Bio-NEXUS 0.76
- Released by
- ARLIN
- Version
- Release Date
- 2010-09-23
- Kwalitee
- 125
- Core Kwalitee
- 84.38
- LINKS
Bio-NEXUS 0.76
Kwalitee Issues
This is not the latest release. The following issues may have already been fixed in the newer releases.
- has_changelog
-
Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.
- buildtool_not_executable
-
Change the permissions of Build.PL/Makefile.PL to not-executable.
- has_license_in_source_file
-
Add =head1 LICENSE and the text of the license to the main module in your code.
- 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 (445) does not match dist (223):
- Duplicates in MANIFEST: Build.PL, LICENSE, MANIFEST, META.yml, Makefile.PL, README, README_admin, data/Liang_et_al_Figure.nex, data/SPAN_Family3il.nex, data/SPAN_Family3il.pdf, data/SPAN_Family3il.ps, data/basic.nex, data/color-my-taxsets.nex, doc/Installation.pod, doc/NEXUS_coverage.html, doc/ToDo.txt, doc/Tutorial.pod, doc/UserManual.pod, doc/buglist.txt, doc/changes.txt, doc/example1.nex, exec/align2nex.pl, exec/bugs.cmd.pl, exec/bugs.pl, exec/extract_taxset.pl, exec/history.pl, exec/jags.pl, exec/newtonex.pl, exec/nex2text_tree.pl, exec/nexdiff.pl, exec/nexdump.pl, exec/nexfix.pl, exec/nexplot.pl, exec/nextool.pl, exec/nexus-convert.pl, exec/p3treeplot.pl, exec/pppplot.pl, exec/readin_tcoffee.pl, exec/roundtrip.pl, exec/setmaker.pl, exec/tree2nex.pl, exec/tree_equality.pl, exec/tree_length.pl, lib/Bio/NEXUS.pm, lib/Bio/NEXUS/AssumptionsBlock.pm, lib/Bio/NEXUS/Block.pm, lib/Bio/NEXUS/CharactersBlock.pm, lib/Bio/NEXUS/CodonsBlock.pm, lib/Bio/NEXUS/DataBlock.pm, lib/Bio/NEXUS/DistancesBlock.pm, lib/Bio/NEXUS/Functions.pm, lib/Bio/NEXUS/HistoryBlock.pm, lib/Bio/NEXUS/Matrix.pm, lib/Bio/NEXUS/NHXCmd.pm, lib/Bio/NEXUS/Node.pm, lib/Bio/NEXUS/NotesBlock.pm, lib/Bio/NEXUS/SetsBlock.pm, lib/Bio/NEXUS/SpanBlock.pm, lib/Bio/NEXUS/TaxUnit.pm, lib/Bio/NEXUS/TaxUnitSet.pm, lib/Bio/NEXUS/TaxaBlock.pm, lib/Bio/NEXUS/Tools/GraphicsParams.pm, lib/Bio/NEXUS/Tools/NexModifier.pm, lib/Bio/NEXUS/Tools/NexPlott.swp, lib/Bio/NEXUS/Tools/NexPlotter.pm, lib/Bio/NEXUS/Tree.pm, lib/Bio/NEXUS/TreesBlock.pm, lib/Bio/NEXUS/UnalignedBlock.pm, lib/Bio/NEXUS/UnknownBlock.pm, lib/Bio/NEXUS/Util/Exceptions.pm, lib/Bio/NEXUS/Util/Logger.pm, lib/Bio/NEXUS/WeightSet.pm, t/_perl_module-loading.t, t/_perl_perlpod.t, t/_perl_podcoverage.t, t/assumptionsblock_options.t, t/assumptionsblock_wtset-scores.t, t/block_link-and-title.t, t/charactersblock_methods-01.t, t/charactersblock_methods-02.t, t/data/compliant/01_basic.nex, t/data/compliant/01_taxa-labels-squarebrackets.nex, t/data/compliant/02_assumptions-block_options_01.nex, t/data/compliant/02_assumptions-block_options_02.nex, t/data/compliant/02_character-polymorphic-doublequotes.nex, t/data/compliant/02_character-polymorphic-uncertain.nex, t/data/compliant/02_character-polymorphic.nex, t/data/compliant/02_character-state-frequency.nex, t/data/compliant/02_character-uncertain.nex, t/data/compliant/02_characters-block_format_01.nex, t/data/compliant/02_characters-block_format_02.nex, t/data/compliant/02_characters-block_initial.nex, t/data/compliant/02_notes-text.nex, t/data/compliant/02_wtset-scores.nex, t/data/compliant/04_block_level_methods.nex, t/data/compliant/04_charactersblock_methods_01.nex, t/data/compliant/04_charactersblock_methods_02.nex, t/data/compliant/04_charactersblock_methods_03.nex, t/data/compliant/04_charactersblock_methods_04.nex, t/data/compliant/04_charactersblock_methods_05.nex, t/data/compliant/04_characterstatelabels_05.nex, t/data/compliant/04_equals_methods.nex, t/data/compliant/04_object-file-equality_01.nex, t/data/compliant/04_object-file-equality_02.nex, t/data/compliant/04_private-commands.nex, t/data/compliant/04_shared_commands_01.nex, t/data/compliant/04_shared_commands_02.nex, t/data/compliant/04_shared_commands_03.nex, t/data/compliant/04_shared_commands_04.nex, t/data/compliant/04_shared_commands_05.nex, t/data/compliant/Bird_Ovomucoids.nex, t/data/compliant/FaresWolfeCCT.nex, t/data/compliant/HCRT_all_orths_pep1_msfed1.aln.nxs, t/data/compliant/Human_mt_DNA.nex, t/data/compliant/KOG0003.nex, t/data/compliant/Kingdoms_DNA.nex, t/data/compliant/Marsupial_Wolf.nex, t/data/compliant/Omland-Orioles.nex, t/data/compliant/Omland-Ravens.nex, t/data/compliant/Primate_mtDNA.nex, t/data/compliant/SPAN_Family10i.nex, t/data/compliant/SPAN_Family1nlw.nex, t/data/compliant/SPAN_Family2alw.nex, t/data/compliant/SPAN_Family3il.nex, t/data/compliant/SPAN_Family4nl.nex, t/data/compliant/SPAN_Family5alw.nex, t/data/compliant/SPAN_Family6iw.nex, t/data/compliant/SPAN_Family7n.nex, t/data/compliant/SPAN_Family8a.nex, t/data/compliant/SPAN_Family9iw.nex, t/data/compliant/Treebase-chlamy-dna.nex, t/data/compliant/Treebase-horsetails-classic.nex, t/data/compliant/Treebase-horsetails-dna.nex, t/data/compliant/Treebase-liverwort-rbcl.nex, t/data/compliant/UnaSmithHIV-both.nex, t/data/compliant/barns-combined.nex, t/data/compliant/basic-bush-dos.nex, t/data/compliant/basic-bush-mac.nex, t/data/compliant/basic-bush-unix.nex, t/data/compliant/basic-bush.nex, t/data/compliant/basic-ladder.nex, t/data/compliant/basic-rake.nex, t/data/compliant/basic-trees.nex, t/data/compliant/char-interleave.nex, t/data/compliant/char-matrix-spaces.nex, t/data/compliant/characters-block-interleave.nex, t/data/compliant/data-block_clustalw.nex, t/data/compliant/dist_interleave_lower.nex, t/data/compliant/dist_interleave_lower_nodiag.nex, t/data/compliant/dist_interleave_rect_nodiag.nex, t/data/compliant/dist_interleave_upper.nex, t/data/compliant/dist_interleave_upper_nodiag.nex, t/data/compliant/dist_lower.nex, t/data/compliant/dist_lower_no-diag.nex, t/data/compliant/dist_rect.nex, t/data/compliant/dist_upper.nex, t/data/compliant/dist_upper_no-diag.nex, t/data/compliant/example1.nex, t/data/compliant/history-block_probab-distrib.nex, t/data/compliant/intrablock-comment.nex, t/data/compliant/long-names.nex, t/data/compliant/multiline-intrablock-comment.nex, t/data/compliant/quoted-strings1.nex, t/data/compliant/quoted-strings2.nex, t/data/compliant/radical-whitespace.nex, t/data/compliant/really-long-names.nex, t/data/compliant/simple_taxa_and_chars.nex, t/data/compliant/temp.nex, t/data/compliant/top-level-comment.nex, t/data/compliant/tree-nhx.nex, t/data/compliant/trees-translate.nex, t/data/compliant/trees-tree-basal-trifurcation.nex, t/data/compliant/trees-tree-bush-branchlength-negative.nex, t/data/compliant/trees-tree-bush-branchlength-scientific.nex, t/data/compliant/trees-tree-bush-branchlength-zero.nex, t/data/compliant/trees-tree-bush-cladogram.nex, t/data/compliant/trees-tree-bush-extended-root-branch.nex, t/data/compliant/trees-tree-bush-inode-labels-partial.nex, t/data/compliant/trees-tree-bush-inode-labels-quoted1.nex, t/data/compliant/trees-tree-bush-inode-labels-quoted2.nex, t/data/compliant/trees-tree-bush-inode-labels.nex, t/data/compliant/trees-tree-bush-quoted-string-name1.nex, t/data/compliant/trees-tree-bush-quoted-string-name2.nex, t/data/compliant/trees-tree-bush-uneven.nex, t/data/compliant/trees-tree-bush.nex, t/data/compliant/trees-tree-ladder-cladogram.nex, t/data/compliant/trees-tree-ladder-uneven.nex, t/data/compliant/trees-tree-ladder.nex, t/data/compliant/trees-tree-multiple-challenges.nex, t/data/compliant/trees-tree-multiple.nex, t/data/compliant/trees-tree-rake-cladogram.nex, t/data/compliant/trees-tree-rake.nex, t/data/compliant/trees_branch-support-values.nex, t/data/compliant/unaligned_simple_01.nex, t/matrix_character-state-frequency.t, t/matrix_charactersblock-interleave.t, t/matrix_historyblock-probab-distrib.t, t/matrix_polymorphic-and-uncertain.t, t/nexus_add-otu-clone.t, t/nexus_block-level-commands.t, t/nexus_taxa-labels-quoted.t, t/nexus_taxa-labels-squarebrackets.t, t/nexus_taxa-labels.t, t/nexus_wrong_format.t, t/nhxcmd_parsing.t, t/notesblock_methods.t, t/tree_equals.t, t/tree_methods-01.t, t/tree_methods-02.t, t/tree_parsing.t, t/tree_parsing_quotemeta.t, t/tree_support-values.t, t/treesblock_methods.t, t/uncat_clone_methods.t, t/uncat_datablock_clustalw.t, t/uncat_equals_methods.t, t/uncat_excessive_whitespace.t, t/uncat_ntax-nchar-dimensions.t, t/uncat_object-file-equality.t, t/uncat_shared-commands.t, t/uncat_todo.t, t/uncat_write.t
- no_pod_errors
-
Remove the POD errors. You can check for POD errors automatically by including Test::Pod to your test suite.
Error: Bio-NEXUS-0.76/exec/jags.pl -- Around line 68: Unknown directive: =ignore
- 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.
- has_known_license_in_source_file
-
Add =head1 LICENSE and/or the proper text of the well-known license to the main module in your code.
- 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::NEXUS, Bio::NEXUS::AssumptionsBlock, Bio::NEXUS::Block, Bio::NEXUS::CharactersBlock, Bio::NEXUS::CodonsBlock, Bio::NEXUS::DataBlock, Bio::NEXUS::DistancesBlock, Bio::NEXUS::Functions, Bio::NEXUS::HistoryBlock, Bio::NEXUS::Matrix, Bio::NEXUS::NHXCmd, Bio::NEXUS::Node, Bio::NEXUS::NotesBlock, Bio::NEXUS::SetsBlock, Bio::NEXUS::SpanBlock, Bio::NEXUS::TaxUnit, Bio::NEXUS::TaxUnitSet, Bio::NEXUS::TaxaBlock, Bio::NEXUS::Tools::GraphicsParams, Bio::NEXUS::Tools::NexModifier, Bio::NEXUS::Tools::NexPlotter, Bio::NEXUS::Tree, Bio::NEXUS::TreesBlock, Bio::NEXUS::UnalignedBlock, Bio::NEXUS::UnknownBlock, Bio::NEXUS::Util::Exceptions, Bio::NEXUS::Util::Logger, Bio::NEXUS::WeightSet
- no_invalid_versions
-
Fix the version numbers so that version::is_lax($version) returns true.
Error:
- lib/Bio/NEXUS/AssumptionsBlock.pm: HASH(0x55c8cee8c258)
- lib/Bio/NEXUS/Block.pm: HASH(0x55c8d16302b8)
- lib/Bio/NEXUS/CharactersBlock.pm: HASH(0x55c8d14d6e70)
- lib/Bio/NEXUS/CodonsBlock.pm: HASH(0x55c8d15ba560)
- lib/Bio/NEXUS/DataBlock.pm: HASH(0x55c8d1516348)
- lib/Bio/NEXUS/DistancesBlock.pm: HASH(0x55c8d1536f50)
- lib/Bio/NEXUS/Functions.pm: HASH(0x55c8d15930a8)
- lib/Bio/NEXUS/HistoryBlock.pm: HASH(0x55c8ceeb3ba8)
- lib/Bio/NEXUS/Matrix.pm: HASH(0x55c8d15fc740)
- lib/Bio/NEXUS/NHXCmd.pm: HASH(0x55c8d14a0e18)
- lib/Bio/NEXUS/Node.pm: HASH(0x55c8d14afce8)
- lib/Bio/NEXUS/NotesBlock.pm: HASH(0x55c8d14b9728)
- lib/Bio/NEXUS/SetsBlock.pm: HASH(0x55c8d162a580)
- lib/Bio/NEXUS/SpanBlock.pm: HASH(0x55c8d14f8a50)
- lib/Bio/NEXUS/TaxUnit.pm: HASH(0x55c8d14721f0)
- lib/Bio/NEXUS/TaxUnitSet.pm: HASH(0x55c8d1622048)
- lib/Bio/NEXUS/TaxaBlock.pm: HASH(0x55c8d1489070)
- lib/Bio/NEXUS/Tools/GraphicsParams.pm: HASH(0x55c8d1601ce0)
- lib/Bio/NEXUS/Tools/NexModifier.pm: HASH(0x55c8d1608a00)
- lib/Bio/NEXUS/Tools/NexPlotter.pm: HASH(0x55c8d1471e78)
- lib/Bio/NEXUS/Tree.pm: HASH(0x55c8d15ed350)
- lib/Bio/NEXUS/TreesBlock.pm: HASH(0x55c8d1608460)
- lib/Bio/NEXUS/UnalignedBlock.pm: HASH(0x55c8d14b9698)
- lib/Bio/NEXUS/UnknownBlock.pm: HASH(0x55c8d14c7ea8)
- lib/Bio/NEXUS/WeightSet.pm: HASH(0x55c8d162ffb8)
- 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::NEXUS | An object-oriented Perl Applications Programming Interface (API) for the NEXUS file format | 0.76 | metacpan |
| Bio::NEXUS::AssumptionsBlock | Represents ASSUMPTIONS block of a NEXUS file | metacpan | |
| Bio::NEXUS::Block | Provides useful functions for blocks in NEXUS file (parent class). | metacpan | |
| Bio::NEXUS::CharactersBlock | Represents a CHARACTERS Block (Data or Characters) of a NEXUS file | metacpan | |
| Bio::NEXUS::CodonsBlock | Represents CODONS block in NEXUS file | metacpan | |
| Bio::NEXUS::DataBlock | Represents the deprecated DATA Block in NEXUS file. | metacpan | |
| Bio::NEXUS::DistancesBlock | Represents DISTANCES block in NEXUS file | metacpan | |
| Bio::NEXUS::Functions | Provides private utiliy functions for the module | metacpan | |
| Bio::NEXUS::HistoryBlock | Represents a HISTORY block of a NEXUS file | metacpan | |
| Bio::NEXUS::Matrix | Provides functions for handling blocks that have matrices | metacpan | |
| Bio::NEXUS::NHXCmd | Provides functions for manipulating nodes in trees | metacpan | |
| Bio::NEXUS::Node | Provides functions for manipulating nodes in trees | metacpan | |
| Bio::NEXUS::NotesBlock | Represents a NOTES block in a NEXUS file. | metacpan | |
| Bio::NEXUS::SetsBlock | Represents SETS block of a NEXUS file | metacpan | |
| Bio::NEXUS::SpanBlock | Represent SPAN block in a NEXUS file (contains meta data). | metacpan | |
| Bio::NEXUS::TaxUnit | Represents a taxon unit in a NEXUS file | metacpan | |
| Bio::NEXUS::TaxUnitSet | Represents a sets of OTUS (Bio::NEXUS::TaxUnits objects) in a NEXUS file | metacpan | |
| Bio::NEXUS::TaxaBlock | Represents TAXA block of a NEXUS file | metacpan | |
| Bio::NEXUS::Tools::GraphicsParams | metacpan | ||
| Bio::NEXUS::Tools::NexModifier | metacpan | ||
| Bio::NEXUS::Tools::NexPlotter | metacpan | ||
| Bio::NEXUS::Tree | Provides functions for manipulating trees | metacpan | |
| Bio::NEXUS::TreesBlock | Represents TREES block of a NEXUS file | metacpan | |
| Bio::NEXUS::UnalignedBlock | Represents an UNALIGNED block of a NEXUS file | metacpan | |
| Bio::NEXUS::UnknownBlock | Represents a simple object for storing information unrecognized blocks by the Bio::NEXUS module. | metacpan | |
| Bio::NEXUS::Util::Exceptions | Exception classes for Bio::NEXUS. | metacpan | |
| Bio::NEXUS::Util::Logger | Logging for Bio::NEXUS. | metacpan | |
| Bio::NEXUS::WeightSet | Represents column weights in alignment ( for each character) | metacpan |