Kwalitee Issues

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.

has_meta_yml

Add a META.yml to the distribution. Your buildtool should be able to autogenerate it.

no_pod_errors

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

Error: Bio-Genex-2.6.0/pod/Genex.pod -- Around line 215: '=item' outside of any '=over'Around line 223: '=item' outside of any '=over' Bio-Genex-2.6.0/pod/control-bundle.pl.pod -- Around line 31: You forgot a '=back' before '=head1' Bio-Genex-2.6.0/scripts/create_genex_class.pl -- Around line 1780: You can't have =items (as at line 1800) unless the first thing after the =over is an =itemAround line 1912: You can't have =items (as at line 1918) unless the first thing after the =over is an =item

package_version_matches_dist_version

Fix the version(s).

prereq_matches_use

List all used modules in META.yml requires

Error:

  • DBI

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.

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.

proper_libs

Move your *.pm files in a directory named 'lib'. The directory structure should look like 'lib/Your/Module.pm' for a module named 'Your::Module'. If you need to provide additional files, e.g. for testing, that should not be considered for Kwalitee, then you should look at the 'provides' map in META.yml to limit the files scanned; or use the 'no_index' map to exclude parts of the distribution.

Error: AL_Spots/AL_Spots.pm, AM_FactorValues/AM_FactorValues.pm, AM_Spots/AM_Spots.pm, AM_SuspectSpots/AM_SuspectSpots.pm, ArrayLayout/ArrayLayout.pm, ArrayMeasurement/ArrayMeasurement.pm, BlastHits/BlastHits.pm, Chromosome/Chromosome.pm, Citation/Citation.pm, Contact/Contact.pm, ControlledVocab/ControlledVocab.pm, ExperimentFactors/ExperimentFactors.pm, ExperimentSet/ExperimentSet.pm, ExternalDatabase/ExternalDatabase.pm, Fkey/Fkey.pm, GenexAdmin/GenexAdmin.pm, GroupLink/GroupLink.pm, GroupSec/GroupSec.pm, HotSpots/HotSpots.pm, Protocol/Protocol.pm, SampleProtocols/SampleProtocols.pm, Scanner/Scanner.pm, Software/Software.pm, Species/Species.pm, SpotLink/SpotLink.pm, Spotter/Spotter.pm, TL_FactorValues/TL_FactorValues.pm, TreatmentLevel/TreatmentLevel.pm, Treatment_AMs/Treatment_AMs.pm, USF_ExternalDBLink/USF_ExternalDBLink.pm, UserSec/UserSec.pm, UserSequenceFeature/UserSequenceFeature.pm

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::Genex::AL_Spots, Bio::Genex::AM_FactorValues, Bio::Genex::AM_Spots, Bio::Genex::AM_SuspectSpots, Bio::Genex::ArrayLayout, Bio::Genex::ArrayMeasurement, Bio::Genex::BlastHits, Bio::Genex::Chromosome, Bio::Genex::Citation, Bio::Genex::Contact, Bio::Genex::ControlledVocab, Bio::Genex::ExperimentFactors, Bio::Genex::ExperimentSet, Bio::Genex::ExternalDatabase, Bio::Genex::Fkey, Bio::Genex::GenexAdmin, Bio::Genex::GroupLink, Bio::Genex::GroupSec, Bio::Genex::HotSpots, Bio::Genex::Protocol, Bio::Genex::SampleProtocols, Bio::Genex::Scanner, Bio::Genex::Software, Bio::Genex::Species, Bio::Genex::SpotLink, Bio::Genex::Spotter, Bio::Genex::TL_FactorValues, Bio::Genex::TreatmentLevel, Bio::Genex::Treatment_AMs, Bio::Genex::USF_ExternalDBLink, Bio::Genex::UserSec, Bio::Genex::UserSequenceFeature

build_prereq_matches_use

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

Error:

  • XML::DOM

Modules

Name Abstract Version View
Bio::Genex::AL_Spots Methods for processing data from the GeneX DB table: AL_Spots metacpan
Bio::Genex::AM_FactorValues Methods for processing data from the GeneX DB linking table: AM_FactorValues metacpan
Bio::Genex::AM_Spots Methods for processing data from the GeneX DB table: AM_Spots metacpan
Bio::Genex::AM_SuspectSpots Methods for processing data from the GeneX DB linking table: AM_SuspectSpots metacpan
Bio::Genex::ArrayLayout Methods for processing data from the GeneX DB table: ArrayLayout metacpan
Bio::Genex::ArrayMeasurement Methods for processing data from the GeneX DB table: ArrayMeasurement metacpan
Bio::Genex::BlastHits Methods for processing data from the GeneX DB table: BlastHits metacpan
Bio::Genex::Chromosome Methods for processing data from the GeneX DB table: Chromosome metacpan
Bio::Genex::Citation Methods for processing data from the GeneX DB table: Citation metacpan
Bio::Genex::Contact Methods for processing data from the GeneX DB table: Contact metacpan
Bio::Genex::ControlledVocab Methods for processing data from the GeneX DB table: ControlledVocab metacpan
Bio::Genex::ExperimentFactors Methods for processing data from the GeneX DB table: ExperimentFactors metacpan
Bio::Genex::ExperimentSet Methods for processing data from the GeneX DB table: ExperimentSet metacpan
Bio::Genex::ExternalDatabase Methods for processing data from the GeneX DB table: ExternalDatabase metacpan
Bio::Genex::Fkey Perl extension for representing Database Foreign Keys metacpan
Bio::Genex::GenexAdmin Methods for processing data from the GeneX DB table: GenexAdmin metacpan
Bio::Genex::GroupLink Methods for processing data from the GeneX DB linking table: GroupLink metacpan
Bio::Genex::GroupSec Methods for processing data from the GeneX DB table: GroupSec metacpan
Bio::Genex::HotSpots Methods for processing data from the GeneX DB linking table: HotSpots metacpan
Bio::Genex::Protocol Methods for processing data from the GeneX DB table: Protocol metacpan
Bio::Genex::SampleProtocols Methods for processing data from the GeneX DB linking table: SampleProtocols metacpan
Bio::Genex::Scanner Methods for processing data from the GeneX DB table: Scanner metacpan
Bio::Genex::Software Methods for processing data from the GeneX DB table: Software metacpan
Bio::Genex::Species Methods for processing data from the GeneX DB table: Species metacpan
Bio::Genex::SpotLink Methods for processing data from the GeneX DB linking table: SpotLink metacpan
Bio::Genex::Spotter Methods for processing data from the GeneX DB table: Spotter metacpan
Bio::Genex::TL_FactorValues Methods for processing data from the GeneX DB linking table: TL_FactorValues metacpan
Bio::Genex::TreatmentLevel Methods for processing data from the GeneX DB table: TreatmentLevel metacpan
Bio::Genex::Treatment_AMs Methods for processing data from the GeneX DB linking table: Treatment_AMs metacpan
Bio::Genex::USF_ExternalDBLink Methods for processing data from the GeneX DB linking table: USF_ExternalDBLink metacpan
Bio::Genex::UserSec Methods for processing data from the GeneX DB table: UserSec metacpan
Bio::Genex::UserSequenceFeature Methods for processing data from the GeneX DB table: UserSequenceFeature metacpan

Provides

Name File View
Bio::Genex::ALS_SpotType ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::AL_Coating ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::AL_DefaultSpotConcUnits ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::AL_IdentifierCode ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::AL_Medium ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::AL_TechnologyType ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::AM_EquationType ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::AM_SpotMeasurementUnits ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::AM_Type ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::ContactType ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::EF_MajorCategory ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::EF_MinorCategory ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::ES_QuantitySeriesType ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::ES_TreatmentType ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::HS_ThresholdType ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::PRT_Type ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::SCN_ModelDescription ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::SMP_AgeUnits ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::SMP_DevelopmentStageName ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::SMP_DevelopmentStageUnits ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::SMP_GeneticStatus ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::SMP_OrganType ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::SMP_OrganismIntactness ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::SMP_PrimaryCellType ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::SMP_SexMatingType ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::SMP_TissueType ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::SPC_CellStructure ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::SPC_GeneralClassification ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::SPT_ModelDescription ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::SW_Name ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::SW_Type ControlledVocab/ControlledVocab.pm metacpan
Bio::Genex::Sample Sample/Sample.pm metacpan
Bio::Genex::USF_Type ControlledVocab/ControlledVocab.pm metacpan

Other Files

AL_Spots/Makefile.PL metacpan
AM_FactorValues/Makefile.PL metacpan
AM_Spots/Makefile.PL metacpan
AM_SuspectSpots/Makefile.PL metacpan
ArrayLayout/Makefile.PL metacpan
ArrayMeasurement/Makefile.PL metacpan
BlastHits/Makefile.PL metacpan
Changes metacpan
Chromosome/Makefile.PL metacpan
Citation/Makefile.PL metacpan
Contact/Makefile.PL metacpan
ControlledVocab/Makefile.PL metacpan
DBUtils/Makefile.PL metacpan
ExperimentFactors/Makefile.PL metacpan
ExperimentSet/Makefile.PL metacpan
ExternalDatabase/Makefile.PL metacpan
Fkey/Makefile.PL metacpan
GenexAdmin/Makefile.PL metacpan
GroupLink/Makefile.PL metacpan
GroupSec/Makefile.PL metacpan
HTMLUtils/Makefile.PL metacpan
HotSpots/Makefile.PL metacpan
MANIFEST metacpan
Makefile.PL metacpan
Protocol/Makefile.PL metacpan
README metacpan
Sample/Makefile.PL metacpan
SampleProtocols/Makefile.PL metacpan
Scanner/Makefile.PL metacpan
Software/Makefile.PL metacpan
Species/Makefile.PL metacpan
SpotLink/Makefile.PL metacpan
Spotter/Makefile.PL metacpan
TL_FactorValues/Makefile.PL metacpan
TreatmentLevel/Makefile.PL metacpan
Treatment_AMs/Makefile.PL metacpan
USF_ExternalDBLink/Makefile.PL metacpan
UserSec/Makefile.PL metacpan
UserSequenceFeature/Makefile.PL metacpan
XMLUtils/Makefile.PL metacpan