[med-svn] [bowtie2] 07/10: Refresh patches
Andreas Tille
tille at debian.org
Mon Jan 9 12:30:42 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository bowtie2.
commit 1ec379336d0799f1e7011c35aa02dcf6d7d9222f
Author: Andreas Tille <tille at debian.org>
Date: Mon Jan 9 12:55:58 2017 +0100
Refresh patches
---
debian/patches/hardening.patch | 32 ++++++++++++++++----------------
debian/patches/reproducible.patch | 16 ++++++++--------
2 files changed, 24 insertions(+), 24 deletions(-)
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
index 8f05d40..297a245 100644
--- a/debian/patches/hardening.patch
+++ b/debian/patches/hardening.patch
@@ -5,7 +5,7 @@ Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Last-Update: Thu, 25 Aug 2016 13:47:22 +0000
--- a/Makefile
+++ b/Makefile
-@@ -254,7 +254,9 @@
+@@ -270,7 +270,9 @@ DEFS=-fno-strict-aliasing \
$(FILE_FLAGS) \
$(PREF_DEF) \
$(MM_DEF) \
@@ -16,7 +16,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000
#
# bowtie2-build targets
-@@ -266,7 +268,7 @@
+@@ -282,7 +284,7 @@ bowtie2-build-s: bt2_build.cpp $(SHARED_
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(BUILD_CPPS_MAIN) \
@@ -25,7 +25,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000
bowtie2-build-l: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
-@@ -274,7 +276,7 @@
+@@ -290,7 +292,7 @@ bowtie2-build-l: bt2_build.cpp $(SHARED_
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(BUILD_CPPS_MAIN) \
@@ -34,7 +34,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000
bowtie2-build-s-debug: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
-@@ -282,7 +284,7 @@
+@@ -298,7 +300,7 @@ bowtie2-build-s-debug: bt2_build.cpp $(S
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(BUILD_CPPS_MAIN) \
@@ -43,7 +43,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000
bowtie2-build-l-debug: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
-@@ -290,7 +292,7 @@
+@@ -306,7 +308,7 @@ bowtie2-build-l-debug: bt2_build.cpp $(S
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(BUILD_CPPS_MAIN) \
@@ -52,7 +52,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000
#
# bowtie2-align targets
-@@ -302,7 +304,7 @@
+@@ -318,7 +320,7 @@ bowtie2-align-s: bt2_search.cpp $(SEARCH
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \
@@ -61,7 +61,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000
bowtie2-align-l: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
-@@ -310,7 +312,7 @@
+@@ -326,7 +328,7 @@ bowtie2-align-l: bt2_search.cpp $(SEARCH
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \
@@ -70,7 +70,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000
bowtie2-align-s-debug: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(DEBUG_FLAGS) \
-@@ -319,7 +321,7 @@
+@@ -335,7 +337,7 @@ bowtie2-align-s-debug: bt2_search.cpp $(
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \
@@ -79,7 +79,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000
bowtie2-align-l-debug: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(DEBUG_FLAGS) \
-@@ -328,7 +330,7 @@
+@@ -344,7 +346,7 @@ bowtie2-align-l-debug: bt2_search.cpp $(
$(INC) \
-o $@ $< \
$(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \
@@ -88,7 +88,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000
#
# bowtie2-inspect targets
-@@ -341,7 +343,7 @@
+@@ -357,7 +359,7 @@ bowtie2-inspect-s: bt2_inspect.cpp $(HEA
$(INC) -I . \
-o $@ $< \
$(SHARED_CPPS) \
@@ -97,16 +97,16 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000
bowtie2-inspect-l: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
$(CXX) $(RELEASE_FLAGS) \
-@@ -350,7 +352,7 @@
+@@ -366,7 +368,7 @@ bowtie2-inspect-l: bt2_inspect.cpp $(HEA
$(INC) -I . \
-o $@ $< \
$(SHARED_CPPS) \
- $(LIBS) $(INSPECT_LIBS)
+ $(LIBS) $(INSPECT_LIBS) $(LDFLAGS)
- bowtie2-inspect-s-debug: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
+ bowtie2-inspect-s-debug: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
$(CXX) $(DEBUG_FLAGS) \
-@@ -359,7 +361,7 @@
+@@ -375,7 +377,7 @@ bowtie2-inspect-s-debug: bt2_inspect.cpp
$(INC) -I . \
-o $@ $< \
$(SHARED_CPPS) \
@@ -115,7 +115,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000
bowtie2-inspect-l-debug: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
$(CXX) $(DEBUG_FLAGS) \
-@@ -368,7 +370,7 @@
+@@ -384,7 +386,7 @@ bowtie2-inspect-l-debug: bt2_inspect.cpp
$(INC) -I . \
-o $@ $< \
$(SHARED_CPPS) \
@@ -124,7 +124,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000
#
# bowtie2-dp targets
-@@ -381,7 +383,7 @@
+@@ -397,7 +399,7 @@ bowtie2-dp: bt2_dp.cpp $(HEADERS) $(SHAR
$(INC) -I . \
-o $@ $< \
$(DP_CPPS) $(SHARED_CPPS) \
@@ -133,7 +133,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000
bowtie2-dp-debug: bt2_dp.cpp $(HEADERS) $(SHARED_CPPS) $(DP_CPPS)
$(CXX) $(DEBUG_FLAGS) \
-@@ -390,7 +392,7 @@
+@@ -406,7 +408,7 @@ bowtie2-dp-debug: bt2_dp.cpp $(HEADERS)
$(INC) -I . \
-o $@ $< \
$(DP_CPPS) $(SHARED_CPPS) \
diff --git a/debian/patches/reproducible.patch b/debian/patches/reproducible.patch
index f9cc79b..2ca2aff 100644
--- a/debian/patches/reproducible.patch
+++ b/debian/patches/reproducible.patch
@@ -5,7 +5,7 @@ Description: make build reproducible
Author: Sascha Steinbiss <sascha at steinbiss.name>
--- a/Makefile
+++ b/Makefile
-@@ -30,7 +30,7 @@
+@@ -30,7 +30,7 @@ GCC_SUFFIX =
CC ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
CPP ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
CXX ?= $(CPP)
@@ -14,7 +14,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
BOWTIE_MM = 1
BOWTIE_SHARED_MEM = 0
-@@ -145,7 +145,7 @@
+@@ -161,7 +161,7 @@ DP_CPPS = qual.cpp aligner_sw.cpp aligne
BUILD_CPPS = diff_sample.cpp
BUILD_CPPS_MAIN = $(BUILD_CPPS) bowtie_build_main.cpp
@@ -23,7 +23,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
VERSION = $(shell cat VERSION)
BITS=32
-@@ -187,14 +187,14 @@
+@@ -203,14 +203,14 @@ BOWTIE2_BIN_LIST_AUX = bowtie2-build-s-d
bowtie2-inspect-s-debug \
bowtie2-inspect-l-debug
@@ -43,7 +43,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
example/reference/lambda_virus.fa \
$(PTHREAD_PKG) \
bowtie2 \
-@@ -221,11 +221,11 @@
+@@ -237,11 +237,11 @@ endif
# the Windows FIND tool instead.
FIND=$(shell which find)
@@ -60,7 +60,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
doc/strip_markdown.pl \
Makefile \
$(GENERAL_LIST)
-@@ -248,9 +248,9 @@
+@@ -264,9 +264,9 @@ both-debug: bowtie2-align-s-debug bowtie
DEFS=-fno-strict-aliasing \
-DBOWTIE2_VERSION="\"`cat VERSION`\"" \
@@ -75,7 +75,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
$(MM_DEF) \
--- a/bt2_build.cpp
+++ b/bt2_build.cpp
-@@ -533,15 +533,15 @@
+@@ -533,15 +533,15 @@ int bowtie_build(int argc, const char **
} else {
cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl;
}
@@ -102,7 +102,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
--- a/bt2_inspect.cpp
+++ b/bt2_inspect.cpp
-@@ -445,15 +445,15 @@
+@@ -443,15 +443,15 @@ int main(int argc, char **argv) {
} else {
cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl;
}
@@ -129,7 +129,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
--- a/bt2_search.cpp
+++ b/bt2_search.cpp
-@@ -4648,15 +4648,15 @@
+@@ -4653,15 +4653,15 @@ int bowtie(int argc, const char **argv)
} else {
cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl;
}
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bowtie2.git
More information about the debian-med-commit
mailing list