Bio-Phylo 0.13
- Released by
- RVOSA
- Version
- Release Date
- 2006-09-07
- Kwalitee
- 140.62
- Core Kwalitee
- 96.88
- LINKS
Bio-Phylo 0.13 Deleted
Kwalitee Issues
- 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-0.13/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::IO, Bio::Phylo::Listable, Bio::Phylo::Matrices, Bio::Phylo::Matrices::Datum, Bio::Phylo::Matrices::Matrix, 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::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
- no_invalid_versions
-
Fix the version numbers so that version::is_lax($version) returns true.
Error:
- lib/Bio/Phylo/Forest.pm: HASH(0x55607bc5ebd0)
- lib/Bio/Phylo/Forest/Node.pm: HASH(0x55607bd3f3b0)
- lib/Bio/Phylo/Forest/Tree.pm: HASH(0x55607bc863c0)
- lib/Bio/Phylo/Generator.pm: HASH(0x55607bd8d550)
- lib/Bio/Phylo/IO.pm: HASH(0x55607be21d58)
- lib/Bio/Phylo/Listable.pm: HASH(0x55607bc6e5d8)
- lib/Bio/Phylo/Matrices.pm: HASH(0x55607bc6ec38)
- lib/Bio/Phylo/Matrices/Datum.pm: HASH(0x55607bc687f0)
- lib/Bio/Phylo/Matrices/Matrix.pm: HASH(0x55607bc68af0)
- lib/Bio/Phylo/Parsers/Newick.pm: HASH(0x55607bcadcb0)
- lib/Bio/Phylo/Parsers/Nexus.pm: HASH(0x55607bc55db8)
- lib/Bio/Phylo/Parsers/Table.pm: HASH(0x55607bdf1bd0)
- lib/Bio/Phylo/Parsers/Taxlist.pm: HASH(0x55607bc86648)
- lib/Bio/Phylo/Taxa.pm: HASH(0x55607bd133c8)
- lib/Bio/Phylo/Taxa/Taxon.pm: HASH(0x55607bc6ece0)
- lib/Bio/Phylo/Treedrawer.pm: HASH(0x55607bd52728)
- lib/Bio/Phylo/Treedrawer/Svg.pm: HASH(0x55607bd52800)
- lib/Bio/Phylo/Unparsers/Mrp.pm: HASH(0x55607bdb3740)
- lib/Bio/Phylo/Unparsers/Newick.pm: HASH(0x55607bca3988)
- lib/Bio/Phylo/Unparsers/Nexus.pm: HASH(0x55607bcc46b0)
- lib/Bio/Phylo/Unparsers/Pagel.pm: HASH(0x55607bca3e80)
- lib/Bio/Phylo/Util/CONSTANT.pm: HASH(0x55607bd60bc0)
- lib/Bio/Phylo/Util/Exceptions.pm: HASH(0x55607bded618)
- 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. | 0.13 | 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::Datum | The single observations object. | metacpan | |
| Bio::Phylo::Matrices::Matrix | Character state matrix, implements Bio::CDAT::CharMatrixI | 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 | 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. No serviceable parts inside. | metacpan | |
| Bio::Phylo::Util::IDPool | Utility class for generating object IDs | metacpan |
Provides
| Name | File | View |
|---|---|---|
| Bio::Phylo::Deprecated | lib/Bio/Phylo.pm | metacpan |
| Bio::Phylo::Matrices::Alignment | lib/Bio/Phylo.pm | metacpan |
| Bio::Phylo::Matrices::CharSeq | lib/Bio/Phylo/Matrices/Matrix.pm | metacpan |
| Bio::Phylo::Matrices::Matrix::categorical | lib/Bio/Phylo/Matrices/Matrix.pm | metacpan |
| Bio::Phylo::Matrices::Matrix::continuous | lib/Bio/Phylo/Matrices/Matrix.pm | metacpan |
| Bio::Phylo::Matrices::Matrix::dna | lib/Bio/Phylo/Matrices/Matrix.pm | metacpan |
| Bio::Phylo::Matrices::Matrix::protein | lib/Bio/Phylo/Matrices/Matrix.pm | metacpan |
| Bio::Phylo::Matrices::Matrix::restriction | lib/Bio/Phylo/Matrices/Matrix.pm | metacpan |
| Bio::Phylo::Matrices::Matrix::rna | lib/Bio/Phylo/Matrices/Matrix.pm | metacpan |
| Bio::Phylo::Matrices::Matrix::standard | lib/Bio/Phylo/Matrices/Matrix.pm | metacpan |
| Bio::Phylo::Matrices::Sequence | lib/Bio/Phylo.pm | metacpan |
| Bio::Phylo::Parsers | lib/Bio/Phylo.pm | metacpan |
| Bio::Phylo::Parsers::Fastnewick | lib/Bio/Phylo.pm | metacpan |
| Bio::Phylo::Parsers::Fastnexus | lib/Bio/Phylo.pm | metacpan |
| Bio::Phylo::Unparsers | lib/Bio/Phylo.pm | metacpan |