debian/patches/perl_5.28.patch

@@ -4,7 +4,7 @@ Description: Can't use 'defined(@array)' (Maybe you should just omit the defined
 
 --- a/src/gff2aplot.pl
 +++ b/src/gff2aplot.pl
-@@ -1733,7 +1733,7 @@ sub varscheck() {
+@@ -1733,7 +1734,7 @@ sub varscheck() {
        || return $F;
      $flag && do {
          my @tmpary = ();
@@ -13,3 +13,26 @@ Description: Can't use 'defined(@array)' (Maybe you should just omit the defined
              @{ $varec->{$class}{ $$rec[1] } } = ();
          };
          @tmpary = &find_regexp( $$rec[0] );
+@@ -2930,7 +2931,8 @@ sub set_page_axes() {
+         ( $vrf->{_x_sequence_name}, $vrf->{_y_sequence_name} ) = split /:/o,
+           $vrf->{alignment_name}, 2;
+     }
+-    elsif ( scalar( @{ $Order{ALN} } ) > 0 ) {
++    elsif ( $Order{ALN} &&
++	    scalar( @{ $Order{ALN} } ) > 0 ) {
+         ( $vrf->{_x_sequence_name}, $vrf->{_y_sequence_name} ) = split /:/o,
+           $Order{ALN}[0][0], 2;
+     }
+@@ -3730,7 +3732,11 @@ sub fill_mid() {
+ 
+ sub counter {    # $_[0]~current_pos++ $_[1]~char
+     my $str;
+-    $str = "$_[1]";
++    if ( length scalar(@_) == 1 ) {
++        $str = "";
++    } else {
++        $str = "$_[1]";
++    }
+     ( ( $_[0] % 50 ) == 0 )
+       && ( $str .= " [" . &fill_left( $_[0], 6, "0" ) . "]\n" );
+     &prt_to_stderr($str);

debian/tests/run-unit-test

@@ -19,7 +19,7 @@ ERR=0
 for script in `find . -name README` ; do
    cd $(dirname $script)
    # Suppress verbose output for testing
-   sed -i -e '/^[[:space:]]\+--verbose[[:space:]]\+\\$/d' -e 's/--verbose//' -e 's/MG *-verbose/MG -quiet/' README
+   sed -i -e '/^[[:space:]]\+--verbose[[:space:]]\+\\$/d' -e 's/--verbose//' -e 's/MG *-verbose/MG -quiet/' -e 's?$BIN/\([a-z0-9]\+\).pl?\1?' -e 's?^$BIN/??' -e '1i set -x' -e '1i set -e' README
    sh README | grep -v -e '^KCRB.GT.hs-mm.log' -e '^#'
    if grep -q -v -e '^#' -e '^|' *.log ; then
      ERR=1