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 <[email protected]> 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 <[email protected]> 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 <[email protected]> --- 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> $(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 <[email protected]> --- 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 <[email protected]> --- 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
