[med-svn] [bowtie2] 05/06: Refresh patches
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Mon Sep 11 11:23:09 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 9565661790d14d54e8278479d706c00ff86065c8
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
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 <debian-med-packaging at lists.alioth.debian.org>
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 <sascha at steinbiss.name>
+ $(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 <sascha at steinbiss.name>
$(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 <sascha at steinbiss.name>
--- 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 <satta at debian.org>
--- 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` ; \
--
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