[med-svn] [bowtie2] 03/03: Refresh patches
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Tue Jan 2 15:55:51 UTC 2018
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository bowtie2.
commit d8fd31183b500e7536cda0531593c2c0f2491bb0
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
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 <satta at debian.org>
--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 <alex at biotec.tu-dresden.de>
Sascha Steinbiss <satta at debian.org>
Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-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 <sascha at steinbiss.name>
--- 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 <sascha at steinbiss.name>
--- 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
--
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