[med-svn] [hyphy] 03/07: Fix gcc-6 build issue by incorporating upstream patch

[Andreas Tille]

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tille pushed a commit to branch master
in repository hyphy.

commit 0c8e1a8380d5efe7b6d5d7e9d7d14494750ade5d
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jul 22 14:41:48 2016 +0200

    Fix gcc-6 build issue by incorporating upstream patch
---
 debian/changelog           |  7 +++++++
 debian/patches/gcc-6.patch | 24 ++++++++++++++++++++++++
 debian/patches/series      |  1 +
 3 files changed, 32 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 74e0e83..b10b761 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+hyphy (2.2.6+dfsg-4) UNRELEASED; urgency=medium
+
+  * Fix gcc-6 build issue by incorporating upstream patch
+    Closes: #811866
+
+ -- Andreas Tille <tille at debian.org>  Fri, 22 Jul 2016 14:40:33 +0200
+
 hyphy (2.2.6+dfsg-3) unstable; urgency=medium
 
   * Change build-dep on python3-dev to python3-all-dev to enable building for
diff --git a/debian/patches/gcc-6.patch b/debian/patches/gcc-6.patch
new file mode 100644
index 0000000..b2ea4fc
--- /dev/null
+++ b/debian/patches/gcc-6.patch
@@ -0,0 +1,24 @@
+Author: Steven Weaver <sweaver at ucsd.edu>
+Last-Update:   Tue Feb 23 13:00:41 2016 -0500
+Origin: Upstream commit 778573019bbf0eaa9173cf04bc3e3baf1b18a7b1
+Bug-Debian: https://bugs.debian.org/811866
+Description: Build with gcc-6
+    fixes #374: adding -fno-strict-aliasing and -fpermissive for gcc-6 compatibility
+
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 9ce7fc1..e446e4d 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -122,6 +122,11 @@ if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
+     if(${GCC46})
+         set(DEFAULT_WARNING_FLAGS "-Wno-int-to-pointer-cast -Wno-conversion-null")
+     endif(${GCC46})
++
++    if(${GCC_VERSION} VERSION_GREATER 6.0 OR ${GCC_VERSION} VERSION_EQUAL 6.0)
++        set(DEFAULT_COMPILE_FLAGS "-fno-strict-aliasing -fpermissive")
++    endif(${GCC_VERSION} VERSION_GREATER 6.0 OR ${GCC_VERSION} VERSION_EQUAL 6.0)
++
+     
+     PCL_CHECK_FOR_AVX()
+     if(${HAVE_AVX_EXTENSIONS})
diff --git a/debian/patches/series b/debian/patches/series
index 8b4b4a4..1847aaf 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -7,3 +7,4 @@ msse_option_only_if_available.patch
 setup_fix_clean_target.patch
 python3.5.patch
 remove_arch_specific_flags.patch
+gcc-6.patch

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