[med-svn] [Git][med-team/ugene][master] 2 commits: Adapt patches
Andreas Tille
gitlab at salsa.debian.org
Mon Jan 28 11:51:59 GMT 2019
Andreas Tille pushed to branch master at Debian Med / ugene
Commits:
f3b185da by Andreas Tille at 2019-01-27T15:34:36Z
Adapt patches
- - - - -
3f868ce3 by Andreas Tille at 2019-01-28T11:51:38Z
Use Debian packaged libs
- - - - -
5 changed files:
- debian/control
- + debian/patches/debian_packaged_libs.patch
- debian/patches/hardening.patch
- debian/patches/series
- debian/patches/use_debian_sqlite.patch
Changes:
=====================================
debian/control
=====================================
@@ -14,6 +14,7 @@ Build-Depends: qtbase5-dev,
qtscript5-dev,
qt5-qmake,
qtchooser,
+ qttools5-dev,
zlib1g-dev,
debhelper (>= 12~),
libxtst-dev,
=====================================
debian/patches/debian_packaged_libs.patch
=====================================
@@ -0,0 +1,170 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -35,8 +35,6 @@ set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS
+ # 3rd party libs
+ add_subdirectory(src/libs_3rdparty/breakpad)
+ add_subdirectory(src/libs_3rdparty/samtools)
+-add_subdirectory(src/libs_3rdparty/sqlite3)
+-add_subdirectory(src/libs_3rdparty/zlib)
+
+ # Core libs
+ add_subdirectory(src/corelibs/U2Core)
+--- a/src/libs_3rdparty/samtools/src/samtools/bam.h
++++ b/src/libs_3rdparty/samtools/src/samtools/bam.h
+@@ -61,7 +61,7 @@ typedef BGZF *bamFile;
+ #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
+ #else
+ #define BAM_TRUE_OFFSET
+-#include <3rdparty/zlib/zlib.h>
++#include <zlib.h>
+ typedef gzFile bamFile;
+ #define bam_open(fn, mode) gzopen(fn, mode)
+ #define bam_dopen(fd, mode) gzdopen(fd, mode)
+--- a/src/libs_3rdparty/samtools/src/samtools/bam_rmdup.c
++++ b/src/libs_3rdparty/samtools/src/samtools/bam_rmdup.c
+@@ -1,7 +1,7 @@
+ #include <stdlib.h>
+ #include <string.h>
+ #include <stdio.h>
+-#include <3rdparty/zlib/zlib.h>
++#include <zlib.h>
+ #include <unistd.h>
+ #include "sam.h"
+
+--- a/src/libs_3rdparty/samtools/src/samtools/bgzf.h
++++ b/src/libs_3rdparty/samtools/src/samtools/bgzf.h
+@@ -26,7 +26,7 @@
+
+ #include <stdint.h>
+ #include <stdio.h>
+-#include <3rdparty/zlib/zlib.h>
++#include <zlib.h>
+ #ifdef _USE_KNETFILE
+ #include "knetfile.h"
+ #endif
+--- a/src/libs_3rdparty/samtools/src/samtools/phase.c
++++ b/src/libs_3rdparty/samtools/src/samtools/phase.c
+@@ -3,7 +3,7 @@
+ #include <unistd.h>
+ #include <stdint.h>
+ #include <math.h>
+-#include <3rdparty/zlib/zlib.h>
++#include <zlib.h>
+ #include "bam.h"
+ #include "errmod.h"
+
+--- a/src/libs_3rdparty/samtools/src/samtools/razf.h
++++ b/src/libs_3rdparty/samtools/src/samtools/razf.h
+@@ -35,7 +35,7 @@
+
+ #include <stdint.h>
+ #include <stdio.h>
+-#include <3rdparty/zlib/zlib.h>
++#include <zlib.h>
+
+ #ifdef _USE_KNETFILE
+ #include "knetfile.h"
+--- a/src/corelibs/U2Core/src/io/ZlibAdapter.cpp
++++ b/src/corelibs/U2Core/src/io/ZlibAdapter.cpp
+@@ -27,7 +27,7 @@
+
+ #include "ZlibAdapter.h"
+
+-#include <3rdparty/zlib/zlib.h>
++#include <zlib.h>
+
+ #include <assert.h>
+
+--- a/src/libs_3rdparty/samtools/src/samtools/bam_import.c
++++ b/src/libs_3rdparty/samtools/src/samtools/bam_import.c
+@@ -1,4 +1,4 @@
+-#include <3rdparty/zlib/zlib.h>
++#include <zlib.h>
+ #include <stdio.h>
+ #include <ctype.h>
+ #include <string.h>
+--- a/src/libs_3rdparty/samtools/src/samtools/bcftools/bcf.h
++++ b/src/libs_3rdparty/samtools/src/samtools/bcftools/bcf.h
+@@ -31,7 +31,7 @@
+ #define BCF_VERSION "0.1.17-dev (r973:277)"
+
+ #include <stdint.h>
+-#include <3rdparty/zlib/zlib.h>
++#include <zlib.h>
+
+ #ifndef BCF_LITE
+ #include "bgzf.h"
+--- a/src/libs_3rdparty/samtools/src/samtools/bcftools/call1.c
++++ b/src/libs_3rdparty/samtools/src/samtools/bcftools/call1.c
+@@ -1,7 +1,7 @@
+ #include <unistd.h>
+ #include <stdlib.h>
+ #include <math.h>
+-#include <3rdparty/zlib/zlib.h>
++#include <zlib.h>
+ #include <errno.h>
+ #include "bcf.h"
+ #include "prob1.h"
+--- a/src/libs_3rdparty/samtools/src/samtools/bcftools/vcf.c
++++ b/src/libs_3rdparty/samtools/src/samtools/bcftools/vcf.c
+@@ -1,4 +1,4 @@
+-#include <3rdparty/zlib/zlib.h>
++#include <zlib.h>
+ #include <stdlib.h>
+ #include <stdio.h>
+ #include <string.h>
+--- a/src/libs_3rdparty/samtools/src/samtools/bedidx.c
++++ b/src/libs_3rdparty/samtools/src/samtools/bedidx.c
+@@ -2,7 +2,7 @@
+ #include <stdint.h>
+ #include <string.h>
+ #include <stdio.h>
+-#include <3rdparty/zlib/zlib.h>
++#include <zlib.h>
+
+ #ifdef _WIN32
+ #define drand48() ((double)rand() / RAND_MAX)
+--- a/src/plugins/biostruct3d_view/src/gl2ps/gl2ps.cpp
++++ b/src/plugins/biostruct3d_view/src/gl2ps/gl2ps.cpp
+@@ -72,7 +72,7 @@
+ #endif
+
+ #if defined(GL2PS_HAVE_ZLIB)
+-#include <3rdparty/zlib/zlib.h>
++#include <zlib.h>
+ #endif
+
+ #if defined(GL2PS_HAVE_LIBPNG)
+--- a/src/plugins/dbi_bam/src/BAMFormat.cpp
++++ b/src/plugins/dbi_bam/src/BAMFormat.cpp
+@@ -19,7 +19,7 @@
+ * MA 02110-1301, USA.
+ */
+
+-#include <3rdparty/zlib/zlib.h>
++#include <zlib.h>
+
+ #include <U2Core/DocumentModel.h>
+ #include <U2Core/L10n.h>
+--- a/src/plugins/dbi_bam/src/BgzfReader.h
++++ b/src/plugins/dbi_bam/src/BgzfReader.h
+@@ -22,7 +22,7 @@
+ #ifndef _U2_BAM_BGZF_READER_H_
+ #define _U2_BAM_BGZF_READER_H_
+
+-#include <3rdparty/zlib/zlib.h>
++#include <zlib.h>
+
+ #include <U2Core/IOAdapter.h>
+ #include "VirtualOffset.h"
+--- a/src/plugins/dbi_bam/src/BgzfWriter.h
++++ b/src/plugins/dbi_bam/src/BgzfWriter.h
+@@ -22,7 +22,7 @@
+ #ifndef _U2_BAM_BGZF_WRITER_H_
+ #define _U2_BAM_BGZF_WRITER_H_
+
+-#include <3rdparty/zlib/zlib.h>
++#include <zlib.h>
+
+ #include <U2Core/IOAdapter.h>
+ #include "VirtualOffset.h"
=====================================
debian/patches/hardening.patch
=====================================
@@ -22,8 +22,8 @@ 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
-@@ -29,6 +34,10 @@ macx {
- QMAKE_CXXFLAGS += -Wall -Wno-ignored-attributes
+@@ -34,6 +39,10 @@ linux-g++ {
+ QMAKE_CXXFLAGS += -Wno-expansion-to-defined
}
+QMAKE_CXXFLAGS += $$(CXXFLAGS)
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
use_debian_sqlite.patch
hardening.patch
+debian_packaged_libs.patch
=====================================
debian/patches/use_debian_sqlite.patch
=====================================
@@ -127,21 +127,21 @@ Last-Updated: 2013-11-30
DEFINES+= QT_DLL QT_FATAL_ASSERT
INCLUDEPATH += src _tmp ../include ../corelibs/U2Private/src
--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
+-LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Lang -lU2Private -lugenedb -lbreakpad -lQSpec
++LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Lang -lU2Private -lsqlite3 -lbreakpad -lQSpec
if(exclude_list_enabled()|!exists( ../libs_3rdparty/QSpec/QSpec.pro )) {
- LIBS -= -lhumimit
+ LIBS -= -lQSpec
}
@@ -26,8 +26,8 @@ if(exclude_list_enabled()|!exists( ../li
DESTDIR=../_debug
MOC_DIR=_tmp/moc/debug
OBJECTS_DIR=_tmp/obj/debug
-- 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
+- LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Lang -lU2Private -lugenedb -lbreakpad -lQSpec
+- LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Testd -lU2Langd -lU2Privated -lugenedbd -lbreakpadd -lQSpecd
++ LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Lang -lU2Private -lbreakpad -lQSpec
++ LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Testd -lU2Langd -lU2Privated -lbreakpadd -lQSpecd
if(exclude_list_enabled()|!exists( ../libs_3rdparty/QSpec/QSpec.pro )) {
- LIBS -= -lhumimitd
+ LIBS -= -lQSpecd
}
--- a/src/ugeneui/ugeneui.pri
+++ b/src/ugeneui/ugeneui.pri
@@ -149,19 +149,19 @@ Last-Updated: 2013-11-30
INCLUDEPATH += src _tmp ../include ../corelibs/U2Private/src ../libs_3rdparty/QSpec/src
macx : INCLUDEPATH += /System/Library/Frameworks/Security.framework/Headers
--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
+-LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Lang -lU2Private -lugenedb -lbreakpad -lQSpec
++LIBS += -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Lang -lU2Private -lsqlite3 -lbreakpad -lQSpec
macx: LIBS += /System/Library/Frameworks/Security.framework/Security
if(exclude_list_enabled()|!exists( ../libs_3rdparty/QSpec/QSpec.pro )) {
- LIBS -= -lhumimit
+ LIBS -= -lQSpec
@@ -31,8 +31,8 @@ if(exclude_list_enabled()|!exists( ../li
DESTDIR=../_debug
MOC_DIR=_tmp/moc/debug
OBJECTS_DIR=_tmp/obj/debug
-- 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
+- LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Lang -lU2Private -lugenedb -lbreakpad -lQSpec
+- LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Viewd -lU2Testd -lU2Langd -lU2Privated -lugenedbd -lbreakpadd -lQSpecd
++ LIBS -= -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2View -lU2Test -lU2Lang -lU2Private -lbreakpad -lQSpec
++ LIBS += -L../_debug -lU2Cored -lU2Algorithmd -lU2Formatsd -lU2Guid -lU2Viewd -lU2Testd -lU2Langd -lU2Privated -lbreakpadd -lQSpecd
if(exclude_list_enabled()|!exists( ../libs_3rdparty/QSpec/QSpec.pro )) {
- LIBS -= -lhumimitd
+ LIBS -= -lQSpecd
}
View it on GitLab: https://salsa.debian.org/med-team/ugene/compare/b567a5b51bd4f54be8098f53b16122b4400ef0cb...3f868ce36dfc0f67461765453cd04526e218a956
--
View it on GitLab: https://salsa.debian.org/med-team/ugene/compare/b567a5b51bd4f54be8098f53b16122b4400ef0cb...3f868ce36dfc0f67461765453cd04526e218a956
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