[med-svn] [Git][med-team/consensuscore][master] d/patches/portable_simd: remove baseline violation and enable compilation on...
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Sat Mar 23 18:46:07 GMT 2024
Michael R. Crusoe pushed to branch master at Debian Med / consensuscore
Commits:
8da604a4 by Michael R. Crusoe at 2024-03-23T19:42:15+01:00
d/patches/portable_simd: remove baseline violation and enable compilation on other 64-bit architectures.
- - - - -
4 changed files:
- debian/changelog
- debian/control
- + debian/patches/portable_simd.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+consensuscore (1.1.1+dfsg-6) unstable; urgency=medium
+
+ * Team upload.
+ * d/patches/portable_simd: remove baseline violation and enable
+ compilation on other 64-bit architectures.
+
+ -- Michael R. Crusoe <crusoe at debian.org> Sat, 23 Mar 2024 19:42:10 +0100
+
consensuscore (1.1.1+dfsg-5) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -5,13 +5,16 @@ Section: science
Testsuite: autopkgtest-pkg-python
Priority: optional
Build-Depends: debhelper-compat (= 13),
+ architecture-is-64-bit,
+ architecture-is-little-endian,
dh-sequence-python3,
dh-exec,
libboost-dev,
swig,
python3-setuptools,
python3-all-dev,
- python3-numpy
+ python3-numpy,
+ libsimde-dev
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/consensuscore
Vcs-Git: https://salsa.debian.org/med-team/consensuscore.git
@@ -19,7 +22,7 @@ Homepage: https://github.com/PacificBiosciences/ConsensusCore
Rules-Requires-Root: no
Package: libconsensuscore-dev
-Architecture: any-amd64 any-i386
+Architecture: any
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends}
@@ -33,7 +36,7 @@ Description: algorithms for PacBio multiple sequence consensus -- development fi
It provides the header files and static library.
Package: python3-pbconsensuscore
-Architecture: any-amd64 any-i386
+Architecture: any
Section: python
Depends: ${shlibs:Depends},
${misc:Depends},
=====================================
debian/patches/portable_simd.patch
=====================================
@@ -0,0 +1,136 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Enable compilation on other 64-bit systems besidex amd64
+--- consensuscore.orig/include/ConsensusCore/Edna/EdnaEvaluator.hpp
++++ consensuscore/include/ConsensusCore/Edna/EdnaEvaluator.hpp
+@@ -2,8 +2,8 @@
+
+ #pragma once
+
+-#include <pmmintrin.h>
+-#include <xmmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse3.h>
+
+ #include <algorithm>
+ #include <cassert>
+--- consensuscore.orig/include/ConsensusCore/LFloat.hpp
++++ consensuscore/include/ConsensusCore/LFloat.hpp
+@@ -1,7 +1,8 @@
+ // Author: David Alexander
+
+ #pragma once
+-#include <xmmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse.h>
+ #include <cfloat>
+ #include <ostream>
+
+--- consensuscore.orig/include/ConsensusCore/Matrix/DenseMatrix.hpp
++++ consensuscore/include/ConsensusCore/Matrix/DenseMatrix.hpp
+@@ -2,7 +2,8 @@
+
+ #pragma once
+
+-#include <xmmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse.h>
+
+ #include <boost/numeric/ublas/matrix.hpp>
+ #include <utility>
+--- consensuscore.orig/include/ConsensusCore/Matrix/SparseMatrix.hpp
++++ consensuscore/include/ConsensusCore/Matrix/SparseMatrix.hpp
+@@ -2,7 +2,8 @@
+
+ #pragma once
+
+-#include <xmmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse.h>
+ #include <utility>
+ #include <vector>
+
+--- consensuscore.orig/include/ConsensusCore/Matrix/SparseVector.hpp
++++ consensuscore/include/ConsensusCore/Matrix/SparseVector.hpp
+@@ -2,7 +2,8 @@
+
+ #pragma once
+
+-#include <xmmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse.h>
+ #include <utility>
+ #include <vector>
+
+--- consensuscore.orig/include/ConsensusCore/Quiver/QvEvaluator.hpp
++++ consensuscore/include/ConsensusCore/Quiver/QvEvaluator.hpp
+@@ -2,8 +2,8 @@
+
+ #pragma once
+
+-#include <pmmintrin.h>
+-#include <xmmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse3.h>
+
+ #include <algorithm>
+ #include <cassert>
+--- consensuscore.orig/include/ConsensusCore/Quiver/detail/SseMath.hpp
++++ consensuscore/include/ConsensusCore/Quiver/detail/SseMath.hpp
+@@ -2,7 +2,8 @@
+
+ #pragma once
+
+-#include <xmmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse.h>
+ #include <limits>
+
+ #include <ConsensusCore/Quiver/detail/sse_mathfun.h>
+--- consensuscore.orig/src/C++/Edna/EdnaCounts.cpp
++++ consensuscore/src/C++/Edna/EdnaCounts.cpp
+@@ -1,7 +1,7 @@
+ // Author: Patrick Marks
+
+-#include <pmmintrin.h>
+-#include <xmmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse3.h>
+ #include <cassert>
+ #include <cfloat>
+ #include <climits>
+--- consensuscore.orig/make/Defs.mk
++++ consensuscore/make/Defs.mk
+@@ -46,10 +46,10 @@
+ endif
+
+ ifeq ($(GXX),clang++)
+- CXX_FLAGS = $(GXX_FLAGS) $(CXX_OPT_FLAGS) -msse3 -fPIC -Qunused-arguments -fno-omit-frame-pointer
++ CXX_FLAGS = $(GXX_FLAGS) $(CXX_OPT_FLAGS) -fPIC -Qunused-arguments -fno-omit-frame-pointer
+ CXX_STRICT_FLAGS = $(GXX_FLAGS) $(CXX_FLAGS) -pedantic -std=$(CPP_STD) -Wall
+ else
+- CXX_FLAGS = $(CXX_OPT_FLAGS) $(CXX_EXTRA_ARGS) -msse3 -fPIC -fno-omit-frame-pointer
++ CXX_FLAGS = $(CXX_OPT_FLAGS) $(CXX_EXTRA_ARGS) -fPIC -fno-omit-frame-pointer
+ CXX_STRICT_FLAGS = $(CXX_FLAGS) -pedantic -std=$(CPP_STD) -Wall
+ endif
+
+--- consensuscore.orig/include/ConsensusCore/Quiver/detail/sse_mathfun.h
++++ consensuscore/include/ConsensusCore/Quiver/detail/sse_mathfun.h
+@@ -31,7 +31,8 @@
+
+ #pragma once
+
+-#include <xmmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse.h>
+ #include <limits>
+ #define USE_SSE2
+
+@@ -49,7 +50,7 @@
+ typedef __m128 v4sf; // vector of 4 float (sse1)
+
+ #ifdef USE_SSE2
+-#include <emmintrin.h>
++#include <simde/x86/sse2.h>
+ typedef __m128i v4si; // vector of 4 int (sse2)
+ #else
+ typedef __m64 v2si; // vector of 2 int (mmx)
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ gcc-6.patch
2to3.patch
check_boost_version.patch
sequence_setuptools.patch
+portable_simd.patch
View it on GitLab: https://salsa.debian.org/med-team/consensuscore/-/commit/8da604a464daf463cfe4c4e214a569ce2aeedd55
--
View it on GitLab: https://salsa.debian.org/med-team/consensuscore/-/commit/8da604a464daf463cfe4c4e214a569ce2aeedd55
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