[med-svn] r15228 - in trunk/packages/ugene/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Wed Nov 20 22:24:57 UTC 2013
Author: tille
Date: 2013-11-20 22:24:57 +0000 (Wed, 20 Nov 2013)
New Revision: 15228
Modified:
trunk/packages/ugene/trunk/debian/changelog
trunk/packages/ugene/trunk/debian/control
trunk/packages/ugene/trunk/debian/copyright
trunk/packages/ugene/trunk/debian/patches/series
trunk/packages/ugene/trunk/debian/patches/use_debian_sqlite.patch
trunk/packages/ugene/trunk/debian/rules
Log:
Some enhancements for ugene packaging
Modified: trunk/packages/ugene/trunk/debian/changelog
===================================================================
--- trunk/packages/ugene/trunk/debian/changelog 2013-11-20 22:14:19 UTC (rev 15227)
+++ trunk/packages/ugene/trunk/debian/changelog 2013-11-20 22:24:57 UTC (rev 15228)
@@ -1,9 +1,9 @@
-ugene (1.11.3+dfsg-1) UNRELEASED; urgency=low
+ugene (1.12.3+dfsg-1) UNRELEASED; urgency=low
* New upstream version
Closes: #693655, #675298
* debian/control
- - Standards-Version: 3.9.4 (no changes needed)
+ - cme fix dpkg-control
- Build-Depends: libxtst-dev
- Moved to non-free (and reported the issue upstream as
https://ugene.unipro.ru/tracker/browse/UGENE-1310
@@ -11,7 +11,7 @@
* debhelper 9 (control+compat)
* debian/rules: Rewritten to use short dh
- -- Andreas Tille <tille at debian.org> Tue, 11 Dec 2012 09:45:46 +0100
+ -- Andreas Tille <tille at debian.org> Mon, 18 Nov 2013 17:29:54 +0100
ugene (1.9.8+repack-1) experimental; urgency=low
Modified: trunk/packages/ugene/trunk/debian/control
===================================================================
--- trunk/packages/ugene/trunk/debian/control 2013-11-20 22:14:19 UTC (rev 15227)
+++ trunk/packages/ugene/trunk/debian/control 2013-11-20 22:24:57 UTC (rev 15228)
@@ -1,20 +1,31 @@
Source: ugene
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Ivan Efremov <iefremov at unipro.ru>,
+ Steffen Moeller <moeller at debian.org>,
+ Andreas Tille <tille at debian.org>
Section: non-free/science
+XS-Autobuild: yes
Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Ivan Efremov <iefremov at unipro.ru>,
- Steffen Moeller <moeller at debian.org>,
- Andreas Tille <tille at debian.org>
-Build-Depends: libqt4-dev (>= 4.7.0), libqtwebkit-dev, libqt4-opengl-dev (>= 4.7.0),
- zlib1g-dev, debhelper (>= 9), libxtst-dev
+Build-Depends: libqt4-dev,
+ libqtwebkit-dev,
+ libqt4-opengl-dev,
+ zlib1g-dev,
+ debhelper (>= 9),
+ libxtst-dev,
+ libsqlite3-dev,
+ libprocps-dev
Standards-Version: 3.9.4
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ugene/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/ugene/trunk/
Homepage: http://ugene.unipro.ru
-Vcs-svn: svn://svn.debian.org/debian-med/trunk/packages/ugene/trunk
-Vcs-browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ugene/trunk/
Package: ugene
Architecture: any
-Depends: ${shlibs:Depends}, libqt4-gui (>=4.7.0), libqt4-core (>=4.7.0), ugene-data, ${misc:Depends}
+Depends: ${shlibs:Depends},
+ libqt4-gui,
+ libqt4-core,
+ ugene-data,
+ ${misc:Depends}
Description: integrated bioinformatics toolkit
Unipro UGENE is a cross-platform visual environment for DNA and protein
sequence analysis. UGENE integrates the most important bioinformatics
@@ -33,9 +44,10 @@
Package: ugene-dbg
Architecture: any
+Section: non-free/debug
Priority: extra
-Section: non-free/debug
-Depends: ${misc:Depends}, ugene (= ${binary:Version})
+Depends: ${misc:Depends},
+ ugene (= ${binary:Version})
Description: integrated bioinformatics toolkit (degugging information)
Unipro UGENE is a cross-platform visual environment for DNA and protein
sequence analysis. UGENE integrates the most important bioinformatics
Modified: trunk/packages/ugene/trunk/debian/copyright
===================================================================
--- trunk/packages/ugene/trunk/debian/copyright 2013-11-20 22:14:19 UTC (rev 15227)
+++ trunk/packages/ugene/trunk/debian/copyright 2013-11-20 22:24:57 UTC (rev 15228)
@@ -5,6 +5,8 @@
Source: http://ugene.unipro.ru/downloads/ugene_get_latest_source.html
Files-Excluded:
src/libs_3rdparty/zlib
+ installer/macosx
+ installer/windows
Files: *
Copyright: © 2008-2012 UniPro <ugene at unipro.ru>
Modified: trunk/packages/ugene/trunk/debian/patches/series
===================================================================
--- trunk/packages/ugene/trunk/debian/patches/series 2013-11-20 22:14:19 UTC (rev 15227)
+++ trunk/packages/ugene/trunk/debian/patches/series 2013-11-20 22:24:57 UTC (rev 15228)
@@ -1,2 +1,2 @@
#do_not_strip.patch
-#use_debian_sqlite.patch
+use_debian_sqlite.patch
Modified: trunk/packages/ugene/trunk/debian/patches/use_debian_sqlite.patch
===================================================================
--- trunk/packages/ugene/trunk/debian/patches/use_debian_sqlite.patch 2013-11-20 22:14:19 UTC (rev 15227)
+++ trunk/packages/ugene/trunk/debian/patches/use_debian_sqlite.patch 2013-11-20 22:24:57 UTC (rev 15228)
@@ -14,12 +14,111 @@
src/corelibs/U2Core \
--- a/src/corelibs/U2Core/U2Core.pri
+++ b/src/corelibs/U2Core/U2Core.pri
-@@ -17,8 +17,6 @@ use_bundled_zlib() {
+@@ -15,9 +15,7 @@ use_bundled_zlib() {
+ }
+
LIBS += -L../../_release
- LIBS += -lugenedb
+-LIBS += -lugenedb
+-
+-INCLUDEPATH += ../../libs_3rdparty/sqlite3/src
++LIBS += -lsqlite3
--INCLUDEPATH += ../../libs_3rdparty/sqlite3/src
--
!debug_and_release|build_pass {
+@@ -29,8 +27,6 @@ INCLUDEPATH += ../../libs_3rdparty/sqlit
+ LIBS += -lzlibd
+ LIBS -= -lzlib
+ }
+- LIBS -= -lugenedb
+- LIBS += -lugenedbd
+ }
+
+ CONFIG(release, debug|release) {
+--- a/src/corelibs/U2Formats/U2Formats.pri
++++ b/src/corelibs/U2Formats/U2Formats.pri
+@@ -12,7 +12,7 @@ UGENE_RELATIVE_DESTDIR = ''
+ DEFINES+= QT_FATAL_ASSERT BUILDING_U2FORMATS_DLL
+
+ LIBS += -L../../_release -lU2Core -lU2Algorithm
+-LIBS += -lugenedb -lsamtools
++LIBS += -lsqlite3 -lsamtools
+
+ # Force re-linking when lib changes
+ unix:POST_TARGETDEPS += ../../_release/libsamtools.a
+@@ -29,8 +29,8 @@ INCLUDEPATH += ../../libs_3rdparty/sqlit
+
CONFIG(debug, debug|release) {
+ DESTDIR=../../_debug
+- LIBS -= -L../../_release -lU2Core -lU2Algorithm -lugenedb -lsamtools
+- LIBS += -L../../_debug -lU2Cored -lU2Algorithmd -lugenedbd -lsamtoolsd
++ LIBS -= -L../../_release -lU2Core -lU2Algorithm -lsamtools
++ LIBS += -L../../_debug -lU2Cored -lU2Algorithmd -lsamtoolsd
+
+ unix:POST_TARGETDEPS -= ../../_release/libsamtools.a
+ unix:POST_TARGETDEPS += ../../_debug/libsamtoolsd.a
+--- a/src/plugins/dbi_bam/dbi_bam.pri
++++ b/src/plugins/dbi_bam/dbi_bam.pri
+@@ -10,7 +10,7 @@ use_bundled_zlib() {
+ INCLUDEPATH += ../../libs_3rdparty/zlib/src
+ }
+
+-LIBS += -lugenedb -lsamtools
++LIBS += -lsqlite3 -lsamtools
+
+ # Force re-linking when lib changes
+ unix:POST_TARGETDEPS += ../../_release/libsamtools.a
+@@ -24,8 +24,8 @@ win32:DEFINES += _USE_MATH_DEFINES "inli
+ !debug_and_release|build_pass {
+
+ CONFIG(debug, debug|release) {
+- LIBS -= -lugenedb -lsamtools
+- LIBS += -lugenedbd -lsamtoolsd
++ LIBS -= -lsamtools
++ LIBS += -lsamtoolsd
+
+ unix:POST_TARGETDEPS -= ../../_release/libsamtools.a
+ unix:POST_TARGETDEPS += ../../_debug/libsamtoolsd.a
+--- a/src/ugenecl/ugenecl.pri
++++ b/src/ugenecl/ugenecl.pri
+@@ -14,7 +14,7 @@ CONFIG +=qt dll thread debug_and_release
+ DEFINES+= QT_DLL QT_FATAL_ASSERT
+ INCLUDEPATH += src _tmp ../include ../corelibs/U2Private/src
+
+-LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Remote -lU2Lang -lU2Private -lugenedb
++LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Remote -lU2Lang -lU2Private -lsqlite3
+
+ !debug_and_release|build_pass {
+
+@@ -24,8 +24,8 @@ LIBS += -L../_release -lU2Core -lU2Algor
+ DESTDIR=../_debug
+ MOC_DIR=_tmp/moc/debug
+ OBJECTS_DIR=_tmp/obj/debug
+- LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Remote -lU2Lang -lU2Private -lugenedb
+- LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Testd -lU2Remoted -lU2Langd -lU2Privated -lugenedbd
++ LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Remote -lU2Lang -lU2Private
++ LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Testd -lU2Remoted -lU2Langd -lU2Privated
+ }
+
+ CONFIG(release, debug|release) {
+--- a/src/ugeneui/ugeneui.pri
++++ b/src/ugeneui/ugeneui.pri
+@@ -15,7 +15,7 @@ DEFINES+= QT_DLL QT_FATAL_ASSERT
+ INCLUDEPATH += src _tmp ../include ../corelibs/U2Private/src
+ macx : INCLUDEPATH += /System/Library/Frameworks/Security.framework/Headers
+
+-LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Remote -lU2Lang -lU2Private -lugenedb
++LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Remote -lU2Lang -lU2Private -lsqlite3
+ macx: LIBS += /System/Library/Frameworks/Security.framework/Security
+
+ !debug_and_release|build_pass {
+@@ -27,8 +27,8 @@ macx: LIBS += /System/Library/Frameworks
+ DESTDIR=../_debug
+ MOC_DIR=_tmp/moc/debug
+ OBJECTS_DIR=_tmp/obj/debug
+- LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Remote -lU2Lang -lU2Private -lugenedb
+- LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Viewd -lU2Testd -lU2Remoted -lU2Langd -lU2Privated -lugenedbd
++ LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Remote -lU2Lang -lU2Private
++ LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Viewd -lU2Testd -lU2Remoted -lU2Langd -lU2Privated
+ }
+
+ CONFIG(release, debug|release) {
Modified: trunk/packages/ugene/trunk/debian/rules
===================================================================
--- trunk/packages/ugene/trunk/debian/rules 2013-11-20 22:14:19 UTC (rev 15227)
+++ trunk/packages/ugene/trunk/debian/rules 2013-11-20 22:24:57 UTC (rev 15228)
@@ -9,7 +9,8 @@
dh $@
override_dh_auto_configure:
- qmake-qt4 -r
+ # exclude non-free plugins
+ qmake-qt4 -r UGENE_WITHOUT_NON_FREE=1
find . -name Makefile.* | xargs -r sed -i '/STRIP/d'
#override_dh_auto_build:
@@ -27,7 +28,7 @@
rm -rf debian/$(pkg)/usr/share/$(pkg)
override_dh_shlibdeps:
- export LD_LIBRARY_PATH=$$(pwd)/debian/$(pkg)/usr/lib/$(pkg):$$(pwd)/debian/$(pkg)/usr/lib64/$(pkg) && dh_shlibdeps
+ dh_shlibdeps -l$(CURDIR)/debian/$(pkg)/usr/lib/$(pkg) -l$(CURDIR)/debian/$(pkg)/usr/lib64/$(pkg)
# Remark: The following uscan command requires devscripts > 2.12.4 which is not
# yet released at the time of this package release. The code can be obtained
More information about the debian-med-commit
mailing list