debian/changelog

+diamond-aligner (0.9.22+dfsg-2) unstable; urgency=medium
+
+  * Do not use march=native flag
+    Closes: #906615
+  * Standards-Version: 4.2.0
+
+ -- Andreas Tille <tille@debian.org>  Sun, 19 Aug 2018 06:41:39 +0200
+
 diamond-aligner (0.9.22+dfsg-1) unstable; urgency=medium
 
   * New upstream version

debian/control

@@ -6,7 +6,7 @@ Priority: optional
 Build-Depends: debhelper (>= 11~),
                cmake,
                zlib1g-dev
-Standards-Version: 4.1.4
+Standards-Version: 4.2.0
 Vcs-Browser: https://salsa.debian.org/med-team/diamond-aligner
 Vcs-Git: https://salsa.debian.org/med-team/diamond-aligner.git
 Homepage: https://github.com/bbuchfink/diamond

debian/patches/no_march_native.patch

+Description: Do not use march=native flag
+Bug-Debian: https://bugs.debian.org/906615
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sun, 19 Aug 2018 06:38:58 +0200
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -14,10 +14,10 @@ if(CMAKE_BUILD_MARCH)
+   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=${CMAKE_BUILD_MARCH}")
+ else()
+   include(CheckCXXCompilerFlag)
+-  CHECK_CXX_COMPILER_FLAG("-march=native" COMPILER_SUPPORTS_MARCHNATIVE)
+-  if(COMPILER_SUPPORTS_MARCHNATIVE)
+-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
+-  endif()
++  #CHECK_CXX_COMPILER_FLAG("-march=native" COMPILER_SUPPORTS_MARCHNATIVE)
++  #if(COMPILER_SUPPORTS_MARCHNATIVE)
++  #  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
++  #endif()
+ endif()
+ 
+ find_package(ZLIB REQUIRED)

debian/patches/series

 avoid_unwanted_optimisation.patch
+no_march_native.patch