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commit 30add480bf686857675efe07c3806c9d4a0fd71f Author: Andreas Tille <[email protected]> Date: Mon Aug 31 12:22:55 2015 +0200 iqtree upstream changes interface of sprng so we can not easily replace this lib by the Debian packaged version --- debian/copyright | 1 - debian/patches/debian_packaged_sprng.patch | 55 +++++++++++++++++++++++++++ debian/patches/use_debian_packaged_libs.patch | 17 ++++----- 3 files changed, 63 insertions(+), 10 deletions(-) diff --git a/debian/copyright b/debian/copyright index 209f2b4..7972492 100644 --- a/debian/copyright +++ b/debian/copyright @@ -3,7 +3,6 @@ Upstream-Name: IQ-TREE Source: http://www.cibiv.at/software/iqtree/download/ Files-Excluded: lib*/* zlib-* - sprng Eigen .* */.* diff --git a/debian/patches/debian_packaged_sprng.patch b/debian/patches/debian_packaged_sprng.patch new file mode 100644 index 0000000..ad93557 --- /dev/null +++ b/debian/patches/debian_packaged_sprng.patch @@ -0,0 +1,55 @@ +Author: Andreas Tille <[email protected]> +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} ${THREAD_LIB}) + endif() + + ################################################################## diff --git a/debian/patches/use_debian_packaged_libs.patch b/debian/patches/use_debian_packaged_libs.patch index 4d5e8d5..49a80da 100644 --- a/debian/patches/use_debian_packaged_libs.patch +++ b/debian/patches/use_debian_packaged_libs.patch @@ -1,6 +1,6 @@ Author: Andreas Tille <[email protected]> Last-Update: Mon, 31 Aug 2015 09:22:55 +0200 -Description: Use Debian packaged zlib, libsprng and libeigen +Description: Use Debian packaged zlib and libeigen --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -12,33 +12,32 @@ Description: Use Debian packaged zlib, libsprng and libeigen ################################################################## -@@ -327,8 +326,6 @@ add_subdirectory(pllrepo/src) - add_subdirectory(ncl) +@@ -328,7 +327,6 @@ add_subdirectory(ncl) add_subdirectory(lbfgsb) add_subdirectory(whtest) --add_subdirectory(sprng) + add_subdirectory(sprng) -add_subdirectory(zlib-1.2.7) add_subdirectory(vectorclass) add_subdirectory(model) -@@ -402,7 +399,7 @@ upperbounds.cpp +@@ -402,7 +400,7 @@ upperbounds.cpp ) if (NOT IQTREE_FLAGS MATCHES "avx" AND NOT IQTREE_FLAGS MATCHES "fma") - set_target_properties(iqtree pll ncl lbfgsb whtest zlibstatic sprng vectorclass model PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}") -+ set_target_properties(iqtree pll ncl lbfgsb whtest 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 +433,9 @@ if (IQTREE_FLAGS MATCHES "omp") +@@ -436,9 +434,9 @@ 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 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 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() ################################################################## -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/iqtree.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
