added "use strict;" and "use warnings;" to all files that were missing these lines

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');
 

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;

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;

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;

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;
 

modules/Bio/EnsEMBL/Hive/Cacheable.pm

 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 {

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');
 

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;
 

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');

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');
 

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;

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;
 

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;

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;

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;
 

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');
 

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');

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');

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');
 

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');