Kwalitee Issues


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


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


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

Error: *** ERROR: '=item' outside of any '=over' at line 160 in file Bio-Graphics-2.25/lib/Bio/Graphics/ *** ERROR: =cut found outside a pod block. Skipping to next block. at line 272 in file Bio-Graphics-2.25/lib/Bio/Graphics/ *** ERROR: You forgot a '=back' before '=head1' at line 274 in file Bio-Graphics-2.25/lib/Bio/Graphics/


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::Iterator, Bio::Graphics::Glyph::read_pair


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

Error: 1.0,2.25


Add =head1 LICENSE and/or the proper text of the well-known license to the main module in your code.


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.


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::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::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::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::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::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_density, Bio::Graphics::Glyph::wiggle_minmax, 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


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


Add a 'repository' resource to the META.yml via 'meta_add' accessor (for Module::Build) or META_ADD parameter (for ExtUtils::MakeMaker).


Name Abstract Version View
Bio::Graphics Generate GD images of Bio::Seq objects 2.25 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). 0 metacpan
Bio::Graphics::DrawTransmembrane draw a cartoon of an Alpha-helical transmembrane protein. 0 metacpan
Bio::Graphics::Feature A simple feature object for use with Bio::Graphics::Panel 0 metacpan
Bio::Graphics::FeatureBase Compatibility module 0 metacpan
Bio::Graphics::FeatureDir A directory of feature files and conf files 0 metacpan
Bio::Graphics::FeatureFile A set of Bio::Graphics features, stored in a file 0 metacpan
Bio::Graphics::FeatureFile::Iterator Iterator across a Bio::Graphics::FeatureFile 0 metacpan
Bio::Graphics::FileSplitter 0 metacpan
Bio::Graphics::Glyph Base class for Bio::Graphics::Glyph objects 0 metacpan
Bio::Graphics::Glyph::Factory Factory for Bio::Graphics::Glyph objects 0 metacpan
Bio::Graphics::Glyph::alignment The "alignment" glyph 0 metacpan
Bio::Graphics::Glyph::allele_tower The "allele_tower" glyph 0 metacpan
Bio::Graphics::Glyph::anchored_arrow The "anchored_arrow" glyph 0 metacpan
Bio::Graphics::Glyph::arrow the "arrow" glyph 0 metacpan
Bio::Graphics::Glyph::box The "box" glyph 0 metacpan
Bio::Graphics::Glyph::broken_line The "broken line" glyph 0 metacpan
Bio::Graphics::Glyph::cds The "cds" glyph 0 metacpan
Bio::Graphics::Glyph::christmas_arrow The "christmas arrow" glyph 0 metacpan
Bio::Graphics::Glyph::cross 0 metacpan
Bio::Graphics::Glyph::crossbox The "crossbox" glyph 0 metacpan
Bio::Graphics::Glyph::dashed_line The "dashed line" glyph 0 metacpan
Bio::Graphics::Glyph::diamond The "diamond" glyph 0 metacpan
Bio::Graphics::Glyph::dna The "dna" glyph 0 metacpan
Bio::Graphics::Glyph::dot The "dot" glyph 0 metacpan
Bio::Graphics::Glyph::dumbbell A glyph that draws a "dumbbell" with the same shapes on both ends. 0 metacpan
Bio::Graphics::Glyph::ellipse The "ellipse" glyph 0 metacpan
Bio::Graphics::Glyph::ex the "ex", or "crossed box" glyph 0 metacpan
Bio::Graphics::Glyph::extending_arrow The "extending arrow" glyph 0 metacpan
Bio::Graphics::Glyph::fixedwidth A base class fixed width glyphs 0 metacpan
Bio::Graphics::Glyph::flag the "flag" glyph 0 metacpan
Bio::Graphics::Glyph::gene A GFF3-compatible gene glyph 0 metacpan
Bio::Graphics::Glyph::generic The "generic" glyph 0 metacpan
Bio::Graphics::Glyph::graded_segments The "graded_segments" glyph 0 metacpan
Bio::Graphics::Glyph::group The "group" glyph 0 metacpan
Bio::Graphics::Glyph::hat The "hat" glyph 0 metacpan
Bio::Graphics::Glyph::heat_map The "heat_map" glyph 0 metacpan
Bio::Graphics::Glyph::heat_map_ideogram The "heat_map_ideogram" glyph 0 metacpan
Bio::Graphics::Glyph::heterogeneous_segments The "heterogeneous_segments" glyph 0 metacpan
Bio::Graphics::Glyph::hidden The "hidden" glyph 0 metacpan
Bio::Graphics::Glyph::hybrid_plot An xyplot plot drawing dual graph using data from two wiggle files per track 1.0 metacpan
Bio::Graphics::Glyph::ideogram The "ideogram" glyph 0 metacpan
Bio::Graphics::Glyph::image A glyph that draws photographs & other images 0 metacpan
Bio::Graphics::Glyph::lightning The "lightning" glyph 0 metacpan
Bio::Graphics::Glyph::line The "line" glyph 0 metacpan
Bio::Graphics::Glyph::merge_parts a base class which suppors semantic zooming of scored alignment features 0 metacpan
Bio::Graphics::Glyph::merged_alignment The "merged_alignment" glyph 0 metacpan
Bio::Graphics::Glyph::minmax The minmax glyph 0 metacpan
Bio::Graphics::Glyph::operon The "polycistronic operon" glyph 0 metacpan
Bio::Graphics::Glyph::oval The "oval" glyph 0 metacpan
Bio::Graphics::Glyph::pairplot The "pairwise plot" glyph 0 metacpan
Bio::Graphics::Glyph::pentagram The "pentagram" glyph 0 metacpan
Bio::Graphics::Glyph::phylo_align The "phylogenetic alignment" glyph 0 metacpan
Bio::Graphics::Glyph::pinsertion The "Drosophila P-element Insertion" glyph 0 metacpan
Bio::Graphics::Glyph::primers The "STS primers" glyph 0 metacpan
Bio::Graphics::Glyph::processed_transcript The sequence ontology transcript glyph 0 metacpan
Bio::Graphics::Glyph::protein The "protein" glyph 0 metacpan
Bio::Graphics::Glyph::ragged_ends The "ragged ends" glyph 0 metacpan
Bio::Graphics::Glyph::rainbow_gene 0 metacpan
Bio::Graphics::Glyph::read_pair 0 metacpan
Bio::Graphics::Glyph::redgreen_box The "redgreen_box" glyph 0 metacpan
Bio::Graphics::Glyph::redgreen_segment The "redgreen_segments" glyph 0 metacpan
Bio::Graphics::Glyph::repeating_shape A glyph that draws the same shape repeatedly. 0 metacpan
Bio::Graphics::Glyph::rndrect The "round rect" glyph 0 metacpan
Bio::Graphics::Glyph::ruler_arrow glyph for drawing an arrow as ruler (5' and 3' are marked as label) 0 metacpan
Bio::Graphics::Glyph::saw_teeth The "saw teeth" glyph 0 metacpan
Bio::Graphics::Glyph::segmented_keyglyph The "segmented_keyglyph" glyph 0 metacpan
Bio::Graphics::Glyph::segments The "segments" glyph 0 metacpan
Bio::Graphics::Glyph::smoothing 0 metacpan
Bio::Graphics::Glyph::so_transcript The sequence ontology transcript glyph 0 metacpan
Bio::Graphics::Glyph::span The "span" glyph 0 metacpan
Bio::Graphics::Glyph::spectrogram The "spectrogram" glyph 0 metacpan
Bio::Graphics::Glyph::splice_site The "splice_site" glyph 0 metacpan
Bio::Graphics::Glyph::stackedplot The stackedplot glyph 0 metacpan
Bio::Graphics::Glyph::ternary_plot Draw ternary plot data 0 metacpan
Bio::Graphics::Glyph::text_in_box The "text in box" glyph 0 metacpan
Bio::Graphics::Glyph::three_letters DAS-compatible package to use for drawing a line of groups of three letters 0 metacpan
Bio::Graphics::Glyph::tic_tac_toe The "tic-tac-toe" glyph 0 metacpan
Bio::Graphics::Glyph::toomany The "too many to show" glyph 0 metacpan
Bio::Graphics::Glyph::trace A glyph that visualizes a trace file 0 metacpan
Bio::Graphics::Glyph::track The "track" glyph 0 metacpan
Bio::Graphics::Glyph::transcript The "transcript" glyph 0 metacpan
Bio::Graphics::Glyph::transcript2 The "transcript2" glyph 0 metacpan
Bio::Graphics::Glyph::translation The "6-frame translation" glyph 0 metacpan
Bio::Graphics::Glyph::triangle The "triangle" glyph 0 metacpan
Bio::Graphics::Glyph::two_bolts The "two bolts" glyph 0 metacpan
Bio::Graphics::Glyph::vista_plot The "vista_plot" glyph 1.0 metacpan
Bio::Graphics::Glyph::wave The "wave" glyph 0 metacpan
Bio::Graphics::Glyph::weighted_arrow The "weighted arrow" glyph 0 metacpan
Bio::Graphics::Glyph::whiskerplot The whiskerplot glyph 0 metacpan
Bio::Graphics::Glyph::wiggle_box A generic box glyph compatible with dense "wig"data 0 metacpan
Bio::Graphics::Glyph::wiggle_density A density plot compatible with dense "wig"data 0 metacpan
Bio::Graphics::Glyph::wiggle_minmax 0 metacpan
Bio::Graphics::Glyph::wiggle_whiskers 0 metacpan
Bio::Graphics::Glyph::wiggle_xyplot An xyplot plot compatible with dense "wig"data 0 metacpan
Bio::Graphics::Glyph::xyplot The xyplot glyph 0 metacpan
Bio::Graphics::Layout 0 metacpan
Bio::Graphics::Layout::Contour 0 metacpan
Bio::Graphics::Math 0 metacpan
Bio::Graphics::Panel Generate GD images of Bio::Seq objects 0 metacpan
Bio::Graphics::Pictogram generate SVG output of Pictogram display for consensus motifs 0 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. 0 metacpan
Bio::Graphics::Util non-object-oriented utilities used in Bio::Graphics modules 0 metacpan
Bio::Graphics::Wiggle Binary storage for dense genomic features 1.0 metacpan
Bio::Graphics::Wiggle::Loader 0 metacpan

Other Files

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