[med-svn] [iqtree] 03/08: Patches not needed for new upstream version
Andreas Tille
tille at debian.org
Thu Dec 17 16:19:04 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository iqtree.
commit 501bea5edeea9f50d0c822e2c83f82872eec5027
Author: Andreas Tille <tille at debian.org>
Date: Thu Dec 17 17:10:57 2015 +0100
Patches not needed for new upstream version
---
debian/patches/debian_packaged_sprng.patch | 55 ----------------
debian/patches/series | 2 -
debian/patches/use_debian_packaged_libs.patch | 82 ------------------------
debian/patches/work_around_missing_example.patch | 15 -----
4 files changed, 154 deletions(-)
diff --git a/debian/patches/debian_packaged_sprng.patch b/debian/patches/debian_packaged_sprng.patch
deleted file mode 100644
index ad93557..0000000
--- a/debian/patches/debian_packaged_sprng.patch
+++ /dev/null
@@ -1,55 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 31 Aug 2015 09:22:55 +0200
-Description: iqtree upstream changes sprng interface so for
- the moment we can not replace this library :-(
- ...
- /usr/bin/c++ -DIQ_TREE -D__SSE3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -I/tmp/buildd/iqtree-1.3.8+dfsg -I/tmp/buildd/iqtree-1.3.8+dfsg/obj-x86_64-linux-gnu -
- msse3 -o CMakeFiles/iqtree.dir/tools.cpp.o -c /tmp/buildd/iqtree-1.3.8+dfsg/tools.cpp
- /tmp/buildd/iqtree-1.3.8+dfsg/tools.cpp: In function 'int init_random(int)':
- /tmp/buildd/iqtree-1.3.8+dfsg/tools.cpp:3312:54: error: too few arguments to function 'int* init_rng(int, int, int, int, int)'
- randstream = init_sprng(0, 1, seed, SPRNG_DEFAULT); /*init stream*/
- ^
- In file included from /usr/include/sprng/sprng.h:12:0,
- from /tmp/buildd/iqtree-1.3.8+dfsg/tools.h:44,
- from /tmp/buildd/iqtree-1.3.8+dfsg/tools.cpp:28:
- /usr/include/sprng/interface.h:22:6: note: declared here
- int *init_rng ANSI_ARGS((int rng_type, int gennum, int total_gen, int seed,
- ^
- CMakeFiles/iqtree.dir/build.make:1092: recipe for target 'CMakeFiles/iqtree.dir/tools.cpp.o' failed
- make[3]: *** [CMakeFiles/iqtree.dir/tools.cpp.o] Error 1
- make[3]: Leaving directory '/tmp/buildd/iqtree-1.3.8+dfsg/obj-x86_64-linux-gnu'
- CMakeFiles/Makefile2:105: recipe for target 'CMakeFiles/iqtree.dir/all' failed
- make[2]: *** [CMakeFiles/iqtree.dir/all] Error 2
-
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -326,7 +326,6 @@ add_subdirectory(pllrepo/src)
- add_subdirectory(ncl)
- add_subdirectory(lbfgsb)
- add_subdirectory(whtest)
--add_subdirectory(sprng)
- add_subdirectory(vectorclass)
- add_subdirectory(model)
-
-@@ -400,7 +399,7 @@ upperbounds.cpp
- )
-
- if (NOT IQTREE_FLAGS MATCHES "avx" AND NOT IQTREE_FLAGS MATCHES "fma")
-- set_target_properties(iqtree pll ncl lbfgsb whtest sprng vectorclass model PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
-+ set_target_properties(iqtree pll ncl lbfgsb whtest vectorclass model PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
- if (NOT BINARY32 AND NOT IQTREE_FLAGS MATCHES "novx")
- set_target_properties(avxkernel pllavx PROPERTIES COMPILE_FLAGS "${AVX_FLAGS}")
- endif()
-@@ -434,9 +433,9 @@ if (IQTREE_FLAGS MATCHES "omp")
- endif()
-
- if (BINARY32 OR IQTREE_FLAGS MATCHES "novx")
-- target_link_libraries(iqtree pll ncl lbfgsb whtest sprng vectorclass model ${PLATFORM_LIB} ${THREAD_LIB})
-+ target_link_libraries(iqtree pll ncl lbfgsb whtest vectorclass model ${PLATFORM_LIB} ${THREAD_LIB})
- else()
-- target_link_libraries(iqtree pll pllavx ncl lbfgsb whtest sprng vectorclass model avxkernel ${PLATFORM_LIB} ${THREAD_LIB})
-+ target_link_libraries(iqtree pll pllavx ncl lbfgsb whtest vectorclass model avxkernel ${PLATFORM_LIB} ${THREAD_LIB})
- endif()
-
- ##################################################################
diff --git a/debian/patches/series b/debian/patches/series
deleted file mode 100644
index 2f0121e..0000000
--- a/debian/patches/series
+++ /dev/null
@@ -1,2 +0,0 @@
-work_around_missing_example.patch
-use_debian_packaged_libs.patch
diff --git a/debian/patches/use_debian_packaged_libs.patch b/debian/patches/use_debian_packaged_libs.patch
deleted file mode 100644
index 108f027..0000000
--- a/debian/patches/use_debian_packaged_libs.patch
+++ /dev/null
@@ -1,82 +0,0 @@
-Author: Andreas Tille <tille at debian.org>,
- Gianfranco Costamagna <costamagnagianfranco at yahoo.it>
-Last-Update: Mon, 31 Aug 2015 09:22:55 +0200
-Description: Use Debian packaged zlib and libeigen
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -317,7 +317,6 @@ configure_file (
- # add the binary tree to the search path for include files
- # so that we will find iqtree_config.h
- include_directories("${PROJECT_BINARY_DIR}")
--include_directories("${PROJECT_BINARY_DIR}/zlib-1.2.7")
-
-
- ##################################################################
-@@ -328,8 +327,11 @@ add_subdirectory(ncl)
- add_subdirectory(lbfgsb)
- add_subdirectory(whtest)
- add_subdirectory(sprng)
--add_subdirectory(zlib-1.2.7)
- add_subdirectory(vectorclass)
-+find_package(Eigen3)
-+if(EIGEN3_FOUND)
-+ include_directories(${EIGEN3_INCLUDE_DIR})
-+endif(EIGEN3_FOUND)
- add_subdirectory(model)
-
- ##################################################################
-@@ -401,8 +403,18 @@ checkpoint.cpp
- upperbounds.cpp
- )
-
-+find_package(ZLIB)
-+if(ZLIB_FOUND)
-+ include_directories(${ZLIB_INCLUDE_DIRS})
-+ target_link_libraries(iqtree ${ZLIB_LIBRARIES})
-+else(ZLIB_FOUND)
-+ include_directories("${PROJECT_BINARY_DIR}/zlib-1.2.7")
-+ add_subdirectory(zlib-1.2.7)
-+ target_link_libraries(iqtree zlibstatic)
-+endif(ZLIB_FOUND)
-+
- if (NOT IQTREE_FLAGS MATCHES "avx" AND NOT IQTREE_FLAGS MATCHES "fma")
-- set_target_properties(iqtree pll ncl lbfgsb whtest zlibstatic sprng vectorclass model PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
-+ set_target_properties(iqtree pll ncl lbfgsb whtest sprng vectorclass model PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
- if (NOT BINARY32 AND NOT IQTREE_FLAGS MATCHES "novx")
- set_target_properties(avxkernel pllavx PROPERTIES COMPILE_FLAGS "${AVX_FLAGS}")
- endif()
-@@ -436,9 +448,9 @@ if (IQTREE_FLAGS MATCHES "omp")
- endif()
-
- if (BINARY32 OR IQTREE_FLAGS MATCHES "novx")
-- target_link_libraries(iqtree pll ncl lbfgsb whtest zlibstatic sprng vectorclass model ${PLATFORM_LIB} ${THREAD_LIB})
-+ target_link_libraries(iqtree pll ncl lbfgsb whtest sprng vectorclass model ${PLATFORM_LIB} ${THREAD_LIB})
- else()
-- target_link_libraries(iqtree pll pllavx ncl lbfgsb whtest zlibstatic sprng vectorclass model avxkernel ${PLATFORM_LIB} ${THREAD_LIB})
-+ target_link_libraries(iqtree pll pllavx ncl lbfgsb whtest sprng vectorclass model avxkernel ${PLATFORM_LIB} ${THREAD_LIB})
- endif()
-
- ##################################################################
---- a/phylotree.h
-+++ b/phylotree.h
-@@ -22,7 +22,7 @@
-
- //#define EIGEN_TUNE_FOR_CPU_CACHE_SIZE (512*256)
- //#define EIGEN_TUNE_FOR_CPU_CACHE_SIZE (8*512*512)
--#include "Eigen/Core"
-+#include "eigen3/Eigen/Core"
- #include "mtree.h"
- #include "alignment.h"
- #include "model/modelsubst.h"
---- a/gzstream.h
-+++ b/gzstream.h
-@@ -32,7 +32,7 @@
- // standard C++ with new header file names and std:: namespace
- #include <iostream>
- #include <fstream>
--#include "zlib-1.2.7/zlib.h"
-+#include <zlib.h>
-
- #ifdef GZSTREAM_NAMESPACE
- namespace GZSTREAM_NAMESPACE {
diff --git a/debian/patches/work_around_missing_example.patch b/debian/patches/work_around_missing_example.patch
deleted file mode 100644
index e661bbe..0000000
--- a/debian/patches/work_around_missing_example.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 31 Aug 2015 09:22:55 +0200
-Description: Example is missing in upstream tarball and installed in wrong directory anyway
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -474,7 +474,7 @@ endif()
- ##############################################################
- install (TARGETS iqtree DESTINATION bin)
- install (FILES "${PROJECT_SOURCE_DIR}/model/models.nex" DESTINATION bin)
--install (FILES "${PROJECT_SOURCE_DIR}/examples/example.phy" DESTINATION .)
-+#File is missing in archive# install (FILES "${PROJECT_SOURCE_DIR}/examples/example.phy" DESTINATION .)
- install (FILES "${PROJECT_SOURCE_DIR}/Documents/iqtree-manual-1.0.pdf" DESTINATION .)
-
- if (WIN32)
--
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