Bio-Phylo 0.17_RC6

Released by
RVOSA
Version
Release Date
2007-07-20
Kwalitee
137.5
Core Kwalitee
93.75
LINKS

Kwalitee Issues

has_proper_version

Remove all letters from the version number. If you want to mark a release as a developer release, use the scheme 'Module-1.00_01'

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::Phylo::Adaptor::Bioperl::Datum, Bio::Phylo::Adaptor::Bioperl::Node, Bio::Phylo::Adaptor::Bioperl::Tree

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::Adaptor, Bio::Phylo::Adaptor::Bioperl::Datum, Bio::Phylo::Adaptor::Bioperl::Matrix, Bio::Phylo::Adaptor::Bioperl::Node, Bio::Phylo::Adaptor::Bioperl::Tree, Bio::Phylo::Forest::Node, Bio::Phylo::Forest::Tree, Bio::Phylo::Generator, Bio::Phylo::IO, Bio::Phylo::Matrices::Datatype, Bio::Phylo::Matrices::Datatype::Continuous, Bio::Phylo::Matrices::Datatype::Custom, Bio::Phylo::Matrices::Datatype::Dna, Bio::Phylo::Matrices::Datatype::Mixed, Bio::Phylo::Matrices::Datatype::Protein, Bio::Phylo::Matrices::Datatype::Restriction, Bio::Phylo::Matrices::Datatype::Rna, Bio::Phylo::Matrices::Datatype::Standard, Bio::Phylo::Matrices::Datum, Bio::Phylo::Matrices::Matrix, Bio::Phylo::Matrices::TypeSafeData, Bio::Phylo::Parsers::Newick, Bio::Phylo::Parsers::Nexus, Bio::Phylo::Parsers::Table, Bio::Phylo::Parsers::Taxlist, Bio::Phylo::Taxa, Bio::Phylo::Taxa::TaxaLinker, Bio::Phylo::Taxa::Taxon, Bio::Phylo::Taxa::TaxonLinker, Bio::Phylo::Treedrawer, Bio::Phylo::Treedrawer::Svg, Bio::Phylo::Unparsers::Mrp, Bio::Phylo::Unparsers::Newick, Bio::Phylo::Unparsers::Nexus, Bio::Phylo::Unparsers::Pagel, Bio::Phylo::Util::CONSTANT, Bio::Phylo::Util::Exceptions, Bio::Phylo::Util::IDPool, Bio::Phylo::Util::XMLWritable

no_invalid_versions

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

Error:

  • lib/Bio/Phylo/Forest.pm: HASH(0x55607ba64850)
  • lib/Bio/Phylo/Forest/Node.pm: HASH(0x55607baa8c78)
  • lib/Bio/Phylo/Forest/Tree.pm: HASH(0x55607baf3510)
  • lib/Bio/Phylo/Generator.pm: HASH(0x55607ba64430)
  • lib/Bio/Phylo/IO.pm: HASH(0x55607ba73360)
  • lib/Bio/Phylo/Listable.pm: HASH(0x55607bb4eb80)
  • lib/Bio/Phylo/Matrices.pm: HASH(0x55607bb0bc40)
  • lib/Bio/Phylo/Parsers/Newick.pm: HASH(0x55607ba645e0)
  • lib/Bio/Phylo/Parsers/Nexus.pm: HASH(0x55607bb36cd8)
  • lib/Bio/Phylo/Parsers/Table.pm: HASH(0x55607bb6c4d8)
  • lib/Bio/Phylo/Parsers/Taxlist.pm: HASH(0x55607ba9a140)
  • lib/Bio/Phylo/Taxa.pm: HASH(0x55607ba8bcf0)
  • lib/Bio/Phylo/Taxa/Taxon.pm: HASH(0x55607baa43f8)
  • lib/Bio/Phylo/Treedrawer.pm: HASH(0x55607bab2750)
  • lib/Bio/Phylo/Treedrawer/Svg.pm: HASH(0x55607bb10668)
  • lib/Bio/Phylo/Unparsers/Mrp.pm: HASH(0x55607ba7d058)
  • lib/Bio/Phylo/Unparsers/Newick.pm: HASH(0x55607bb4e400)
  • lib/Bio/Phylo/Unparsers/Nexus.pm: HASH(0x55607bbc3be8)
  • lib/Bio/Phylo/Unparsers/Pagel.pm: HASH(0x55607bad0d38)
  • lib/Bio/Phylo/Util/CONSTANT.pm: HASH(0x55607baf8648)
  • lib/Bio/Phylo/Util/Exceptions.pm: HASH(0x55607bb0b058)

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.

Modules

Name Abstract Version View
Bio::Phylo Phylogenetic analysis using perl. 0.17_RC6 metacpan
Bio::Phylo::Adaptor Object adaptor for compatibility metacpan
Bio::Phylo::Adaptor::Bioperl::Datum Adaptor class for bioperl compatibility metacpan
Bio::Phylo::Adaptor::Bioperl::Matrix Adaptor class for bioperl compatibility metacpan
Bio::Phylo::Adaptor::Bioperl::Node Adaptor class for bioperl compatibility metacpan
Bio::Phylo::Adaptor::Bioperl::Tree Adaptor class for bioperl compatibility 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::Datatype Superclass for objects that validate character data. metacpan
Bio::Phylo::Matrices::Datatype::Continuous Datatype subclass, no serviceable parts inside metacpan
Bio::Phylo::Matrices::Datatype::Custom Datatype subclass, no serviceable parts inside metacpan
Bio::Phylo::Matrices::Datatype::Dna Datatype subclass, no serviceable parts inside metacpan
Bio::Phylo::Matrices::Datatype::Mixed Datatype subclass, no serviceable parts inside metacpan
Bio::Phylo::Matrices::Datatype::Protein Datatype subclass, no serviceable parts inside metacpan
Bio::Phylo::Matrices::Datatype::Restriction Datatype subclass, no serviceable parts inside metacpan
Bio::Phylo::Matrices::Datatype::Rna Datatype subclass, no serviceable parts inside metacpan
Bio::Phylo::Matrices::Datatype::Standard Datatype subclass, no serviceable parts inside metacpan
Bio::Phylo::Matrices::Datum The character state sequence object. metacpan
Bio::Phylo::Matrices::Matrix Character state matrix. metacpan
Bio::Phylo::Matrices::TypeSafeData Superclass for objects that hold character data. metacpan
Bio::Phylo::Mediators::NodeMediator Mediator class to manage links between nodes. metacpan
Bio::Phylo::Mediators::TaxaMediator Mediator class to manage links between objects. 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::TaxaLinker Superclass for objects that link to taxa objects. metacpan
Bio::Phylo::Taxa::Taxon The operational taxonomic unit. metacpan
Bio::Phylo::Taxa::TaxonLinker Superclass for objects that link to taxon objects. metacpan
Bio::Phylo::Treedrawer An object-oriented facade for drawing trees. metacpan
Bio::Phylo::Treedrawer::Svg Creates svg tree drawings. No serviceable parts inside. 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 This package defines global constants and utility functions that operate on them. metacpan
Bio::Phylo::Util::Exceptions Exception classes for Bio::Phylo. metacpan
Bio::Phylo::Util::IDPool Utility class for generating object IDs. No serviceable parts inside. metacpan
Bio::Phylo::Util::Logger Logging for Bio::Phylo. metacpan
Bio::Phylo::Util::XMLWritable Superclass for objects that stringify to xml metacpan

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