[med-svn] [hyphy] 04/05: New upstream with adapted patches
Andreas Tille
tille at debian.org
Thu Aug 25 09:30:11 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository hyphy.
commit 5c0441bd3ca1ada625678a072323b26ec54f887e
Author: Andreas Tille <tille at debian.org>
Date: Tue Aug 16 09:37:08 2016 +0200
New upstream with adapted patches
---
debian/changelog | 3 +-
debian/patches/arch_all_files_to_usr_share.patch | 16 -----
debian/patches/drop_profiling_option.patch | 4 +-
debian/patches/gcc-6.1_false_is_not_nil.patch | 50 --------------
debian/patches/gcc-6.1_narrowing_conversion.patch | 34 ----------
debian/patches/gcc-6.patch | 22 ------
debian/patches/msse_option_only_if_available.patch | 2 +-
debian/patches/python3.5.patch | 78 ----------------------
debian/patches/remove_arch_specific_flags.patch | 4 +-
debian/patches/series | 6 --
debian/patches/setup_fix_clean_target.patch | 18 -----
debian/patches/spelling.patch | 11 ---
debian/patches/use_debian_sqlite.patch | 56 +++-------------
13 files changed, 15 insertions(+), 289 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index c465dba..c8259f8 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,6 @@
-hyphy (2.2.6+dfsg-6) UNRELEASED; urgency=medium
+hyphy (2.2.7+dfsg-1) UNRELEASED; urgency=medium
+ * New upstream version
* Use xz compression in d/watch
-- Andreas Tille <tille at debian.org> Tue, 16 Aug 2016 09:22:40 +0200
diff --git a/debian/patches/arch_all_files_to_usr_share.patch b/debian/patches/arch_all_files_to_usr_share.patch
deleted file mode 100644
index c840d6f..0000000
--- a/debian/patches/arch_all_files_to_usr_share.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 29 Jun 2015 11:13:57 +0200
-Description: Move arch all files to /usr/share
- Deactivated since it does not work this way
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -277,7 +277,7 @@ target_link_libraries(hyphy_mp ${DEFAULT
-
- install(
- TARGETS hyphy_mp
-- LIBRARY DESTINATION lib
-+ LIBRARY DESTINATION share
- OPTIONAL
- )
-
diff --git a/debian/patches/drop_profiling_option.patch b/debian/patches/drop_profiling_option.patch
index 4e6ed65..df88584 100644
--- a/debian/patches/drop_profiling_option.patch
+++ b/debian/patches/drop_profiling_option.patch
@@ -5,7 +5,7 @@ Bug-Debian: http://bugs.debian.org/793345
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -432,8 +432,8 @@ add_custom_target(DEBUG DEPENDS HYPHYDEB
+@@ -441,8 +441,8 @@ add_custom_target(DEBUG DEPENDS HYPHYDEB
set_target_properties(
HYPHYDEBUG
PROPERTIES
@@ -16,7 +16,7 @@ Bug-Debian: http://bugs.debian.org/793345
)
-@@ -457,8 +457,8 @@ set_property(
+@@ -466,8 +466,8 @@ set_property(
set_target_properties(
HYPHYGTEST
PROPERTIES
diff --git a/debian/patches/gcc-6.1_false_is_not_nil.patch b/debian/patches/gcc-6.1_false_is_not_nil.patch
deleted file mode 100644
index 6a62861..0000000
--- a/debian/patches/gcc-6.1_false_is_not_nil.patch
+++ /dev/null
@@ -1,50 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 14 Aug 2016 21:42:54 +0200
-Bug-Debian: https://bugs.debian.org/811866
-Description: Previous versions of the compiler allow conversion from false to
- a null pointer, so this used to work, though maybe with a warning. Replacing
- false with nil fixed this.
- Thanks for the hint to Jason Crain <jason at inspiresomeone.us>
-
---- a/src/gui/HYChartWindow.cpp
-+++ b/src/gui/HYChartWindow.cpp
-@@ -3007,7 +3007,7 @@ bool ReadDataFromFile (_String fileNa
- for (long k=0; k<columns; k++) {
- _String * thisString = (_String*)readStrings (lastRead*columns+k);
- if ((thisString->sLength)&&(thisString->FirstNonSpaceIndex (0,-1)>=0)) {
-- _Formula f (*thisString,nil,false);
-+ _Formula f (*thisString,nil,nil);
- v.SetValue (k);
- if (!f.IsEmpty()) {
- data.MStore (&h,&v,f);
-@@ -4527,7 +4527,7 @@ void _HYDistributionChartWindow::AddV
-
- aPrompt = newExpression;
-
-- _Formula f (newExpression, nil,false);
-+ _Formula f (newExpression, nil, nil);
-
- if (f.IsEmpty()) {
- newExpression = _String("Failed to parse the expression :") & aPrompt;
---- a/src/gui/gtk/WindowClasses/HYPlatformModelWindow.cpp
-+++ b/src/gui/gtk/WindowClasses/HYPlatformModelWindow.cpp
-@@ -173,7 +173,7 @@ bool _HYModelWindow::_CheckClipboard (vo
- {
- _String cText ((char*)scrapHandle);
- skipWarningMessages = true;
-- _Formula f (cText,nil,false);
-+ _Formula f (cText,nil,nil);
- skipWarningMessages = false;
- if (f.GetList().lLength)
- {
---- a/src/gui/HYModelWindow.cpp
-+++ b/src/gui/HYModelWindow.cpp
-@@ -857,7 +857,7 @@ bool _HYModelWindow::ProcessEvent (_H
- _HYButtonBar* bb3 = (_HYButtonBar*)GetCellObject (MODEL_BUTTON_ROW,6);
-
- _String cText (tl->GetText());
-- _Formula f (cText,nil,false);
-+ _Formula f (cText,nil,nil);
- if (f.GetList().lLength) {
- clipboardString = cText;
- SyncEditBox ();
diff --git a/debian/patches/gcc-6.1_narrowing_conversion.patch b/debian/patches/gcc-6.1_narrowing_conversion.patch
deleted file mode 100644
index bcc6240..0000000
--- a/debian/patches/gcc-6.1_narrowing_conversion.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 14 Aug 2016 21:42:54 +0200
-Bug-Debian: https://bugs.debian.org/811866
-Description: Fix error: narrowing conversion from 'double' to 'unsigned char'
-
---- a/src/gui/HYChartWindow.cpp
-+++ b/src/gui/HYChartWindow.cpp
-@@ -100,16 +100,16 @@ extern _String
- windowTypeDistribTable;
-
- _HYColor chartColors [HY_CHART_COLOR_COUNT] = {
-- {255*.94, 255*.12, 255*.11 },//(Red)
-- {255*.41, 255*.46, 255*.91 },//(Evening Blue)
-- {255 , 255*.91, 255*.34 },//(Banana)
-- {255*.18, 255*.55, 255*.13 },//(Clover)
-- {255*.55, 255*.38, 255*.21 },//(Dirt)
-- {255*.42, 255*.09, 255*.69 },//(Royal Violet)
-- {255*.09, 255*.29, 255*.51 },//(Sea Blue)
-- {255 , 255*.57, 255*.09 },//(Orange)
-- {255*.67, 255*.67, 255*.67 },//(Concrete)
-- {255*.85, 255*.27, 255*.42 } //(Carnation)
-+ {255*94/100, 255*12/100, 255*11/100 },//(Red)
-+ {255*41/100, 255*46/100, 255*91/100 },//(Evening Blue)
-+ {255 , 255*91/100, 255*34/100 },//(Banana)
-+ {255*18/100, 255*55/100, 255*13/100 },//(Clover)
-+ {255*55/100, 255*38/100, 255*21/100 },//(Dirt)
-+ {255*42/100, 255*9/100, 255*69/100 },//(Royal Violet)
-+ {255*9/100, 255*29/100, 255*51/100 },//(Sea Blue)
-+ {255 , 255*57/100, 255*9/100 },//(Orange)
-+ {255*67/100, 255*67/100, 255*67/100 },//(Concrete)
-+ {255*85/100, 255*27/100, 255*42/100 } //(Carnation)
- };
-
- extern _Parameter pi_const;
diff --git a/debian/patches/gcc-6.patch b/debian/patches/gcc-6.patch
deleted file mode 100644
index 174a25b..0000000
--- a/debian/patches/gcc-6.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-Author: Steven Weaver <sweaver at ucsd.edu>
-Last-Update: Tue Feb 23 13:00:41 2016 -0500
-Origin: Upstream commit 778573019bbf0eaa9173cf04bc3e3baf1b18a7b1
-Bug-Debian: https://bugs.debian.org/811866
-Description: Build with gcc-6
- fixes #374: adding -fno-strict-aliasing and -fpermissive for gcc-6 compatibility
-
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -122,6 +122,11 @@ if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMP
- if(${GCC46})
- set(DEFAULT_WARNING_FLAGS "-Wno-int-to-pointer-cast -Wno-conversion-null")
- endif(${GCC46})
-+
-+ if(${GCC_VERSION} VERSION_GREATER 6.0 OR ${GCC_VERSION} VERSION_EQUAL 6.0)
-+ set(DEFAULT_COMPILE_FLAGS "-fno-strict-aliasing -fpermissive")
-+ endif(${GCC_VERSION} VERSION_GREATER 6.0 OR ${GCC_VERSION} VERSION_EQUAL 6.0)
-+
-
- PCL_CHECK_FOR_AVX()
- if(${HAVE_AVX_EXTENSIONS})
diff --git a/debian/patches/msse_option_only_if_available.patch b/debian/patches/msse_option_only_if_available.patch
index 1f70cd8..ff41f52 100644
--- a/debian/patches/msse_option_only_if_available.patch
+++ b/debian/patches/msse_option_only_if_available.patch
@@ -5,7 +5,7 @@ Last-Update: Thu, 23 Jul 2015 13:12:54 +0200
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -454,13 +454,23 @@ set_property(
+@@ -463,13 +463,23 @@ set_property(
TARGET HYPHYGTEST
APPEND PROPERTY COMPILE_DEFINITIONS __UNITTEST__
)
diff --git a/debian/patches/python3.5.patch b/debian/patches/python3.5.patch
deleted file mode 100644
index 4fc77fd..0000000
--- a/debian/patches/python3.5.patch
+++ /dev/null
@@ -1,78 +0,0 @@
-Author: Matthias Klose <doko at debian.org>
-Last-Update: Sun, 25 Oct 2015 22:24:40 +0200
-Bug-Debian: http://bugs.debian.org/802999
-Description: make generated swig file ready for Python 3.5
- Remark: How to autogenerate this file properly?
-
---- a/src/lib/SWIGWrappers/THyPhy_py3.cpp
-+++ b/src/lib/SWIGWrappers/THyPhy_py3.cpp
-@@ -5632,6 +5632,13 @@ static PyHeapTypeObject SwigPyBuiltin___
- (int) 0, /* tp_version_tag */
- #endif
- },
-+#if PY_VERSION_HEX >= 0x03050000
-+ {
-+ (unaryfunc) 0, /* am_await */
-+ (unaryfunc) 0, /* am_aiter */
-+ (unaryfunc) 0, /* am_anext */
-+ },
-+#endif
- {
- (binaryfunc) 0, /* nb_add */
- (binaryfunc) 0, /* nb_subtract */
-@@ -5830,6 +5837,13 @@ static PyHeapTypeObject SwigPyBuiltin___
- (int) 0, /* tp_version_tag */
- #endif
- },
-+#if PY_VERSION_HEX >= 0x03050000
-+ {
-+ (unaryfunc) 0, /* am_await */
-+ (unaryfunc) 0, /* am_aiter */
-+ (unaryfunc) 0, /* am_anext */
-+ },
-+#endif
- {
- (binaryfunc) 0, /* nb_add */
- (binaryfunc) 0, /* nb_subtract */
-@@ -6025,6 +6039,13 @@ static PyHeapTypeObject SwigPyBuiltin___
- (int) 0, /* tp_version_tag */
- #endif
- },
-+#if PY_VERSION_HEX >= 0x03050000
-+ {
-+ (unaryfunc) 0, /* am_await */
-+ (unaryfunc) 0, /* am_aiter */
-+ (unaryfunc) 0, /* am_anext */
-+ },
-+#endif
- {
- (binaryfunc) 0, /* nb_add */
- (binaryfunc) 0, /* nb_subtract */
-@@ -6227,6 +6248,13 @@ static PyHeapTypeObject SwigPyBuiltin___
- (int) 0, /* tp_version_tag */
- #endif
- },
-+#if PY_VERSION_HEX >= 0x03050000
-+ {
-+ (unaryfunc) 0, /* am_await */
-+ (unaryfunc) 0, /* am_aiter */
-+ (unaryfunc) 0, /* am_anext */
-+ },
-+#endif
- {
- (binaryfunc) 0, /* nb_add */
- (binaryfunc) 0, /* nb_subtract */
-@@ -6433,6 +6461,13 @@ static PyHeapTypeObject SwigPyBuiltin___
- (int) 0, /* tp_version_tag */
- #endif
- },
-+#if PY_VERSION_HEX >= 0x03050000
-+ {
-+ (unaryfunc) 0, /* am_await */
-+ (unaryfunc) 0, /* am_aiter */
-+ (unaryfunc) 0, /* am_anext */
-+ },
-+#endif
- {
- (binaryfunc) 0, /* nb_add */
- (binaryfunc) 0, /* nb_subtract */
diff --git a/debian/patches/remove_arch_specific_flags.patch b/debian/patches/remove_arch_specific_flags.patch
index 1bd27f3..3102069 100644
--- a/debian/patches/remove_arch_specific_flags.patch
+++ b/debian/patches/remove_arch_specific_flags.patch
@@ -14,8 +14,8 @@ Description: remove optimizations for the local machine
endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
check_cxx_source_runs("
-@@ -125,7 +125,7 @@ if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMP
-
+@@ -134,7 +134,7 @@ if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMP
+
PCL_CHECK_FOR_AVX()
if(${HAVE_AVX_EXTENSIONS})
- set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -march=corei7-avx -mtune=corei7-avx")
diff --git a/debian/patches/series b/debian/patches/series
index 8509f78..8b772cc 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,12 +1,6 @@
-# arch_all_files_to_usr_share.patch
use_debian_sqlite.patch
spelling.patch
drop_profiling_option.patch
remove_unneeded_test.patch
msse_option_only_if_available.patch
-setup_fix_clean_target.patch
-python3.5.patch
remove_arch_specific_flags.patch
-gcc-6.patch
-gcc-6.1_narrowing_conversion.patch
-gcc-6.1_false_is_not_nil.patch
diff --git a/debian/patches/setup_fix_clean_target.patch b/debian/patches/setup_fix_clean_target.patch
deleted file mode 100644
index 56399d5..0000000
--- a/debian/patches/setup_fix_clean_target.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 22 Sep 2015 17:00:57 +0200
-Forwarde-Upstream: yes
-Description: Brute force hack to get rid of a mac-ism
-
---- a/src/lib/setup.py
-+++ b/src/lib/setup.py
-@@ -51,8 +51,8 @@ includePaths += [linkPath, contribPath]
- define_macros = [('__HYPHY_64__', None)] if '64' in architecture()[0] else []
-
- # openmp on Mac OS X Lion is broken
--major, minor, patch = mac_ver()[0].split('.')
--openmp = ['-fopenmp'] if int(major) < 10 or (int(major) == 10 and int(minor) < 7) else []
-+#major, minor, patch = mac_ver()[0].split('.')
-+openmp = ['-fopenmp'] #if int(major) < 10 or (int(major) == 10 and int(minor) < 7) else []
-
- setup(
- name = 'HyPhy',
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
index ce8d4ba..428e1be 100644
--- a/debian/patches/spelling.patch
+++ b/debian/patches/spelling.patch
@@ -64,14 +64,3 @@ Description: Fix two spelling issues
and a string (key "CONSENSUS");
The first cell contains the number of splits in *this
The second cell contains the number of splits in the argument that are present in *this
---- a/src/lib/Link/THyPhy.h
-+++ b/src/lib/Link/THyPhy.h
-@@ -58,7 +58,7 @@ SOFTWARE OR THE USE OR OTHER DEALINGS IN
-
- typedef bool _ProgressCancelHandler (char*,int,double);
- /* if the function returns false, then HyPhy will attempt to terminate the task and return
-- HyPhy will also populate three agruments
-+ HyPhy will also populate three arguments
- -- char * : pointer to an (internally handled by HyPhy) string
- that describes what task HyPhy is working on at the moment
- -- int : integer progress value (as in % done)
diff --git a/debian/patches/use_debian_sqlite.patch b/debian/patches/use_debian_sqlite.patch
index aaf48fd..d51a9ec 100644
--- a/debian/patches/use_debian_sqlite.patch
+++ b/debian/patches/use_debian_sqlite.patch
@@ -6,7 +6,7 @@ Description: Use Debian packaged sqlite3
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -179,6 +179,36 @@ if(${CURL_FOUND})
+@@ -188,6 +188,36 @@ if(${CURL_FOUND})
endif(${CURL_FOUND})
#-------------------------------------------------------------------------------
@@ -43,9 +43,9 @@ Description: Use Debian packaged sqlite3
# gtest dependency
#-------------------------------------------------------------------------------
add_subdirectory(contrib/gtest-1.7.0)
-@@ -211,13 +241,12 @@ file(GLOB SRC_NEW src/new/*.cpp)
+@@ -220,13 +250,12 @@ file(GLOB SRC_NEW src/new/*.cpp)
- set(SRC_LINK src/lib/Link/THyPhy.cpp)
+ set(SRC_LINK src/lib/link/THyPhy.cpp)
set(SRC_PREFS src/gui/preferences.cpp)
-set(SRC_SQLITE3 contrib/SQLite-3.8.2/sqlite3.c)
set(SRC_UNIXMAIN src/mains/unix.cpp)
@@ -58,7 +58,7 @@ Description: Use Debian packaged sqlite3
#-------------------------------------------------------------------------------
-@@ -229,11 +258,6 @@ set_property(
+@@ -238,11 +267,6 @@ set_property(
)
set_property(
@@ -70,7 +70,7 @@ Description: Use Debian packaged sqlite3
SOURCE src/core/calcnode2.cpp
PROPERTY COMPILE_FLAGS "-fstrict-aliasing -funroll-loops"
)
-@@ -250,7 +274,6 @@ endif(CMAKE_SIZEOF_VOID_P EQUAL 8)
+@@ -259,7 +283,6 @@ endif(CMAKE_SIZEOF_VOID_P EQUAL 8)
include_directories(
src/core/include
src/lib/Link src/new/include
@@ -78,7 +78,7 @@ Description: Use Debian packaged sqlite3
src/gui/include
src/gui/include/Components
src/gui/include/WindowClasses
-@@ -438,11 +461,11 @@ set_target_properties(
+@@ -447,11 +470,11 @@ set_target_properties(
LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS} -msse3 -g -fprofile-arcs -ftest-coverage -pg"
)
@@ -91,7 +91,7 @@ Description: Use Debian packaged sqlite3
find_package(GTK2 2.6)
if((${GTK2_FOUND}))
-@@ -454,6 +477,7 @@ if((${GTK2_FOUND}))
+@@ -463,6 +486,7 @@ if((${GTK2_FOUND}))
)
include_directories(
${GTK2_INCLUDE_DIRS}
@@ -99,7 +99,7 @@ Description: Use Debian packaged sqlite3
src/gui/gtk/include
src/gui/gtk/include/Components
/Developer/Headers/FlatCarbon
-@@ -544,7 +568,7 @@ if(APPLE AND NOT ${MACOSX_GT_LION})
+@@ -553,7 +577,7 @@ if(APPLE AND NOT ${MACOSX_GT_LION})
add_executable(HyPhy
MACOSX_BUNDLE
EXCLUDE_FROM_ALL
@@ -108,43 +108,3 @@ Description: Use Debian packaged sqlite3
${RES_MACGUI}
)
---- a/src/lib/setup.py
-+++ b/src/lib/setup.py
-@@ -21,7 +21,7 @@ hyphyPath, srcDir = path.split(srcPath)
- # resFiles = [(f, path.join(*(['..'] * 5 + f.split('/')))) for f in fh.read().split('\n') if f != '']
-
- contribPath = path.join(hyphyPath, 'contrib')
--sqlitePath = path.join(contribPath, 'SQLite-3.8.2')
-+#sqlitePath = path.join(contribPath, 'SQLite-3.8.2')
-
- linkPath = path.join(scriptPath, 'Link')
- coreSrcPath = path.join(srcPath, 'core')
-@@ -36,14 +36,16 @@ else:
-
- coreSrcFiles = glob(path.join(coreSrcPath, '*.cpp'))
- newSrcFiles = glob(path.join(newSrcPath, '*.cpp'))
--sqliteFiles = glob(path.join(sqlitePath, '*.c'))
-+#sqliteFiles = glob(path.join(sqlitePath, '*.c'))
- linkFiles = glob(path.join(linkPath, '*.cpp')) # + glob(path.join(linkPath, '*.cxx'))
- utilFiles = glob(path.join(srcPath, 'utils', '*.cpp'))
-
--sourceFiles = coreSrcFiles + newSrcFiles + sqliteFiles + prefFile + linkFiles + swigFile + utilFiles
-+# sourceFiles = coreSrcFiles + newSrcFiles + sqliteFiles + prefFile + linkFiles + swigFile + utilFiles
-+sourceFiles = coreSrcFiles + newSrcFiles + prefFile + linkFiles + swigFile + utilFiles
-
- includePaths = [path.join(p, 'include') for p in [coreSrcPath, newSrcPath, guiSrcPath]]
--includePaths += [linkPath, contribPath, sqlitePath]
-+# includePaths += [linkPath, contribPath, sqlitePath]
-+includePaths += [linkPath, contribPath]
-
- # check for 64bit and define as such
- define_macros = [('__HYPHY_64__', None)] if '64' in architecture()[0] else []
-@@ -74,7 +76,7 @@ setup(
- ('__AFYP_REWRITE_BGM__', None),
- ('__HEADLESS__', None),
- ('_HYPHY_LIBDIRECTORY_', '"/usr/local/lib/hyphy"')] + define_macros,
-- libraries = ['pthread', 'ssl', 'crypto', 'curl'],
-+ libraries = ['pthread', 'ssl', 'crypto', 'curl', 'sqlite3'],
- extra_compile_args = [
- '-Wno-int-to-pointer-cast',
- # '-Wno-pointer-to-int-cast',
--
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