Author: tille Date: 2012-01-25 13:26:57 +0000 (Wed, 25 Jan 2012) New Revision: 9431
Added: trunk/packages/libhmsbeagle/trunk/debian/patches/disable_cpu_sse_plugin.patch trunk/packages/libhmsbeagle/trunk/debian/rules_peter Modified: trunk/packages/libhmsbeagle/trunk/debian/changelog trunk/packages/libhmsbeagle/trunk/debian/patches/series trunk/packages/libhmsbeagle/trunk/debian/rules Log: Applied a patch from Peter Green and enabled compiling with SSE in debian/rules Modified: trunk/packages/libhmsbeagle/trunk/debian/changelog =================================================================== --- trunk/packages/libhmsbeagle/trunk/debian/changelog 2012-01-25 12:53:26 UTC (rev 9430) +++ trunk/packages/libhmsbeagle/trunk/debian/changelog 2012-01-25 13:26:57 UTC (rev 9431) @@ -1,3 +1,12 @@ +libhmsbeagle (1.0-4) unstable; urgency=low + + * debian/patches/disable_cpu_sse_plugin.patch: Apply patch from Peter + Green (thanks for your help, Peter) and + debian/rules: Enable sse for amd64 (only) to profit from plugin library + Closes: #656755 + + -- Andreas Tille <[email protected]> Wed, 25 Jan 2012 13:54:59 +0100 + libhmsbeagle (1.0-3) unstable; urgency=low * debian/patches/enable_static.patch: Enable building static Added: trunk/packages/libhmsbeagle/trunk/debian/patches/disable_cpu_sse_plugin.patch =================================================================== --- trunk/packages/libhmsbeagle/trunk/debian/patches/disable_cpu_sse_plugin.patch (rev 0) +++ trunk/packages/libhmsbeagle/trunk/debian/patches/disable_cpu_sse_plugin.patch 2012-01-25 13:26:57 UTC (rev 9431) @@ -0,0 +1,59 @@ +Description: Disable CPU_SSE plugin when building without SSE + The CPU_SSE plugin does not build without -msse +Author: Peter Green <[email protected]> +Bug-Debian: http://bugs.debian.org/656755 + +--- +The information above should follow the Patch Tagging Guidelines, please +checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here +are templates for supplementary fields that you might want to add: + +Origin: <vendor|upstream|other>, <url of original patch> +Bug: <url in upstream bugtracker> +Bug-Debian: http://bugs.debian.org/<bugnumber> +Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber> +Forwarded: <no|not-needed|url proving that it has been forwarded> +Reviewed-By: <name and email of someone who approved the patch> +Last-Update: <YYYY-MM-DD> + +Index: libhmsbeagle-1.0.new/libhmsbeagle/CPU/Makefile.am +=================================================================== +--- libhmsbeagle-1.0.new.orig/libhmsbeagle/CPU/Makefile.am 2012-01-25 10:09:40.000000000 +0000 ++++ libhmsbeagle-1.0.new/libhmsbeagle/CPU/Makefile.am 2012-01-25 10:09:40.000000000 +0000 +@@ -1,4 +1,4 @@ +-lib_LTLIBRARIES=libhmsbeagle-cpu.la libhmsbeagle-cpu-sse.la ++lib_LTLIBRARIES=libhmsbeagle-cpu.la + + BEAGLE_CPU_COMMON = Precision.h EigenDecomposition.h \ + EigenDecompositionCube.hpp EigenDecompositionCube.h \ +@@ -19,6 +19,8 @@ + # + # CPU plugin with custom SSE code + # ++if HAVE_SSE ++lib_LTLIBRARIES += libhmsbeagle-cpu-sse.la + libhmsbeagle_cpu_sse_la_SOURCES = $(BEAGLE_CPU_COMMON) \ + SSEDefinitions.h BeagleCPU4StateSSEImpl.hpp BeagleCPU4StateSSEImpl.h \ + BeagleCPUSSEImpl.hpp BeagleCPUSSEImpl.h \ +@@ -26,6 +28,7 @@ + + libhmsbeagle_cpu_sse_la_CXXFLAGS = $(AM_CXXFLAGS) + libhmsbeagle_cpu_sse_la_LDFLAGS= -version-info $(GENERIC_LIBRARY_VERSION) ++endif + + # + # CPU plugin with OpenMP parallel threads +Index: libhmsbeagle-1.0.new/configure.ac +=================================================================== +--- libhmsbeagle-1.0.new.orig/configure.ac 2012-01-25 10:41:40.000000000 +0000 ++++ libhmsbeagle-1.0.new/configure.ac 2012-01-25 10:41:59.000000000 +0000 +@@ -222,6 +222,9 @@ + if test "$enable_sse" = yes; then + SSE_CFLAGS+="-DENABLE_SSE" + AM_CXXFLAGS="$AM_CXXFLAGS -msse2" ++ AM_CONDITIONAL(HAVE_SSE,true) ++else ++ AM_CONDITIONAL(HAVE_SSE,false) + fi + + # ------------------------------------------------------------------------------ Modified: trunk/packages/libhmsbeagle/trunk/debian/patches/series =================================================================== --- trunk/packages/libhmsbeagle/trunk/debian/patches/series 2012-01-25 12:53:26 UTC (rev 9430) +++ trunk/packages/libhmsbeagle/trunk/debian/patches/series 2012-01-25 13:26:57 UTC (rev 9431) @@ -1 +1,2 @@ enable_static.patch +disable_cpu_sse_plugin.patch Modified: trunk/packages/libhmsbeagle/trunk/debian/rules =================================================================== --- trunk/packages/libhmsbeagle/trunk/debian/rules 2012-01-25 12:53:26 UTC (rev 9430) +++ trunk/packages/libhmsbeagle/trunk/debian/rules 2012-01-25 13:26:57 UTC (rev 9431) @@ -6,13 +6,14 @@ #export DH_VERBOSE=1 pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') +use_sse := $(shell if [ `dpkg-architecture -qDEB_BUILD_ARCH` = amd64 ] ; then echo yes ; else echo no ; fi) %: dh $@ --with autoreconf --with javahelper override_dh_auto_configure: ./autogen.sh - dh_auto_configure -- --enable-doxygen-man --enable-march-native=no --enable-sse=no + dh_auto_configure -- --enable-doxygen-man --enable-march-native=no --enable-sse=$(use_sse) override_dh_auto_build: $(MAKE) Added: trunk/packages/libhmsbeagle/trunk/debian/rules_peter =================================================================== --- trunk/packages/libhmsbeagle/trunk/debian/rules_peter (rev 0) +++ trunk/packages/libhmsbeagle/trunk/debian/rules_peter 2012-01-25 13:26:57 UTC (rev 9431) @@ -0,0 +1,107 @@ +#!/usr/bin/make -f +# -*- makefile -*- +# debian/rules of libhmsbeagle + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') + +%: + dh $@ --with autoreconf --with javahelper + +override_dh_auto_configure: + ./autogen.sh + dh_auto_configure -- --enable-doxygen-man --enable-march-native=no --enable-sse=no + +override_dh_auto_build: + $(MAKE) + $(MAKE) doxygen-doc + ant + +override_dh_auto_install: + dh_auto_install + #Shunt jni .so to jni directory. + mkdir -p -m755 debian/tmp/usr/lib/jni + mv debian/tmp/usr/lib/*jni.* debian/tmp/usr/lib/jni + + # will be removed later anyway (see below) + # sed -i "s/libdir='\/usr\/lib'/libdir='\/usr\/lib\/jni'/" debian/tmp/usr/lib/jni/libhmsbeagle-jni.la + + # Remove unneeded *.la files according to + # http://lists.debian.org/debian-devel/2009/08/msg00783.html + # Release goal: Getting rid of unneeded *.la / emptying dependency_libs + find debian -name "*.la" -delete + +override_dh_installman: + # Fix whatis entry of doxygen generated man pages if possible + find doc/man/man3 -name "*.3" -exec sed -i "/^.SH NAME/{;N;N;N;s/\(.SH NAME\)[[:space:]]*\([A-Za-z].*-\).*.PP[[:space:]]*\([A-Za-z].*\)/\1\n\2 \3/g;}" \{\} \; + dh_installman + +override_dh_auto_clean: + $(MAKE) -f Makefile distclean || true + rm -rf doc .config configure + rm -rf lib build + rm -f acinclude.m4 + rm -f INSTALL + rm -f libhmsbeagle/config.h.in + rm -f examples/*/Makefile.in + rm -f examples/Makefile.in + rm -f examples/*/*.o + rm -rf examples/*/.libs + rm -rf libhmsbeagle/*/.libs + rm -rf libhmsbeagle/.libs + rm -rf libhmsbeagle/*.o + rm -rf libhmsbeagle/*/*.o + rm -f Makefile + rm -f config.log + rm -f config.status + rm -f examples/Makefile + rm -f examples/complextest/Makefile + rm -f examples/complextest/complextest + rm -f examples/fourtaxon/Makefile + rm -f examples/fourtaxon/check_lnL_using_paup.nex + rm -f examples/fourtaxon/fourtaxon + rm -f examples/fourtaxon/fourtaxonrun.sh + rm -f examples/genomictest/Makefile + rm -f examples/genomictest/genomictest + rm -f examples/genomictest/genomictest.sh + rm -f examples/matrixtest/Makefile + rm -f examples/matrixtest/matrixtest + rm -f examples/oddstatetest/Makefile + rm -f examples/oddstatetest/oddstatetest + rm -f examples/tinytest/Makefile + rm -f examples/tinytest/tinytest + rm -f hmsbeagle-1.pc + rm -f libhmsbeagle/CPU/Makefile + rm -f libhmsbeagle/CPU/libhmsbeagle-cpu.la + rm -f libhmsbeagle/CPU/libhmsbeagle_cpu_la-BeagleCPUPlugin.lo + rm -f libhmsbeagle/GPU/Makefile + rm -f libhmsbeagle/GPU/kernels/Makefile + rm -f libhmsbeagle/Makefile + rm -f libhmsbeagle/config.h + rm -f libhmsbeagle/libhmsbeagle-jni.la + rm -f libhmsbeagle/libhmsbeagle.la + rm -f libhmsbeagle/libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.lo + rm -f libhmsbeagle/libhmsbeagle_la-beagle.lo + rm -f libhmsbeagle/plugin/Makefile + rm -f libhmsbeagle/plugin/libplugin.la + rm -f libhmsbeagle/plugin/libplugin_la-Plugin.lo + rm -f libhmsbeagle/plugin/libplugin_la-UnixSharedLibrary.lo + rm -f libhmsbeagle/stamp-h1 + rm -f libtool + rm -f aclocal.m4 + rm -f m4/libtool.m4 + rm -f m4/ltoptions.m4 + rm -f m4/ltsugar.m4 + rm -f m4/ltversion.m4 + rm -f m4/lt~obsolete.m4 + + +# Does not help to fix the lintian issue ... hmmm +#override_dh_shlibdeps: +# # somehow shlibdeps is not called for jni subdir +# dh_shlibdeps -- debian/$(pkg)1/usr/lib/jni/* debian/$(pkg)1/usr/lib/lib* + +get-orig-source: + . debian/get-orig-source Property changes on: trunk/packages/libhmsbeagle/trunk/debian/rules_peter ___________________________________________________________________ Added: svn:executable + * _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
