Bio-Phylo 0.18
- Released by
- RVOSA
- Version
- Release Date
- 2010-03-02
- Kwalitee
- 128.12
- Core Kwalitee
- 87.5
- LINKS
Bio-Phylo 0.18 Deleted
Kwalitee Issues
- meta_yml_conforms_to_known_spec
-
Take a look at the META.yml Spec at https://metacpan.org/pod/CPAN::Meta::History::Meta_1_4 (for version 1.4) or https://metacpan.org/pod/CPAN::Meta::Spec (for version 2), and change your META.yml accordingly.
Error: Expected a map structure from string or file. (requires) [Validation: 1.3];License '<undef>' is invalid (license) [Validation: 1.3];Missing mandatory field, 'abstract' (abstract) [Validation: 1.3];Missing mandatory field, 'license' (license) [Validation: 1.3];value is an undefined string (abstract) [Validation: 1.3]
- has_changelog
-
Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.
- 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 (113) does not match dist (118):
- Missing in MANIFEST: lib/Bio/._Phylo.pm, t/._28-reroot.t, t/._regress_35511.t, t/._regress_51602.t, t/._regress_52960.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, Bio::Phylo::Factory, Bio::Phylo::Meta::XMLLiteral, Bio::Phylo::PhyloWS::Resource, Bio::Phylo::PhyloWS::Resource::Description, Bio::Phylo::PhyloWS::Service::Tolweb, Bio::Phylo::Set
- 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:
- lib/Bio/._Phylo.pm
- t/._28-reroot.t
- t/._regress_35511.t
- t/._regress_51602.t
- t/._regress_52960.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, Bio::Phylo, Bio::Phylo::Annotation, Bio::Phylo::Dictionary, Bio::Phylo::Factory, Bio::Phylo::Forest, Bio::Phylo::Forest::DrawNode, Bio::Phylo::Forest::DrawTree, Bio::Phylo::Forest::Node, Bio::Phylo::Forest::Tree, Bio::Phylo::Generator, Bio::Phylo::IO, Bio::Phylo::Listable, Bio::Phylo::Matrices, 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::Mediators::NodeMediator, Bio::Phylo::Mediators::TaxaMediator, Bio::Phylo::Meta, Bio::Phylo::Meta::XMLLiteral, Bio::Phylo::Parsers::Newick, Bio::Phylo::Parsers::Nexml, Bio::Phylo::Parsers::Nexus, Bio::Phylo::Parsers::Table, Bio::Phylo::Parsers::Taxlist, Bio::Phylo::PhyloWS, Bio::Phylo::PhyloWS::Client, Bio::Phylo::PhyloWS::Resource, Bio::Phylo::PhyloWS::Resource::Description, Bio::Phylo::PhyloWS::Service, Bio::Phylo::PhyloWS::Service::Tolweb, Bio::Phylo::Project, Bio::Phylo::Set, 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::Nexml, Bio::Phylo::Unparsers::Nexus, Bio::Phylo::Unparsers::Pagel, Bio::Phylo::Util::CONSTANT, Bio::Phylo::Util::DOM, Bio::Phylo::Util::Exceptions, Bio::Phylo::Util::IDPool, Bio::Phylo::Util::Logger, Bio::Phylo::Util::XMLWritable
- no_invalid_versions
-
Fix the version numbers so that version::is_lax($version) returns true.
Error:
- lib/Bio/Phylo/Parsers/Nexml.pm: HASH(0x55607c6621a0)
- lib/Bio/Phylo/Parsers/Tolweb.pm: HASH(0x55607c904ea8)
- lib/Bio/Phylo/Unparsers/Nexml.pm: HASH(0x55607c5b5180)
- 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).
Modules
| Name | Abstract | Version | View |
|---|---|---|---|
| Bio::Phylo | Phylogenetic analysis using perl | 0.18 | metacpan |
| Bio::Phylo::Annotation | Single key/value annotation, used within dictionary | metacpan | |
| Bio::Phylo::Dictionary | Container for annotations, attaches to other objects | metacpan | |
| Bio::Phylo::Factory | Creator of objects, reduces hardcoded class names in code | metacpan | |
| Bio::Phylo::Forest | Container for tree objects | metacpan | |
| Bio::Phylo::Forest::DrawNode | Tree node with extra methods for tree drawing | metacpan | |
| Bio::Phylo::Forest::DrawTree | Tree with extra methods for tree drawing | metacpan | |
| Bio::Phylo::Forest::Node | Node in a phylogenetic tree | metacpan | |
| Bio::Phylo::Forest::Tree | Phylogenetic tree | metacpan | |
| Bio::Phylo::Generator | Generator of tree topologies | metacpan | |
| Bio::Phylo::IO | Front end for parsers and serializers | metacpan | |
| Bio::Phylo::Listable | List of things, super class for many objects | metacpan | |
| Bio::Phylo::Matrices | Container of matrix objects | metacpan | |
| Bio::Phylo::Matrices::Datatype | Validator of character state data | metacpan | |
| Bio::Phylo::Matrices::Datatype::Continuous | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datatype::Custom | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datatype::Dna | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datatype::Mixed | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datatype::Protein | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datatype::Restriction | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datatype::Rna | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datatype::Standard | Validator subclass, no serviceable parts inside | metacpan | |
| Bio::Phylo::Matrices::Datum | Character state sequence | metacpan | |
| Bio::Phylo::Matrices::Matrix | Character state matrix | metacpan | |
| Bio::Phylo::Matrices::TypeSafeData | Superclass for objects that contain character data | metacpan | |
| Bio::Phylo::Mediators::NodeMediator | Mediator for links between tree nodes | metacpan | |
| Bio::Phylo::Mediators::TaxaMediator | Mediator for links between taxa and other objects | metacpan | |
| Bio::Phylo::Meta | Single predicate/object annotation, attached to an xml-writable subject | metacpan | |
| Bio::Phylo::Meta::XMLLiteral | Annotation value adaptor, no direct usage | metacpan | |
| Bio::Phylo::Parsers::Newick | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Nexml | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Nexus | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Table | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Taxlist | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Parsers::Tolweb | Parser used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::PhyloWS | Base class for phylogenetic web services | metacpan | |
| Bio::Phylo::PhyloWS::Client | Base class for phylogenetic web service clients | metacpan | |
| Bio::Phylo::PhyloWS::Resource | Represents a PhyloWS web resource | metacpan | |
| Bio::Phylo::PhyloWS::Resource::Description | Represents a PhyloWS resource description | metacpan | |
| Bio::Phylo::PhyloWS::Service | Base class for phylogenetic web services | metacpan | |
| Bio::Phylo::PhyloWS::Service::Timetree | PhyloWS service wrapper for Timetree | metacpan | |
| Bio::Phylo::PhyloWS::Service::Tolweb | PhyloWS service wrapper for Tree of Life | metacpan | |
| Bio::Phylo::Project | Container for related data | metacpan | |
| Bio::Phylo::Set | Subset of the parts inside a container | metacpan | |
| Bio::Phylo::Taxa | Container of taxon objects | metacpan | |
| Bio::Phylo::Taxa::TaxaLinker | Superclass for objects that link to taxa objects | metacpan | |
| Bio::Phylo::Taxa::Taxon | Operational taxonomic unit | metacpan | |
| Bio::Phylo::Taxa::TaxonLinker | Superclass for objects that link to taxon objects | metacpan | |
| Bio::Phylo::Treedrawer | Visualizer of tree shapes | metacpan | |
| Bio::Phylo::Treedrawer::Svg | Graphics format writer used by treedrawer, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Mrp | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Newick | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Nexml | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Nexus | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Unparsers::Pagel | Serializer used by Bio::Phylo::IO, no serviceable parts inside | metacpan | |
| Bio::Phylo::Util::CONSTANT | Global constants and utility functions | metacpan | |
| Bio::Phylo::Util::DOM | Drop-in XML DOM support for C<Bio::Phylo> | metacpan | |
| Bio::Phylo::Util::DOM::Document::libxml | XML DOM document mappings to the C<XML::LibXML> package | metacpan | |
| Bio::Phylo::Util::DOM::Document::twig | XML DOM document mappings to the C<XML::Twig> package | metacpan | |
| Bio::Phylo::Util::DOM::DocumentI | Abstract interface class for flexible XML document object model implementation | metacpan | |
| Bio::Phylo::Util::DOM::Element::libxml | XML DOM element mappings to the C<XML::LibXML> package | metacpan | |
| Bio::Phylo::Util::DOM::Element::twig | XML DOM mappings to the C<XML::Twig> package | metacpan | |
| Bio::Phylo::Util::DOM::ElementI | Abstract interface class for flexible XML document object model implementation | metacpan | |
| Bio::Phylo::Util::Exceptions | Errors ($@) that are objects | metacpan | |
| Bio::Phylo::Util::IDPool | Utility class for generating object IDs. No serviceable parts inside. | metacpan | |
| Bio::Phylo::Util::Logger | Logger of internal messages of several severity levels | metacpan | |
| Bio::Phylo::Util::XMLWritable | Superclass for objects that serialize to NeXML | metacpan |
Provides
| Name | File | View |
|---|---|---|
| Bio::Phylo::Util::StackTrace | lib/Bio/Phylo/Util/Exceptions.pm | metacpan |