[med-svn] [Git][med-team/bedops][master] 3 commits: Add parallel.patch: toplevel Makefile should use our -jN argument.
Andreas Tille
gitlab at salsa.debian.org
Fri Feb 19 13:33:49 GMT 2021
Andreas Tille pushed to branch master at Debian Med / bedops
Commits:
3c31bfc9 by Juhani Numminen at 2021-02-19T11:59:54+02:00
Add parallel.patch: toplevel Makefile should use our -jN argument.
- - - - -
cb88f2b7 by Juhani Numminen at 2021-02-19T12:04:08+02:00
Update hardening.patch: our optimization flags now override upstream -O3.
- - - - -
bc5da57a by Andreas Tille at 2021-02-19T14:15:50+01:00
Upload to unstable
- - - - -
4 changed files:
- debian/changelog
- debian/patches/hardening.patch
- + debian/patches/parallel.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+bedops (2.4.39+dfsg1-2) unstable; urgency=medium
+
+ * Team upload.
+ * Add parallel.patch: toplevel Makefile should use our -jN argument.
+ * Update hardening.patch: our optimization flags now override upstream -O3.
+
+ -- Juhani Numminen <juhaninumminen0 at gmail.com> Fri, 19 Feb 2021 11:50:32 +0200
+
bedops (2.4.39+dfsg1-1) unstable; urgency=medium
[ Helmut Grohne ]
=====================================
debian/patches/hardening.patch
=====================================
@@ -1,108 +1,141 @@
Description: Propagate hardening options
Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 20 Mar 2018 15:43:55 +0100
+Last-Update: Fri, 19 Feb 2021 11:39:51 +0200
--- a/applications/bed/conversion/src/Makefile
+++ b/applications/bed/conversion/src/Makefile
-@@ -47,7 +47,7 @@ $(DISTDIR)/gprof.%-${BINARY_TYPE}: %.c g
- @echo -e "\nNote: To profile convert2bed with gprof/pthreads, run:\n\t$$ LD_PRELOAD=/path/to/gprof-helper.so convert2bed"
+@@ -1,6 +1,6 @@
+ BLDFLAGS = -Wall -Wextra -pedantic -std=c99
+ COMMONFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1
+-CFLAGS = -O3
++CFLAGS := -O3 $(CFLAGS)
+ CDFLAGS = -DDEBUG=1 -g -O0 -fno-inline
+ CPFLAGS = -pg
+ LIBS = -lpthread
+@@ -27,7 +27,7 @@
+ rm -rf $(OBJDIR)
- %.so: %.c
-- $(CC) -shared -fPIC $^ -o $@ $(LIBS) -ldl
-+ $(CC) $(CFLAGS) -shared -fPIC $^ -o $@ $(LIBS) -ldl $(LDFLAGS)
+ $(DISTDIR)/$(PROG)-${BINARY_TYPE}: $(PROG).c
+- mkdir -p $(DISTDIR) && $(CC) $(BLDFLAGS) ${MEGAFLAGS} $(COMMONFLAGS) $(CFLAGS) $(SFLAGS) $(INCLUDES) $^ -o $@ $(LIBS)
++ mkdir -p $(DISTDIR) && $(CC) $(BLDFLAGS) ${MEGAFLAGS} $(COMMONFLAGS) $(CPPFLAGS) $(CFLAGS) $(SFLAGS) $(INCLUDES) $(LDFLAGS) $^ -o $@ $(LIBS)
- clean:
- rm -rf $(DISTDIR)
+ $(DISTDIR)/%-${BINARY_TYPE}: %.c
+ mkdir -p $(DISTDIR) && $(CC) $(BLDFLAGS) ${MEGAFLAGS} $(COMMONFLAGS) $(CFLAGS) $(SFLAGS) $(INCLUDES) $^ -o $@ $(LIBS)
--- a/applications/bed/sort-bed/src/Makefile
+++ b/applications/bed/sort-bed/src/Makefile
-@@ -36,8 +36,8 @@ dependency_names = starchConstants st
+@@ -29,14 +29,14 @@
+ BINDIR = ../bin
+ OBJDIR = objects-${BINARY_TYPE}
+ WARNINGS = -Wall -Wextra -pedantic
+-BLDFLAGS = ${WARNINGS} -O3 -std=c++11 ${MEGAFLAGS}
++BLDFLAGS = ${WARNINGS} -O3 -std=c++11 ${MEGAFLAGS} $(CPPFLAGS) $(CXXFLAGS)
+ SFLAGS =
+
+ dependency_names = starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding SortDetails Sort CheckSort
dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
debug_dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .do, $(dependency_names)))
-FLAGS = $(SFLAGS) ${MEGAFLAGS} -s ${BLDFLAGS} ${LIBLOCATION} ${INCLUDES}
--DFLAGS = $(SFLAGS) ${MEGAFLAGS} -g -O0 -std=c++11 -Wall -fno-inline -pedantic ${LIBLOCATION} ${INCLUDES}
-+FLAGS = $(CFLAGS) $(SFLAGS) ${MEGAFLAGS} -s ${BLDFLAGS} ${LIBLOCATION} ${INCLUDES} $(LDFLAGS)
-+DFLAGS = $(CFLAGS) $(SFLAGS) ${MEGAFLAGS} -g -O0 -std=c++11 -Wall -fno-inline -pedantic ${LIBLOCATION} ${INCLUDES} $(LDFLAGS)
++FLAGS = $(SFLAGS) ${MEGAFLAGS} -s ${BLDFLAGS} ${LIBLOCATION} ${INCLUDES} $(LDFLAGS)
+ DFLAGS = $(SFLAGS) ${MEGAFLAGS} -g -O0 -std=c++11 -Wall -fno-inline -pedantic ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = $(SFLAGS) ${MEGAFLAGS} -O -std=c++11 -Wall -pedantic -pg ${LIBLOCATION} ${INCLUDES}
- ifneq ($(shell uname -s),CYGWIN_NT-6.1)
--- a/applications/bed/starch/src/Makefile
+++ b/applications/bed/starch/src/Makefile
-@@ -38,8 +38,8 @@ TEST_LINUX_BINDIR = ${TEST}/bina
+@@ -38,7 +38,7 @@
TEST_OSX_BINDIR = ${TEST}/binaries/osx/${ARCH_VERSION}/bin
AR = ar
SFLAGS =
-CXXFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 ${SFLAGS} -s
--CXXDFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O0 -g -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -DDEBUG_VERBOSE=1 ${SFLAGS} -DDEBUG=1
-+CXXFLAGS += -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 ${SFLAGS} -s
-+CXXDFLAGS = $(CXXFLAGS) -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O0 -g -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -DDEBUG_VERBOSE=1 ${SFLAGS} -DDEBUG=1
++CXXFLAGS := -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 ${SFLAGS} -s $(CXXFLAGS)
+ CXXDFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O0 -g -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -DDEBUG_VERBOSE=1 ${SFLAGS} -DDEBUG=1
CXXGFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -DDEBUG_VERBOSE=1 ${SFLAGS} -DDEBUG=1 -pg
- STARCH_NAMES = starchConstants unstarchHelpers starchHelpers starchMetadataHelpers starchFileHelpers starchSha1Digest starchBase64Coding
-@@ -68,12 +68,12 @@ starchstrip: $(BINDIR)/starchstrip-$(BIN
+@@ -67,8 +67,8 @@
+
$(BINDIR)/%-$(BINARY_TYPE) : %.c $(LOCALSTARCHLIB)
mkdir -p $(BINDIR)
- ${CXX} ${CXXFLAGS} ${MEGAFLAGS} -c $*.c -o $(LOCALOBJDIR)/$*.o ${INCLUDES}
+- ${CXX} ${CXXFLAGS} ${MEGAFLAGS} -c $*.c -o $(LOCALOBJDIR)/$*.o ${INCLUDES}
- ${CXX} ${CXXFLAGS} ${MEGAFLAGS} $(LOCALOBJDIR)/$*.o -o $@ ${LOCALSTARCHLIB} ${LIBRARIES}
-+ ${CXX} ${CXXFLAGS} ${MEGAFLAGS} $(LOCALOBJDIR)/$*.o -o $@ ${LOCALSTARCHLIB} ${LIBRARIES} $(LDFLAGS)
++ ${CXX} $(CPPFLAGS) ${CXXFLAGS} ${MEGAFLAGS} -c $*.c -o $(LOCALOBJDIR)/$*.o ${INCLUDES}
++ ${CXX} $(CPPFLAGS) ${CXXFLAGS} ${MEGAFLAGS} $(LOCALOBJDIR)/$*.o -o $@ ${LOCALSTARCHLIB} ${LIBRARIES} $(LDFLAGS)
$(BINDIR)/debug.% : %.c $(LOCALSTARCHLIB) $(LIBRARIES)
mkdir -p $(BINDIR)
- ${CXX} ${CXXDFLAGS} ${MEGAFLAGS} -c $*.c -o $(LOCALOBJDIR)/$*.o ${INCLUDES}
-- ${CXX} ${CXXDFLAGS} ${MEGAFLAGS} $(LOCALOBJDIR)/$*.o -o $@-$(BINARY_TYPE) ${LOCALSTARCHLIB} ${LIBRARIES}
-+ ${CXX} ${CXXDFLAGS} ${MEGAFLAGS} $(LOCALOBJDIR)/$*.o -o $@-$(BINARY_TYPE) ${LOCALSTARCHLIB} ${LIBRARIES} $(LDFLAGS)
+@@ -104,7 +104,7 @@
- $(BINDIR)/gprof.% : %.c $(LOCALSTARCHLIB) $(LIBRARIES)
- mkdir -p $(BINDIR)
+ $(LOCALOBJDIR)/%.o : $(OBJDIR)/%.c
+ mkdir -p $(LOCALOBJDIR)
+- ${CXX} ${CXXFLAGS} ${MEGAFLAGS} -c $< -o $@ ${INCLUDES}
++ ${CXX} $(CPPFLAGS) ${CXXFLAGS} ${MEGAFLAGS} -c $< -o $@ ${INCLUDES}
+
+ test: starch unstarch starchcat
+ cp ${BINDIR}/starch-${BINARY_TYPE} ${TEST_LINUX_BINDIR}/starch-${BINARY_TYPE}
--- a/applications/bed/bedextract/src/Makefile
+++ b/applications/bed/bedextract/src/Makefile
-@@ -29,8 +29,8 @@ SFLAGS = ${MEGAFLAGS}
+@@ -24,12 +24,12 @@
+ INCLUDES = -iquote$(HEAD)
+ LIBLOCATION =
+ LIBRARIES = -ljansson -lz -lbz2
+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
++BLDFLAGS = -Wall -pedantic -O3 -std=c++11 $(CPPFLAGS) $(CXXFLAGS)
+ SFLAGS = ${MEGAFLAGS}
dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
-FLAGS = $(SFLAGS) -s $(BLDFLAGS) $(dependencies) ${LIBLOCATION} ${INCLUDES}
--DFLAGS = $(SFLAGS) -g -O0 -std=c++11 -Wall -fno-inline -pedantic $(dependencies) ${LIBLOCATION} ${INCLUDES}
-+FLAGS = $(CFLAGS) $(SFLAGS) -s $(BLDFLAGS) $(dependencies) ${LIBLOCATION} ${INCLUDES} $(LDFLAGS)
-+DFLAGS = $(CFLAGS) $(SFLAGS) -g -O0 -std=c++11 -Wall -fno-inline -pedantic $(dependencies) ${LIBLOCATION} ${INCLUDES} $(LDFLAGS)
++FLAGS = $(SFLAGS) -s $(BLDFLAGS) $(dependencies) ${LIBLOCATION} ${INCLUDES} $(LDFLAGS)
+ DFLAGS = $(SFLAGS) -g -O0 -std=c++11 -Wall -fno-inline -pedantic $(dependencies) ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = $(SFLAGS) -O -std=c++11 -Wall -pedantic -pg $(dependencies) ${LIBLOCATION} ${INCLUDES}
- SOURCE1 = ExtractRows.cpp
--- a/applications/bed/bedmap/src/Makefile
+++ b/applications/bed/bedmap/src/Makefile
-@@ -28,8 +28,8 @@ SFLAGS =
+@@ -23,12 +23,12 @@
+ INCLUDES = -iquote${HEAD}
+ LIBLOCATION =
+ LIBRARIES = -ljansson -lz -lbz2
+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
++BLDFLAGS = -Wall -pedantic -O3 -std=c++11 $(CPPFLAGS) $(CXXFLAGS)
+ SFLAGS =
dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
-FLAGS = ${SFLAGS} ${MEGAFLAGS} -s ${BLDFLAGS} $(dependencies) ${LIBLOCATION} ${INCLUDES}
--DFLAGS = ${SFLAGS} ${MEGAFLAGS} -g -O0 -std=c++11 -DDEBUG=1 -fno-inline -Wall -pedantic $(dependencies) ${LIBLOCATION} ${INCLUDES}
-+FLAGS = $(CFLAGS) ${SFLAGS} ${MEGAFLAGS} -s ${BLDFLAGS} $(dependencies) ${LIBLOCATION} ${INCLUDES} $(LDFLAGS)
-+DFLAGS = $(CFLAGS) ${SFLAGS} ${MEGAFLAGS} -g -O0 -std=c++11 -DDEBUG=1 -fno-inline -Wall -pedantic $(dependencies) ${LIBLOCATION} ${INCLUDES} $(LDFLAGS)
++FLAGS = ${SFLAGS} ${MEGAFLAGS} -s ${BLDFLAGS} $(dependencies) ${LIBLOCATION} ${INCLUDES} $(LDFLAGS)
+ DFLAGS = ${SFLAGS} ${MEGAFLAGS} -g -O0 -std=c++11 -DDEBUG=1 -fno-inline -Wall -pedantic $(dependencies) ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = ${SFLAGS} ${MEGAFLAGS} -pg -O -std=c++11 -Wall -pedantic $(dependencies) ${LIBLOCATION} ${INCLUDES}
- SOURCE1 = Bedmap.cpp
--- a/applications/bed/bedops/src/Makefile
+++ b/applications/bed/bedops/src/Makefile
-@@ -30,8 +30,8 @@ SFLAGS =
+@@ -25,12 +25,12 @@
+ INCLUDES = -iquote$(HEAD)
+ LIBLOCATION =
+ LIBRARIES = -ljansson -lz -lbz2
+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
++BLDFLAGS = -Wall -pedantic -O3 -std=c++11 $(CPPFLAGS) $(CXXFLAGS)
+ SFLAGS =
dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
-FLAGS = $(SFLAGS) ${MEGAFLAGS} -s $(BLDFLAGS) $(dependencies) ${LIBLOCATION} ${INCLUDES}
--DFLAGS = $(SFLAGS) ${MEGAFLAGS} -g -O0 -DDEBUG_VERBOSE=1 -std=c++11 -Wall -fno-inline -pedantic -DDEBUG=1 $(dependencies) ${LIBLOCATION} ${INCLUDES}
-+FLAGS = $(CFLAGS) $(SFLAGS) ${MEGAFLAGS} -s $(BLDFLAGS) $(dependencies) ${LIBLOCATION} ${INCLUDES} $(LDFLAGS)
-+DFLAGS = $(CFLAGS) $(SFLAGS) ${MEGAFLAGS} -g -O0 -DDEBUG_VERBOSE=1 -std=c++11 -Wall -fno-inline -pedantic -DDEBUG=1 $(dependencies) ${LIBLOCATION} ${INCLUDES} $(LDFLAGS)
++FLAGS = $(SFLAGS) ${MEGAFLAGS} -s $(BLDFLAGS) $(dependencies) ${LIBLOCATION} ${INCLUDES} $(LDFLAGS)
+ DFLAGS = $(SFLAGS) ${MEGAFLAGS} -g -O0 -DDEBUG_VERBOSE=1 -std=c++11 -Wall -fno-inline -pedantic -DDEBUG=1 $(dependencies) ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = $(SFLAGS) ${MEGAFLAGS} -O -std=c++11 -Wall -pedantic -pg $(dependencies) ${LIBLOCATION} ${INCLUDES}
SOURCE1 = Bedops.cpp
- BINDIR = ../bin
--- a/applications/bed/closestfeats/src/Makefile
+++ b/applications/bed/closestfeats/src/Makefile
-@@ -28,8 +28,8 @@ SFLAGS =
+@@ -23,12 +23,12 @@
+ INCLUDES = -iquote$(HEAD)
+ LIBLOCATION =
+ LIBRARIES = -ljansson -lz -lbz2
+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
++BLDFLAGS = -Wall -pedantic -O3 -std=c++11 $(CPPFLAGS) $(CXXFLAGS)
+ SFLAGS =
dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
-FLAGS = $(SFLAGS) ${MEGAFLAGS} -s $(BLDFLAGS) $(dependencies) ${LIBLOCATION} ${INCLUDES}
--DFLAGS = $(SFLAGS) ${MEGAFLAGS} -g -O0 -std=c++11 -Wall -fno-inline -pedantic $(dependencies) ${LIBLOCATION} ${INCLUDES}
-+FLAGS = $(CFLAGS) $(SFLAGS) ${MEGAFLAGS} -s $(BLDFLAGS) $(dependencies) ${LIBLOCATION} ${INCLUDES} $(LDFLAGS)
-+DFLAGS = $(CFLAGS) $(SFLAGS) ${MEGAFLAGS} -g -O0 -std=c++11 -Wall -fno-inline -pedantic $(dependencies) ${LIBLOCATION} ${INCLUDES} $(LDFLAGS)
++FLAGS = $(SFLAGS) ${MEGAFLAGS} -s $(BLDFLAGS) $(dependencies) ${LIBLOCATION} ${INCLUDES} $(LDFLAGS)
+ DFLAGS = $(SFLAGS) ${MEGAFLAGS} -g -O0 -std=c++11 -Wall -fno-inline -pedantic $(dependencies) ${LIBLOCATION} ${INCLUDES}
GPROFFLAGS = $(SFLAGS) ${MEGAFLAGS} -O -std=c++11 -Wall -pedantic -pg $(dependencies) ${LIBLOCATION} ${INCLUDES}
SOURCE1 = ClosestFeature.cpp
- BINDIR = ../bin
=====================================
debian/patches/parallel.patch
=====================================
@@ -0,0 +1,29 @@
+Description: Let GNU make jobserver handle parallel make jobs.
+ dh calls toplevel make with a suitable "-j", so let's not override that.
+Author: Juhani Numminen <juhaninumminen0 at gmail.com>
+Last-Update: Fri, 19 Feb 2021 10:30:30 +0200
+Forwarded: no
+
+--- a/Makefile
++++ b/Makefile
+@@ -10,7 +10,7 @@
+ MASSIVE_ID_EXP = 18
+ MASSIVE_CHROM_EXP = 8
+ MEASURE128BIT = 'long double'
+-JPARALLEL = 8
++#JPARALLEL = 8
+ MEGAROW = megarow
+ TYPICAL = typical
+ FLOAT128 = float128
+@@ -26,9 +26,9 @@
+
+ default:
+ ifeq ($(KERNEL), Darwin)
+- $(MAKE) $(MAKECMDGOALS) -j $(JPARALLEL) -f system.mk/Makefile.darwin
++ $(MAKE) $(MAKECMDGOALS) -f system.mk/Makefile.darwin
+ else
+- $(MAKE) $(MAKECMDGOALS) -j $(JPARALLEL) -f system.mk/Makefile.linux
++ $(MAKE) $(MAKECMDGOALS) -f system.mk/Makefile.linux
+ endif
+
+ clean: default
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ tests_use_installed_binaries.patch
2to3.patch
use_debian_libs
hardening.patch
+parallel.patch
View it on GitLab: https://salsa.debian.org/med-team/bedops/-/compare/4bc8b525ae977a6b2ee4699b844c26a053f48a19...bc5da57ac05ff505ac1dae8014c4d40e54167c79
--
View it on GitLab: https://salsa.debian.org/med-team/bedops/-/compare/4bc8b525ae977a6b2ee4699b844c26a053f48a19...bc5da57ac05ff505ac1dae8014c4d40e54167c79
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