[med-svn] [bowtie2] 05/09: Refresh patches
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Fri Oct 13 13:48:17 UTC 2017
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository bowtie2.
commit 3c1f09de011ba1c681554269f609695c70a82d44
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Fri Oct 13 14:47:50 2017 +0200
Refresh patches
---
debian/patches/hardening.patch | 30 +++++++++++-----------
debian/patches/reproducible.patch | 12 ++++-----
debian/patches/single-cpu-for-test.patch | 2 +-
...st_requiring_non-free_libmath-random-perl.patch | 11 +++-----
4 files changed, 25 insertions(+), 30 deletions(-)
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
index 2d60c31..1df586d 100644
--- a/debian/patches/hardening.patch
+++ b/debian/patches/hardening.patch
@@ -5,7 +5,7 @@ Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Last-Update: Thu, 25 Aug 2016 13:47:22 +0000
--- bowtie2.orig/Makefile
+++ bowtie2/Makefile
-@@ -270,7 +270,9 @@
+@@ -273,7 +273,9 @@
$(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 @@
+@@ -285,7 +287,7 @@
$(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 @@
+@@ -293,7 +295,7 @@
$(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 @@
+@@ -301,7 +303,7 @@
$(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 @@
+@@ -309,7 +311,7 @@
$(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 @@
+@@ -321,7 +323,7 @@
$(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 @@
+@@ -329,7 +331,7 @@
$(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 @@
+@@ -338,7 +340,7 @@
$(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 @@
+@@ -347,7 +349,7 @@
$(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 @@
+@@ -360,7 +362,7 @@
$(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 @@
+@@ -369,7 +371,7 @@
$(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 @@
+@@ -378,7 +380,7 @@
$(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 @@
+@@ -387,7 +389,7 @@
$(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 @@
+@@ -400,7 +402,7 @@
$(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 @@
+@@ -409,7 +411,7 @@
$(INC) -I . \
-o $@ $< \
$(DP_CPPS) $(SHARED_CPPS) \
diff --git a/debian/patches/reproducible.patch b/debian/patches/reproducible.patch
index 36546f3..a0642d4 100644
--- a/debian/patches/reproducible.patch
+++ b/debian/patches/reproducible.patch
@@ -12,9 +12,9 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
-HEADERS = $(wildcard *.h)
+HEADERS = $(sort $(wildcard *.h))
BOWTIE_MM = 1
- BOWTIE_SHARED_MEM = 0
+ BOWTIE_SHARED_MEM =
-@@ -162,7 +162,7 @@
+@@ -165,7 +165,7 @@
BUILD_CPPS = diff_sample.cpp
BUILD_CPPS_MAIN = $(BUILD_CPPS) bowtie_build_main.cpp
@@ -23,7 +23,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
VERSION = $(shell cat VERSION)
BITS=32
-@@ -204,14 +204,14 @@
+@@ -207,14 +207,14 @@
bowtie2-inspect-s-debug \
bowtie2-inspect-l-debug
@@ -43,7 +43,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
example/reference/lambda_virus.fa \
$(PTHREAD_PKG) \
bowtie2 \
-@@ -238,11 +238,11 @@
+@@ -241,11 +241,11 @@
# the Windows FIND tool instead.
FIND=$(shell which find)
@@ -60,7 +60,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
Makefile \
$(GENERAL_LIST)
-@@ -264,9 +264,9 @@
+@@ -267,9 +267,9 @@
DEFS=-fno-strict-aliasing \
-DBOWTIE2_VERSION="\"`cat VERSION`\"" \
@@ -129,7 +129,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
--- bowtie2.orig/bt2_search.cpp
+++ bowtie2/bt2_search.cpp
-@@ -4988,15 +4988,15 @@
+@@ -5000,15 +5000,15 @@
} 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 8631659..d4c838a 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 <satta at debian.org>
--- bowtie2.orig/Makefile
+++ bowtie2/Makefile
-@@ -491,7 +491,7 @@
+@@ -493,7 +493,7 @@
.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 cf1f841..5c4881e 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
-@@ -483,13 +483,13 @@
+@@ -485,13 +485,13 @@
cp -f $$file $(DESTDIR)$(bindir) ; \
done
@@ -183,16 +183,11 @@ Description: Math::Random is in package libmath-random-perl which is
eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
sh ./scripts/sim/run.sh $(if $(NUM_CORES), $(NUM_CORES), 2)
-@@ -500,11 +500,10 @@
+@@ -502,7 +502,6 @@
mkdir .perllib.tmp ; \
$$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 ; \
fi
- .PHONY: test
--test: simple-test random-test
-+test: simple-test #random-test
-
- .PHONY: clean
- clean:
+ static-libs:
--
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