CPANTS

InSilicoSpectro 0.9.13

Kwalitee Issues

This is not the latest release. The following issues may have already been fixed in the newer releases.

Upgrade your YAML generator so it produces valid YAML.

Error: CPAN::Meta::YAML does not support a feature in line '! >-'

Add a MANIFEST to the distribution. Your buildtool should be able to autogenerate it (eg "make manifest" or "./Build manifest")

has_changelog

Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.

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: Cannot find MANIFEST in dist.

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: CGIUtils

prereq_matches_use

List all used modules in META.yml requires

Error:

AI::NNFlex::Backprop
AI::NNFlex::Dataset
Archive::Zip
Compress::Zlib
File::Find::Rule
Math::Spline
Statistics::Regression
XML::Dumper
XML::Parser::PerlSAX
XML::Twig

no_pod_errors

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

Error: InSilicoSpectro-0.9.13/cgi/DefEnv.pm -- Around line 14: Unknown directive: =FUNCTIONS InSilicoSpectro-0.9.13/lib/InSilicoSpectro/InSilico/AASequence.pm -- Around line 64: Expected text after =item, not a bullet InSilicoSpectro-0.9.13/lib/InSilicoSpectro/Spectra/PhenyxPeakDescriptor.pm -- Around line 54: You forgot a '=back' before '=head1'

5 Extra Issues

has_meta_json

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

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: cgi/CGIUtils.pm, cgi/DefEnv.pm

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.

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: CGIUtils, DefEnv, InSilicoSpectro, InSilicoSpectro::InSilico::AASequence, InSilicoSpectro::InSilico::CleavEnzyme, InSilicoSpectro::InSilico::ExpCalibrator, InSilicoSpectro::InSilico::InternIonSeries, InSilicoSpectro::InSilico::IonSeries, InSilicoSpectro::InSilico::IsoelPoint, InSilicoSpectro::InSilico::MSMSOutput, InSilicoSpectro::InSilico::MSMSTheoSpectrum, InSilicoSpectro::InSilico::MassCalculator, InSilicoSpectro::InSilico::ModRes, InSilicoSpectro::InSilico::PMFMatch, InSilicoSpectro::InSilico::Peptide, InSilicoSpectro::InSilico::RetentionTimer, InSilicoSpectro::InSilico::RetentionTimer::Hodges, InSilicoSpectro::InSilico::RetentionTimer::Petritis, InSilicoSpectro::InSilico::Sequence, InSilicoSpectro::InSilico::TermIonSeries, InSilicoSpectro::Spectra::ExpSpectrum, InSilicoSpectro::Spectra::MSMSCmpd, InSilicoSpectro::Spectra::MSMSSpectra, InSilicoSpectro::Spectra::MSRun, InSilicoSpectro::Spectra::MSSpectra, InSilicoSpectro::Spectra::PeakDescriptor, InSilicoSpectro::Spectra::PhenyxPeakDescriptor, InSilicoSpectro::Utils::Files, InSilicoSpectro::Utils::XML::SaxIndexMaker, InSilicoSpectro::Utils::io

consistent_version

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

Error: 0.009013,0.9

4 Experimental Issues

has_separate_license_file: This is not a critical issue. Currently mainly informative for the CPANTS authors. It might be removed later.
has_security_doc: Add SECURITY(.pod|md). See Software::Security::Policy.
security_doc_contains_contact: Add SECURITY(.pod|md) and add a contact address. See Software::Security::Policy.
has_contributing_doc: Add CONTRIBUTING(.pod|md). See https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/setting-guidelines-for-repository-contributors.

Modules

Name	Abstract	Version	View
CGIUtils			metacpan
DefEnv		0.9	metacpan
InSilicoSpectro	Open source Perl library for proteomics	0.009013	metacpan
InSilicoSpectro::InSilico::AASequence	Elementary protein sequence.		metacpan
InSilicoSpectro::InSilico::CleavEnzyme			metacpan
InSilicoSpectro::InSilico::ExpCalibrator	Calibrates a RetentionTimer predictor based on experimental data		metacpan
InSilicoSpectro::InSilico::InternIonSeries			metacpan
InSilicoSpectro::InSilico::IonSeries			metacpan
InSilicoSpectro::InSilico::IsoelPoint	A class for peptide isoelectric point (pI) prediction		metacpan
InSilicoSpectro::InSilico::MSMSOutput			metacpan
InSilicoSpectro::InSilico::MSMSTheoSpectrum			metacpan
InSilicoSpectro::InSilico::MassCalculator			metacpan
InSilicoSpectro::InSilico::ModRes			metacpan
InSilicoSpectro::InSilico::PMFMatch			metacpan
InSilicoSpectro::InSilico::Peptide	A class for digestion products		metacpan
InSilicoSpectro::InSilico::RetentionTimer	A base class for implementing a peptide retention time predictor		metacpan
InSilicoSpectro::InSilico::RetentionTimer::Hodges			metacpan
InSilicoSpectro::InSilico::RetentionTimer::Petritis			metacpan
InSilicoSpectro::InSilico::Sequence	Elementary sequence object		metacpan
InSilicoSpectro::InSilico::TermIonSeries			metacpan
InSilicoSpectro::Spectra::ExpSpectrum	A class for representing spectra.		metacpan
InSilicoSpectro::Spectra::MSMSCmpd			metacpan
InSilicoSpectro::Spectra::MSMSSpectra			metacpan
InSilicoSpectro::Spectra::MSRun			metacpan
InSilicoSpectro::Spectra::MSSpectra			metacpan
InSilicoSpectro::Spectra::PeakDescriptor	Description of peak properties		metacpan
InSilicoSpectro::Spectra::PhenyxPeakDescriptor			metacpan
InSilicoSpectro::Utils::Files			metacpan
InSilicoSpectro::Utils::XML::SaxIndexMaker			metacpan
InSilicoSpectro::Utils::io			metacpan

Other Files


META.yml	metacpan
Makefile.PL	metacpan
README	metacpan