From c07503cbad4fdb922c08f00639cd27476f0015c7 Mon Sep 17 00:00:00 2001
From: Chris Fields <cjfields@bioperl.org>
Date: Tue, 19 Feb 2013 08:38:49 -0600
Subject: [PATCH] Graph::Directed is giving warnings when using 'require', but
 using actual module required is more direct w/o the warning

---
 Bio/Root/Test.pm          | 18 +++++++++---------
 t/Annotation/Annotation.t | 12 ++++++------
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/Bio/Root/Test.pm b/Bio/Root/Test.pm
index 95fce7ad6..fafd1bb81 100644
--- a/Bio/Root/Test.pm
+++ b/Bio/Root/Test.pm
@@ -26,7 +26,7 @@ Bio::Root::Test - A common base for all Bioperl test scripts.
 
   my $do_network_tests = test_network();
   my $output_debugging = test_debug();
-  
+
   # Bio::Root::Test rewraps Test::Most, so one can carry out tests with
   # Test::More, Test::Exception, Test::Warn, Test::Deep, Test::Diff syntax
 
@@ -142,12 +142,12 @@ our @ISA = qw(Test::Builder::Module);
 
 {
     my $Tester = Test::Builder->new;
-    
+
     no warnings 'redefine';
     sub Test::Warn::_canonical_got_warning {
         my ($called_from, $msg) = @_;
         my $warn_kind = $called_from eq 'Carp' ? 'carped' : ($called_from =~ /Bio::/ ? 'Bioperl' : 'warn');
-        
+
         my $warning;
         if ($warn_kind eq 'Bioperl') {
             ($warning) = $msg =~ /\n--------------------- WARNING ---------------------\nMSG: (.+)\n---------------------------------------------------\n$/m;
@@ -157,10 +157,10 @@ our @ISA = qw(Test::Builder::Module);
             my @warning_stack = split /\n/, $msg;   # some stuff of uplevel is included
             $warning = $warning_stack[0];
         }
-        
+
         return {$warn_kind => $warning}; # return only the real message
     }
-    
+
     sub Test::Warn::_diag_found_warning {
         foreach (@_) {
             if (ref($_) eq 'HASH') {
@@ -173,12 +173,12 @@ our @ISA = qw(Test::Builder::Module);
         }
         $Tester->diag( "didn't find a warning" ) unless @_;
     }
-    
+
     sub Test::Warn::_cmp_got_to_exp_warning {
         my ($got_kind, $got_msg) = %{ shift() };
         my ($exp_kind, $exp_msg) = %{ shift() };
         return 0 if ($got_kind eq 'warn') && ($exp_kind eq 'carped');
-        
+
         my $cmp;
         if ($got_kind eq 'Bioperl') {
             $cmp = $got_msg =~ /^\Q$exp_msg\E$/;
@@ -186,7 +186,7 @@ our @ISA = qw(Test::Builder::Module);
         else {
             $cmp = $got_msg =~ /^\Q$exp_msg\E at \S+ line \d+\.?$/;
         }
-        
+
         return $cmp;
     }
 }
@@ -194,7 +194,7 @@ our @ISA = qw(Test::Builder::Module);
 our @EXPORT = (@Test::Most::EXPORT,
                #@Bio::Root::Test::Warn::EXPORT,
                # Test::Warn method wrappers
-               
+
                # BioPerl-specific
                qw(
                 test_begin
diff --git a/t/Annotation/Annotation.t b/t/Annotation/Annotation.t
index 2394b8a2b..1583f1aef 100644
--- a/t/Annotation/Annotation.t
+++ b/t/Annotation/Annotation.t
@@ -3,12 +3,12 @@
 
 use strict;
 
-BEGIN { 
+BEGIN {
     use lib '.';
     use Bio::Root::Test;
-    
+
     test_begin(-tests => 159);
-	
+
     use_ok('Bio::Annotation::Collection');
     use_ok('Bio::Annotation::DBLink');
     use_ok('Bio::Annotation::Comment');
@@ -160,7 +160,7 @@ is (scalar($nested_ac->get_Annotations()), 7);
 is (scalar($nested_ac->get_all_Annotations()), 7);
 
 SKIP: {
-  test_skip(-tests => 7, -requires_modules => [qw(Graph::Directed Bio::Annotation::OntologyTerm)]);
+  test_skip(-tests => 7, -requires_modules => [qw(Bio::Annotation::OntologyTerm)]);
   use_ok('Bio::Annotation::OntologyTerm');
   # OntologyTerm annotation
   my $termann = Bio::Annotation::OntologyTerm->new(-label => 'test case',
@@ -252,7 +252,7 @@ my $ann_tree = Bio::Annotation::Tree->new(
 isa_ok($ann_tree, 'Bio::AnnotationI');
 $ann_tree->tree_id('test');
 is $ann_tree->tree_id(), 'test', "tree_id()";
-$ann_tree->tagname('tree'); 
+$ann_tree->tagname('tree');
 is $ann_tree->tagname(), 'tree', "tagname()";
 my $aln_filename = test_input_file('longnames.aln');
 use Bio::AlignIO;
@@ -311,7 +311,7 @@ my $ann_struct2 = Bio::Annotation::TagTree->new(-tagname => 'gn',
 						-value => $val);
 is($ann_struct2->value, $val,'roundtrip');
 
-# formats 
+# formats
 like($ann_struct2->value, qr/Name: CALM1/,'itext');
 $ann_struct2->tagformat('sxpr');
 like($ann_struct2->value, qr/\(Name "CALM1"\)/,'spxr');
-- 
2.11.4.GIT