fixed some warnings/test errors

modules/t/attributeAdaptor.t

@@ -97,7 +97,7 @@ ok($count == 0);
 #
 # make sure the attribute is no longer retrievable
 #
-my @attribs = @{$aa->fetch_all_by_MiscFeature($mf)};
+@attribs = @{$aa->fetch_all_by_MiscFeature($mf)};
 ok(@attribs == 0);
 
 
@@ -107,10 +107,10 @@ ok(@attribs == 0);
 #
 
 
-my $attrib = Bio::EnsEMBL::Attribute->new(-NAME => 'test_name2',
-                                          -CODE => 'test_code2',
-                                          -DESCRIPTION => 'test_desc2',
-                                          -VALUE => 'test_value2');
+$attrib = Bio::EnsEMBL::Attribute->new(-NAME => 'test_name2',
+                                       -CODE => 'test_code2',
+                                       -DESCRIPTION => 'test_desc2',
+                                       -VALUE => 'test_value2');
 
 
 my $slice = $slice_adaptor->fetch_by_region('chromosome', '20');
@@ -120,7 +120,7 @@ $aa->store_on_Slice($slice, [$attrib]);
 #
 # make sure the seq_region_attrib table was updated
 #
-my $count = $db->db_handle->selectall_arrayref
+$count = $db->db_handle->selectall_arrayref
   ("SELECT count(*) FROM seq_region_attrib " .
    "WHERE seq_region_id = ".$slice->get_seq_region_id())->[0]->[0];
 
@@ -137,7 +137,7 @@ ok($count == 1);
 #
 # test that we can now retrieve this attribute
 #
-my @attribs = @{$aa->fetch_all_by_Slice($slice)};
+@attribs = @{$aa->fetch_all_by_Slice($slice)};
 
 ok(@attribs == 1);
 
@@ -157,7 +157,7 @@ $aa->remove_from_Slice($slice);
 #
 # make sure the seq_region_attrib table was updated
 #
-my $count = $db->db_handle->selectall_arrayref
+$count = $db->db_handle->selectall_arrayref
   ("SELECT count(*) FROM seq_region_attrib " .
    "WHERE seq_region_id = " . $slice->get_seq_region_id())->[0]->[0];
 
@@ -166,7 +166,7 @@ ok($count == 0);
 #
 # make sure the attribute is no longer retrievable
 #
-my @attribs = @{$aa->fetch_all_by_Slice($slice)};
+@attribs = @{$aa->fetch_all_by_Slice($slice)};
 ok(@attribs == 0);
 
 
@@ -179,7 +179,7 @@ $aa->store_on_Slice($slice, [$attrib]);
 #
 # make sure the seq_region_attrib table was updated
 #
-my $count = $db->db_handle->selectall_arrayref
+$count = $db->db_handle->selectall_arrayref
   ("SELECT count(*) FROM seq_region_attrib " .
    "WHERE seq_region_id = ".$slice->get_seq_region_id())->[0]->[0];
 
@@ -193,7 +193,7 @@ $count = $db->db_handle->selectall_arrayref
    "WHERE code = 'test_code2'")->[0]->[0];
 ok($count == 1);
 
-my @attribs = @{$aa->fetch_all_by_Slice($slice)};
+@attribs = @{$aa->fetch_all_by_Slice($slice)};
 ok(@attribs == 1);
 
 

modules/t/miscFeature.t

@@ -26,17 +26,15 @@ ok($mf->start() == 10 && $mf->end() == 100);
 #
 # Test add_set, get_set, get_set_codes
 #
-my $ms1 = Bio::EnsEMBL::MiscSet->new(3, undef,
-                                     '1mbcloneset',
-                                     '1mb Clone Set',
-                                     'This is a 1MB cloneset',
-                                     1e7);
-
-my $ms2 = Bio::EnsEMBL::MiscSet->new(4, undef,
-                                     'tilepath',
-                                     'Tiling Path',
-                                     'NCBI33 Tiling Path',
-                                     1e6);
+my $ms1 = Bio::EnsEMBL::MiscSet->new(-CODE => '1mbcloneset',
+                                     -NAME => '1mb Clone Set',
+                                     -DESCRIPTION => 'This is a 1MB cloneset',
+                                     -LONGEST_FEATURE => 1e7);
+
+my $ms2 = Bio::EnsEMBL::MiscSet->new(-CODE => 'tilepath',
+                                     -NAME => 'Tiling Path',
+                                     -DESCRIPTION => 'NCBI33 Tiling Path',
+                                     -LONGEST_FEATURE => 1e6);
 
 
 

modules/t/miscFeatureAdaptor.t

@@ -118,7 +118,7 @@ $mfa->store($mf);
 ok($mf->dbID() && $mf->adaptor());
 ok($misc_set->dbID() && $misc_set->adaptor());
 
-my $mf = $mfa->fetch_by_dbID($mf->dbID());
+$mf = $mfa->fetch_by_dbID($mf->dbID());
 
 my @attribs = @{$mf->get_all_Attributes()};
 ok(@attribs == 1);

modules/t/miscSetAdaptor.t

@@ -91,7 +91,7 @@ ok($misc_set->longest_feature == 1000);
 
 
 # try to store a misc_set with the same code
-my $misc_set = Bio::EnsEMBL::MiscSet->new
+$misc_set = Bio::EnsEMBL::MiscSet->new
   (-code => 'code',
    -name => 'name',
    -description => 'description',