[med-svn] [ugene] 06/10: refresh patches
Sascha Steinbiss
satta at debian.org
Thu Jul 28 06:06:36 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository ugene.
commit ea26930dbde3ffc3aaaaf160162b36b8267c2c1e
Author: Sascha Steinbiss <satta at debian.org>
Date: Wed Jul 27 21:55:46 2016 +0000
refresh patches
---
debian/patches/hardening.patch | 4 +-
debian/patches/use_debian_sqlite.patch | 79 +++++++++++++++-------------------
2 files changed, 37 insertions(+), 46 deletions(-)
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
index 4b4179c..1a68852 100644
--- a/debian/patches/hardening.patch
+++ b/debian/patches/hardening.patch
@@ -10,7 +10,7 @@ Forwarded: no
--- a/src/ugene_globals.pri
+++ b/src/ugene_globals.pri
-@@ -23,6 +23,11 @@ win32 : QMAKE_CXXFLAGS += /MP # use para
+@@ -21,6 +21,11 @@
win32 : DEFINES+= _WINDOWS
win32-msvc2013 : DEFINES += _SCL_SECURE_NO_WARNINGS
@@ -22,7 +22,7 @@ Forwarded: no
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 {
+@@ -33,6 +38,10 @@
QMAKE_CXXFLAGS += -Wall -Wno-ignored-attributes
}
diff --git a/debian/patches/use_debian_sqlite.patch b/debian/patches/use_debian_sqlite.patch
index 909264f..d53a8c3 100644
--- a/debian/patches/use_debian_sqlite.patch
+++ b/debian/patches/use_debian_sqlite.patch
@@ -6,18 +6,16 @@ Forwarded: no
Last-Updated: 2013-11-30
--- a/src/corelibs/U2Core/U2Core.pri
+++ b/src/corelibs/U2Core/U2Core.pri
-@@ -19,9 +19,7 @@ use_bundled_zlib() {
+@@ -21,7 +21,7 @@
unix: QMAKE_CXXFLAGS += -Wno-char-subscripts
LIBS += -L../../_release
-LIBS += -lugenedb
--
--INCLUDEPATH += ../../libs_3rdparty/sqlite3/src
+LIBS += -lsqlite3
!debug_and_release|build_pass {
-@@ -33,8 +31,6 @@ INCLUDEPATH += ../../libs_3rdparty/sqlit
+@@ -33,8 +33,6 @@
LIBS += -lzlibd
LIBS -= -lzlib
}
@@ -28,8 +26,8 @@ Last-Updated: 2013-11-30
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
+@@ -14,7 +14,7 @@
+ DEFINES += QT_FATAL_ASSERT BUILDING_U2FORMATS_DLL
LIBS += -L../../_release -lU2Core -lU2Algorithm
-LIBS += -lugenedb -lsamtools
@@ -37,7 +35,7 @@ Last-Updated: 2013-11-30
win32-msvc2013 {
DEFINES += NOMINMAX _XKEYCHECK_H
-@@ -36,8 +36,8 @@ INCLUDEPATH += ../../libs_3rdparty/sqlit
+@@ -38,8 +38,8 @@
CONFIG(debug, debug|release) {
DESTDIR=../../_debug
@@ -50,8 +48,8 @@ Last-Updated: 2013-11-30
LIBS -= -lzlib
--- 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
+@@ -12,7 +12,7 @@
+ macx: LIBS += -lz
}
-LIBS += -lugenedb -lsamtools
@@ -59,7 +57,7 @@ Last-Updated: 2013-11-30
win32-msvc2013 {
DEFINES += NOMINMAX _XKEYCHECK_H
-@@ -29,8 +29,8 @@ win32:DEFINES += _USE_MATH_DEFINES "inli
+@@ -31,8 +31,8 @@
!debug_and_release|build_pass {
CONFIG(debug, debug|release) {
@@ -72,35 +70,28 @@ Last-Updated: 2013-11-30
LIBS -= -lzlib
--- a/src/corelibs/U2Script/U2Script.pri
+++ b/src/corelibs/U2Script/U2Script.pri
-@@ -21,15 +21,15 @@ INCLUDEPATH += ../../include \
+@@ -21,15 +21,15 @@
# $${UGENE_NODE_DIR}/deps/uv/include
#}
--LIBS += -L../../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Remote -lU2Lang -lU2Private -lugenedb -lU2Gui -lU2Test
-+LIBS += -L../../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Remote -lU2Lang -lU2Private -lsqlite3 -lU2Gui -lU2Test
+-LIBS += -L../../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Lang -lU2Private -lugenedb -lU2Gui -lU2Test
++LIBS += -L../../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Lang -lU2Private -lsqlite3 -lU2Gui -lU2Test
!debug_and_release|build_pass {
CONFIG( debug, debug|release ) {
DESTDIR = ../../_debug
-- LIBS -= -L../../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Remote -lU2Lang -lU2Private -lugenedb -lU2Gui -lU2Test
-- LIBS += -L../../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Remoted -lU2Langd -lU2Privated -lugenedbd -lU2Guid -lU2Testd
-+ LIBS -= -L../../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Remote -lU2Lang -lU2Private -lsqlite3 -lU2Gui -lU2Test
-+ LIBS += -L../../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Remoted -lU2Langd -lU2Privated -lsqlite3 -lU2Guid -lU2Testd
+- LIBS -= -L../../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Lang -lU2Private -lugenedb -lU2Gui -lU2Test
+- LIBS += -L../../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Langd -lU2Privated -lugenedbd -lU2Guid -lU2Testd
++ LIBS -= -L../../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Lang -lU2Private -lsqlite3 -lU2Gui -lU2Test
++ LIBS += -L../../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Langd -lU2Privated -lsqlite3 -lU2Guid -lU2Testd
# count( UGENE_NODE_DIR, 1 ) {
# LIBS += -l$${UGENE_NODE_DIR}/Debug/node
-@@ -48,4 +48,4 @@ LIBS += -L../../_release -lU2Core -lU2Al
- unix {
- target.path = $$UGENE_INSTALL_DIR/$$UGENE_RELATIVE_DESTDIR
- INSTALLS += target
--}
-\ No newline at end of file
-+}
--- a/src/plugins_checker/plugins_checker.pri
+++ b/src/plugins_checker/plugins_checker.pri
-@@ -16,7 +16,7 @@ CONFIG -= app_bundle
+@@ -15,7 +15,7 @@
DEFINES+= QT_DLL QT_FATAL_ASSERT
INCLUDEPATH += src _tmp ../include ../corelibs/U2Private/src
@@ -109,7 +100,7 @@ Last-Updated: 2013-11-30
!debug_and_release|build_pass {
-@@ -26,8 +26,8 @@ LIBS += -L../_release -lU2Core -lU2Algor
+@@ -25,8 +25,8 @@
DESTDIR=../_debug
MOC_DIR=_tmp/moc/debug
OBJECTS_DIR=_tmp/obj/debug
@@ -122,55 +113,55 @@ Last-Updated: 2013-11-30
CONFIG(release, debug|release) {
--- a/ugene.pro
+++ b/ugene.pro
-@@ -22,7 +22,6 @@ use_bundled_zlib() {
+@@ -22,7 +22,6 @@
SUBDIRS += \
src/libs_3rdparty/breakpad \
src/libs_3rdparty/qscore \
- src/libs_3rdparty/sqlite3 \
- src/libs_3rdparty/gtest \
src/libs_3rdparty/samtools \
src/libs_3rdparty/QSpec \
+ src/corelibs/U2Core \
--- a/src/ugenecl/ugenecl.pri
+++ b/src/ugenecl/ugenecl.pri
-@@ -14,7 +14,7 @@ CONFIG +=qt dll thread debug_and_release
+@@ -14,7 +14,7 @@
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
+-LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Lang -lU2Private -lugenedb -lbreakpad -lhumimit
++LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Lang -lU2Private -lsqlite3 -lbreakpad -lhumimit
if(exclude_list_enabled()|!exists( ../libs_3rdparty/QSpec/QSpec.pro )) {
LIBS -= -lhumimit
}
-@@ -26,8 +26,8 @@ if(exclude_list_enabled()|!exists( ../li
+@@ -26,8 +26,8 @@
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
+- LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Lang -lU2Private -lugenedb -lbreakpad -lhumimit
+- LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Testd -lU2Langd -lU2Privated -lugenedbd -lbreakpadd -lhumimitd
++ LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Lang -lU2Private -lbreakpad -lhumimit
++ LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Testd -lU2Langd -lU2Privated -lbreakpadd -lhumimitd
if(exclude_list_enabled()|!exists( ../libs_3rdparty/QSpec/QSpec.pro )) {
LIBS -= -lhumimitd
}
--- a/src/ugeneui/ugeneui.pri
+++ b/src/ugeneui/ugeneui.pri
-@@ -16,7 +16,7 @@ DEFINES+= QT_DLL QT_FATAL_ASSERT
+@@ -16,7 +16,7 @@
INCLUDEPATH += src _tmp ../include ../corelibs/U2Private/src ../libs_3rdparty/QSpec/src
macx : INCLUDEPATH += /System/Library/Frameworks/Security.framework/Headers
--LIBS += -L../_release -L../libs_3rdparty/humimit/ -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Remote -lU2Lang -lU2Private -lugenedb -lbreakpad -lhumimit
-+LIBS += -L../_release -L../libs_3rdparty/humimit/ -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Remote -lU2Lang -lU2Private -lsqlite3 -lbreakpad -lhumimit
+-LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Lang -lU2Private -lugenedb -lbreakpad -lhumimit
++LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Lang -lU2Private -lsqlite3 -lbreakpad -lhumimit
macx: LIBS += /System/Library/Frameworks/Security.framework/Security
if(exclude_list_enabled()|!exists( ../libs_3rdparty/QSpec/QSpec.pro )) {
LIBS -= -lhumimit
-@@ -31,8 +31,8 @@ if(exclude_list_enabled()|!exists( ../li
+@@ -31,8 +31,8 @@
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
+- LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Lang -lU2Private -lugenedb -lbreakpad -lhumimit
+- LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Viewd -lU2Testd -lU2Langd -lU2Privated -lugenedbd -lbreakpadd -lhumimitd
++ LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Lang -lU2Private -lbreakpad -lhumimit
++ LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Viewd -lU2Testd -lU2Langd -lU2Privated -lbreakpadd -lhumimitd
if(exclude_list_enabled()|!exists( ../libs_3rdparty/QSpec/QSpec.pro )) {
LIBS -= -lhumimitd
}
--
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