[med-svn] [ugene] 02/03: Refreshed patches

Andreas Tille tille at debian.org
Wed Dec 9 16:36:31 UTC 2015 

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tille pushed a commit to branch master
in repository ugene.

commit 8718ab2848f0d805e52efa444f2758c4710f40be
Author: Andreas Tille <tille at debian.org>
Date:   Wed Dec 9 15:11:06 2015 +0100

    Refreshed patches
---
 debian/patches/hardening.patch         | 13 ++------
 debian/patches/use_debian_sqlite.patch | 58 +++++++++++++++++-----------------
 2 files changed, 32 insertions(+), 39 deletions(-)

diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
index 407a83e..125ff69 100644
--- a/debian/patches/hardening.patch
+++ b/debian/patches/hardening.patch
@@ -5,9 +5,9 @@ Last-Updated: 2013-11-30
 Forwarded: no
 --- a/src/ugene_globals.pri
 +++ b/src/ugene_globals.pri
-@@ -7,6 +7,15 @@
- DEFINES+=UGENE_VER_MINOR=$${UGENE_VER_MINOR}
- DEFINES+=UGENE_VER_PATCH=$${UGENE_VER_PATCH}
+@@ -14,6 +14,15 @@ DEFINES+=UGENE_VER_PATCH=$${UGENE_VER_PA
+ _UGENE_NGS = $$(UGENE_NGS)
+ contains(_UGENE_NGS, 1) : DEFINES += UGENE_NGS
  
 +CFLAGS += $(CFLAGS)
 +CXXFLAGS += $(CXXFLAGS)
@@ -21,10 +21,3 @@ Forwarded: no
  #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
-@@ -133,4 +142,4 @@
- defineTest( without_non_free ) {
-     contains( UGENE_WITHOUT_NON_FREE, 1 ) : return (true)
-     return (false)
--}
-\ No newline at end of file
-+}
diff --git a/debian/patches/use_debian_sqlite.patch b/debian/patches/use_debian_sqlite.patch
index 789c25b..a3cfe18 100644
--- a/debian/patches/use_debian_sqlite.patch
+++ b/debian/patches/use_debian_sqlite.patch
@@ -6,9 +6,9 @@ Forwarded: no
 Last-Updated: 2013-11-30
 --- a/ugene.pro
 +++ b/ugene.pro
-@@ -8,7 +8,6 @@ use_bundled_zlib() {
- 
+@@ -11,7 +11,6 @@ use_bundled_zlib() {
  SUBDIRS += \
+           src/libs_3rdparty/breakpad \
            src/libs_3rdparty/qscore \
 -          src/libs_3rdparty/sqlite3 \
            src/libs_3rdparty/gtest \
@@ -16,8 +16,8 @@ Last-Updated: 2013-11-30
            src/corelibs/U2Core \
 --- a/src/corelibs/U2Core/U2Core.pri
 +++ b/src/corelibs/U2Core/U2Core.pri
-@@ -15,9 +15,7 @@ use_bundled_zlib() {
- }
+@@ -19,9 +19,7 @@ use_bundled_zlib() {
+ unix: QMAKE_CXXFLAGS += -Wno-char-subscripts
  
  LIBS += -L../../_release
 -LIBS += -lugenedb
@@ -27,7 +27,7 @@ Last-Updated: 2013-11-30
  
  !debug_and_release|build_pass {
  
-@@ -29,8 +27,6 @@ INCLUDEPATH += ../../libs_3rdparty/sqlit
+@@ -33,8 +31,6 @@ INCLUDEPATH += ../../libs_3rdparty/sqlit
              LIBS += -lzlibd
              LIBS -= -lzlib
          }
@@ -45,9 +45,9 @@ Last-Updated: 2013-11-30
 -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
+ win32-msvc2013 {
+     DEFINES += NOMINMAX _XKEYCHECK_H
+@@ -36,8 +36,8 @@ INCLUDEPATH += ../../libs_3rdparty/sqlit
  
      CONFIG(debug, debug|release) {
          DESTDIR=../../_debug
@@ -56,8 +56,8 @@ Last-Updated: 2013-11-30
 +        LIBS -= -L../../_release -lU2Core -lU2Algorithm -lsamtools
 +        LIBS += -L../../_debug -lU2Cored -lU2Algorithmd -lsamtoolsd
  
-         unix:POST_TARGETDEPS -= ../../_release/libsamtools.a
-         unix:POST_TARGETDEPS += ../../_debug/libsamtoolsd.a
+         win32-msvc2013 {
+             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() {
@@ -67,9 +67,9 @@ Last-Updated: 2013-11-30
 -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
+ win32-msvc2013 {
+     DEFINES += NOMINMAX _XKEYCHECK_H
+@@ -29,8 +29,8 @@ win32:DEFINES += _USE_MATH_DEFINES "inli
  !debug_and_release|build_pass {
  
      CONFIG(debug, debug|release) {
@@ -78,16 +78,16 @@ Last-Updated: 2013-11-30
 +        LIBS -= -lsamtools
 +        LIBS += -lsamtoolsd
  
-         unix:POST_TARGETDEPS -= ../../_release/libsamtools.a
-         unix:POST_TARGETDEPS += ../../_debug/libsamtoolsd.a
+         win32-msvc2013 {
+             LIBS -= -lzlib
 --- 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
+-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 {
  
@@ -95,32 +95,32 @@ Last-Updated: 2013-11-30
          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
+-        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) {
 --- a/src/ugeneui/ugeneui.pri
 +++ b/src/ugeneui/ugeneui.pri
-@@ -15,7 +15,7 @@ DEFINES+= QT_DLL QT_FATAL_ASSERT
+@@ -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
-+LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Remote -lU2Lang -lU2Private -lsqlite3
+-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 {
-@@ -27,8 +27,8 @@ macx: LIBS += /System/Library/Frameworks
+@@ -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
--        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
+-        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) {

-- 
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