From cd061795dbd0dc572bc49404ff6a8b82edb49e08 Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Fri, 23 May 2014 13:16:46 +0100
Subject: [PATCH] added "use strict;" and "use warnings;" to all files that
were missing these lines
---
modules/Bio/EnsEMBL/Hive/Accumulator.pm | 1 +
modules/Bio/EnsEMBL/Hive/Analysis.pm | 1 +
modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm | 1 +
modules/Bio/EnsEMBL/Hive/AnalysisJob.pm | 1 +
modules/Bio/EnsEMBL/Hive/AnalysisStats.pm | 1 +
modules/Bio/EnsEMBL/Hive/Cacheable.pm | 5 ++++-
modules/Bio/EnsEMBL/Hive/DBSQL/AccumulatorAdaptor.pm | 1 +
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisAdaptor.pm | 1 +
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisCtrlRuleAdaptor.pm | 1 +
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisDataAdaptor.pm | 1 +
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm | 1 +
modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisStatsAdaptor.pm | 1 +
modules/Bio/EnsEMBL/Hive/DBSQL/CoreDBConnection.pm | 1 +
modules/Bio/EnsEMBL/Hive/DBSQL/DBAdaptor.pm | 1 +
modules/Bio/EnsEMBL/Hive/DBSQL/DataflowRuleAdaptor.pm | 1 +
modules/Bio/EnsEMBL/Hive/DBSQL/LogMessageAdaptor.pm | 1 +
modules/Bio/EnsEMBL/Hive/DBSQL/MetaAdaptor.pm | 1 +
modules/Bio/EnsEMBL/Hive/DBSQL/NakedTableAdaptor.pm | 1 +
modules/Bio/EnsEMBL/Hive/DBSQL/ObjectAdaptor.pm | 1 +
.../Bio/EnsEMBL/Hive/DBSQL/PipelineWideParametersAdaptor.pm | 1 +
modules/Bio/EnsEMBL/Hive/DBSQL/ResourceClassAdaptor.pm | 1 +
modules/Bio/EnsEMBL/Hive/DBSQL/ResourceDescriptionAdaptor.pm | 1 +
modules/Bio/EnsEMBL/Hive/DBSQL/RoleAdaptor.pm | 1 +
modules/Bio/EnsEMBL/Hive/DBSQL/SqlSchemaAdaptor.pm | 1 +
modules/Bio/EnsEMBL/Hive/DataflowRule.pm | 1 +
modules/Bio/EnsEMBL/Hive/Limiter.pm | 3 +++
modules/Bio/EnsEMBL/Hive/Meadow/LOCAL.pm | 1 +
modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm | 1 +
modules/Bio/EnsEMBL/Hive/MetaParameters.pm | 1 +
modules/Bio/EnsEMBL/Hive/NakedTable.pm | 1 +
modules/Bio/EnsEMBL/Hive/PipelineWideParameters.pm | 1 +
modules/Bio/EnsEMBL/Hive/Queen.pm | 1 +
modules/Bio/EnsEMBL/Hive/ResourceClass.pm | 1 +
modules/Bio/EnsEMBL/Hive/ResourceDescription.pm | 1 +
modules/Bio/EnsEMBL/Hive/Role.pm | 1 +
modules/Bio/EnsEMBL/Hive/RunnableDB/FailureTest.pm | 1 +
modules/Bio/EnsEMBL/Hive/RunnableDB/FastaFactory.pm | 1 +
modules/Bio/EnsEMBL/Hive/RunnableDB/JobFactory.pm | 1 +
modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/AddTogether.pm | 1 +
modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/DigitFactory.pm | 1 +
modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/PartMultiply.pm | 1 +
modules/Bio/EnsEMBL/Hive/RunnableDB/NotifyByEmail.pm | 1 +
modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm | 1 +
modules/Bio/EnsEMBL/Hive/RunnableDB/SystemCmd.pm | 1 +
modules/Bio/EnsEMBL/Hive/URLFactory.pm | 1 +
modules/Bio/EnsEMBL/Hive/Utils/Config.pm | 2 ++
modules/Bio/EnsEMBL/Hive/Utils/Stopwatch.pm | 1 +
modules/Bio/EnsEMBL/Hive/Worker.pm | 1 +
48 files changed, 54 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/Hive/Accumulator.pm b/modules/Bio/EnsEMBL/Hive/Accumulator.pm
index 2e3935cd9..cb3aade04 100644
--- a/modules/Bio/EnsEMBL/Hive/Accumulator.pm
+++ b/modules/Bio/EnsEMBL/Hive/Accumulator.pm
@@ -32,6 +32,7 @@
package Bio::EnsEMBL::Hive::Accumulator;
use strict;
+use warnings;
use Bio::EnsEMBL::Hive::Utils ('stringify');
diff --git a/modules/Bio/EnsEMBL/Hive/Analysis.pm b/modules/Bio/EnsEMBL/Hive/Analysis.pm
index 1a0a2ee96..663fd0ba6 100644
--- a/modules/Bio/EnsEMBL/Hive/Analysis.pm
+++ b/modules/Bio/EnsEMBL/Hive/Analysis.pm
@@ -36,6 +36,7 @@
package Bio::EnsEMBL::Hive::Analysis;
use strict;
+use warnings;
use Bio::EnsEMBL::Hive::Utils ('stringify');
use Bio::EnsEMBL::Hive::AnalysisCtrlRule;
diff --git a/modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm b/modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm
index b725d8a35..f84bc9cc1 100644
--- a/modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm
+++ b/modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm
@@ -42,6 +42,7 @@
package Bio::EnsEMBL::Hive::AnalysisCtrlRule;
use strict;
+use warnings;
use Bio::EnsEMBL::Hive::Utils ('throw');
use Bio::EnsEMBL::Hive::URLFactory;
diff --git a/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm b/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
index 21c10ecbd..cfee0f96c 100644
--- a/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
+++ b/modules/Bio/EnsEMBL/Hive/AnalysisJob.pm
@@ -37,6 +37,7 @@
package Bio::EnsEMBL::Hive::AnalysisJob;
use strict;
+use warnings;
use Bio::EnsEMBL::Hive::Utils ('stringify', 'destringify');
use Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
diff --git a/modules/Bio/EnsEMBL/Hive/AnalysisStats.pm b/modules/Bio/EnsEMBL/Hive/AnalysisStats.pm
index 14ff51bd6..3bed6ebc6 100644
--- a/modules/Bio/EnsEMBL/Hive/AnalysisStats.pm
+++ b/modules/Bio/EnsEMBL/Hive/AnalysisStats.pm
@@ -36,6 +36,7 @@
package Bio::EnsEMBL::Hive::AnalysisStats;
use strict;
+use warnings;
use List::Util 'sum';
use POSIX;
diff --git a/modules/Bio/EnsEMBL/Hive/Cacheable.pm b/modules/Bio/EnsEMBL/Hive/Cacheable.pm
index b543b5457..873f5e812 100644
--- a/modules/Bio/EnsEMBL/Hive/Cacheable.pm
+++ b/modules/Bio/EnsEMBL/Hive/Cacheable.pm
@@ -1,9 +1,12 @@
package Bio::EnsEMBL::Hive::Cacheable;
+use strict;
+use warnings;
+
use Bio::EnsEMBL::Hive::Utils ('stringify');
use Bio::EnsEMBL::Hive::Utils::Collection;
-our $cache_by_class; # global Hash-of-Hashes
+our %cache_by_class; # global Hash-of-Hashes
sub collection {
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/AccumulatorAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/AccumulatorAdaptor.pm
index 7455c176b..e17982c4b 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/AccumulatorAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/AccumulatorAdaptor.pm
@@ -35,6 +35,7 @@
package Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor;
use strict;
+use warnings;
use Bio::EnsEMBL::Hive::Utils ('destringify');
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisAdaptor.pm
index adf9ba90b..de65d17a6 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisAdaptor.pm
@@ -38,6 +38,7 @@
package Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor;
use strict;
+use warnings;
use Bio::EnsEMBL::Hive::Analysis;
use Bio::EnsEMBL::Hive::URLFactory;
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisCtrlRuleAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisCtrlRuleAdaptor.pm
index c9bafbd9b..b305be6ff 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisCtrlRuleAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisCtrlRuleAdaptor.pm
@@ -37,6 +37,7 @@
package Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor;
use strict;
+use warnings;
use Bio::EnsEMBL::Hive::AnalysisCtrlRule;
use base ('Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor');
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisDataAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisDataAdaptor.pm
index df3ad31e7..62721ee7c 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisDataAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisDataAdaptor.pm
@@ -41,6 +41,7 @@
package Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor;
use strict;
+use warnings;
use base ('Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor');
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
index 7012c9103..00a18c339 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
@@ -42,6 +42,7 @@
package Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
use strict;
+use warnings;
use Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor;
use Bio::EnsEMBL::Hive::AnalysisJob;
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisStatsAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisStatsAdaptor.pm
index 9c2b9f31b..f9bf93984 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisStatsAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisStatsAdaptor.pm
@@ -42,6 +42,7 @@
package Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor;
use strict;
+use warnings;
use Bio::EnsEMBL::Hive::AnalysisStats;
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/CoreDBConnection.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/CoreDBConnection.pm
index 60438cac4..e45cbbdb7 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/CoreDBConnection.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/CoreDBConnection.pm
@@ -68,6 +68,7 @@ the Bio::EnsEMBL::Registry and will not be instantiated directly.
package Bio::EnsEMBL::Hive::DBSQL::CoreDBConnection;
use strict;
+use warnings;
use DBI;
use Bio::EnsEMBL::Hive::DBSQL::StatementHandle;
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/DBAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/DBAdaptor.pm
index b24d102e2..a8c78f01a 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/DBAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/DBAdaptor.pm
@@ -35,6 +35,7 @@
package Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
use strict;
+use warnings;
use Bio::EnsEMBL::Hive;
use Bio::EnsEMBL::Hive::DBSQL::DBConnection;
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/DataflowRuleAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/DataflowRuleAdaptor.pm
index 91cf5ae21..7ac5d6db7 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/DataflowRuleAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/DataflowRuleAdaptor.pm
@@ -37,6 +37,7 @@
package Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor;
use strict;
+use warnings;
use Bio::EnsEMBL::Hive::Utils ('stringify');
use Bio::EnsEMBL::Hive::DataflowRule;
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/LogMessageAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/LogMessageAdaptor.pm
index 5a0afe91f..b9ae452c6 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/LogMessageAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/LogMessageAdaptor.pm
@@ -37,6 +37,7 @@
package Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor;
use strict;
+use warnings;
use base ('Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor');
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/MetaAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/MetaAdaptor.pm
index d98d20eb1..2ce424281 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/MetaAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/MetaAdaptor.pm
@@ -35,6 +35,7 @@
package Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor;
use strict;
+use warnings;
use Bio::EnsEMBL::Hive::MetaParameters;
use base ('Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor');
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/NakedTableAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/NakedTableAdaptor.pm
index 240b809f4..ae5995ee5 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/NakedTableAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/NakedTableAdaptor.pm
@@ -37,6 +37,7 @@
package Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor;
use strict;
+use warnings;
use Bio::EnsEMBL::Hive::NakedTable;
use base ('Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor');
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/ObjectAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/ObjectAdaptor.pm
index 12a29e9df..d727eced2 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/ObjectAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/ObjectAdaptor.pm
@@ -37,6 +37,7 @@
package Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor;
use strict;
+use warnings;
use base ('Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor');
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/PipelineWideParametersAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/PipelineWideParametersAdaptor.pm
index a4142b9e9..c9538dc5d 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/PipelineWideParametersAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/PipelineWideParametersAdaptor.pm
@@ -35,6 +35,7 @@
package Bio::EnsEMBL::Hive::DBSQL::PipelineWideParametersAdaptor;
use strict;
+use warnings;
use Bio::EnsEMBL::Hive::Utils ('stringify', 'destringify');
use base ('Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor');
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/ResourceClassAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/ResourceClassAdaptor.pm
index 2360ebcf4..dd3873394 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/ResourceClassAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/ResourceClassAdaptor.pm
@@ -38,6 +38,7 @@
package Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor;
use strict;
+use warnings;
use Bio::EnsEMBL::Hive::ResourceClass;
use base ('Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor');
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/ResourceDescriptionAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/ResourceDescriptionAdaptor.pm
index 726db149c..cd6820e3f 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/ResourceDescriptionAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/ResourceDescriptionAdaptor.pm
@@ -38,6 +38,7 @@
package Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor;
use strict;
+use warnings;
use Bio::EnsEMBL::Hive::ResourceDescription;
use base ('Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor');
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/RoleAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/RoleAdaptor.pm
index 09e8b49ee..c0db4a4b5 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/RoleAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/RoleAdaptor.pm
@@ -38,6 +38,7 @@
package Bio::EnsEMBL::Hive::DBSQL::RoleAdaptor;
use strict;
+use warnings;
use Bio::EnsEMBL::Hive::Role;
use base ('Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor');
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/SqlSchemaAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/SqlSchemaAdaptor.pm
index a6784c99b..4666a77b6 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/SqlSchemaAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/SqlSchemaAdaptor.pm
@@ -35,6 +35,7 @@
package Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor;
use strict;
+use warnings;
sub find_all_sql_schema_patches {
diff --git a/modules/Bio/EnsEMBL/Hive/DataflowRule.pm b/modules/Bio/EnsEMBL/Hive/DataflowRule.pm
index dfc5f3a49..8646296d2 100644
--- a/modules/Bio/EnsEMBL/Hive/DataflowRule.pm
+++ b/modules/Bio/EnsEMBL/Hive/DataflowRule.pm
@@ -52,6 +52,7 @@
package Bio::EnsEMBL::Hive::DataflowRule;
use strict;
+use warnings;
use Bio::EnsEMBL::Hive::Utils ('stringify', 'throw');
use Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor;
diff --git a/modules/Bio/EnsEMBL/Hive/Limiter.pm b/modules/Bio/EnsEMBL/Hive/Limiter.pm
index cff847308..cce455a4e 100644
--- a/modules/Bio/EnsEMBL/Hive/Limiter.pm
+++ b/modules/Bio/EnsEMBL/Hive/Limiter.pm
@@ -31,6 +31,9 @@
package Bio::EnsEMBL::Hive::Limiter;
+use strict;
+use warnings;
+
sub new {
my ($class, $description, $available_capacity) = @_;
diff --git a/modules/Bio/EnsEMBL/Hive/Meadow/LOCAL.pm b/modules/Bio/EnsEMBL/Hive/Meadow/LOCAL.pm
index 0eac97f42..3d5dbb93c 100644
--- a/modules/Bio/EnsEMBL/Hive/Meadow/LOCAL.pm
+++ b/modules/Bio/EnsEMBL/Hive/Meadow/LOCAL.pm
@@ -31,6 +31,7 @@
package Bio::EnsEMBL::Hive::Meadow::LOCAL;
use strict;
+use warnings;
use Sys::Hostname;
use base ('Bio::EnsEMBL::Hive::Meadow');
diff --git a/modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm b/modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm
index d710b45ab..84f585cc7 100644
--- a/modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm
+++ b/modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm
@@ -31,6 +31,7 @@
package Bio::EnsEMBL::Hive::Meadow::LSF;
use strict;
+use warnings;
use Time::Piece;
use Time::Seconds;
diff --git a/modules/Bio/EnsEMBL/Hive/MetaParameters.pm b/modules/Bio/EnsEMBL/Hive/MetaParameters.pm
index ddb77d4ad..d31278e21 100644
--- a/modules/Bio/EnsEMBL/Hive/MetaParameters.pm
+++ b/modules/Bio/EnsEMBL/Hive/MetaParameters.pm
@@ -31,6 +31,7 @@
package Bio::EnsEMBL::Hive::MetaParameters;
use strict;
+use warnings;
use base ( 'Bio::EnsEMBL::Hive::Cacheable' );
diff --git a/modules/Bio/EnsEMBL/Hive/NakedTable.pm b/modules/Bio/EnsEMBL/Hive/NakedTable.pm
index cafba6b77..444bdc0d0 100644
--- a/modules/Bio/EnsEMBL/Hive/NakedTable.pm
+++ b/modules/Bio/EnsEMBL/Hive/NakedTable.pm
@@ -32,6 +32,7 @@
package Bio::EnsEMBL::Hive::NakedTable;
use strict;
+use warnings;
use base ( 'Bio::EnsEMBL::Hive::Storable' );
diff --git a/modules/Bio/EnsEMBL/Hive/PipelineWideParameters.pm b/modules/Bio/EnsEMBL/Hive/PipelineWideParameters.pm
index 8588ba9b4..d610330d6 100644
--- a/modules/Bio/EnsEMBL/Hive/PipelineWideParameters.pm
+++ b/modules/Bio/EnsEMBL/Hive/PipelineWideParameters.pm
@@ -31,6 +31,7 @@
package Bio::EnsEMBL::Hive::PipelineWideParameters;
use strict;
+use warnings;
use base ( 'Bio::EnsEMBL::Hive::Cacheable' );
diff --git a/modules/Bio/EnsEMBL/Hive/Queen.pm b/modules/Bio/EnsEMBL/Hive/Queen.pm
index 62b17d2a3..eab5c0692 100644
--- a/modules/Bio/EnsEMBL/Hive/Queen.pm
+++ b/modules/Bio/EnsEMBL/Hive/Queen.pm
@@ -66,6 +66,7 @@
package Bio::EnsEMBL::Hive::Queen;
use strict;
+use warnings;
use File::Path 'make_path';
use Bio::EnsEMBL::Hive::Utils ('destringify', 'dir_revhash'); # NB: needed by invisible code
diff --git a/modules/Bio/EnsEMBL/Hive/ResourceClass.pm b/modules/Bio/EnsEMBL/Hive/ResourceClass.pm
index ed998f587..a38ae572f 100644
--- a/modules/Bio/EnsEMBL/Hive/ResourceClass.pm
+++ b/modules/Bio/EnsEMBL/Hive/ResourceClass.pm
@@ -38,6 +38,7 @@
package Bio::EnsEMBL::Hive::ResourceClass;
use strict;
+use warnings;
use base ( 'Bio::EnsEMBL::Hive::Cacheable', 'Bio::EnsEMBL::Hive::Storable' );
diff --git a/modules/Bio/EnsEMBL/Hive/ResourceDescription.pm b/modules/Bio/EnsEMBL/Hive/ResourceDescription.pm
index e77147045..83996fe68 100644
--- a/modules/Bio/EnsEMBL/Hive/ResourceDescription.pm
+++ b/modules/Bio/EnsEMBL/Hive/ResourceDescription.pm
@@ -40,6 +40,7 @@
package Bio::EnsEMBL::Hive::ResourceDescription;
use strict;
+use warnings;
use base ( 'Bio::EnsEMBL::Hive::Cacheable', 'Bio::EnsEMBL::Hive::Storable' );
diff --git a/modules/Bio/EnsEMBL/Hive/Role.pm b/modules/Bio/EnsEMBL/Hive/Role.pm
index f47fdc585..6338a4caf 100644
--- a/modules/Bio/EnsEMBL/Hive/Role.pm
+++ b/modules/Bio/EnsEMBL/Hive/Role.pm
@@ -36,6 +36,7 @@
package Bio::EnsEMBL::Hive::Role;
use strict;
+use warnings;
use base ( 'Bio::EnsEMBL::Hive::Storable' );
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/FailureTest.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/FailureTest.pm
index eb01110ff..407d8a4d0 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/FailureTest.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/FailureTest.pm
@@ -61,6 +61,7 @@
package Bio::EnsEMBL::Hive::RunnableDB::FailureTest;
use strict;
+use warnings;
use base ('Bio::EnsEMBL::Hive::Process');
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/FastaFactory.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/FastaFactory.pm
index 70cf0385f..6e0122ad7 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/FastaFactory.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/FastaFactory.pm
@@ -52,6 +52,7 @@
package Bio::EnsEMBL::Hive::RunnableDB::FastaFactory;
use strict;
+use warnings;
use base ('Bio::EnsEMBL::Hive::Process');
use Bio::SeqIO;
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/JobFactory.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/JobFactory.pm
index e2deb26bc..6dca245c9 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/JobFactory.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/JobFactory.pm
@@ -49,6 +49,7 @@
package Bio::EnsEMBL::Hive::RunnableDB::JobFactory;
use strict;
+use warnings;
use base ('Bio::EnsEMBL::Hive::Process');
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/AddTogether.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/AddTogether.pm
index 36b08be51..1114eab10 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/AddTogether.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/AddTogether.pm
@@ -37,6 +37,7 @@
package Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether;
use strict;
+use warnings;
use base ('Bio::EnsEMBL::Hive::Process');
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/DigitFactory.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/DigitFactory.pm
index 16b350e1d..be3756937 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/DigitFactory.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/DigitFactory.pm
@@ -42,6 +42,7 @@
package Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory;
use strict;
+use warnings;
use base ('Bio::EnsEMBL::Hive::Process');
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/PartMultiply.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/PartMultiply.pm
index 2380e5c97..50c358172 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/PartMultiply.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/PartMultiply.pm
@@ -37,6 +37,7 @@
package Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply;
use strict;
+use warnings;
use base ('Bio::EnsEMBL::Hive::Process');
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/NotifyByEmail.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/NotifyByEmail.pm
index 3a35374cf..b00303b55 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/NotifyByEmail.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/NotifyByEmail.pm
@@ -46,6 +46,7 @@
package Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail;
use strict;
+use warnings;
use base ('Bio::EnsEMBL::Hive::Process');
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm
index bb965117a..55a432ed8 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/SqlCmd.pm
@@ -51,6 +51,7 @@
package Bio::EnsEMBL::Hive::RunnableDB::SqlCmd;
use strict;
+use warnings;
use base ('Bio::EnsEMBL::Hive::Process');
diff --git a/modules/Bio/EnsEMBL/Hive/RunnableDB/SystemCmd.pm b/modules/Bio/EnsEMBL/Hive/RunnableDB/SystemCmd.pm
index 3a9c8f3bc..91f624f0d 100644
--- a/modules/Bio/EnsEMBL/Hive/RunnableDB/SystemCmd.pm
+++ b/modules/Bio/EnsEMBL/Hive/RunnableDB/SystemCmd.pm
@@ -61,6 +61,7 @@
package Bio::EnsEMBL::Hive::RunnableDB::SystemCmd;
use strict;
+use warnings;
use base ('Bio::EnsEMBL::Hive::Process');
diff --git a/modules/Bio/EnsEMBL/Hive/URLFactory.pm b/modules/Bio/EnsEMBL/Hive/URLFactory.pm
index 921116650..196b7d6c3 100644
--- a/modules/Bio/EnsEMBL/Hive/URLFactory.pm
+++ b/modules/Bio/EnsEMBL/Hive/URLFactory.pm
@@ -45,6 +45,7 @@ my $_URLFactory_global_instance;
package Bio::EnsEMBL::Hive::URLFactory;
use strict;
+use warnings;
use Bio::EnsEMBL::Hive::Utils::URL;
use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
diff --git a/modules/Bio/EnsEMBL/Hive/Utils/Config.pm b/modules/Bio/EnsEMBL/Hive/Utils/Config.pm
index 915c77000..9c65c78d0 100644
--- a/modules/Bio/EnsEMBL/Hive/Utils/Config.pm
+++ b/modules/Bio/EnsEMBL/Hive/Utils/Config.pm
@@ -30,6 +30,8 @@
package Bio::EnsEMBL::Hive::Utils::Config;
+use strict;
+use warnings;
use JSON;
sub default_config_files { # a class method, returns a list
diff --git a/modules/Bio/EnsEMBL/Hive/Utils/Stopwatch.pm b/modules/Bio/EnsEMBL/Hive/Utils/Stopwatch.pm
index a51a92544..59931385e 100644
--- a/modules/Bio/EnsEMBL/Hive/Utils/Stopwatch.pm
+++ b/modules/Bio/EnsEMBL/Hive/Utils/Stopwatch.pm
@@ -52,6 +52,7 @@
package Bio::EnsEMBL::Hive::Utils::Stopwatch;
use strict;
+use warnings;
use Time::HiRes qw(time);
my $default_unit = 1000; # milliseconds
diff --git a/modules/Bio/EnsEMBL/Hive/Worker.pm b/modules/Bio/EnsEMBL/Hive/Worker.pm
index df8f993ed..88a08e2fa 100644
--- a/modules/Bio/EnsEMBL/Hive/Worker.pm
+++ b/modules/Bio/EnsEMBL/Hive/Worker.pm
@@ -72,6 +72,7 @@
package Bio::EnsEMBL::Hive::Worker;
use strict;
+use warnings;
use POSIX;
use Bio::EnsEMBL::Hive::Analysis;
--
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