[med-svn] [Git][med-team/hmmer][simde2] 2 commits: test
Michael R. Crusoe
gitlab at salsa.debian.org
Thu Jun 25 13:20:30 BST 2020
Michael R. Crusoe pushed to branch simde2 at Debian Med / hmmer
Commits:
f1a7c6e8 by Michael R. Crusoe at 2020-06-23T16:17:38+02:00
test
- - - - -
c5bdc9cb by Michael R. Crusoe at 2020-06-25T12:33:55+02:00
fix test result parsing
- - - - -
4 changed files:
- debian/control
- debian/patches/series
- + debian/patches/simde
- debian/rules
Changes:
=====================================
debian/control
=====================================
@@ -5,6 +5,7 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
libdivsufsort-dev,
+ libsimde-dev,
python3
Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/hmmer
@@ -12,7 +13,7 @@ Vcs-Git: https://salsa.debian.org/med-team/hmmer.git
Homepage: http://hmmer.org/
Package: hmmer
-Architecture: any-amd64 any-i386 powerpc ppc64 x32
+Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
Suggests: hmmer-doc (>= ${source:Version})
=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ hardening
skip_threads_check
sub_make_parallel
spelling
+simde
=====================================
debian/patches/simde
=====================================
@@ -0,0 +1,240 @@
+--- hmmer.orig/easel/m4/esl_sse.m4
++++ hmmer/easel/m4/esl_sse.m4
+@@ -38,7 +38,7 @@
+ if test "x$SSE_CFLAGS" != x; then
+ esl_sse_try_flags=$SSE_CFLAGS
+ else
+- esl_sse_try_flags="none -msse2"
++ esl_sse_try_flags="none"
+ fi
+
+ save_CFLAGS=$CFLAGS
+@@ -50,7 +50,8 @@
+
+ AC_LINK_IFELSE(
+ [AC_LANG_SOURCE([[
+-#include <x86intrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+ #include <stdint.h>
+ int stub_sse(void) {
+ __m128i v1 = _mm_set1_epi32(42);
+--- hmmer.orig/easel/esl_sse.c
++++ hmmer/easel/esl_sse.c
+@@ -37,7 +37,8 @@
+ #include <math.h>
+ #include <float.h>
+
+-#include <x86intrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+
+ #include "easel.h"
+ #include "esl_sse.h"
+--- hmmer.orig/easel/esl_sse.h
++++ hmmer/easel/esl_sse.h
+@@ -22,7 +22,8 @@
+ #include "easel.h"
+
+ #include <stdio.h>
+-#include <x86intrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+
+
+ /*****************************************************************
+--- hmmer.orig/src/fm_sse.c
++++ hmmer/src/fm_sse.c
+@@ -3,8 +3,8 @@
+ #include <stdio.h>
+
+ #if defined eslENABLE_SSE
+-#include <xmmintrin.h> /* SSE */
+-#include <emmintrin.h> /* SSE2 */
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+ #endif
+
+ #include "easel.h"
+--- hmmer.orig/src/impl_sse/decoding.c
++++ hmmer/src/impl_sse/decoding.c
+@@ -12,7 +12,8 @@
+ #include <stdio.h>
+ #include <math.h>
+
+-#include <x86intrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+
+ #include "easel.h"
+ #include "esl_sse.h"
+--- hmmer.orig/src/impl_sse/fwdback.c
++++ hmmer/src/impl_sse/fwdback.c
+@@ -34,8 +34,8 @@
+ #include <stdio.h>
+ #include <math.h>
+
+-#include <xmmintrin.h> /* SSE */
+-#include <emmintrin.h> /* SSE2 */
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+
+ #include "easel.h"
+ #include "esl_sse.h"
+--- hmmer.orig/src/impl_sse/impl_sse.h
++++ hmmer/src/impl_sse/impl_sse.h
+@@ -11,8 +11,9 @@
+ #include "esl_alphabet.h"
+ #include "esl_random.h"
+
+-#include <xmmintrin.h> /* SSE */
+-#include <emmintrin.h> /* SSE2 */
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
++
+ #ifdef __SSE3__
+ #include <pmmintrin.h> /* DENORMAL_MODE */
+ #endif
+--- hmmer.orig/src/impl_sse/io.c
++++ hmmer/src/impl_sse/io.c
+@@ -35,8 +35,8 @@
+ #include <pthread.h>
+ #endif
+
+-#include <xmmintrin.h> /* SSE */
+-#include <emmintrin.h> /* SSE2 */
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+
+ #include "easel.h"
+
+--- hmmer.orig/src/impl_sse/ssvfilter.c
++++ hmmer/src/impl_sse/ssvfilter.c
+@@ -407,8 +407,8 @@
+
+ #include <math.h>
+
+-#include <xmmintrin.h> /* SSE */
+-#include <emmintrin.h> /* SSE2 */
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+
+ #include "easel.h"
+ #include "esl_sse.h"
+--- hmmer.orig/src/impl_sse/mpi.c
++++ hmmer/src/impl_sse/mpi.c
+@@ -17,8 +17,8 @@
+
+ #include "mpi.h"
+
+-#include <xmmintrin.h> /* SSE */
+-#include <emmintrin.h> /* SSE2 */
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+
+ #include "easel.h"
+ #include "esl_mpi.h"
+--- hmmer.orig/src/impl_sse/msvfilter.c
++++ hmmer/src/impl_sse/msvfilter.c
+@@ -20,8 +20,8 @@
+ #include <stdio.h>
+ #include <math.h>
+
+-#include <xmmintrin.h> /* SSE */
+-#include <emmintrin.h> /* SSE2 */
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+
+ #include "easel.h"
+ #include "esl_sse.h"
+--- hmmer.orig/src/impl_sse/null2.c
++++ hmmer/src/impl_sse/null2.c
+@@ -13,8 +13,8 @@
+ #include <stdlib.h>
+ #include <string.h>
+
+-#include <xmmintrin.h> /* SSE */
+-#include <emmintrin.h> /* SSE2 */
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+
+ #include "easel.h"
+ #include "esl_sse.h"
+--- hmmer.orig/src/impl_sse/optacc.c
++++ hmmer/src/impl_sse/optacc.c
+@@ -14,8 +14,8 @@
+
+ #include <float.h>
+
+-#include <xmmintrin.h>
+-#include <emmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+
+ #include "easel.h"
+ #include "esl_sse.h"
+--- hmmer.orig/src/impl_sse/p7_omx.c
++++ hmmer/src/impl_sse/p7_omx.c
+@@ -15,8 +15,8 @@
+ #include <math.h>
+ #include <float.h>
+
+-#include <xmmintrin.h> /* SSE */
+-#include <emmintrin.h> /* SSE2 */
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+
+ #include "easel.h"
+ #include "esl_alphabet.h"
+--- hmmer.orig/src/impl_sse/p7_oprofile.c
++++ hmmer/src/impl_sse/p7_oprofile.c
+@@ -17,8 +17,8 @@
+ #include <string.h>
+ #include <math.h> /* roundf() */
+
+-#include <xmmintrin.h> /* SSE */
+-#include <emmintrin.h> /* SSE2 */
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+
+ #include "easel.h"
+ #include "esl_random.h"
+--- hmmer.orig/src/impl_sse/stotrace.c
++++ hmmer/src/impl_sse/stotrace.c
+@@ -16,8 +16,8 @@
+ #include <stdio.h>
+ #include <math.h>
+
+-#include <xmmintrin.h> /* SSE */
+-#include <emmintrin.h> /* SSE2 */
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+
+ #include "easel.h"
+ #include "esl_random.h"
+--- hmmer.orig/src/impl_sse/vitfilter.c
++++ hmmer/src/impl_sse/vitfilter.c
+@@ -21,8 +21,8 @@
+ #include <stdio.h>
+ #include <math.h>
+
+-#include <xmmintrin.h> /* SSE */
+-#include <emmintrin.h> /* SSE2 */
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+
+ #include "easel.h"
+ #include "esl_sse.h"
+--- hmmer.orig/src/impl_sse/vitscore.c
++++ hmmer/src/impl_sse/vitscore.c
+@@ -25,8 +25,8 @@
+ #include <stdio.h>
+ #include <math.h>
+
+-#include <xmmintrin.h> /* SSE */
+-#include <emmintrin.h> /* SSE2 */
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
+
+ #include "easel.h"
+ #include "esl_sse.h"
=====================================
debian/rules
=====================================
@@ -38,7 +38,7 @@ override_dh_auto_configure:
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
export V=VERBOSE ; make check -j$(shell nproc) | tee debian/test_log
- if tail -n 6 debian/test_log | head -n 1 | grep -q FAILED ; then false ; fi
+ grep -v -q FAILED debian/test_log
endif
override_dh_auto_build:
View it on GitLab: https://salsa.debian.org/med-team/hmmer/-/compare/82bbdfcbcc60314e51bd7c95d230535886b57543...c5bdc9cbd2be0cb6e13f7fa4862eb5da34a102e7
--
View it on GitLab: https://salsa.debian.org/med-team/hmmer/-/compare/82bbdfcbcc60314e51bd7c95d230535886b57543...c5bdc9cbd2be0cb6e13f7fa4862eb5da34a102e7
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