[med-svn] [Git][med-team/mummer][master] 9 commits: Fix Perl compatibility error in mummerplot
Andreas Tille
gitlab at salsa.debian.org
Wed Apr 15 07:42:06 BST 2020
Andreas Tille pushed to branch master at Debian Med / mummer
Commits:
962ccdd9 by Andreas Tille at 2020-04-15T08:22:41+02:00
Fix Perl compatibility error in mummerplot
- - - - -
c0d8bc22 by Andreas Tille at 2020-04-15T08:31:01+02:00
routine-update: Standards-Version: 4.5.0
- - - - -
32654f0b by Andreas Tille at 2020-04-15T08:31:01+02:00
routine-update: debhelper-compat 12
- - - - -
84d6f586 by Andreas Tille at 2020-04-15T08:31:53+02:00
routine-update: DEB_BUILD_OPTIONS allow override_dh_auto_test
- - - - -
e1b33728 by Andreas Tille at 2020-04-15T08:31:53+02:00
routine-update: Add salsa-ci file
- - - - -
e904f3b0 by Andreas Tille at 2020-04-15T08:31:53+02:00
routine-update: Rules-Requires-Root: no
- - - - -
fa307ada by Andreas Tille at 2020-04-15T08:37:27+02:00
Build-Depends: csh to enable build-time tests
- - - - -
5fdb7378 by Andreas Tille at 2020-04-15T08:40:29+02:00
Upload to unstable
- - - - -
f21066df by Andreas Tille at 2020-04-15T08:41:36+02:00
Rename debian/NEWS.Debian to NEWS as suggested by lintian
- - - - -
8 changed files:
- debian/NEWS.Debian → debian/NEWS
- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/mummerplot.patch
- debian/patches/series
- debian/rules
- + debian/salsa-ci.yml
Changes:
=====================================
debian/NEWS.Debian → debian/NEWS
=====================================
=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+mummer (3.23+dfsg-5) unstable; urgency=medium
+
+ [ Charles Plessy ]
+ * Fix Perl compatibility error in mummerplot
+ Closes: #956746
+
+ [ Andreas Tille ]
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 12 (routine-update)
+ * Build-Depends: csh to enable build-time tests
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Wed, 15 Apr 2020 08:37:33 +0200
+
mummer (3.23+dfsg-4) unstable; urgency=medium
[ Helmut Grohne ]
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -5,14 +5,16 @@ Uploaders: Steffen Moeller <moeller at debian.org>,
Charles Plessy <plessy at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
texlive-latex-base,
texlive-latex-recommended,
- texlive-fonts-recommended
-Standards-Version: 4.1.4
+ texlive-fonts-recommended,
+ csh | c-shell <!nocheck>
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/mummer
Vcs-Git: https://salsa.debian.org/med-team/mummer.git
Homepage: http://mummer.sourceforge.net/
+Rules-Requires-Root: no
Package: mummer
Architecture: any
=====================================
debian/patches/mummerplot.patch
=====================================
@@ -0,0 +1,61 @@
+From: Charles Plessy <plessy at debian.org>
+Date: Wed, 15 Apr 2020 13:53:51 +0900
+Bug-Debian: https://bugs.debian.org/956746
+Description: Fix Perl compatibility error in mummerplot
+
+--- a/scripts/mummerplot.pl
++++ b/scripts/mummerplot.pl
+@@ -881,7 +881,7 @@ sub PlotData ($$$)
+ my ($refoff, $reflen, $refdir);
+ my ($qryoff, $qrylen, $qrydir);
+
+- if ( defined (%$rref) ) {
++ if ( %$rref ) {
+ #-- skip reference sequence or set atts from hash
+ if ( !exists ($rref->{$idR}) ) { next; }
+ else { ($refoff, $reflen, $refdir) = @{$rref->{$idR}}; }
+@@ -891,7 +891,7 @@ sub PlotData ($$$)
+ ($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 @@ sub PlotData ($$$)
+ my ($refoff, $reflen, $refdir);
+ my ($qryoff, $qrylen, $qrydir);
+
+- if ( defined (%$rref) ) {
++ if ( %$rref ) {
+ #-- skip reference sequence or set atts from hash
+ if ( !exists ($rref->{$idR}) ) { next; }
+ else { ($refoff, $reflen, $refdir) = @{$rref->{$idR}}; }
+@@ -988,7 +988,7 @@ sub PlotData ($$$)
+ ($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 @@ sub PlotData ($$$)
+ }
+
+
+- if ( !defined (%$rref) ) {
++ if ( !%$rref ) {
+ if ( $ismultiref ) {
+ print STDERR
+ "WARNING: Multiple ref sequences overlaid, try -R or -r\n";
+@@ -1041,7 +1041,7 @@ sub PlotData ($$$)
+ }
+ }
+
+- if ( !defined (%$qref) ) {
++ if ( !%$qref ) {
+ if ( $ismultiqry && !$OPT_coverage ) {
+ print STDERR
+ "WARNING: Multiple qry sequences overlaid, try -Q, -q or -c\n";
=====================================
debian/patches/series
=====================================
@@ -8,3 +8,4 @@ addition_from_mugsy.patch
0009-improve-performance-of-delta2maf.patch
# most probably broken see bug #843621
# addition_from_report_duplicates.patch
+mummerplot.patch
=====================================
debian/rules
=====================================
@@ -25,9 +25,6 @@ override_dh_auto_build:
CFLAGS="$(CFLAGS)" CXXFLAGS="$(CXXFLAGS)" LDFLAGS="$(LDFLAGS)"
$(MAKE) -C docs
-override_dh_auto_test:
- $(MAKE) check
-
override_dh_prep:
# Unfortunately the upstream makefile does not separate the build and install steps.
dh_prep -X debian/tmp
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
View it on GitLab: https://salsa.debian.org/med-team/mummer/-/compare/f3c976f4c6723355dc32f2324611598ae74b41a7...f21066df592925adfe0ce299fb9da010bae413e4
--
View it on GitLab: https://salsa.debian.org/med-team/mummer/-/compare/f3c976f4c6723355dc32f2324611598ae74b41a7...f21066df592925adfe0ce299fb9da010bae413e4
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