bioperl-db 1.5.2_005-RC

Released by
SENDU
Version
Release Date
2006-11-24
Kwalitee
134.38
Core Kwalitee
90.62
LINKS

Kwalitee Issues

has_proper_version

Remove all letters from the version number. If you want to mark a release as a developer release, use the scheme 'Module-1.00_01'

has_license_in_source_file

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

main_module_version_matches_dist_version

Make sure that the main module name and version are the same of the distribution.

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: Bio/BioEntry.pm, Bio/DB/BioDB.pm, Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm, Bio/DB/BioSQL/BaseDriver.pm, Bio/DB/BioSQL/BasePersistenceAdaptor.pm, Bio/DB/BioSQL/BioNamespaceAdaptor.pm, Bio/DB/BioSQL/BiosequenceAdaptor.pm, Bio/DB/BioSQL/ClusterAdaptor.pm, Bio/DB/BioSQL/CommentAdaptor.pm, Bio/DB/BioSQL/DBAdaptor.pm, Bio/DB/BioSQL/DBLinkAdaptor.pm, Bio/DB/BioSQL/LocationAdaptor.pm, Bio/DB/BioSQL/MultiDB.pm, Bio/DB/BioSQL/OBDA.pm, Bio/DB/BioSQL/OntologyAdaptor.pm, Bio/DB/BioSQL/Oracle/AnnotationCollectionAdaptorDriver.pm, Bio/DB/BioSQL/Oracle/BasePersistenceAdaptorDriver.pm, Bio/DB/BioSQL/Oracle/BiosequenceAdaptorDriver.pm, Bio/DB/BioSQL/Oracle/PathAdaptorDriver.pm, Bio/DB/BioSQL/Oracle/SpeciesAdaptorDriver.pm, Bio/DB/BioSQL/Oracle/TermAdaptorDriver.pm, Bio/DB/BioSQL/PathAdaptor.pm, Bio/DB/BioSQL/Pg/AnnotationCollectionAdaptorDriver.pm, Bio/DB/BioSQL/Pg/BasePersistenceAdaptorDriver.pm, Bio/DB/BioSQL/Pg/BiosequenceAdaptorDriver.pm, Bio/DB/BioSQL/Pg/PathAdaptorDriver.pm, Bio/DB/BioSQL/Pg/SpeciesAdaptorDriver.pm, Bio/DB/BioSQL/Pg/TermAdaptorDriver.pm, Bio/DB/BioSQL/PrimarySeqAdaptor.pm, Bio/DB/BioSQL/ReferenceAdaptor.pm, Bio/DB/BioSQL/RelationshipAdaptor.pm, Bio/DB/BioSQL/SeqAdaptor.pm, Bio/DB/BioSQL/SeqFeatureAdaptor.pm, Bio/DB/BioSQL/SimpleValueAdaptor.pm, Bio/DB/BioSQL/SpeciesAdaptor.pm, Bio/DB/BioSQL/TermAdaptor.pm, Bio/DB/BioSQL/mysql/AnnotationCollectionAdaptorDriver.pm, Bio/DB/BioSQL/mysql/BasePersistenceAdaptorDriver.pm, Bio/DB/BioSQL/mysql/BiosequenceAdaptorDriver.pm, Bio/DB/BioSQL/mysql/PathAdaptorDriver.pm, Bio/DB/BioSQL/mysql/SpeciesAdaptorDriver.pm, Bio/DB/BioSQL/mysql/TermAdaptorDriver.pm, Bio/DB/CacheServer/SeqDB.pm, Bio/DB/DBAdaptorI.pm, Bio/DB/DBContextI.pm, Bio/DB/DBD.pm, Bio/DB/DBI.pm, Bio/DB/DBI/Oracle.pm, Bio/DB/DBI/Pg.pm, Bio/DB/DBI/Transaction.pm, Bio/DB/DBI/TransactionListener.pm, Bio/DB/DBI/base.pm, Bio/DB/DBI/mysql.pm, Bio/DB/EasyArgv.pm, Bio/DB/PersistenceAdaptorI.pm, Bio/DB/Persistent/BioNamespace.pm, Bio/DB/Persistent/ObjectRelMapperI.pm, Bio/DB/Persistent/PersistentObject.pm, Bio/DB/Persistent/PersistentObjectFactory.pm, Bio/DB/Persistent/PrimarySeq.pm, Bio/DB/Persistent/Seq.pm, Bio/DB/Persistent/SeqFeature.pm, Bio/DB/PersistentObjectI.pm, Bio/DB/Query/AbstractQuery.pm, Bio/DB/Query/BioQuery.pm, Bio/DB/Query/DBQueryResult.pm, Bio/DB/Query/PrebuiltResult.pm, Bio/DB/Query/QueryConstraint.pm, Bio/DB/Query/QueryResultI.pm, Bio/DB/Query/SqlGenerator.pm, Bio/DB/Query/SqlQuery.pm, Bio/DB/SimpleDBContext.pm

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.

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::BioEntry, Bio::DB::BioDB, Bio::DB::BioSQL::AnnotationCollectionAdaptor, Bio::DB::BioSQL::BaseDriver, Bio::DB::BioSQL::BasePersistenceAdaptor, Bio::DB::BioSQL::BioNamespaceAdaptor, Bio::DB::BioSQL::BiosequenceAdaptor, Bio::DB::BioSQL::ClusterAdaptor, Bio::DB::BioSQL::CommentAdaptor, Bio::DB::BioSQL::DBAdaptor, Bio::DB::BioSQL::DBLinkAdaptor, Bio::DB::BioSQL::LocationAdaptor, Bio::DB::BioSQL::MultiDB, Bio::DB::BioSQL::OBDA, Bio::DB::BioSQL::OntologyAdaptor, Bio::DB::BioSQL::Oracle::AnnotationCollectionAdaptorDriver, Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver, Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver, Bio::DB::BioSQL::Oracle::PathAdaptorDriver, Bio::DB::BioSQL::Oracle::SpeciesAdaptorDriver, Bio::DB::BioSQL::Oracle::TermAdaptorDriver, Bio::DB::BioSQL::PathAdaptor, Bio::DB::BioSQL::Pg::AnnotationCollectionAdaptorDriver, Bio::DB::BioSQL::Pg::BasePersistenceAdaptorDriver, Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver, Bio::DB::BioSQL::Pg::PathAdaptorDriver, Bio::DB::BioSQL::Pg::SpeciesAdaptorDriver, Bio::DB::BioSQL::Pg::TermAdaptorDriver, Bio::DB::BioSQL::PrimarySeqAdaptor, Bio::DB::BioSQL::ReferenceAdaptor, Bio::DB::BioSQL::RelationshipAdaptor, Bio::DB::BioSQL::SeqAdaptor, Bio::DB::BioSQL::SeqFeatureAdaptor, Bio::DB::BioSQL::SimpleValueAdaptor, Bio::DB::BioSQL::SpeciesAdaptor, Bio::DB::BioSQL::TermAdaptor, Bio::DB::BioSQL::mysql::AnnotationCollectionAdaptorDriver, Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver, Bio::DB::BioSQL::mysql::BiosequenceAdaptorDriver, Bio::DB::BioSQL::mysql::PathAdaptorDriver, Bio::DB::BioSQL::mysql::SpeciesAdaptorDriver, Bio::DB::BioSQL::mysql::TermAdaptorDriver, Bio::DB::CacheServer::SeqDB, Bio::DB::DBAdaptorI, Bio::DB::DBContextI, Bio::DB::DBD, Bio::DB::DBI, Bio::DB::DBI::Oracle, Bio::DB::DBI::Pg, Bio::DB::DBI::Transaction, Bio::DB::DBI::TransactionListener, Bio::DB::DBI::base, Bio::DB::DBI::mysql, Bio::DB::EasyArgv, Bio::DB::PersistenceAdaptorI, Bio::DB::Persistent::BioNamespace, Bio::DB::Persistent::PersistentObject, Bio::DB::Persistent::PersistentObjectFactory, Bio::DB::Persistent::PrimarySeq, Bio::DB::Persistent::Seq, Bio::DB::Persistent::SeqFeature, Bio::DB::PersistentObjectI, Bio::DB::Query::AbstractQuery, Bio::DB::Query::BioQuery, Bio::DB::Query::DBQueryResult, Bio::DB::Query::PrebuiltResult, Bio::DB::Query::QueryConstraint, Bio::DB::Query::QueryResultI, Bio::DB::Query::SqlGenerator, Bio::DB::Query::SqlQuery, Bio::DB::SimpleDBContext

no_unauthorized_packages

Ask the owner of the distribution (the one who released it first, or the one who is designated in x_authority) to give you a (co-)maintainer's permission.

Error:

  • Bio::BioEntry
  • Bio::DB::BioDB
  • Bio::DB::BioSQL::AnnotationCollectionAdaptor
  • Bio::DB::BioSQL::BaseDriver
  • Bio::DB::BioSQL::BasePersistenceAdaptor
  • Bio::DB::BioSQL::BioNamespaceAdaptor
  • Bio::DB::BioSQL::BiosequenceAdaptor
  • Bio::DB::BioSQL::ClusterAdaptor
  • Bio::DB::BioSQL::CommentAdaptor
  • Bio::DB::BioSQL::DBAdaptor
  • Bio::DB::BioSQL::DBLinkAdaptor
  • Bio::DB::BioSQL::LocationAdaptor
  • Bio::DB::BioSQL::MultiDB
  • Bio::DB::BioSQL::OBDA
  • Bio::DB::BioSQL::OntologyAdaptor
  • Bio::DB::BioSQL::Oracle::AnnotationCollectionAdaptorDriver
  • Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver
  • Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver
  • Bio::DB::BioSQL::Oracle::PathAdaptorDriver
  • Bio::DB::BioSQL::Oracle::SpeciesAdaptorDriver
  • Bio::DB::BioSQL::Oracle::TermAdaptorDriver
  • Bio::DB::BioSQL::PathAdaptor
  • Bio::DB::BioSQL::Pg::AnnotationCollectionAdaptorDriver
  • Bio::DB::BioSQL::Pg::BasePersistenceAdaptorDriver
  • Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver
  • Bio::DB::BioSQL::Pg::PathAdaptorDriver
  • Bio::DB::BioSQL::Pg::SpeciesAdaptorDriver
  • Bio::DB::BioSQL::Pg::TermAdaptorDriver
  • Bio::DB::BioSQL::PrimarySeqAdaptor
  • Bio::DB::BioSQL::ReferenceAdaptor
  • Bio::DB::BioSQL::RelationshipAdaptor
  • Bio::DB::BioSQL::SeqAdaptor
  • Bio::DB::BioSQL::SeqFeatureAdaptor
  • Bio::DB::BioSQL::SimpleValueAdaptor
  • Bio::DB::BioSQL::SpeciesAdaptor
  • Bio::DB::BioSQL::TermAdaptor
  • Bio::DB::BioSQL::mysql::AnnotationCollectionAdaptorDriver
  • Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver
  • Bio::DB::BioSQL::mysql::BiosequenceAdaptorDriver
  • Bio::DB::BioSQL::mysql::PathAdaptorDriver
  • Bio::DB::BioSQL::mysql::SpeciesAdaptorDriver
  • Bio::DB::BioSQL::mysql::TermAdaptorDriver
  • Bio::DB::CacheServer::SeqDB
  • Bio::DB::DBAdaptorI
  • Bio::DB::DBContextI
  • Bio::DB::DBD
  • Bio::DB::DBI
  • Bio::DB::DBI::Oracle
  • Bio::DB::DBI::Pg
  • Bio::DB::DBI::Transaction
  • Bio::DB::DBI::TransactionListener
  • Bio::DB::DBI::base
  • Bio::DB::DBI::mysql
  • Bio::DB::EasyArgv
  • Bio::DB::PersistenceAdaptorI
  • Bio::DB::Persistent::BioNamespace
  • Bio::DB::Persistent::ObjectRellMapperI
  • Bio::DB::Persistent::PersistentObject
  • Bio::DB::Persistent::PersistentObjectFactory
  • Bio::DB::Persistent::PrimarySeq
  • Bio::DB::Persistent::Seq
  • Bio::DB::Persistent::SeqFeature
  • Bio::DB::PersistentObjectI
  • Bio::DB::Query::AbstractQuery
  • Bio::DB::Query::BioQuery
  • Bio::DB::Query::DBQueryResult
  • Bio::DB::Query::PrebuiltResult
  • Bio::DB::Query::QueryConstraint
  • Bio::DB::Query::QueryResultI
  • Bio::DB::Query::SqlGenerator
  • Bio::DB::Query::SqlQuery
  • Bio::DB::SimpleDBContext

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).

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
Bio::BioEntry DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioDB class creating the adaptor factory for a particular database 1.005002005 metacpan
Bio::DB::BioSQL::AnnotationCollectionAdaptor DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::BaseDriver DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::BasePersistenceAdaptor DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::BioNamespaceAdaptor DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::BiosequenceAdaptor DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::ClusterAdaptor DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::CommentAdaptor DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::DBAdaptor 1.005002005 metacpan
Bio::DB::BioSQL::DBLinkAdaptor DBLink Adaptor 1.005002005 metacpan
Bio::DB::BioSQL::LocationAdaptor DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::MultiDB 1.005002005 metacpan
Bio::DB::BioSQL::OBDA 1.005002005 metacpan
Bio::DB::BioSQL::OntologyAdaptor DB Adaptor for Ontology objects 1.005002005 metacpan
Bio::DB::BioSQL::Oracle::AnnotationCollectionAdaptorDriver DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::Oracle::PathAdaptorDriver DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::Oracle::SpeciesAdaptorDriver DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::Oracle::TermAdaptorDriver DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::PathAdaptor DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::Pg::AnnotationCollectionAdaptorDriver DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::Pg::BasePersistenceAdaptorDriver DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::Pg::PathAdaptorDriver DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::Pg::SpeciesAdaptorDriver DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::Pg::TermAdaptorDriver DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::PrimarySeqAdaptor DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::ReferenceAdaptor DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::RelationshipAdaptor DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::SeqAdaptor DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::SeqFeatureAdaptor DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::SimpleValueAdaptor DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::SpeciesAdaptor DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::TermAdaptor DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::mysql::AnnotationCollectionAdaptorDriver DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::mysql::BiosequenceAdaptorDriver DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::mysql::PathAdaptorDriver DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::mysql::SpeciesAdaptorDriver DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::BioSQL::mysql::TermAdaptorDriver DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::CacheServer::SeqDB Caching DB object 1.005002005 metacpan
Bio::DB::DBAdaptorI DESCRIPTION of Interface 1.005002005 metacpan
Bio::DB::DBContextI Interface for a class implementing a database context 1.005002005 metacpan
Bio::DB::DBD DESCRIPTION of Interface 1.005002005 metacpan
Bio::DB::DBI 1.005002005 metacpan
Bio::DB::DBI::Oracle DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::DBI::Pg DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::DBI::Transaction DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::DBI::TransactionListener a simple transaction listener 1.005002005 metacpan
Bio::DB::DBI::base base class for drivers implementing Bio::DB::DBI 1.005002005 metacpan
Bio::DB::DBI::mysql DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::EasyArgv 1.005002005 metacpan
Bio::DB::PersistenceAdaptorI DESCRIPTION of Interface 1.005002005 metacpan
Bio::DB::Persistent::BioNamespace DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::Persistent::ObjectRellMapperI 1.005002005 metacpan
Bio::DB::Persistent::PersistentObject makes a given object persistent 1.005002005 metacpan
Bio::DB::Persistent::PersistentObjectFactory DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::Persistent::PrimarySeq Proxy object for database PrimarySeq representations 1.005002005 metacpan
Bio::DB::Persistent::Seq 1.005002005 metacpan
Bio::DB::Persistent::SeqFeature Proxy object for database SeqFeatureI representations 1.005002005 metacpan
Bio::DB::PersistentObjectI DESCRIPTION of Interface 1.005002005 metacpan
Bio::DB::Query::AbstractQuery Abstract Query class 1.005002005 metacpan
Bio::DB::Query::BioQuery Object representing a query on a bioperldb 1.005002005 metacpan
Bio::DB::Query::DBQueryResult DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::Query::PrebuiltResult DESCRIPTION of Object 1.005002005 metacpan
Bio::DB::Query::QueryConstraint a constraint on a variable value in a query 1.005002005 metacpan
Bio::DB::Query::QueryResultI DESCRIPTION of Interface 1.005002005 metacpan
Bio::DB::Query::SqlGenerator Object representing an SQL Query 1.005002005 metacpan
Bio::DB::Query::SqlQuery Object representing an SQL Query 1.005002005 metacpan
Bio::DB::SimpleDBContext a base implementation of Bio::DB::DBContextI 1.005002005 metacpan

Other Files
Build.PL metacpan
Changes metacpan
MANIFEST metacpan
META.yml metacpan
Makefile.PL metacpan
README metacpan