[med-svn] r12627 - in trunk/packages/libhmsbeagle/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Sat Dec 15 18:47:05 UTC 2012
Author: tille
Date: 2012-12-15 18:47:05 +0000 (Sat, 15 Dec 2012)
New Revision: 12627
Removed:
trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle-dev.lintian-overrides
Modified:
trunk/packages/libhmsbeagle/trunk/debian/changelog
trunk/packages/libhmsbeagle/trunk/debian/compat
trunk/packages/libhmsbeagle/trunk/debian/control
trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle-dev.install
trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle-dev.manpages
trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle1.install
trunk/packages/libhmsbeagle/trunk/debian/patches/disable_cpu_sse_plugin.patch
trunk/packages/libhmsbeagle/trunk/debian/patches/series
trunk/packages/libhmsbeagle/trunk/debian/rules
Log:
New upstream version; adapted to changes needed to the multi-arch build which seems to happen now automagically when using standard build method
Modified: trunk/packages/libhmsbeagle/trunk/debian/changelog
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/changelog 2012-12-15 10:53:11 UTC (rev 12626)
+++ trunk/packages/libhmsbeagle/trunk/debian/changelog 2012-12-15 18:47:05 UTC (rev 12627)
@@ -4,8 +4,12 @@
- debian/patches/disable_cpu_sse_plugin.patch: Seems upstream
has solved the problem a bit differently than in this patch
-> droping it for the moment
+ * debian/get-orig-source: use xz compression
+ * debhelper 9 (control+compat)
+ * debian/libhmsbeagle-dev.lintian-overrides: deleted; no need for overrides
+ any more
- -- Andreas Tille <tille at debian.org> Fri, 25 May 2012 14:48:52 +0200
+ -- Andreas Tille <tille at debian.org> Fri, 14 Dec 2012 19:23:52 +0100
libhmsbeagle (1.0-6) unstable; urgency=low
Modified: trunk/packages/libhmsbeagle/trunk/debian/compat
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/compat 2012-12-15 10:53:11 UTC (rev 12626)
+++ trunk/packages/libhmsbeagle/trunk/debian/compat 2012-12-15 18:47:05 UTC (rev 12627)
@@ -1 +1 @@
-8
+9
Modified: trunk/packages/libhmsbeagle/trunk/debian/control
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/control 2012-12-15 10:53:11 UTC (rev 12626)
+++ trunk/packages/libhmsbeagle/trunk/debian/control 2012-12-15 18:47:05 UTC (rev 12627)
@@ -4,7 +4,7 @@
DM-Upload-Allowed: yes
Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 8), autotools-dev, dh-autoreconf,
+Build-Depends: debhelper (>= 9), autotools-dev, dh-autoreconf,
doxygen, javahelper (>=0.25), openjdk-6-jdk, ant
Standards-Version: 3.9.3
Section: libs
@@ -36,6 +36,7 @@
Package: libhmsbeagle1
Section: libs
Architecture: linux-any
+Pre-Depend: multiarch-support
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: High-performance lib for Bayesian and Maximum Likelihood phylogenetics
BEAGLE is a high-performance library that can perform the core calculations at
Modified: trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle-dev.install
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle-dev.install 2012-12-15 10:53:11 UTC (rev 12626)
+++ trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle-dev.install 2012-12-15 18:47:05 UTC (rev 12627)
@@ -1,4 +1,6 @@
usr/include/*
-usr/lib/pkgconfig/*
-usr/lib/lib*.so
-usr/lib/lib*.a
+usr/lib/*/pkgconfig/*
+usr/lib/*/lib*-cpu*.so
+usr/lib/*/lib*-cpu*.a
+usr/lib/*/libhmsbeagle.a
+usr/lib/*/libhmsbeagle.so
Deleted: trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle-dev.lintian-overrides
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle-dev.lintian-overrides 2012-12-15 10:53:11 UTC (rev 12626)
+++ trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle-dev.lintian-overrides 2012-12-15 18:47:05 UTC (rev 12627)
@@ -1,51 +0,0 @@
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/BeagleOperation.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/Dim3Int.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/FourTaxonExample.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/GPUInterface.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/KernelLauncher.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/KernelResource.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/VecUnion.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_Beagle.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_BeagleException.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_BeagleErrorCode.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_BeagleFactory.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_BeagleFlag.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_BeagleImpl.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_BeagleImplFactory.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_BeagleInfo.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_BeagleJNIImpl.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_BeagleJNIWrapper.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_BeaglePlugin.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_DependencyAwareBeagleImpl.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_FourStateBeagleImpl.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_GeneralBeagleImpl.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_InstanceDetails.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_ResourceDetails.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_cpu_BeagleCPU4StateImpl.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_cpu_BeagleCPU4StateImplFactory.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_cpu_BeagleCPU4StateSSEImpl.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_cpu_BeagleCPU4StateSSEImplFactory.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_cpu_BeagleCPU4StateSSEImpl_ BEAGLE_CPU_4_SSE_DOUBLE _.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_cpu_BeagleCPU4StateSSEImpl_ BEAGLE_CPU_4_SSE_FLOAT _.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_cpu_BeagleCPUImpl.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_cpu_BeagleCPUImplFactory.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_cpu_BeagleCPUOpenMPPlugin.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_cpu_BeagleCPUPlugin.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_cpu_BeagleCPUSSEImpl.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_cpu_BeagleCPUSSEImplFactory.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_cpu_BeagleCPUSSEImpl_ BEAGLE_CPU_SSE_DOUBLE _.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_cpu_BeagleCPUSSEImpl_ BEAGLE_CPU_SSE_FLOAT _.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_cpu_BeagleCPUSSEPlugin.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_cpu_EigenDecomposition.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_cpu_EigenDecompositionCube.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_cpu_EigenDecompositionSquare.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_gpu_BeagleGPUImpl.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_gpu_BeagleGPUImplFactory.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_gpu_CUDAPlugin.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_gpu_OpenCLPlugin.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_plugin_Plugin.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_plugin_PluginManager.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_plugin_SharedLibrary.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_plugin_SharedLibraryException.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_plugin_UnixSharedLibrary.3.gz
-libhmsbeagle-dev: manpage-has-bad-whatis-entry usr/share/man/man3/beagle_plugin_WinSharedLibrary.3.gz
Modified: trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle-dev.manpages
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle-dev.manpages 2012-12-15 10:53:11 UTC (rev 12626)
+++ trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle-dev.manpages 2012-12-15 18:47:05 UTC (rev 12627)
@@ -1 +1 @@
-doc/man/man3/*
+doc/man/man3/[bB]*
Modified: trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle1.install
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle1.install 2012-12-15 10:53:11 UTC (rev 12626)
+++ trunk/packages/libhmsbeagle/trunk/debian/libhmsbeagle1.install 2012-12-15 18:47:05 UTC (rev 12627)
@@ -1,2 +1,2 @@
-usr/lib/lib*.so.*
-usr/lib/jni/*.so
+usr/lib/*/lib*.so.*
+usr/lib/*/lib*jni.so
Modified: trunk/packages/libhmsbeagle/trunk/debian/patches/disable_cpu_sse_plugin.patch
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/patches/disable_cpu_sse_plugin.patch 2012-12-15 10:53:11 UTC (rev 12626)
+++ trunk/packages/libhmsbeagle/trunk/debian/patches/disable_cpu_sse_plugin.patch 2012-12-15 18:47:05 UTC (rev 12627)
@@ -4,46 +4,17 @@
Bug-Debian: http://bugs.debian.org/656755
Forwarded: "Marc A. Suchard" <msuchard at ucla.edu>, Aaron Darling <aarondarling at ucdavis.edu>
Reviewed-By: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 25 Jan 2012
+Last-Update: Fri, 14 Dec 2012 19:23:52 +0100
-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 $(GENERIC_LIBRARY_VERSION)
-+endif
-
- #
- # CPU plugin with OpenMP parallel threads
-Index: libhmsbeagle-1.0.new/configure.ac
-===================================================================
---- libhmsbeagle-1.0.new.orig/configure.ac 2012-01-25 10:41:40.000000000 +0000
-+++ libhmsbeagle-1.0.new/configure.ac 2012-01-25 10:41:59.000000000 +0000
-@@ -222,6 +222,9 @@
+--- libhmsbeagle-1.1.orig/configure.ac
++++ libhmsbeagle-1.1/configure.ac
+@@ -211,6 +211,9 @@
if test "$enable_sse" = yes; then
SSE_CFLAGS+="-DENABLE_SSE"
AM_CXXFLAGS="$AM_CXXFLAGS -msse2"
-+ AM_CONDITIONAL(HAVE_SSE,true)
++ AM_CONDITIONAL(HAVE_SSE2,true)
+else
-+ AM_CONDITIONAL(HAVE_SSE,false)
++ AM_CONDITIONAL(HAVE_SSE2,false)
fi
# ------------------------------------------------------------------------------
Modified: trunk/packages/libhmsbeagle/trunk/debian/patches/series
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/patches/series 2012-12-15 10:53:11 UTC (rev 12626)
+++ trunk/packages/libhmsbeagle/trunk/debian/patches/series 2012-12-15 18:47:05 UTC (rev 12627)
@@ -1 +1,3 @@
enable_static.patch
+disable_cpu_sse_plugin.patch
+gcc-4.7.patch
Modified: trunk/packages/libhmsbeagle/trunk/debian/rules
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/rules 2012-12-15 10:53:11 UTC (rev 12626)
+++ trunk/packages/libhmsbeagle/trunk/debian/rules 2012-12-15 18:47:05 UTC (rev 12627)
@@ -6,6 +6,7 @@
#export DH_VERBOSE=1
pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
+lib := $(pkg)1
use_sse := $(shell if [ `dpkg-architecture -qDEB_BUILD_ARCH` = amd64 ] ; then echo yes ; else echo no ; fi)
%:
@@ -20,20 +21,12 @@
$(MAKE) doxygen-doc
ant
-override_dh_auto_install:
- dh_auto_install
- #Shunt jni .so to jni directory.
- mkdir -p -m755 debian/tmp/usr/lib/jni
- mv debian/tmp/usr/lib/*jni.* debian/tmp/usr/lib/jni
+override_dh_install:
+ dh_install
+ jniso=`find debian/$(lib) -name $(pkg)-jni.so` ; \
+ mkdir -p `dirname $$jniso`/jni ; \
+ mv $$jniso `dirname $$jniso`/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;}" \{\} \;
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