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commit 9565661790d14d54e8278479d706c00ff86065c8 Author: Alexandre Mestiashvili <[email protected]> Date: Mon Sep 11 11:00:11 2017 +0200 Refresh patches --- debian/patches/hardening.patch | 30 +++++++++++----------- debian/patches/reproducible.patch | 8 +++--- debian/patches/single-cpu-for-test.patch | 2 +- ...st_requiring_non-free_libmath-random-perl.patch | 4 +-- 4 files changed, 22 insertions(+), 22 deletions(-) diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch index 63f96c0..2d60c31 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 --- bowtie2.orig/Makefile +++ bowtie2/Makefile -@@ -271,7 +271,9 @@ +@@ -270,7 +270,9 @@ $(FILE_FLAGS) \ $(PREF_DEF) \ $(MM_DEF) \ @@ -16,7 +16,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000 # # bowtie2-build targets -@@ -283,7 +285,7 @@ +@@ -282,7 +284,7 @@ $(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) \ -@@ -291,7 +293,7 @@ +@@ -290,7 +292,7 @@ $(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) \ -@@ -299,7 +301,7 @@ +@@ -298,7 +300,7 @@ $(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) \ -@@ -307,7 +309,7 @@ +@@ -306,7 +308,7 @@ $(INC) \ -o $@ $< \ $(SHARED_CPPS) $(BUILD_CPPS_MAIN) \ @@ -52,7 +52,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000 # # bowtie2-align targets -@@ -319,7 +321,7 @@ +@@ -318,7 +320,7 @@ $(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) \ -@@ -327,7 +329,7 @@ +@@ -326,7 +328,7 @@ $(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) \ -@@ -336,7 +338,7 @@ +@@ -335,7 +337,7 @@ $(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) \ -@@ -345,7 +347,7 @@ +@@ -344,7 +346,7 @@ $(INC) \ -o $@ $< \ $(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \ @@ -88,7 +88,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000 # # bowtie2-inspect targets -@@ -358,7 +360,7 @@ +@@ -357,7 +359,7 @@ $(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) \ -@@ -367,7 +369,7 @@ +@@ -366,7 +368,7 @@ $(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) \ -@@ -376,7 +378,7 @@ +@@ -375,7 +377,7 @@ $(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) \ -@@ -385,7 +387,7 @@ +@@ -384,7 +386,7 @@ $(INC) -I . \ -o $@ $< \ $(SHARED_CPPS) \ @@ -124,7 +124,7 @@ Last-Update: Thu, 25 Aug 2016 13:47:22 +0000 # # bowtie2-dp targets -@@ -398,7 +400,7 @@ +@@ -397,7 +399,7 @@ $(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) \ -@@ -407,7 +409,7 @@ +@@ -406,7 +408,7 @@ $(INC) -I . \ -o $@ $< \ $(DP_CPPS) $(SHARED_CPPS) \ diff --git a/debian/patches/reproducible.patch b/debian/patches/reproducible.patch index 8dafbda..36546f3 100644 --- a/debian/patches/reproducible.patch +++ b/debian/patches/reproducible.patch @@ -57,10 +57,10 @@ Author: Sascha Steinbiss <[email protected]> + $(sort $(wildcard *.c)) \ + $(sort $(wildcard *.cpp)) \ + $(sort $(wildcard third_party/*)) \ - doc/strip_markdown.pl \ Makefile \ $(GENERAL_LIST) -@@ -265,9 +265,9 @@ + +@@ -264,9 +264,9 @@ DEFS=-fno-strict-aliasing \ -DBOWTIE2_VERSION="\"`cat VERSION`\"" \ @@ -75,7 +75,7 @@ Author: Sascha Steinbiss <[email protected]> $(MM_DEF) \ --- bowtie2.orig/bt2_build.cpp +++ bowtie2/bt2_build.cpp -@@ -533,15 +533,15 @@ +@@ -548,15 +548,15 @@ } else { cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl; } @@ -129,7 +129,7 @@ Author: Sascha Steinbiss <[email protected]> --- bowtie2.orig/bt2_search.cpp +++ bowtie2/bt2_search.cpp -@@ -4697,15 +4697,15 @@ +@@ -4988,15 +4988,15 @@ } 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 8debdb5..8631659 100644 --- a/debian/patches/single-cpu-for-test.patch +++ b/debian/patches/single-cpu-for-test.patch @@ -3,7 +3,7 @@ Description: only use single CPU for testing Author: Sascha Steinbiss <[email protected]> --- bowtie2.orig/Makefile +++ bowtie2/Makefile -@@ -492,7 +492,7 @@ +@@ -491,7 +491,7 @@ .PHONY: random-test perl-deps random-test: all eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \ 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 43928ae..cf1f841 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 @@ -165,7 +165,7 @@ Description: Math::Random is in package libmath-random-perl which is print STDERR "DONE\n"; --- bowtie2.orig/Makefile +++ bowtie2/Makefile -@@ -484,13 +484,13 @@ +@@ -483,13 +483,13 @@ cp -f $$file $(DESTDIR)$(bindir) ; \ done @@ -183,7 +183,7 @@ Description: Math::Random is in package libmath-random-perl which is eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \ sh ./scripts/sim/run.sh $(if $(NUM_CORES), $(NUM_CORES), 2) -@@ -501,11 +501,10 @@ +@@ -500,11 +500,10 @@ mkdir .perllib.tmp ; \ $$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
