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commit d8fd31183b500e7536cda0531593c2c0f2491bb0 Author: Alexandre Mestiashvili <[email protected]> Date: Tue Jan 2 16:46:44 2018 +0100 Refresh patches --- debian/patches/do-not-rebuild-during-test.patch | 18 ++- debian/patches/hardening.patch | 150 ++------------------- debian/patches/reproducible.patch | 69 +--------- ...st_requiring_non-free_libmath-random-perl.patch | 19 ++- 4 files changed, 38 insertions(+), 218 deletions(-) diff --git a/debian/patches/do-not-rebuild-during-test.patch b/debian/patches/do-not-rebuild-during-test.patch index 10cb763..817291a 100644 --- a/debian/patches/do-not-rebuild-during-test.patch +++ b/debian/patches/do-not-rebuild-during-test.patch @@ -31,26 +31,34 @@ Author: Sascha Steinbiss <[email protected]> --bowtie2-build=./bowtie2-build \ --- bowtie2.orig/scripts/test/simple_tests.sh +++ bowtie2/scripts/test/simple_tests.sh -@@ -21,14 +21,14 @@ - - # simple_tests.sh +@@ -24,18 +24,18 @@ + export ASAN_OPTIONS=halt_on_error=1 + export UBSAN_OPTIONS=halt_on_error=1 -make $* bowtie2-align-s \ - bowtie2-align-l \ - bowtie2-align-s-debug \ - bowtie2-align-l-debug \ +- bowtie2-align-s-sanitized \ +- bowtie2-align-l-sanitized \ - bowtie2-build-s \ - bowtie2-build-l \ - bowtie2-build-s-debug \ -- bowtie2-build-l-debug && \ +- bowtie2-build-l-debug \ +- bowtie2-build-s-sanitized \ +- bowtie2-build-l-sanitized && \ +#make $* bowtie2-align-s \ +# bowtie2-align-l \ +# bowtie2-align-s-debug \ +# bowtie2-align-l-debug \ ++# bowtie2-align-s-sanitized \ ++# bowtie2-align-l-sanitized \ +# bowtie2-build-s \ +# bowtie2-build-l \ +# bowtie2-build-s-debug \ -+# bowtie2-build-l-debug && \ ++# bowtie2-build-l-debug \ ++# bowtie2-build-s-sanitized \ ++# bowtie2-build-l-sanitized && \ perl scripts/test/simple_tests.pl \ --bowtie2=./bowtie2 \ --bowtie2-build=./bowtie2-build \ diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch index 1df586d..9739edc 100644 --- a/debian/patches/hardening.patch +++ b/debian/patches/hardening.patch @@ -2,143 +2,17 @@ Description: Patch injects hardening C(PP,XX) FLAGS and LDFLAGS Author: Alexandre Mestiashvili <[email protected]> Sascha Steinbiss <[email protected]> Origin: Debian Med Packaging Team <[email protected]> -Last-Update: Thu, 25 Aug 2016 13:47:22 +0000 +Last-Update: Tue, 2 Jan 2018 16:20:02 +0100 --- bowtie2.orig/Makefile +++ bowtie2/Makefile -@@ -273,7 +273,9 @@ - $(FILE_FLAGS) \ - $(PREF_DEF) \ - $(MM_DEF) \ -- $(SHMEM_DEF) -+ $(SHMEM_DEF)\ -+ $(CPPFLAGS) \ -+ $(CFLAGS) - - # - # bowtie2-build targets -@@ -285,7 +287,7 @@ - $(INC) \ - -o $@ $< \ - $(SHARED_CPPS) $(BUILD_CPPS_MAIN) \ -- $(LIBS) $(BUILD_LIBS) -+ $(LIBS) $(BUILD_LIBS) $(LDFLAGS) - - bowtie2-build-l: bt2_build.cpp $(SHARED_CPPS) $(HEADERS) - $(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \ -@@ -293,7 +295,7 @@ - $(INC) \ - -o $@ $< \ - $(SHARED_CPPS) $(BUILD_CPPS_MAIN) \ -- $(LIBS) $(BUILD_LIBS) -+ $(LIBS) $(BUILD_LIBS) $(LDFLAGS) - - bowtie2-build-s-debug: bt2_build.cpp $(SHARED_CPPS) $(HEADERS) - $(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \ -@@ -301,7 +303,7 @@ - $(INC) \ - -o $@ $< \ - $(SHARED_CPPS) $(BUILD_CPPS_MAIN) \ -- $(LIBS) $(BUILD_LIBS) -+ $(LIBS) $(BUILD_LIBS) $(LDFLAGS) - - bowtie2-build-l-debug: bt2_build.cpp $(SHARED_CPPS) $(HEADERS) - $(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \ -@@ -309,7 +311,7 @@ - $(INC) \ - -o $@ $< \ - $(SHARED_CPPS) $(BUILD_CPPS_MAIN) \ -- $(LIBS) $(BUILD_LIBS) -+ $(LIBS) $(BUILD_LIBS) $(LDFLAGS) - - # - # bowtie2-align targets -@@ -321,7 +323,7 @@ - $(INC) \ - -o $@ $< \ - $(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \ -- $(LIBS) $(SEARCH_LIBS) -+ $(LIBS) $(SEARCH_LIBS) $(LDFLAGS) - - bowtie2-align-l: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS) - $(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \ -@@ -329,7 +331,7 @@ - $(INC) \ - -o $@ $< \ - $(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \ -- $(LIBS) $(SEARCH_LIBS) -+ $(LIBS) $(SEARCH_LIBS) $(LDFLAGS) - - bowtie2-align-s-debug: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS) - $(CXX) $(DEBUG_FLAGS) \ -@@ -338,7 +340,7 @@ - $(INC) \ - -o $@ $< \ - $(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \ -- $(LIBS) $(SEARCH_LIBS) -+ $(LIBS) $(SEARCH_LIBS) $(LDFLAGS) - - bowtie2-align-l-debug: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS) - $(CXX) $(DEBUG_FLAGS) \ -@@ -347,7 +349,7 @@ - $(INC) \ - -o $@ $< \ - $(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \ -- $(LIBS) $(SEARCH_LIBS) -+ $(LIBS) $(SEARCH_LIBS) $(LDFLAGS) - - # - # bowtie2-inspect targets -@@ -360,7 +362,7 @@ - $(INC) -I . \ - -o $@ $< \ - $(SHARED_CPPS) \ -- $(LIBS) $(INSPECT_LIBS) -+ $(LIBS) $(INSPECT_LIBS) $(LDFLAGS) - - bowtie2-inspect-l: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS) - $(CXX) $(RELEASE_FLAGS) \ -@@ -369,7 +371,7 @@ - $(INC) -I . \ - -o $@ $< \ - $(SHARED_CPPS) \ -- $(LIBS) $(INSPECT_LIBS) -+ $(LIBS) $(INSPECT_LIBS) $(LDFLAGS) - - bowtie2-inspect-s-debug: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS) - $(CXX) $(DEBUG_FLAGS) \ -@@ -378,7 +380,7 @@ - $(INC) -I . \ - -o $@ $< \ - $(SHARED_CPPS) \ -- $(LIBS) $(INSPECT_LIBS) -+ $(LIBS) $(INSPECT_LIBS) $(LDFLAGS) - - bowtie2-inspect-l-debug: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS) - $(CXX) $(DEBUG_FLAGS) \ -@@ -387,7 +389,7 @@ - $(INC) -I . \ - -o $@ $< \ - $(SHARED_CPPS) \ -- $(LIBS) $(INSPECT_LIBS) -+ $(LIBS) $(INSPECT_LIBS) $(LDFLAGS) - - # - # bowtie2-dp targets -@@ -400,7 +402,7 @@ - $(INC) -I . \ - -o $@ $< \ - $(DP_CPPS) $(SHARED_CPPS) \ -- $(LIBS) $(SEARCH_LIBS) -+ $(LIBS) $(SEARCH_LIBS) $(LDFLAGS) - - bowtie2-dp-debug: bt2_dp.cpp $(HEADERS) $(SHARED_CPPS) $(DP_CPPS) - $(CXX) $(DEBUG_FLAGS) \ -@@ -409,7 +411,7 @@ - $(INC) -I . \ - -o $@ $< \ - $(DP_CPPS) $(SHARED_CPPS) \ -- $(LIBS) $(SEARCH_LIBS) -+ $(LIBS) $(SEARCH_LIBS) $(LDFLAGS) - - bowtie2.bat: - echo "@echo off" > bowtie2.bat +@@ -290,7 +290,9 @@ + $(FILE_FLAGS) \ + $(PREF_DEF) \ + $(MM_DEF) \ +- $(SHMEM_DEF) ++ $(SHMEM_DEF) \ ++ $(CPPFLAGS) \ ++ $(CFLAGS) + + # set compiler flags for all sanitized builds + $(BOWTIE2_BIN_LIST_SAN): CXXFLAGS += $(SANITIZER_FLAGS) diff --git a/debian/patches/reproducible.patch b/debian/patches/reproducible.patch index a0642d4..254aeef 100644 --- a/debian/patches/reproducible.patch +++ b/debian/patches/reproducible.patch @@ -6,73 +6,14 @@ Author: Sascha Steinbiss <[email protected]> --- bowtie2.orig/Makefile +++ bowtie2/Makefile @@ -31,7 +31,7 @@ - CC ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX) CPP ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX) CXX ?= $(CPP) --HEADERS = $(wildcard *.h) -+HEADERS = $(sort $(wildcard *.h)) - BOWTIE_MM = 1 - BOWTIE_SHARED_MEM = -@@ -165,7 +165,7 @@ - BUILD_CPPS = diff_sample.cpp - BUILD_CPPS_MAIN = $(BUILD_CPPS) bowtie_build_main.cpp +-HEADERS := $(wildcard *.h) ++HEADERS := $(sort $(wildcard *.h)) + BOWTIE_MM := 1 + BOWTIE_SHARED_MEM := --SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c) -+SEARCH_FRAGMENTS = $(sort $(wildcard search_*_phase*.c)) - VERSION = $(shell cat VERSION) - - BITS=32 -@@ -207,14 +207,14 @@ - bowtie2-inspect-s-debug \ - bowtie2-inspect-l-debug - --GENERAL_LIST = $(wildcard scripts/*.sh) \ -- $(wildcard scripts/*.pl) \ -+GENERAL_LIST = $(sort $(wildcard scripts/*.sh)) \ -+ $(sort $(wildcard scripts/*.pl)) \ - doc/manual.html \ - doc/README \ - doc/style.css \ -- $(wildcard example/index/*.bt2) \ -- $(wildcard example/reads/*.fq) \ -- $(wildcard example/reads/*.pl) \ -+ $(sort $(wildcard example/index/*.bt2)) \ -+ $(sort $(wildcard example/reads/*.fq)) \ -+ $(sort $(wildcard example/reads/*.pl)) \ - example/reference/lambda_virus.fa \ - $(PTHREAD_PKG) \ - bowtie2 \ -@@ -241,11 +241,11 @@ - # the Windows FIND tool instead. - FIND=$(shell which find) - --SRC_PKG_LIST = $(wildcard *.h) \ -- $(wildcard *.hh) \ -- $(wildcard *.c) \ -- $(wildcard *.cpp) \ -- $(wildcard third_party/*) \ -+SRC_PKG_LIST = $(sort $(wildcard *.h)) \ -+ $(sort $(wildcard *.hh)) \ -+ $(sort $(wildcard *.c)) \ -+ $(sort $(wildcard *.cpp)) \ -+ $(sort $(wildcard third_party/*)) \ - Makefile \ - $(GENERAL_LIST) - -@@ -267,9 +267,9 @@ - - DEFS=-fno-strict-aliasing \ - -DBOWTIE2_VERSION="\"`cat VERSION`\"" \ -- -DBUILD_HOST="\"`hostname`\"" \ -- -DBUILD_TIME="\"`date`\"" \ -- -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \ -+ -DBUILD_HOST="\"\"" \ -+ -DBUILD_TIME="\"\"" \ -+ -DCOMPILER_VERSION="\"\"" \ - $(FILE_FLAGS) \ - $(PREF_DEF) \ - $(MM_DEF) \ --- bowtie2.orig/bt2_build.cpp +++ bowtie2/bt2_build.cpp @@ -548,15 +548,15 @@ @@ -129,7 +70,7 @@ Author: Sascha Steinbiss <[email protected]> --- bowtie2.orig/bt2_search.cpp +++ bowtie2/bt2_search.cpp -@@ -5000,15 +5000,15 @@ +@@ -5006,15 +5006,15 @@ } else { cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl; } diff --git a/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch b/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch index 0b19f6d..7bfce1b 100644 --- a/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch +++ b/debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch @@ -165,33 +165,30 @@ Description: Math::Random is in package libmath-random-perl which is print STDERR "DONE\n"; --- bowtie2.orig/Makefile +++ bowtie2/Makefile -@@ -485,13 +485,13 @@ - cp -f $$file $(DESTDIR)$(bindir) ; \ +@@ -506,12 +506,12 @@ done --.PHONY: simple-test --simple-test: all perl-deps -+.PHONY: simple-test perl-deps + .PHONY: simple-test +-simple-test: perl-deps both both-debug both-sanitized +simple-test: all eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \ sh ./scripts/test/simple_tests.sh --.PHONY: random-test + .PHONY: random-test -random-test: all perl-deps -+.PHONY: random-test perl-deps +random-test: all eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \ sh ./scripts/sim/run.sh $(if $(NUM_CORES), $(NUM_CORES), 2) -@@ -502,7 +502,6 @@ +@@ -522,7 +522,6 @@ mkdir .perllib.tmp ; \ $$DL http://cpanmin.us | perl - -l $(CURDIR)/.perllib.tmp App::cpanminus local::lib ; \ eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \ -- cpanm --force Math::Random Clone Test::Deep Sys::Info ; \ +- $(CURDIR)/.perllib.tmp/bin/cpanm --force Math::Random Clone Test::Deep Sys::Info ; \ fi - static-libs: -@@ -523,7 +522,7 @@ + .PHONY: static-libs +@@ -544,7 +543,7 @@ && cp -r include/tbb $(CURDIR)/.include && cp build/*_release/*.a $(CURDIR)/.lib .PHONY: test -- 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
