[med-svn] [ugene] 05/08: Adapt quilt patches
Andreas Tille
tille at debian.org
Fri Jan 8 18:38:45 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository ugene.
commit 30a2ee190daaf5448c298bf2ced9c55abc25de17
Author: Andreas Tille <tille at debian.org>
Date: Fri Jan 8 19:30:00 2016 +0100
Adapt quilt patches
---
debian/patches/hardening.patch | 36 ++++-----
debian/patches/use_debian_sqlite.patch | 144 +++++++++++++++------------------
2 files changed, 79 insertions(+), 101 deletions(-)
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
index eb7b077..4b4179c 100644
--- a/debian/patches/hardening.patch
+++ b/debian/patches/hardening.patch
@@ -7,35 +7,29 @@ Description: add QMAKE flags to add hardening
overlap.
Last-Updated: 2015-12-10
Forwarded: no
-Index: ugene/src/ugene_globals.pri
-===================================================================
---- ugene.orig/src/ugene_globals.pri
-+++ ugene/src/ugene_globals.pri
-@@ -14,20 +14,14 @@ DEFINES+=UGENE_VER_PATCH=$${UGENE_VER_PA
- _UGENE_NGS = $$(UGENE_NGS)
- contains(_UGENE_NGS, 1) : DEFINES += UGENE_NGS
+
+--- a/src/ugene_globals.pri
++++ b/src/ugene_globals.pri
+@@ -23,6 +23,11 @@ win32 : QMAKE_CXXFLAGS += /MP # use para
+ win32 : DEFINES+= _WINDOWS
+ win32-msvc2013 : DEFINES += _SCL_SECURE_NO_WARNINGS
--#win32 : CONFIG -= flat #group the files within the source/header group depending on the directory they reside in file system
--win32 : QMAKE_CXXFLAGS += /MP # use parallel build with nmake
--win32 : DEFINES+= _WINDOWS
--win32-msvc2013 : DEFINES += _SCL_SECURE_NO_WARNINGS
+CFLAGS += $(CFLAGS)
+CXXFLAGS += $(CXXFLAGS)
+LDFLAGS += $(LDFLAGS)
+CPPFLAGS=$(CPPFLAGS)
++
+ win32 : QMAKE_CFLAGS_RELEASE = -O2 -Oy- -MD -Zi
+ win32 : QMAKE_CXXFLAGS_RELEASE = -O2 -Oy- -MD -Zi
+ win32 : QMAKE_LFLAGS_RELEASE = /INCREMENTAL:NO /MAP /MAPINFO:EXPORTS /DEBUG
+@@ -35,6 +40,10 @@ macx {
+ QMAKE_CXXFLAGS += -Wall -Wno-ignored-attributes
+ }
--win32 : QMAKE_CFLAGS_RELEASE = -O2 -Oy- -MD -Zi
--win32 : QMAKE_CXXFLAGS_RELEASE = -O2 -Oy- -MD -Zi
--win32 : QMAKE_LFLAGS_RELEASE = /INCREMENTAL:NO /MAP /MAPINFO:EXPORTS /DEBUG
--
--macx {
-- CONFIG -= warn_on
-- #Ignore "'weak_import' attribute ignored" warning coming from OpenCL headers
-- QMAKE_CXXFLAGS += -Wall -Wno-ignored-attributes
--}
+QMAKE_CXXFLAGS += $$(CXXFLAGS)
+QMAKE_CFLAGS += $$(CFLAGS)
+QMAKE_LFLAGS += $$(LDFLAGS)
-
++
isEmpty( INSTALL_PREFIX ) : INSTALL_PREFIX = /usr
+ isEmpty( INSTALL_BINDIR ) : INSTALL_BINDIR = $$INSTALL_PREFIX/bin
diff --git a/debian/patches/use_debian_sqlite.patch b/debian/patches/use_debian_sqlite.patch
index 6bb4130..36b613a 100644
--- a/debian/patches/use_debian_sqlite.patch
+++ b/debian/patches/use_debian_sqlite.patch
@@ -4,22 +4,8 @@ Description: Tried to use Debian packages sqlite3
but failed because package does not build that way
Forwarded: no
Last-Updated: 2013-11-30
-Index: ugene/ugene.pro
-===================================================================
---- ugene.orig/ugene.pro
-+++ ugene/ugene.pro
-@@ -11,7 +11,6 @@ use_bundled_zlib() {
- SUBDIRS += \
- src/libs_3rdparty/breakpad \
- src/libs_3rdparty/qscore \
-- src/libs_3rdparty/sqlite3 \
- src/libs_3rdparty/gtest \
- src/libs_3rdparty/samtools \
- src/corelibs/U2Core \
-Index: ugene/src/corelibs/U2Core/U2Core.pri
-===================================================================
---- ugene.orig/src/corelibs/U2Core/U2Core.pri
-+++ ugene/src/corelibs/U2Core/U2Core.pri
+--- a/src/corelibs/U2Core/U2Core.pri
++++ b/src/corelibs/U2Core/U2Core.pri
@@ -19,9 +19,7 @@ use_bundled_zlib() {
unix: QMAKE_CXXFLAGS += -Wno-char-subscripts
@@ -40,10 +26,8 @@ Index: ugene/src/corelibs/U2Core/U2Core.pri
}
CONFIG(release, debug|release) {
-Index: ugene/src/corelibs/U2Formats/U2Formats.pri
-===================================================================
---- ugene.orig/src/corelibs/U2Formats/U2Formats.pri
-+++ ugene/src/corelibs/U2Formats/U2Formats.pri
+--- 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
@@ -64,10 +48,8 @@ Index: ugene/src/corelibs/U2Formats/U2Formats.pri
win32-msvc2013 {
LIBS -= -lzlib
-Index: ugene/src/plugins/dbi_bam/dbi_bam.pri
-===================================================================
---- ugene.orig/src/plugins/dbi_bam/dbi_bam.pri
-+++ ugene/src/plugins/dbi_bam/dbi_bam.pri
+--- 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
}
@@ -88,58 +70,8 @@ Index: ugene/src/plugins/dbi_bam/dbi_bam.pri
win32-msvc2013 {
LIBS -= -lzlib
-Index: ugene/src/ugenecl/ugenecl.pri
-===================================================================
---- ugene.orig/src/ugenecl/ugenecl.pri
-+++ ugene/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 -lbreakpad
-+LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Remote -lU2Lang -lU2Private -lsqlite3 -lbreakpad
-
- !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 -lbreakpad
-- LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Testd -lU2Remoted -lU2Langd -lU2Privated -lugenedbd -lbreakpadd
-+ LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Remote -lU2Lang -lU2Private -lbreakpad
-+ LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Testd -lU2Remoted -lU2Langd -lU2Privated -lbreakpadd
- }
-
- CONFIG(release, debug|release) {
-Index: ugene/src/ugeneui/ugeneui.pri
-===================================================================
---- ugene.orig/src/ugeneui/ugeneui.pri
-+++ ugene/src/ugeneui/ugeneui.pri
-@@ -16,7 +16,7 @@ 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 -lbreakpad
-+LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Remote -lU2Lang -lU2Private -lsqlite3 -lbreakpad
- macx: LIBS += /System/Library/Frameworks/Security.framework/Security
-
- !debug_and_release|build_pass {
-@@ -28,8 +28,8 @@ 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 -lbreakpad
-- LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Viewd -lU2Testd -lU2Remoted -lU2Langd -lU2Privated -lugenedbd -lbreakpadd
-+ LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Remote -lU2Lang -lU2Private -lbreakpad
-+ LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Viewd -lU2Testd -lU2Remoted -lU2Langd -lU2Privated -lbreakpadd
- }
-
- CONFIG(release, debug|release) {
-Index: ugene/src/corelibs/U2Script/U2Script.pri
-===================================================================
---- ugene.orig/src/corelibs/U2Script/U2Script.pri
-+++ ugene/src/corelibs/U2Script/U2Script.pri
+--- a/src/corelibs/U2Script/U2Script.pri
++++ b/src/corelibs/U2Script/U2Script.pri
@@ -21,15 +21,15 @@ INCLUDEPATH += ../../include \
# $${UGENE_NODE_DIR}/deps/uv/include
#}
@@ -166,10 +98,8 @@ Index: ugene/src/corelibs/U2Script/U2Script.pri
-}
\ No newline at end of file
+}
-Index: ugene/src/plugins_checker/plugins_checker.pri
-===================================================================
---- ugene.orig/src/plugins_checker/plugins_checker.pri
-+++ ugene/src/plugins_checker/plugins_checker.pri
+--- a/src/plugins_checker/plugins_checker.pri
++++ b/src/plugins_checker/plugins_checker.pri
@@ -16,7 +16,7 @@ CONFIG -= app_bundle
DEFINES+= QT_DLL QT_FATAL_ASSERT
INCLUDEPATH += src _tmp ../include ../corelibs/U2Private/src
@@ -190,3 +120,57 @@ Index: ugene/src/plugins_checker/plugins_checker.pri
}
CONFIG(release, debug|release) {
+--- a/ugene.pro
++++ b/ugene.pro
+@@ -22,7 +22,6 @@ use_bundled_zlib() {
+ SUBDIRS += \
+ src/libs_3rdparty/breakpad \
+ src/libs_3rdparty/qscore \
+- src/libs_3rdparty/sqlite3 \
+ src/libs_3rdparty/gtest \
+ src/libs_3rdparty/samtools \
+ src/libs_3rdparty/humimit \
+--- 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 -lbreakpad -lhumimit
++LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Remote -lU2Lang -lU2Private -lsqlite3 -lbreakpad -lhumimit
+
+ !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 -lbreakpad -lhumimit
+- LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Testd -lU2Remoted -lU2Langd -lU2Privated -lugenedbd -lbreakpadd -lhumimitd
++ LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Remote -lU2Lang -lU2Private -lbreakpad -lhumimit
++ LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Testd -lU2Remoted -lU2Langd -lU2Privated -lbreakpadd -lhumimitd
+ }
+
+ CONFIG(release, debug|release) {
+--- a/src/ugeneui/ugeneui.pri
++++ b/src/ugeneui/ugeneui.pri
+@@ -16,7 +16,7 @@ DEFINES+= QT_DLL QT_FATAL_ASSERT
+ INCLUDEPATH += src _tmp ../include ../corelibs/U2Private/src ../libs_3rdparty/humimit/src
+ macx : INCLUDEPATH += /System/Library/Frameworks/Security.framework/Headers
+
+-LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Remote -lU2Lang -lU2Private -lugenedb -lbreakpad -lhumimit
++LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Remote -lU2Lang -lU2Private -lsqlite3 -lbreakpad -lhumimit
+ macx: LIBS += /System/Library/Frameworks/Security.framework/Security
+
+ !debug_and_release|build_pass {
+@@ -28,8 +28,8 @@ 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 -lbreakpad -lhumimit
+- LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Viewd -lU2Testd -lU2Remoted -lU2Langd -lU2Privated -lugenedbd -lbreakpadd -lhumimitd
++ LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Remote -lU2Lang -lU2Private -lbreakpad -lhumimit
++ LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Viewd -lU2Testd -lU2Remoted -lU2Langd -lU2Privated -lbreakpadd -lhumimitd
+ }
+
+ CONFIG(release, debug|release) {
--
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