debian/changelog

@@ -7,8 +7,8 @@ ugene (1.31.1+dfsg-1) UNRELEASED; urgency=medium
 
   [ Andreas Tille ]
   * New upstream version
+    Closes: #868885, #887305
   * Standards-Version: 4.3.0
-  * Upstream switched to cmake
   * Cleanup d/watch
   * More Files-Excluded
   * debhelper 12
@@ -17,6 +17,7 @@ ugene (1.31.1+dfsg-1) UNRELEASED; urgency=medium
  -- Andreas Tille <tille@debian.org>  Sun, 03 Dec 2017 19:10:03 +0100
 
 ugene (1.25.0+dfsg-1) unstable; urgency=medium
+
   * New upstream version
     Closes: #846557
   * debhelper 10

debian/control

@@ -19,8 +19,7 @@ Build-Depends: qtbase5-dev,
                debhelper (>= 12~),
                libxtst-dev,
                libsqlite3-dev,
-               libprocps-dev,
-               cmake
+               libprocps-dev
 Build-Conflicts: libqt4-dev,
                  qt4-qmake
 Standards-Version: 4.3.0

debian/patches/add_missing_header.patch

+Author:  Andreas Tille <tille@debian.org>
+Last-Update: Sun, 03 Dec 2017 19:10:03 +0100
+Description: Fix build issue by adding missing headers
+
+--- a/src/plugins/external_tool_support/src/trimmomatic/steps/SlidingWindowStep.cpp
++++ b/src/plugins/external_tool_support/src/trimmomatic/steps/SlidingWindowStep.cpp
+@@ -20,6 +20,7 @@
+  */
+ 
+ #include <U2Core/U2SafePoints.h>
++#include <QIntValidator>
+ 
+ #include "trimmomatic/util/LineEditHighlighter.h"
+ #include "SlidingWindowStep.h"
+--- a/src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp
++++ b/src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp
+@@ -20,6 +20,7 @@
+  */
+ 
+ #include <U2Core/U2SafePoints.h>
++#include <QIntValidator>
+ 
+ #include "LengthSettingsWidget.h"
+ #include "LineEditHighlighter.h"

debian/patches/series

 use_debian_sqlite.patch
 hardening.patch
 debian_packaged_libs.patch
+add_missing_header.patch

debian/rules

@@ -19,7 +19,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 #	dh_strip --dbg-package=ugene-dbg
 
 %:
-	dh $@
+	dh $@ --buildsystem=qmake
 
 override_dh_auto_configure:
 	# exclude non-free plugins
@@ -49,3 +49,9 @@ override_dh_fixperms-indep:
 
 override_dh_shlibdeps:
 	dh_shlibdeps -l$(CURDIR)/debian/$(pkg)/usr/lib/$(pkg)/
+
+override_dh_dwz:
+	echo "Do not run dh_dwz since it just results in:"
+	echo "    dwz: debian/ugene/usr/lib/ugene/libU2View.so.1.0.0: Couldn't find DIE referenced by DW_OP_GNU_parameter_ref"
+	echo "    dwz: debian/ugene/usr/lib/ugene/plugins/libexternal_tool_support.so.1.0.0: Couldn't find DIE referenced by DW_OP_GNU_parameter_ref"
+	echo "    dh_dwz: dwz -q -mdebian/ugene/usr/lib/debug/.dwz/x86_64-linux-gnu/ugene.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/ugene.debug ..."