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-rw-r--r--sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch138
1 files changed, 138 insertions, 0 deletions
diff --git a/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
new file mode 100644
index 000000000..16ac4e2b0
--- /dev/null
+++ b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
@@ -0,0 +1,138 @@
+--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin 2017-04-28 21:53:55.811777276 +0200
+@@ -28,7 +28,7 @@
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+ STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
+-BLDFLAGS = -O3 ${STDFLAGS}
++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
+
+
+ FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
+--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedextract/src/Makefile 2017-04-28 21:54:05.952048644 +0200
+@@ -24,7 +24,7 @@
+ INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
+ SFLAGS = -static
+
+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+@@ -64,4 +64,4 @@
+ rm -rf $(OBJDIR)
+ rm -f $(BINDIR)/$(PROG)
+ rm -f $(BINDIR)/*.$(PROG)
+- rm -rf $(BINDIR)
+\ No newline at end of file
++ rm -rf $(BINDIR)
+--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin 2017-04-28 21:54:12.162214836 +0200
+@@ -28,7 +28,7 @@
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+ STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
+-BLDFLAGS = -O3 ${STDFLAGS}
++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
+
+ FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
+
+--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedmap/src/Makefile 2017-04-28 21:54:19.472410465 +0200
+@@ -23,7 +23,7 @@
+ INCLUDES = -iquote${HEAD} -I${PARTY3} -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
+ SFLAGS = -static
+
+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+--- bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin 2017-04-28 21:54:25.422569698 +0200
+@@ -1,7 +1,7 @@
+ MIN_OSX_VERSION = 10.7
+ BLDFLAGS = -Wall -Wextra -pedantic -std=c99
+ COMMONFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1
+-CFLAGS = -O3
++CFLAGS = ${CXXFLAGS:--O3}
+ CDFLAGS = -DDEBUG=1 -g -O0 -fno-inline
+ CPFLAGS = -pg
+ LIBS = -lpthread
+--- bedops-2.4.26/applications/bed/conversion/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/conversion/src/Makefile 2017-04-28 21:54:30.832714482 +0200
+@@ -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 = ${CXXFLAGS:--O3}
+ CDFLAGS = -DDEBUG=1 -g -O0 -fno-inline
+ CPFLAGS = -pg
+ LIBS = -lpthread
+--- bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin 2017-04-28 21:54:37.312887898 +0200
+@@ -27,7 +27,7 @@
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+ STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
+-BLDFLAGS = -O3 ${STDFLAGS}
++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
+
+ FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
+
+--- bedops-2.4.26/applications/bed/bedops/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedops/src/Makefile 2017-04-28 21:54:43.513053823 +0200
+@@ -25,7 +25,7 @@
+ INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
+ SFLAGS = -static
+
+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+--- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin 2017-04-28 21:54:49.093203153 +0200
+@@ -28,7 +28,7 @@
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+ STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++
+-BLDFLAGS = -O3 ${STDFLAGS}
++BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS}
+
+ FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
+
+--- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile 2017-04-28 21:54:54.283342049 +0200
+@@ -23,7 +23,7 @@
+ INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+ LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+-BLDFLAGS = -Wall -pedantic -O3 -std=c++11
++BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
+ SFLAGS = -static
+
+ dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+--- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin 2017-04-28 21:55:00.023495662 +0200
+@@ -7,7 +7,7 @@
+ PROG = sort-bed
+ DIST_DIR = ../bin
+ OBJ_DIR = objects_${ARCH}
+-OPTIMIZE = -O3 -std=c++11 -stdlib=libc++
++OPTIMIZE = ${CXXFLAGS:--O3} -std=c++11 -stdlib=libc++
+ WARNINGS = -Wall
+ MAIN = ../../../..
+ HEAD = ${MAIN}/interfaces/general-headers
+--- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile 2017-04-28 21:55:05.663646597 +0200
+@@ -29,7 +29,7 @@
+ BINDIR = ../bin
+ OBJDIR = objects
+ WARNINGS = -Wall -Wextra -pedantic
+-BLDFLAGS = ${WARNINGS} -O3 -std=c++11
++BLDFLAGS = ${WARNINGS} ${CXXFLAGS:--O3} -std=c++11
+ SFLAGS = -static
+
+ dependency_names = starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding SortDetails Sort CheckSort