[med-svn] [bowtie2] 04/05: Refresh patches and delete unused patches

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository bowtie2.

commit 7415845295821abd2ede53c74914fc0d828e5d2c
Author: Andreas Tille <tille at debian.org>
Date:   Wed Feb 17 22:10:50 2016 +0100

    Refresh patches and delete unused patches
---
 .../do_not_use_outdated_copy_of_cpuid_h.patch      | 15 -------
 .../patches/fix_makefile_machine_detection.patch   | 51 ----------------------
 debian/patches/hardening.patch                     |  6 +--
 debian/patches/series                              |  1 -
 4 files changed, 3 insertions(+), 70 deletions(-)

diff --git a/debian/patches/do_not_use_outdated_copy_of_cpuid_h.patch b/debian/patches/do_not_use_outdated_copy_of_cpuid_h.patch
deleted file mode 100644
index 24e0d9d..0000000
--- a/debian/patches/do_not_use_outdated_copy_of_cpuid_h.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 03 Sep 2014 09:50:22 +0200
-Description: Do not use copy of outdated gcc header file which destroys
-  portability to other architectures.
-
---- a/Makefile
-+++ b/Makefile
-@@ -59,7 +59,6 @@ endif
- POPCNT_CAPABILITY ?= 1
- ifeq (1, $(POPCNT_CAPABILITY))
-     EXTRA_FLAGS += -DPOPCNT_CAPABILITY
--    INC += -I third_party
- endif
- 
- MM_DEF = 
diff --git a/debian/patches/fix_makefile_machine_detection.patch b/debian/patches/fix_makefile_machine_detection.patch
deleted file mode 100644
index a2e9270..0000000
--- a/debian/patches/fix_makefile_machine_detection.patch
+++ /dev/null
@@ -1,51 +0,0 @@
-Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
-Last-Update: Fri, 11 May 2012 08:41:59 +0200
-Bug-Debian: http://bugs.debian.org/672526
-Description: use -msse2 only for Intel architectures
-
---- bowtie2.orig/Makefile
-+++ bowtie2/Makefile
-@@ -128,21 +128,29 @@
- SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
- VERSION = $(shell cat VERSION)
- 
--BITS=32
--ifeq (x86_64,$(shell uname -m))
--	BITS=64
--endif
--# msys will always be 32 bit so look at the cpu arch instead.
--ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
--	ifeq (1,$(MINGW))
--		BITS=64
--	endif
--endif
--ifeq (32,$(BITS))
--  $(error bowtie2 compilation requires a 64-bit platform )
--endif
-+ifeq (1,$(ENABLE_SSE))
-+ ARCH := $(shell getconf LONG_BIT)
-+ UNAME := $(shell uname -m )
-+ # Convert BITS=?? to a -m flag
-+ BITS=32
-+ BITS_FLAG = -m32
-+ ifeq (64,$(ARCH))
-+       BITS=64
-+       BITS_FLAG = -m64
-+ endif
-+ ifeq ($(UNAME),'Power Macintosh')
-+       ifeq (32,$(BITS))
-+               BITS_FLAG = -m32
-+               SSE_FLAG =
-+       endif
-+       ifeq (64,$(BITS))
-+               BITS_FLAG = -m64
-+               SSE_FLAG =
-+       endif
-+ endif
- 
--SSE_FLAG=-msse2 
-+ SSE_FLAG=-msse2
-+endif
- 
- DEBUG_FLAGS    = -O0 -g3 -m64 $(SSE_FLAG)
- DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
index fdee516..54a1811 100644
--- a/debian/patches/hardening.patch
+++ b/debian/patches/hardening.patch
@@ -2,9 +2,9 @@ Description: Patch injects hardening CPPFLAGS
 Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
 Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Last-Update: Mon, 30 Jul 2012 13:51:31 +0200
---- bowtie2.orig/Makefile
-+++ bowtie2/Makefile
-@@ -232,7 +232,8 @@
+--- a/Makefile
++++ b/Makefile
+@@ -250,7 +250,8 @@ DEFS=-fno-strict-aliasing \
       $(FILE_FLAGS) \
       $(PREF_DEF) \
       $(MM_DEF) \
diff --git a/debian/patches/series b/debian/patches/series
index b4bef34..814900f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1 @@
 hardening.patch
-# do_not_use_outdated_copy_of_cpuid_h.patch

-- 
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