Bio-Gonzales 0.051
- Released by
- JWB
- Version
- Release Date
- 2013-11-23
- Kwalitee
- 131.25
- Core Kwalitee
- 84.38
- LINKS
Bio-Gonzales 0.051
Kwalitee Issues
- 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 (155) does not match dist (174):
- Missing in MANIFEST: LICENSE, MANIFEST.bak, META.yml, _build/auto_features, _build/build_params, _build/cleanup, _build/config_data, _build/features, _build/magicnum, _build/notes, _build/prereqs, _build/runtime_params, bin/gonzconf, bin/gonzlog, bin/profile_time_space.pl, bin/profile_time_space.plot.R, bin/uniq_nodes.pl, dist.ini, lib/Bio/Gonzales/Feat/IO/SWISS.pm, lib/Bio/Gonzales/MiniFeat.pm, lib/Bio/Gonzales/Util.pm, lib/Bio/Gonzales/Util/Cerial.pm, lib/Bio/Gonzales/Util/Development.pm, lib/Bio/Gonzales/Util/Development/File.pm, lib/Bio/Gonzales/Util/Development/Module.pm, lib/Bio/Gonzales/Util/File.pm, lib/Bio/Gonzales/Util/Graphics/Color/Generator.pm, lib/Bio/Gonzales/Util/Log.pm, lib/Bio/Gonzales/Util/Math.pm, lib/Bio/Gonzales/Util/Math/kNN/via/Distances.pm, lib/Bio/Gonzales/Util/Role/FileIO.pm, lib/Bio/Gonzales/Util/Text.pm, lib/Bio/Gonzales/Util/YAML.pm, t/Bio-Gonzales-Feat-IO-SWISS.t, t/Bio-Gonzales-Util-Cerial.t, t/Bio-Gonzales-Util-File.t, t/Bio-Gonzales-Util-Log.t, t/Bio-Gonzales-Util-Log_threads.t, t/Bio-Gonzales-Util-Math.t, t/Bio-Gonzales-Util-Text.t, t/Bio-Gonzales-Util-YAML.t, t/Bio-Gonzales-Util.t, t/Math-kNN-via-Distances.t, t/data/uniprot_sprot.dat, t/data/uniprot_trembl.dat
- Missing in Dist: MANIFEST.SKIP, lib/Bargsten/Bio.pm, lib/Bargsten/Bio/Align/Jalview.pm, lib/Bargsten/Bio/Domain/Identification/HMMER.pm, lib/Bargsten/Bio/Domain/Identification/HMMER/SeqMarks.pm, lib/Bargsten/Bio/Domain/Identification/InterProScan.pm, lib/Bargsten/Bio/IDMapIO.pm, lib/Bargsten/Bio/Matrix/IO/mcl.pm, lib/Bargsten/Bio/Phylo/Dendroscope.pm, lib/Bargsten/Bio/PrimarySeqIX.pm, lib/Bargsten/Bio/Role/BioPerl/Constructor.pm, lib/Bargsten/Bio/SearchIO/HMMResult.pm, lib/Bargsten/Bio/Seq/Filter/DuplicateSeqs.pm, lib/Bargsten/Bio/Seq/Validate/fasta.pm, lib/Bargsten/Bio/SeqIO/fasta/idmap.pm, lib/Bargsten/Bio/Tools/SeqMask.pm, lib/Bargsten/Bio/Tools/SeqStats.pm, t/Align-Jalview.t, t/Domain-Identification-HMMER.t, t/Matrix-IO-mcl.t, t/idmapio.t, t/pod-coverage.t, t/pod.t, t/seq-validate-fasta.t, t/seqio-fasta-idmap.t, t/tools-seqmask.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::Gonzales::Util::Development::Module
- prereq_matches_use
-
List all used modules in META.yml requires
Error:
- Bio::Graphics
- Bio::Graphics::Glyph::generic
- Bio::Phylo::IO
- Color::Spectrum
- Data::Printer
- IO::Uncompress::Bunzip2
- Log::Log4perl
- Params::Validate
- YAML
- parent
- main_module_version_matches_dist_version
-
Make sure that the main module name and version are the same of the distribution.
- no_pod_errors
-
Remove the POD errors. You can check for POD errors automatically by including Test::Pod to your test suite.
Error: Bio-Gonzales-0.051/lib/Bio/Gonzales.pm -- Around line 48: Unknown directive: =head Around line 62: Unknown directive: =head
- has_meta_json
-
Add a META.json to the distribution. Your buildtool should be able to autogenerate it.
- 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::Gonzales::Graphics::Glyph::colorfulBox, Bio::Gonzales::Util::Development::Module
- test_prereq_matches_use
-
List all modules used in the test suite in META.yml test_requires
Error:
- Test::Fatal
- consistent_version
-
Split the distribution, or fix the version numbers to make them consistent (use the highest version number to avoid version downgrade).
Error: 0.0101,0.03
- 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::Gonzales | Speedy functions to manipulate biological data | 0.03 | metacpan |
| Bio::Gonzales::Align | 0.0101 | metacpan | |
| Bio::Gonzales::Align::ConsensePrimer | 0.0101 | metacpan | |
| Bio::Gonzales::Align::ConsensePrimer1 | 0.0101 | metacpan | |
| Bio::Gonzales::Align::IO | 0.0101 | metacpan | |
| Bio::Gonzales::Align::IO::MAF | 0.0101 | metacpan | |
| Bio::Gonzales::Align::IO::Stockholm | IO class for the stockholm format | 0.0101 | metacpan |
| Bio::Gonzales::Align::Jalview | 0.0101 | metacpan | |
| Bio::Gonzales::Assembly::IO | assembly related stuff | 0.0101 | metacpan |
| Bio::Gonzales::Domain::Group | 0.0101 | metacpan | |
| Bio::Gonzales::Domain::Identification::HMMER | 0.0101 | metacpan | |
| Bio::Gonzales::Feat | a sequence feature | 0.0101 | metacpan |
| Bio::Gonzales::Feat::IO | 0.0101 | metacpan | |
| Bio::Gonzales::Feat::IO::BED | 0.0101 | metacpan | |
| Bio::Gonzales::Feat::IO::Base | 0.0101 | metacpan | |
| Bio::Gonzales::Feat::IO::GFF3 | read and write gff files | 0.0101 | metacpan |
| Bio::Gonzales::Graphics::BLAST | make your blast result nice | 0.0101 | metacpan |
| Bio::Gonzales::Graphics::Glyph::colorfulBox | metacpan | ||
| Bio::Gonzales::IDMapIO | remap ids of 'objects', should be used in IO-classes, like Bio::SeqIO | 0.0101 | metacpan |
| Bio::Gonzales::Matrix::IO | Library for simple matrix IO | 0.0101 | metacpan |
| Bio::Gonzales::Matrix::IO::csv | 0.0101 | metacpan | |
| Bio::Gonzales::Matrix::Util | 0.0101 | metacpan | |
| Bio::Gonzales::Phylo::Dendroscope | Color phylogenetic trees in Dendroscope format | 0.0101 | metacpan |
| Bio::Gonzales::Phylo::IO | 0.0101 | metacpan | |
| Bio::Gonzales::Phylo::Util | utility functions for phylogenetic analysis | 0.0101 | metacpan |
| Bio::Gonzales::PrimarySeqIX | 0.0101 | metacpan | |
| Bio::Gonzales::Project | 0.0101 | metacpan | |
| Bio::Gonzales::Range::Cluster | cluster sorted ranges iteratively | 0.0101 | metacpan |
| Bio::Gonzales::Range::GroupedOverlap | cluster overlapping ranges that are in the same group | 0.0101 | metacpan |
| Bio::Gonzales::Range::Overlap | find overlapping ranges | 0.0101 | metacpan |
| Bio::Gonzales::Range::Util | 0.0101 | metacpan | |
| Bio::Gonzales::Role::BioPerl::Constructor | 0.0101 | metacpan | |
| Bio::Gonzales::Search::IO::BLAST | 0.0101 | metacpan | |
| Bio::Gonzales::Search::IO::HMMER3 | 0.0101 | metacpan | |
| Bio::Gonzales::Seq | Gonzales Seqeuence Object | 0.0101 | metacpan |
| Bio::Gonzales::Seq::Filter | filter sequence data | 0.0101 | metacpan |
| Bio::Gonzales::Seq::Filter::DuplicateSeqs | 0.0101 | metacpan | |
| Bio::Gonzales::Seq::Filter::ProteinCleaner | clean protein sequences | 0.0101 | metacpan |
| Bio::Gonzales::Seq::IO | fast utility functions for sequence IO | 0.0101 | metacpan |
| Bio::Gonzales::Seq::IO::Fasta | 0.0101 | metacpan | |
| Bio::Gonzales::Seq::IO::fastq | 0.0101 | metacpan | |
| Bio::Gonzales::Seq::LongestTranscript | 0.0101 | metacpan | |
| Bio::Gonzales::Seq::Util | 0.0101 | metacpan | |
| Bio::Gonzales::Seq::Validate::fasta | 0.0101 | metacpan | |
| Bio::Gonzales::Tools::SeqMask | 0.0101 | metacpan | |
| Bio::Gonzales::Tools::SeqStats | 0.0101 | metacpan |