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debian/control
View file @ 3f868ce3
......@@ -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 → 100644
View file @ 3f868ce3
--- 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
View file @ 3f868ce3
......@@ -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
View file @ 3f868ce3
use_debian_sqlite.patch
hardening.patch
debian_packaged_libs.patch
debian/patches/use_debian_sqlite.patch
View file @ 3f868ce3
......@@ -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
}