[med-svn] [Git][med-team/hisat2][master] forward patches upstream

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / hisat2


Commits:
2ad3dc9b by Michael R. Crusoe at 2020-06-20T17:43:39+02:00
forward patches upstream

- - - - -


3 changed files:

- debian/patches/hardening
- debian/patches/reproducibile
- debian/patches/simde


Changes:

=====================================
debian/patches/hardening
=====================================
@@ -1,5 +1,6 @@
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
-Description: Enable the passing of extra compilation flags, for hardening
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Enable the passing of extra compilation flags, for hardening
+Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/249
 --- hisat2.orig/Makefile
 +++ hisat2/Makefile
 @@ -176,7 +176,7 @@


=====================================
debian/patches/reproducibile
=====================================
@@ -1,5 +1,6 @@
-Author: Michael R. Crusoe
-Description: Make build reproducible
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Make build reproducible
+Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/250
 --- hisat2.orig/Makefile
 +++ hisat2/Makefile
 @@ -26,7 +26,7 @@


=====================================
debian/patches/simde
=====================================
@@ -1,18 +1,14 @@
-From: Michael R. Crusoe <michael.crusoe at gmail.com>
-Description: use the simde header library for greater compatibility
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: use the simde header library for greater compatibility
+Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/251
 --- hisat2.orig/aligner_sw.h
 +++ hisat2/aligner_sw.h
-@@ -66,11 +66,17 @@
+@@ -66,11 +66,12 @@
  
  #define INLINE_CUPS
  
 +#define SIMDE_ENABLE_NATIVE_ALIASES
 +#include <simde/x86/sse2.h>
-+#if defined(__VEC__) && defined(__ALTIVEC__) && !defined(__APPLE_ALTIVEC__)
-+#  undef vector
-+#  undef pixel
-+#  undef bool
-+#endif
  #include <stdint.h>
  #include <iostream>
  #include <limits>
@@ -23,17 +19,12 @@ Description: use the simde header library for greater compatibility
  #include "ds.h"
 --- hisat2.orig/sse_util.h
 +++ hisat2/sse_util.h
-@@ -20,11 +20,18 @@
+@@ -20,11 +20,13 @@
  #ifndef SSE_UTIL_H_
  #define SSE_UTIL_H_
  
 +#define SIMDE_ENABLE_NATIVE_ALIASES
 +#include <simde/x86/sse2.h>
-+#if defined(__VEC__) && defined(__ALTIVEC__) && !defined(__APPLE_ALTIVEC__)
-+#  undef vector
-+#  undef pixel
-+#  undef bool
-+#endif
 +
  #include "assert_helpers.h"
  #include "ds.h"



View it on GitLab: https://salsa.debian.org/med-team/hisat2/-/commit/2ad3dc9b705b8ff32228e498883fb97320a249b4

-- 
View it on GitLab: https://salsa.debian.org/med-team/hisat2/-/commit/2ad3dc9b705b8ff32228e498883fb97320a249b4
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