Kwalitee Issues

buildtool_not_executable

Change the permissions of Build.PL/Makefile.PL to not-executable.

has_human_readable_license

Add a section called "LICENSE" to the documentation, or add a file named LICENSE to the distribution.

has_license_in_source_file

Add =head1 LICENSE and the text of the license to the main module in your code.

no_pod_errors

Remove the POD errors. You can check for POD errors automatically by including Test::Pod to your test suite.

Error: Bio-Graphics-2.39/lib/Bio/Graphics/FeatureDir.pm -- Around line 160: '=item' outside of any '=over'Around line 272: =cut found outside a pod block. Skipping to next block.Around line 274: You forgot a '=back' before '=head1'

prereq_matches_use

List all used modules in META.yml requires

Error:

  • BerkeleyDB
  • Bio::DB::BigWig
  • Bio::SCF
  • GD::Image
  • SVG

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::Graphics::FeatureFile, Bio::Graphics::FeatureFile::Iterator, Bio::Graphics::GDWrapper, Bio::Graphics::Glyph::fb_shmiggle, Bio::Graphics::Glyph::read_pair, Bio::Graphics::Glyph::three_letters, Bio::Graphics::Wiggle::Loader

consistent_version

Split the distribution, or fix the version numbers to make them consistent (use the highest version number to avoid version downgrade).

Error: 1.0,2.39

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.

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.

use_warnings

Add 'use warnings' (or its equivalents) to all modules (this will require perl > 5.6), 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::Graphics, Bio::Graphics::ConfiguratorI, Bio::Graphics::Feature, Bio::Graphics::FeatureBase, Bio::Graphics::FeatureFile, Bio::Graphics::FeatureFile::Iterator, Bio::Graphics::GDWrapper, Bio::Graphics::Glyph, Bio::Graphics::Glyph::Factory, Bio::Graphics::Glyph::alignment, Bio::Graphics::Glyph::allele_tower, Bio::Graphics::Glyph::anchored_arrow, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::box, Bio::Graphics::Glyph::broken_line, Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::christmas_arrow, Bio::Graphics::Glyph::cross, Bio::Graphics::Glyph::crossbox, Bio::Graphics::Glyph::dashed_line, Bio::Graphics::Glyph::decorated_gene, Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::dumbbell, Bio::Graphics::Glyph::ellipse, Bio::Graphics::Glyph::ex, Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::fb_shmiggle, Bio::Graphics::Glyph::fixedwidth, Bio::Graphics::Glyph::flag, Bio::Graphics::Glyph::gene, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments, Bio::Graphics::Glyph::group, Bio::Graphics::Glyph::hat, Bio::Graphics::Glyph::heat_map, Bio::Graphics::Glyph::heat_map_ideogram, Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::hidden, Bio::Graphics::Glyph::hybrid_plot, Bio::Graphics::Glyph::ideogram, Bio::Graphics::Glyph::image, Bio::Graphics::Glyph::lightning, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::merge_parts, Bio::Graphics::Glyph::merged_alignment, Bio::Graphics::Glyph::minmax, Bio::Graphics::Glyph::operon, Bio::Graphics::Glyph::oval, Bio::Graphics::Glyph::pairplot, Bio::Graphics::Glyph::pentagram, Bio::Graphics::Glyph::phylo_align, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::point_glyph, Bio::Graphics::Glyph::primers, Bio::Graphics::Glyph::processed_transcript, Bio::Graphics::Glyph::protein, Bio::Graphics::Glyph::ragged_ends, Bio::Graphics::Glyph::rainbow_gene, Bio::Graphics::Glyph::read_pair, Bio::Graphics::Glyph::redgreen_box, Bio::Graphics::Glyph::redgreen_segment, Bio::Graphics::Glyph::repeating_shape, Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::saw_teeth, Bio::Graphics::Glyph::scale, Bio::Graphics::Glyph::segmented_keyglyph, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::smoothing, Bio::Graphics::Glyph::so_transcript, Bio::Graphics::Glyph::span, Bio::Graphics::Glyph::spectrogram, Bio::Graphics::Glyph::splice_site, Bio::Graphics::Glyph::stackedplot, Bio::Graphics::Glyph::ternary_plot, Bio::Graphics::Glyph::text_in_box, Bio::Graphics::Glyph::three_letters, Bio::Graphics::Glyph::tic_tac_toe, Bio::Graphics::Glyph::toomany, Bio::Graphics::Glyph::trace, Bio::Graphics::Glyph::track, Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::triangle, Bio::Graphics::Glyph::two_bolts, Bio::Graphics::Glyph::vista_plot, Bio::Graphics::Glyph::wave, Bio::Graphics::Glyph::weighted_arrow, Bio::Graphics::Glyph::whiskerplot, Bio::Graphics::Glyph::wiggle_box, Bio::Graphics::Glyph::wiggle_data, Bio::Graphics::Glyph::wiggle_density, Bio::Graphics::Glyph::wiggle_whiskers, Bio::Graphics::Glyph::wiggle_xyplot, Bio::Graphics::Glyph::xyplot, Bio::Graphics::Math, Bio::Graphics::Panel, Bio::Graphics::Pictogram, Bio::Graphics::RendererI, Bio::Graphics::Util, Bio::Graphics::Wiggle::Loader

build_prereq_matches_use

List all modules used in the test suite in META.yml build_requires

Error:

  • ExtUtils::MakeMaker
  • File::Glob
  • File::Spec
  • File::Temp
  • FindBin
  • Test::More
  • constant
  • lib
  • strict

has_separate_license_file

This is not a critical issue. Currently mainly informative for the CPANTS authors. It might be removed later.

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::Graphics Generate GD images of Bio::Seq objects 2.39 metacpan
Bio::Graphics::ConfiguratorI A sectioned map of configuration options (a map of maps), with a default section. Intended to augment existing tag-E<gt>value semantics (ie. of Bio::AnnotationCollectionI) for object-representation information (eg. foreground color), and for general interface preferences (eg. image width in gbrowse). metacpan
Bio::Graphics::DrawTransmembrane draw a cartoon of an Alpha-helical transmembrane protein. metacpan
Bio::Graphics::Feature A simple feature object for use with Bio::Graphics::Panel metacpan
Bio::Graphics::FeatureBase Compatibility module metacpan
Bio::Graphics::FeatureDir A directory of feature files and conf files metacpan
Bio::Graphics::FeatureFile A set of Bio::Graphics features, stored in a file metacpan
Bio::Graphics::FeatureFile::Iterator Iterator across a Bio::Graphics::FeatureFile metacpan
Bio::Graphics::FileSplitter metacpan
Bio::Graphics::GDWrapper metacpan
Bio::Graphics::Glyph Base class for Bio::Graphics::Glyph objects metacpan
Bio::Graphics::Glyph::Factory Factory for Bio::Graphics::Glyph objects metacpan
Bio::Graphics::Glyph::alignment The "alignment" glyph metacpan
Bio::Graphics::Glyph::allele_tower The "allele_tower" glyph metacpan
Bio::Graphics::Glyph::anchored_arrow The "anchored_arrow" glyph metacpan
Bio::Graphics::Glyph::arrow the "arrow" glyph metacpan
Bio::Graphics::Glyph::box The "box" glyph metacpan
Bio::Graphics::Glyph::broken_line The "broken line" glyph metacpan
Bio::Graphics::Glyph::cds The "cds" glyph metacpan
Bio::Graphics::Glyph::christmas_arrow The "christmas arrow" glyph metacpan
Bio::Graphics::Glyph::cross metacpan
Bio::Graphics::Glyph::crossbox The "crossbox" glyph metacpan
Bio::Graphics::Glyph::dashed_line The "dashed line" glyph metacpan
Bio::Graphics::Glyph::decorated_gene A GFF3-compatible gene glyph with protein decorations metacpan
Bio::Graphics::Glyph::decorated_transcript draws processed transcript with protein decorations metacpan
Bio::Graphics::Glyph::diamond The "diamond" glyph metacpan
Bio::Graphics::Glyph::dna The "dna" glyph metacpan
Bio::Graphics::Glyph::dot The "dot" glyph metacpan
Bio::Graphics::Glyph::dumbbell A glyph that draws a "dumbbell" with the same shapes on both ends. metacpan
Bio::Graphics::Glyph::ellipse The "ellipse" glyph metacpan
Bio::Graphics::Glyph::ex the "ex", or "crossed box" glyph metacpan
Bio::Graphics::Glyph::extending_arrow The "extending arrow" glyph metacpan
Bio::Graphics::Glyph::fb_shmiggle metacpan
Bio::Graphics::Glyph::fixedwidth A base class fixed width glyphs metacpan
Bio::Graphics::Glyph::flag the "flag" glyph metacpan
Bio::Graphics::Glyph::gene A GFF3-compatible gene glyph metacpan
Bio::Graphics::Glyph::generic The "generic" glyph metacpan
Bio::Graphics::Glyph::graded_segments The "graded_segments" glyph metacpan
Bio::Graphics::Glyph::group The "group" glyph metacpan
Bio::Graphics::Glyph::hat The "hat" glyph metacpan
Bio::Graphics::Glyph::heat_map The "heat_map" glyph metacpan
Bio::Graphics::Glyph::heat_map_ideogram The "heat_map_ideogram" glyph metacpan
Bio::Graphics::Glyph::heterogeneous_segments The "heterogeneous_segments" glyph metacpan
Bio::Graphics::Glyph::hidden The "hidden" glyph metacpan
Bio::Graphics::Glyph::hybrid_plot An xyplot plot drawing dual graph using data from two or more wiggle files per track 1.0 metacpan
Bio::Graphics::Glyph::ideogram The "ideogram" glyph metacpan
Bio::Graphics::Glyph::image A glyph that draws photographs & other images metacpan
Bio::Graphics::Glyph::lightning The "lightning" glyph metacpan
Bio::Graphics::Glyph::line The "line" glyph metacpan
Bio::Graphics::Glyph::merge_parts a base class which suppors semantic zooming of scored alignment features metacpan
Bio::Graphics::Glyph::merged_alignment The "merged_alignment" glyph metacpan
Bio::Graphics::Glyph::minmax The minmax glyph metacpan
Bio::Graphics::Glyph::operon The "polycistronic operon" glyph metacpan
Bio::Graphics::Glyph::oval The "oval" glyph metacpan
Bio::Graphics::Glyph::pairplot The "pairwise plot" glyph metacpan
Bio::Graphics::Glyph::pentagram The "pentagram" glyph metacpan
Bio::Graphics::Glyph::phylo_align The "phylogenetic alignment" glyph metacpan
Bio::Graphics::Glyph::pinsertion The "Drosophila P-element Insertion" glyph metacpan
Bio::Graphics::Glyph::point_glyph metacpan
Bio::Graphics::Glyph::primers The "STS primers" glyph metacpan
Bio::Graphics::Glyph::processed_transcript The sequence ontology transcript glyph metacpan
Bio::Graphics::Glyph::protein The "protein" glyph metacpan
Bio::Graphics::Glyph::ragged_ends The "ragged ends" glyph metacpan
Bio::Graphics::Glyph::rainbow_gene metacpan
Bio::Graphics::Glyph::read_pair metacpan
Bio::Graphics::Glyph::redgreen_box The "redgreen_box" glyph metacpan
Bio::Graphics::Glyph::redgreen_segment The "redgreen_segments" glyph metacpan
Bio::Graphics::Glyph::repeating_shape A glyph that draws the same shape repeatedly. metacpan
Bio::Graphics::Glyph::rndrect The "round rect" glyph metacpan
Bio::Graphics::Glyph::ruler_arrow glyph for drawing an arrow as ruler (5' and 3' are marked as label) metacpan
Bio::Graphics::Glyph::saw_teeth The "saw teeth" glyph metacpan
Bio::Graphics::Glyph::scale The "scale" glyph metacpan
Bio::Graphics::Glyph::segmented_keyglyph The "segmented_keyglyph" glyph metacpan
Bio::Graphics::Glyph::segments The "segments" glyph metacpan
Bio::Graphics::Glyph::smoothing metacpan
Bio::Graphics::Glyph::so_transcript The sequence ontology transcript glyph metacpan
Bio::Graphics::Glyph::span The "span" glyph metacpan
Bio::Graphics::Glyph::spectrogram The "spectrogram" glyph metacpan
Bio::Graphics::Glyph::splice_site The "splice_site" glyph metacpan
Bio::Graphics::Glyph::stackedplot The stackedplot glyph metacpan
Bio::Graphics::Glyph::ternary_plot Draw ternary plot data metacpan
Bio::Graphics::Glyph::text_in_box The "text in box" glyph metacpan
Bio::Graphics::Glyph::three_letters DAS-compatible package to use for drawing a line of groups of three letters metacpan
Bio::Graphics::Glyph::tic_tac_toe The "tic-tac-toe" glyph metacpan
Bio::Graphics::Glyph::toomany The "too many to show" glyph metacpan
Bio::Graphics::Glyph::trace A glyph that visualizes a trace file metacpan
Bio::Graphics::Glyph::track The "track" glyph metacpan
Bio::Graphics::Glyph::transcript The "transcript" glyph metacpan
Bio::Graphics::Glyph::transcript2 The "transcript2" glyph metacpan
Bio::Graphics::Glyph::translation The "6-frame translation" glyph metacpan
Bio::Graphics::Glyph::triangle The "triangle" glyph metacpan
Bio::Graphics::Glyph::two_bolts The "two bolts" glyph metacpan
Bio::Graphics::Glyph::vista_plot The "vista_plot" glyph 1.0 metacpan
Bio::Graphics::Glyph::wave The "wave" glyph metacpan
Bio::Graphics::Glyph::weighted_arrow The "weighted arrow" glyph metacpan
Bio::Graphics::Glyph::whiskerplot The whiskerplot glyph metacpan
Bio::Graphics::Glyph::wiggle_box A generic box glyph compatible with dense "wig"data metacpan
Bio::Graphics::Glyph::wiggle_data metacpan
Bio::Graphics::Glyph::wiggle_density A density plot compatible with dense "wig"data metacpan
Bio::Graphics::Glyph::wiggle_whiskers metacpan
Bio::Graphics::Glyph::wiggle_xyplot An xyplot plot compatible with dense "wig"data metacpan
Bio::Graphics::Glyph::xyplot The xyplot glyph metacpan
Bio::Graphics::Layout metacpan
Bio::Graphics::Layout::Contour metacpan
Bio::Graphics::Math metacpan
Bio::Graphics::Panel Generate GD images of Bio::Seq objects metacpan
Bio::Graphics::Pictogram generate SVG output of Pictogram display for consensus motifs metacpan
Bio::Graphics::RendererI A renderer for the Bio::Graphics class that renders Bio::SeqFeature::CollectionI objects onto Bio::Graphics::Panels using configuration information provided by a Bio::Graphics::ConfiguratorI. metacpan
Bio::Graphics::Util non-object-oriented utilities used in Bio::Graphics modules metacpan
Bio::Graphics::Wiggle Binary storage for dense genomic features 1.0 metacpan
Bio::Graphics::Wiggle::Loader metacpan

Other Files

Build.PL metacpan
Changes metacpan
MANIFEST metacpan
META.json metacpan
META.yml metacpan
Makefile.PL metacpan
README metacpan
README.bioperl metacpan