- Released by
- RVOSA
- Version
- Release Date
- 2007-03-27
- Kwalitee
- 125
- Core Kwalitee
- 84.38
- LINKS
Bio-Phylo 0.16_RC3 Deleted
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'
- buildtool_not_executable
-
Change the permissions of Build.PL/Makefile.PL to not-executable.
- 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 (85) does not match dist (87):
- Missing in MANIFEST: t/._regress_21209.t, t/._regress_22813.t
- 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 - 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-0.16_RC3/lib/Bio/Phylo/Manual.pod -- Around line 138: 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.
- 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:- t/._regress_21209.t
- t/._regress_22813.t
- 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(0x56553b210730)
- lib/Bio/Phylo/Forest/Node.pm: HASH(0x56553b210508)
- lib/Bio/Phylo/Forest/Tree.pm: HASH(0x56553b1de6d8)
- lib/Bio/Phylo/Generator.pm: HASH(0x56553a930c48)
- lib/Bio/Phylo/IO.pm: HASH(0x56553b243458)
- lib/Bio/Phylo/Listable.pm: HASH(0x56553b11cc50)
- lib/Bio/Phylo/Matrices.pm: HASH(0x56553a9e95a0)
- lib/Bio/Phylo/Parsers/Newick.pm: HASH(0x56553b1e8980)
- lib/Bio/Phylo/Parsers/Nexus.pm: HASH(0x56553b120208)
- lib/Bio/Phylo/Parsers/Table.pm: HASH(0x56553b1e8788)
- lib/Bio/Phylo/Parsers/Taxlist.pm: HASH(0x56553b1d7680)
- lib/Bio/Phylo/Taxa.pm: HASH(0x56553b1dfbe8)
- lib/Bio/Phylo/Taxa/Taxon.pm: HASH(0x56553b118900)
- lib/Bio/Phylo/Treedrawer.pm: HASH(0x56553b244548)
- lib/Bio/Phylo/Treedrawer/Svg.pm: HASH(0x56553b2178e8)
- lib/Bio/Phylo/Unparsers/Mrp.pm: HASH(0x56553b122a78)
- lib/Bio/Phylo/Unparsers/Newick.pm: HASH(0x56553a9c0470)
- lib/Bio/Phylo/Unparsers/Nexus.pm: HASH(0x56553b245bf0)
- lib/Bio/Phylo/Unparsers/Pagel.pm: HASH(0x56553a9f9968)
- lib/Bio/Phylo/Util/CONSTANT.pm: HASH(0x565536d2e750)
- lib/Bio/Phylo/Util/Exceptions.pm: HASH(0x56553aa57ef8)
- 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. | 0.16_RC3 | 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::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 taxa 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::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 |