[med-svn] [bowtie] 03/06: Refresh patches

Alex Mestiashvili malex-guest at moszumanska.debian.org
Sat Dec 16 19:08:01 UTC 2017 

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

malex-guest pushed a commit to branch master
in repository bowtie.

commit 600747edb82e7e1101a05b80d36b026d909ebc0b
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Sat Dec 16 19:01:22 2017 +0100

    Refresh patches
---
 debian/patches/build-as-Cpp03.patch              | 2 +-
 debian/patches/disable_bits_flag.patch           | 2 +-
 debian/patches/enable_arm64.patch                | 2 +-
 debian/patches/gcc-64bit.patch                   | 2 +-
 debian/patches/no_hash_style_both_for_mips.patch | 2 +-
 debian/patches/ppc64el.patch                     | 4 ++--
 debian/patches/reproducible.patch                | 4 ++--
 debian/patches/seqan-rename-ChunkPool.patch      | 8 ++++----
 debian/patches/use-dpkg-buildflags.patch         | 2 +-
 debian/patches/use_debian_seqan.patch            | 2 +-
 10 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/debian/patches/build-as-Cpp03.patch b/debian/patches/build-as-Cpp03.patch
index bc98b01..9ccc871 100644
--- a/debian/patches/build-as-Cpp03.patch
+++ b/debian/patches/build-as-Cpp03.patch
@@ -16,4 +16,4 @@ Subject: build as C++03
 +EXTRA_CXXFLAGS = -std=c++03
  CFLAGS += $(EXTRA_CFLAGS)
  CXXFLAGS += $(EXTRA_CXXFLAGS)
- WARNING_FLAGS = -Wall -Wno-unused-private-field \
+ WARNING_FLAGS = -Wall -Wno-unused-parameter -Wno-reorder \
diff --git a/debian/patches/disable_bits_flag.patch b/debian/patches/disable_bits_flag.patch
index 7811b75..56c2500 100644
--- a/debian/patches/disable_bits_flag.patch
+++ b/debian/patches/disable_bits_flag.patch
@@ -7,7 +7,7 @@ Last-Update: 2014-08-13
 
 --- bowtie.orig/Makefile
 +++ bowtie/Makefile
-@@ -183,8 +183,8 @@
+@@ -182,8 +182,8 @@
      $(error bowtie2 compilation requires a 64-bit platform )
  endif
  
diff --git a/debian/patches/enable_arm64.patch b/debian/patches/enable_arm64.patch
index 1d2f3b7..dc03084 100644
--- a/debian/patches/enable_arm64.patch
+++ b/debian/patches/enable_arm64.patch
@@ -5,7 +5,7 @@ Author: Edmund Grimley Evans <edmund.grimley.evans at gmail.com>
 Last-Update: Wed, 30 Sep 2015 19:09:04 +0100
 --- bowtie.orig/Makefile
 +++ bowtie/Makefile
-@@ -163,7 +163,7 @@
+@@ -162,7 +162,7 @@
  VERSION = $(shell cat VERSION)
  
  BITS=32
diff --git a/debian/patches/gcc-64bit.patch b/debian/patches/gcc-64bit.patch
index 770bb98..72229ae 100644
--- a/debian/patches/gcc-64bit.patch
+++ b/debian/patches/gcc-64bit.patch
@@ -12,7 +12,7 @@ Author: James Cowgill <jcowgill at debian.org>
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
 --- bowtie.orig/Makefile
 +++ bowtie/Makefile
-@@ -163,7 +163,7 @@
+@@ -162,7 +162,7 @@
  VERSION = $(shell cat VERSION)
  
  BITS=32
diff --git a/debian/patches/no_hash_style_both_for_mips.patch b/debian/patches/no_hash_style_both_for_mips.patch
index 29a7598..680f6a7 100644
--- a/debian/patches/no_hash_style_both_for_mips.patch
+++ b/debian/patches/no_hash_style_both_for_mips.patch
@@ -8,7 +8,7 @@ Bug-Debian: https://bugs.debian.org/864439
 
 --- bowtie.orig/Makefile
 +++ bowtie/Makefile
-@@ -63,7 +63,9 @@
+@@ -62,7 +62,9 @@
  LINUX =
  ifneq (,$(findstring Linux,$(shell uname)))
      LINUX = 1
diff --git a/debian/patches/ppc64el.patch b/debian/patches/ppc64el.patch
index 4424943..76d9be0 100644
--- a/debian/patches/ppc64el.patch
+++ b/debian/patches/ppc64el.patch
@@ -13,7 +13,7 @@ Last-Update: Fri, 12 Jun 2015 14:39:07 UTC
  CPP = g++
  CXX = $(CPP)
  CC = gcc
-@@ -104,11 +104,11 @@
+@@ -103,11 +103,11 @@
  	LIBS += $(PTHREAD_LIB)
  endif
  
@@ -30,7 +30,7 @@ Last-Update: Fri, 12 Jun 2015 14:39:07 UTC
  
  PREFETCH_LOCALITY = 2
  PREF_DEF = -DPREFETCH_LOCALITY=$(PREFETCH_LOCALITY)
-@@ -163,7 +163,7 @@
+@@ -162,7 +162,7 @@
  VERSION = $(shell cat VERSION)
  
  BITS=32
diff --git a/debian/patches/reproducible.patch b/debian/patches/reproducible.patch
index e44bca9..39de59f 100644
--- a/debian/patches/reproducible.patch
+++ b/debian/patches/reproducible.patch
@@ -2,7 +2,7 @@ Description: make build reproducible
 Author: Sascha Steinbiss <sascha at steinbiss.name>
 --- bowtie.orig/Makefile
 +++ bowtie/Makefile
-@@ -245,9 +245,9 @@
+@@ -244,9 +244,9 @@
  
  DEFS=-fno-strict-aliasing \
       -DBOWTIE_VERSION="\"`cat VERSION`\"" \
@@ -15,7 +15,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
       $(FILE_FLAGS) \
       $(PTHREAD_DEF) \
       $(PREF_DEF) \
-@@ -255,8 +255,8 @@
+@@ -254,8 +254,8 @@
       $(SHMEM_DEF)
  
  ALL_FLAGS = $(EXTRA_FLAGS) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS)
diff --git a/debian/patches/seqan-rename-ChunkPool.patch b/debian/patches/seqan-rename-ChunkPool.patch
index 77cb74a..9c638c5 100644
--- a/debian/patches/seqan-rename-ChunkPool.patch
+++ b/debian/patches/seqan-rename-ChunkPool.patch
@@ -232,7 +232,7 @@ Last-Update: 2013-04-18
  	chunkVerbose			= false; // have chunk allocator output status messages?
  	useV1					= true;
  	reportSe				= false;
-@@ -1342,7 +1342,7 @@
+@@ -1340,7 +1340,7 @@
  	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
  	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
  
@@ -241,7 +241,7 @@ Last-Update: 2013-04-18
  	UnpairedExactAlignerV1Factory alSEfact(
  			ebwt,
  			NULL,
-@@ -1630,7 +1630,7 @@
+@@ -1631,7 +1631,7 @@
  	// Global initialization
  	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
  	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
@@ -250,7 +250,7 @@ Last-Update: 2013-04-18
  
  	Unpaired1mmAlignerV1Factory alSEfact(
  			ebwtFw,
-@@ -2082,7 +2082,7 @@
+@@ -2084,7 +2084,7 @@
  	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
  	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
  
@@ -259,7 +259,7 @@ Last-Update: 2013-04-18
  	Unpaired23mmAlignerV1Factory alSEfact(
  			ebwtFw,
  			&ebwtBw,
-@@ -2753,7 +2753,7 @@
+@@ -2756,7 +2756,7 @@
  	// Global initialization
  	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
  	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
diff --git a/debian/patches/use-dpkg-buildflags.patch b/debian/patches/use-dpkg-buildflags.patch
index ccb6e69..a475050 100644
--- a/debian/patches/use-dpkg-buildflags.patch
+++ b/debian/patches/use-dpkg-buildflags.patch
@@ -6,7 +6,7 @@ Bug-Closed: http://bugs.debian.org/670230
 
 --- bowtie.orig/Makefile
 +++ bowtie/Makefile
-@@ -255,7 +255,7 @@
+@@ -254,7 +254,7 @@
       $(MM_DEF) \
       $(SHMEM_DEF)
  
diff --git a/debian/patches/use_debian_seqan.patch b/debian/patches/use_debian_seqan.patch
index ca18f17..b5d3111 100644
--- a/debian/patches/use_debian_seqan.patch
+++ b/debian/patches/use_debian_seqan.patch
@@ -15,7 +15,7 @@ Reviewed-by: Ognyan Kulev <ogi at debian.org>
  # treat SeqAn as a sysdir to suppress warnings
  SEQAN_INC = -isystem $(SEQAN_DIR)
  INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party
-@@ -208,7 +208,6 @@
+@@ -207,7 +207,6 @@
                 $(wildcard genomes/NC_008253.fna) \
                 $(wildcard reads/e_coli_1000.*) \
                 $(wildcard reads/e_coli_1000_*) \

-- 
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