[med-svn] [iqtree] 04/04: iqtree upstream changes interface of sprng so we can not easily replace this lib by the Debian packaged version
Andreas Tille
tille at debian.org
Mon Aug 31 13:46:43 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 30add480bf686857675efe07c3806c9d4a0fd71f
Author: Andreas Tille <tille at debian.org>
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 <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} ${THREAD_LIB})
+ endif()
+
+ ##################################################################
diff --git a/debian/patches/use_debian_packaged_libs.patch b/debian/patches/use_debian_packaged_libs.patch
index 4d5e8d5..49a80da 100644
--- a/debian/patches/use_debian_packaged_libs.patch
+++ b/debian/patches/use_debian_packaged_libs.patch
@@ -1,6 +1,6 @@
Author: Andreas Tille <tille at debian.org>
Last-Update: Mon, 31 Aug 2015 09:22:55 +0200
-Description: Use Debian packaged zlib, libsprng and libeigen
+Description: Use Debian packaged zlib and libeigen
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -12,33 +12,32 @@ Description: Use Debian packaged zlib, libsprng and libeigen
##################################################################
-@@ -327,8 +326,6 @@ add_subdirectory(pllrepo/src)
- add_subdirectory(ncl)
+@@ -328,7 +327,6 @@ add_subdirectory(ncl)
add_subdirectory(lbfgsb)
add_subdirectory(whtest)
--add_subdirectory(sprng)
+ add_subdirectory(sprng)
-add_subdirectory(zlib-1.2.7)
add_subdirectory(vectorclass)
add_subdirectory(model)
-@@ -402,7 +399,7 @@ upperbounds.cpp
+@@ -402,7 +400,7 @@ upperbounds.cpp
)
if (NOT IQTREE_FLAGS MATCHES "avx" AND NOT IQTREE_FLAGS MATCHES "fma")
- set_target_properties(iqtree pll ncl lbfgsb whtest zlibstatic sprng vectorclass model PROPERTIES COMPILE_FLAGS "${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()
##################################################################
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