: HASH(0x5609d67f48f0)
  • lib/Bio/Phylo/Unparsers/Mrp.pm: HASH(0x5609d66cf7c8)
  • lib/Bio/Phylo/Unparsers/Newick.pm: HASH(0x5609d3471eb8)
  • lib/Bio/Phylo/Unparsers/Nexus.pm: HASH(0x5609d68354e0)
  • lib/Bio/Phylo/Unparsers/Pagel.pm: HASH(0x5609d6783c10)
  • lib/Bio/Phylo/Util/CONSTANT.pm: HASH(0x5609d67815e8)
  • lib/Bio/Phylo/Util/Exceptions.pm: HASH(0x5609d6769770)

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_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::Phylo Phylogenetic analysis using perl. 0.09 metacpan
Bio::Phylo::Forest The forest object, a set of phylogenetic trees. metacpan
Bio::Phylo::Forest::Node The tree node object. metacpan
Bio::Phylo::Forest::Tree The tree object. metacpan
Bio::Phylo::Generator Generates random trees. metacpan
Bio::Phylo::IO Input and output of phylogenetic data. metacpan
Bio::Phylo::Listable Parent class for listable/iterator objects. metacpan
Bio::Phylo::Matrices Holds a set of matrix objects. metacpan
Bio::Phylo::Matrices::Alignment The alignment object to aggregate sequences. metacpan
Bio::Phylo::Matrices::Datum The single observations object. metacpan
Bio::Phylo::Matrices::Matrix The matrix object to aggregate datum objects. metacpan
Bio::Phylo::Matrices::Sequence The molecular sequence object. metacpan
Bio::Phylo::Parsers::Fastnewick Parses newick trees. No serviceable parts inside. metacpan
Bio::Phylo::Parsers::Fastnexus Parses nexus files. No serviceable parts inside. metacpan
Bio::Phylo::Parsers::Newick Parses newick trees. No serviceable parts inside. metacpan
Bio::Phylo::Parsers::Nexus Parses nexus files. No serviceable parts inside. metacpan
Bio::Phylo::Parsers::Table Parses tab- (or otherwise) delimited matrices. No serviceable parts inside. metacpan
Bio::Phylo::Parsers::Taxlist Parses lists of taxon names. No serviceable parts inside. metacpan
Bio::Phylo::Taxa An object-oriented module for managing taxa. metacpan
Bio::Phylo::Taxa::Taxon The operational taxonomic unit. metacpan
Bio::Phylo::Treedrawer An object-oriented facade for drawing trees. metacpan
Bio::Phylo::Treedrawer::Svg metacpan
Bio::Phylo::Unparsers::Mrp Unparses a forest object into an MRP matrix. No serviceable parts inside. metacpan
Bio::Phylo::Unparsers::Newick Unparses newick trees. No serviceable parts inside. metacpan
Bio::Phylo::Unparsers::Nexus Unparses nexus matrices. No serviceable parts inside. metacpan
Bio::Phylo::Unparsers::Pagel Unparses pagel data files. No serviceable parts inside. metacpan
Bio::Phylo::Util::CONSTANT Global constants for Bio::Phylo. No serviceable parts inside. metacpan
Bio::Phylo::Util::Exceptions Exception classes for Bio::Phylo. No serviceable parts inside. metacpan
Bio::Phylo::Util::IDPool Utility class for generating object IDs metacpan

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