Asking if a dereferenced array ref is undefined is not testing what you think...

Asking if a dereferenced array ref is undefined is not testing what you think it is and is deprecated in Perl 5.16.0. You are seeing if the first element was defined when in actual fact you needed to assert if the array reference was undefined and act accordingly.

modules/Bio/EnsEMBL/OperonTranscript.pm

@@ -224,14 +224,17 @@ sub operon {
 =cut
 sub get_all_Genes {
 	my $self = shift;
-	if ( !defined @{$self->{'_gene_array'}} && defined $self->dbID) {
-		if ( defined $self->adaptor() ) {
-			my $ta = $self->adaptor()->db()->get_OperonTranscriptAdaptor();
-			my $transcripts = $ta->fetch_genes_by_operon_transcript($self);
-			$self->{'_gene_array'} = $transcripts;
-		}
+	if(! defined $self->{_gene_array}) {
+	  if(defined $self->dbID() && defined $self->adaptor()) {
+	    my $ta = $self->adaptor()->db()->get_OperonTranscriptAdaptor();
+      my $transcripts = $ta->fetch_genes_by_operon_transcript($self);
+      $self->{_gene_array} = $transcripts;
+	  }
+	  else {
+	    $self->{_gene_array} = [];
+	  }
 	}
-	return $self->{'_gene_array'};
+	return $self->{_gene_array};
 }
 =head2 add_gene
 
@@ -249,6 +252,7 @@ sub add_gene {
 	push @{$self->get_all_Genes()},$gene;
 	return;
 }
+
 =head2 add_DBEntry
 
   Arg [1]    : Bio::EnsEMBL::DBEntry $dbe