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commit b525e0f8c4793632cdb72433914877f127b266c1 Author: Alexandre Mestiashvili <[email protected]> Date: Tue Mar 7 11:06:13 2017 +0100 Refresh patches --- debian/patches/do-not-rebuild-during-test.patch | 10 +++---- debian/patches/hardening.patch | 34 +++++++++++----------- debian/patches/reproducible.patch | 32 ++++++++++---------- debian/patches/single-cpu-for-test.patch | 14 ++++----- ...st_requiring_non-free_libmath-random-perl.patch | 12 ++++---- 5 files changed, 51 insertions(+), 51 deletions(-) diff --git a/debian/patches/do-not-rebuild-during-test.patch b/debian/patches/do-not-rebuild-during-test.patch index 0d09145..10cb763 100644 --- a/debian/patches/do-not-rebuild-during-test.patch +++ b/debian/patches/do-not-rebuild-during-test.patch @@ -2,8 +2,8 @@ Description: do not rebuild with default settings during test The test suite builds the debug versions of the executables with default flags, while is needs to be built with the flags in d/rules. Author: Sascha Steinbiss <[email protected]> ---- a/scripts/sim/run.sh -+++ b/scripts/sim/run.sh +--- bowtie2.orig/scripts/sim/run.sh ++++ bowtie2/scripts/sim/run.sh @@ -21,15 +21,15 @@ CPUS=$1 @@ -29,8 +29,8 @@ Author: Sascha Steinbiss <[email protected]> perl scripts/sim/run.pl \ --bowtie2=./bowtie2 \ --bowtie2-build=./bowtie2-build \ ---- a/scripts/test/simple_tests.sh -+++ b/scripts/test/simple_tests.sh +--- bowtie2.orig/scripts/test/simple_tests.sh ++++ bowtie2/scripts/test/simple_tests.sh @@ -21,14 +21,14 @@ # simple_tests.sh @@ -53,4 +53,4 @@ Author: Sascha Steinbiss <[email protected]> +# bowtie2-build-l-debug && \ perl scripts/test/simple_tests.pl \ --bowtie2=./bowtie2 \ - --bowtie2-build=./bowtie2-build + --bowtie2-build=./bowtie2-build \ diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch index 297a245..63f96c0 100644 --- a/debian/patches/hardening.patch +++ b/debian/patches/hardening.patch @@ -3,9 +3,9 @@ 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 ---- a/Makefile -+++ b/Makefile -@@ -270,7 +270,9 @@ DEFS=-fno-strict-aliasing \ +--- bowtie2.orig/Makefile ++++ bowtie2/Makefile +@@ -271,7 +271,9 @@ $(FILE_FLAGS) \ $(PREF_DEF) \ $(MM_DEF) \ @@ -16,7 +16,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000 # # bowtie2-build targets -@@ -282,7 +284,7 @@ bowtie2-build-s: bt2_build.cpp $(SHARED_ +@@ -283,7 +285,7 @@ $(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) \ -@@ -290,7 +292,7 @@ bowtie2-build-l: bt2_build.cpp $(SHARED_ +@@ -291,7 +293,7 @@ $(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) \ -@@ -298,7 +300,7 @@ bowtie2-build-s-debug: bt2_build.cpp $(S +@@ -299,7 +301,7 @@ $(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) \ -@@ -306,7 +308,7 @@ bowtie2-build-l-debug: bt2_build.cpp $(S +@@ -307,7 +309,7 @@ $(INC) \ -o $@ $< \ $(SHARED_CPPS) $(BUILD_CPPS_MAIN) \ @@ -52,7 +52,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000 # # bowtie2-align targets -@@ -318,7 +320,7 @@ bowtie2-align-s: bt2_search.cpp $(SEARCH +@@ -319,7 +321,7 @@ $(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) \ -@@ -326,7 +328,7 @@ bowtie2-align-l: bt2_search.cpp $(SEARCH +@@ -327,7 +329,7 @@ $(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) \ -@@ -335,7 +337,7 @@ bowtie2-align-s-debug: bt2_search.cpp $( +@@ -336,7 +338,7 @@ $(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) \ -@@ -344,7 +346,7 @@ bowtie2-align-l-debug: bt2_search.cpp $( +@@ -345,7 +347,7 @@ $(INC) \ -o $@ $< \ $(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \ @@ -88,7 +88,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000 # # bowtie2-inspect targets -@@ -357,7 +359,7 @@ bowtie2-inspect-s: bt2_inspect.cpp $(HEA +@@ -358,7 +360,7 @@ $(INC) -I . \ -o $@ $< \ $(SHARED_CPPS) \ @@ -97,7 +97,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000 bowtie2-inspect-l: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS) $(CXX) $(RELEASE_FLAGS) \ -@@ -366,7 +368,7 @@ bowtie2-inspect-l: bt2_inspect.cpp $(HEA +@@ -367,7 +369,7 @@ $(INC) -I . \ -o $@ $< \ $(SHARED_CPPS) \ @@ -106,7 +106,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000 bowtie2-inspect-s-debug: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS) $(CXX) $(DEBUG_FLAGS) \ -@@ -375,7 +377,7 @@ bowtie2-inspect-s-debug: bt2_inspect.cpp +@@ -376,7 +378,7 @@ $(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) \ -@@ -384,7 +386,7 @@ bowtie2-inspect-l-debug: bt2_inspect.cpp +@@ -385,7 +387,7 @@ $(INC) -I . \ -o $@ $< \ $(SHARED_CPPS) \ @@ -124,7 +124,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000 # # bowtie2-dp targets -@@ -397,7 +399,7 @@ bowtie2-dp: bt2_dp.cpp $(HEADERS) $(SHAR +@@ -398,7 +400,7 @@ $(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) \ -@@ -406,7 +408,7 @@ bowtie2-dp-debug: bt2_dp.cpp $(HEADERS) +@@ -407,7 +409,7 @@ $(INC) -I . \ -o $@ $< \ $(DP_CPPS) $(SHARED_CPPS) \ diff --git a/debian/patches/reproducible.patch b/debian/patches/reproducible.patch index 2ca2aff..3beda9d 100644 --- a/debian/patches/reproducible.patch +++ b/debian/patches/reproducible.patch @@ -3,9 +3,9 @@ Description: make build reproducible hostname, time, etc. from the binary. It also ensures a stable sorting order for all wildcard expansions in the Makefile. Author: Sascha Steinbiss <[email protected]> ---- a/Makefile -+++ b/Makefile -@@ -30,7 +30,7 @@ GCC_SUFFIX = +--- bowtie2.orig/Makefile ++++ bowtie2/Makefile +@@ -31,7 +31,7 @@ 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 -@@ -161,7 +161,7 @@ DP_CPPS = qual.cpp aligner_sw.cpp aligne +@@ -162,7 +162,7 @@ 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 -@@ -203,14 +203,14 @@ BOWTIE2_BIN_LIST_AUX = bowtie2-build-s-d +@@ -204,14 +204,14 @@ bowtie2-inspect-s-debug \ bowtie2-inspect-l-debug @@ -43,7 +43,7 @@ Author: Sascha Steinbiss <[email protected]> example/reference/lambda_virus.fa \ $(PTHREAD_PKG) \ bowtie2 \ -@@ -237,11 +237,11 @@ endif +@@ -238,11 +238,11 @@ # the Windows FIND tool instead. FIND=$(shell which find) @@ -60,7 +60,7 @@ Author: Sascha Steinbiss <[email protected]> doc/strip_markdown.pl \ Makefile \ $(GENERAL_LIST) -@@ -264,9 +264,9 @@ both-debug: bowtie2-align-s-debug bowtie +@@ -265,9 +265,9 @@ DEFS=-fno-strict-aliasing \ -DBOWTIE2_VERSION="\"`cat VERSION`\"" \ @@ -73,9 +73,9 @@ Author: Sascha Steinbiss <[email protected]> $(FILE_FLAGS) \ $(PREF_DEF) \ $(MM_DEF) \ ---- a/bt2_build.cpp -+++ b/bt2_build.cpp -@@ -533,15 +533,15 @@ int bowtie_build(int argc, const char ** +--- bowtie2.orig/bt2_build.cpp ++++ bowtie2/bt2_build.cpp +@@ -533,15 +533,15 @@ } else { cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl; } @@ -100,9 +100,9 @@ Author: Sascha Steinbiss <[email protected]> return 0; } ---- a/bt2_inspect.cpp -+++ b/bt2_inspect.cpp -@@ -443,15 +443,15 @@ int main(int argc, char **argv) { +--- bowtie2.orig/bt2_inspect.cpp ++++ bowtie2/bt2_inspect.cpp +@@ -443,15 +443,15 @@ } else { cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl; } @@ -127,9 +127,9 @@ Author: Sascha Steinbiss <[email protected]> return 0; } ---- a/bt2_search.cpp -+++ b/bt2_search.cpp -@@ -4653,15 +4653,15 @@ int bowtie(int argc, const char **argv) +--- bowtie2.orig/bt2_search.cpp ++++ bowtie2/bt2_search.cpp +@@ -4658,15 +4658,15 @@ } else { cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl; } diff --git a/debian/patches/single-cpu-for-test.patch b/debian/patches/single-cpu-for-test.patch index 015dcfe..8debdb5 100644 --- a/debian/patches/single-cpu-for-test.patch +++ b/debian/patches/single-cpu-for-test.patch @@ -1,9 +1,9 @@ Description: only use single CPU for testing This also frees us of the dependency to the non-packaged libsys-info-perl. Author: Sascha Steinbiss <[email protected]> ---- a/Makefile -+++ b/Makefile -@@ -491,7 +491,7 @@ +--- bowtie2.orig/Makefile ++++ bowtie2/Makefile +@@ -492,7 +492,7 @@ .PHONY: random-test perl-deps random-test: all eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \ @@ -12,8 +12,8 @@ Author: Sascha Steinbiss <[email protected]> .PHONY: perl-deps perl-deps: ---- a/scripts/sim/run.sh -+++ b/scripts/sim/run.sh +--- bowtie2.orig/scripts/sim/run.sh ++++ bowtie2/scripts/sim/run.sh @@ -19,7 +19,7 @@ # along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>. # @@ -23,8 +23,8 @@ Author: Sascha Steinbiss <[email protected]> shift #make -j$CPUS \ # bowtie2-align-s \ ---- a/scripts/sim/Sim.pm -+++ b/scripts/sim/Sim.pm +--- bowtie2.orig/scripts/sim/Sim.pm ++++ bowtie2/scripts/sim/Sim.pm @@ -33,8 +33,8 @@ use Math::Random; use List::Util qw(max min); 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 feec033..23e95f7 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 @@ -5,8 +5,8 @@ Description: Math::Random is in package libmath-random-perl which is this package. Thus the occurences of references and the surrounding code is removed here. ---- a/example/reads/simulate.pl -+++ b/example/reads/simulate.pl +--- bowtie2.orig/example/reads/simulate.pl ++++ bowtie2/example/reads/simulate.pl @@ -33,7 +33,6 @@ use strict; use warnings; @@ -163,9 +163,9 @@ Description: Math::Random is in package libmath-random-perl which is } print STDERR "DONE\n"; ---- a/Makefile -+++ b/Makefile -@@ -483,13 +483,13 @@ +--- bowtie2.orig/Makefile ++++ bowtie2/Makefile +@@ -484,13 +484,13 @@ cp -f $$file $(DESTDIR)$(bindir) ; \ done @@ -183,7 +183,7 @@ Description: Math::Random is in package libmath-random-perl which is eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \ sh ./scripts/sim/run.sh $(if $(NUM_CORES), $(NUM_CORES), 2) -@@ -500,11 +500,10 @@ +@@ -501,11 +501,10 @@ mkdir .perllib.tmp ; \ $$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` ; \ -- 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
