[med-svn] [bowtie2] 03/05: Refresh patches
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Tue Mar 7 11:57:50 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 b525e0f8c4793632cdb72433914877f127b266c1
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
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 <satta at debian.org>
---- 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 <satta at debian.org>
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 <satta at debian.org>
+# 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 <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
---- 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 <sascha at steinbiss.name>
---- 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 <sascha at steinbiss.name>
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 <sascha at steinbiss.name>
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 <sascha at steinbiss.name>
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 <sascha at steinbiss.name>
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 <sascha at steinbiss.name>
$(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 <sascha at steinbiss.name>
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 <sascha at steinbiss.name>
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 <satta at debian.org>
---- 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 <satta at debian.org>
.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 <satta at debian.org>
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` ; \
--
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