[Debian-med-packaging] Bug#956746: Perl compatibility error in mummerplot

[Charles Plessy]

Package: mummer
Version: 3.23+dfsg-4
Severity: important

Hello everybody,

the `mummerplot` Perl script in the mummer package is broken because it
contains some deprecated Perl syntax.  The attached patch solves the
problem.

I am not sure if it is enough for a Stable update.  In Sid, maybe it is
a sign that an upgrade to MUMmer4 (where at least this issue is fixed)
would be useful.

Have a nice day,

Charles

-- System Information:
Debian Release: 10.3
  APT prefers stable
  APT policy: (900, 'stable'), (500, 'stable-updates')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.19.0-8-amd64 (SMP w/4 CPU cores)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=fr_FR.utf8, LC_CTYPE=fr_FR.utf8 (charmap=UTF-8), LANGUAGE=fr_FR.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages mummer depends on:
ii  gawk        1:4.2.1+dfsg-1
ii  libc6       2.28-10
ii  libgcc1     1:8.3.0-6
ii  libstdc++6  8.3.0-6
ii  perl        5.28.1-6

mummer recommends no packages.

mummer suggests no packages.

-- no debconf information
-------------- next part --------------
--- /usr/bin/mummerplot	2018-06-11 15:38:49.000000000 +0900
+++ mummerplot.patched	2020-04-15 13:38:35.483544650 +0900
@@ -881,7 +881,7 @@
         my ($refoff, $reflen, $refdir);
         my ($qryoff, $qrylen, $qrydir);
 
-        if ( defined (%$rref) ) {
+        if ( %$rref ) {
             #-- skip reference sequence or set atts from hash
             if ( !exists ($rref->{$idR}) ) { next; }
             else { ($refoff, $reflen, $refdir) = @{$rref->{$idR}}; }
@@ -891,7 +891,7 @@
             ($refoff, $reflen, $refdir) = (0, $lenR, 1);
         }
 
-        if ( defined (%$qref) ) {
+        if ( %$qref ) {
             #-- skip query sequence or set atts from hash
             if ( !exists ($qref->{$idQ}) ) { next; }
             else { ($qryoff, $qrylen, $qrydir) = @{$qref->{$idQ}}; }
@@ -978,7 +978,7 @@
             my ($refoff, $reflen, $refdir);
             my ($qryoff, $qrylen, $qrydir);
             
-            if ( defined (%$rref) ) {
+            if ( %$rref ) {
                 #-- skip reference sequence or set atts from hash
                 if ( !exists ($rref->{$idR}) ) { next; }
                 else { ($refoff, $reflen, $refdir) = @{$rref->{$idR}}; }
@@ -988,7 +988,7 @@
                 ($refoff, $reflen, $refdir) = (0, $lenR, 1);
             }
             
-            if ( defined (%$qref) ) {
+            if ( %$qref ) {
                 #-- skip query sequence or set atts from hash
                 if ( !exists ($qref->{$idQ}) ) { next; }
                 else { ($qryoff, $qrylen, $qrydir) = @{$qref->{$idQ}}; }
@@ -1031,7 +1031,7 @@
     }
 
 
-    if ( !defined (%$rref) ) {
+    if ( !%$rref ) {
         if ( $ismultiref ) {
             print STDERR
                 "WARNING: Multiple ref sequences overlaid, try -R or -r\n";
@@ -1041,7 +1041,7 @@
         }
     }
 
-    if ( !defined (%$qref) ) {
+    if ( !%$qref ) {
         if ( $ismultiqry && !$OPT_coverage ) {
             print STDERR
                 "WARNING: Multiple qry sequences overlaid, try -Q, -q or -c\n";