[med-svn] r9431 - in trunk/packages/libhmsbeagle/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Wed Jan 25 13:26:57 UTC 2012
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 <tille at debian.org> 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 <plugwash at p10link.net>
+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
+ *
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