debian/changelog

+gmap (2018-07-04-3) unstable; urgency=medium
+
+  * Bump Standards-Version to 4.2.1
+  * Fix a typo in sse2 patch description
+  * d/control: XS-Autobuild: yes
+
+ -- Alexandre Mestiashvili <mestia@debian.org>  Fri, 31 Aug 2018 09:40:16 +0000
+
+gmap (2018-07-04-2) unstable; urgency=medium
+
+  * Add patch from upstream fixing FTBFS when a CPU has only SSE2
+
+ -- Alexandre Mestiashvili <mestia@debian.org>  Thu, 30 Aug 2018 08:51:09 +0000
+
 gmap (2018-07-04-1) unstable; urgency=medium
 
   [ Steffen Möller ]

debian/control

@@ -4,14 +4,14 @@ Uploaders: Shaun Jackman <sjackman@debian.org>,
            Andreas Tille <tille@debian.org>,
            Alexandre Mestiashvili <mestia@debian.org>
 Section: non-free/science
-XS-Autobuild: no
+XS-Autobuild: yes
 Priority: optional
 Build-Depends: debhelper (>= 11~),
                dh-exec,
                help2man,
                libbz2-dev,
                zlib1g-dev
-Standards-Version: 4.1.5
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/gmap
 Vcs-Git: https://salsa.debian.org/med-team/gmap.git
 Homepage: http://research-pub.gene.com/gmap

debian/patches/series

+sse2.patch
 only-do-cpuid-on-amd64-i386.patch
 install-data-local

debian/patches/sse2.patch

+Subject: Apply upstream patch fixing #902820
+ FTBFS on stretch/amd64 if CPU has SSE2 and nothing more
+From: Thomas Wu <wu.thomas@gene.com>
+Forwarded: Yes
+--- gmap.orig/src/extension-search.c
++++ gmap/src/extension-search.c
+@@ -340,13 +340,6 @@
+ 
+ #endif
+ 
+-static void
+-print_vector_dec (__m128i x) {
+-  printf("%d %d %d %d\n",
+-	 _mm_extract_epi32(x,0),_mm_extract_epi32(x,1),_mm_extract_epi32(x,2),_mm_extract_epi32(x,3));
+-  return;
+-}
+-
+ 
+ #if !defined(HAVE_SSE4_2)
+ #define count_leading_zeroes_32(diff) ((diff >> 16) ? clz_table[diff >> 16] : 16 + clz_table[diff])
+--- gmap.orig/src/kmer-search.c
++++ gmap/src/kmer-search.c
+@@ -215,7 +215,8 @@
+ /* Algorithm 2: Stage3end_complete_path_run_gmap: complete_path -> hits */
+ 
+ 
+-#ifdef HAVE_SSE2
++#ifdef DEBUG8
++#ifdef HAVE_SSE4_1
+ static void
+ print_vector_dec (__m128i x) {
+   printf("%d %d %d %d\n",
+@@ -223,6 +224,7 @@
+   return;
+ }
+ #endif
++#endif
+ 
+ 
+ #if !defined(HAVE_SSE4_2)