diff options
Diffstat (limited to 'sci-biology/bedtools/files')
-rw-r--r-- | sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch | 869 |
1 files changed, 869 insertions, 0 deletions
diff --git a/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch new file mode 100644 index 000000000000..fb6be18d7071 --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch @@ -0,0 +1,869 @@ +* Make build system verbose (https://bugs.gentoo.org/show_bug.cgi?id=429308) +* Remove CXX and CXXFLAGS, ebuild sets them +* Handle python via Gentoo's EPYTHON instead + +--- a/Makefile ++++ b/Makefile +@@ -16,17 +16,9 @@ + export BIN_DIR = bin + export SRC_DIR = src + export UTIL_DIR = src/utils +-export CXX = g++ +-ifeq ($(DEBUG),1) +-export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG +-else +-export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES) +-endif + export LIBS = -lz + export BT_ROOT = src/utils/BamTools/ + +-prefix ?= /usr/local +- + SUBDIRS = $(SRC_DIR)/annotateBed \ + $(SRC_DIR)/bamToBed \ + $(SRC_DIR)/bamToFastq \ +@@ -135,13 +127,13 @@ + + all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS) + @echo "- Building main bedtools binary." +- @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES) +- @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES) ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) + @echo "done." + + @echo "- Creating executables for old CLI." +- @python scripts/makeBashScripts.py +- @chmod +x bin/* ++ $(EPYTHON) scripts/makeBashScripts.py ++ chmod +x bin/* + @echo "done." + + +--- a/src/annotateBed/Makefile ++++ b/src/annotateBed/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + + clean: +--- a/src/bamToBed/Makefile ++++ b/src/bamToBed/Makefile +@@ -28,7 +28,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/bamToFastq/Makefile ++++ b/src/bamToFastq/Makefile +@@ -24,7 +24,7 @@ +
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/bed12ToBed6/Makefile ++++ b/src/bed12ToBed6/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/bedpeToBam/Makefile ++++ b/src/bedpeToBam/Makefile +@@ -33,7 +33,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/ +--- a/src/bedToBam/Makefile ++++ b/src/bedToBam/Makefile +@@ -30,7 +30,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/bedToIgv/Makefile ++++ b/src/bedToIgv/Makefile +@@ -28,7 +28,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/closestFile/Makefile ++++ b/src/closestFile/Makefile +@@ -40,7 +40,7 @@ +
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/clusterBed/Makefile ++++ b/src/clusterBed/Makefile +@@ -25,7 +25,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/complementFile/Makefile ++++ b/src/complementFile/Makefile +@@ -42,7 +42,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/coverageFile/Makefile ++++ b/src/coverageFile/Makefile +@@ -38,7 +38,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/expand/Makefile ++++ b/src/expand/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/fastaFromBed/Makefile ++++ b/src/fastaFromBed/Makefile +@@ -30,7 +30,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/fisher/Makefile ++++ b/src/fisher/Makefile +@@ -51,7 +51,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/flankBed/Makefile ++++ b/src/flankBed/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/genomeCoverageBed/Makefile ++++ b/src/genomeCoverageBed/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/getOverlap/Makefile ++++ b/src/getOverlap/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + + clean: +--- a/src/groupBy/Makefile ++++ b/src/groupBy/Makefile +@@ -42,7 +42,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/intersectFile/Makefile ++++ b/src/intersectFile/Makefile +@@ -39,7 +39,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/jaccard/Makefile ++++ b/src/jaccard/Makefile +@@ -43,7 +43,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/linksBed/Makefile ++++ b/src/linksBed/Makefile +@@ -25,7 +25,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/mapFile/Makefile ++++ b/src/mapFile/Makefile +@@ -38,7 +38,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/maskFastaFromBed/Makefile ++++ b/src/maskFastaFromBed/Makefile +@@ -25,7 +25,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/mergeFile/Makefile ++++ b/src/mergeFile/Makefile +@@ -40,7 +40,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/multiBamCov/Makefile ++++ b/src/multiBamCov/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/multiIntersectBed/Makefile ++++ b/src/multiIntersectBed/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/nekSandbox1/Makefile ++++ b/src/nekSandbox1/Makefile +@@ -35,7 +35,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/nucBed/Makefile ++++ b/src/nucBed/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/pairToBed/Makefile ++++ b/src/pairToBed/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/pairToPair/Makefile ++++ b/src/pairToPair/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + + clean: +--- a/src/randomBed/Makefile ++++ b/src/randomBed/Makefile +@@ -23,7 +23,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/regressTest/Makefile ++++ b/src/regressTest/Makefile +@@ -24,24 +24,18 @@ + # ---------------------------------- + # define our source and object files + # ---------------------------------- +-#SOURCES= regressTestMain.cpp RegressTest.cpp RegressTest.h +-#OBJECTS= regressTestMain.o RegressTest.o +-#BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) ++SOURCES= regressTestMain.cpp RegressTest.cpp RegressTest.h ++OBJECTS= regressTestMain.o RegressTest.o ++BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) + PROGRAM= regressTest + +- +-all: #$(BUILT_OBJECTS) +- @echo "compiling RegressTest.cpp" +- @$(CXX) -c -o $(OBJ_DIR)/RegressTest.o RegressTest.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) +- @echo "compiling regressTestMain.cpp" +- @$(CXX) -c -o $(OBJ_DIR)/regressTestMain.o regressTestMain.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++all: $(BUILT_OBJECTS) + + .PHONY: all + +-#$(BUILT_OBJECTS): $(SOURCES) +-# @echo " * compiling" $(*F).cpp +-# @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) +- ++$(BUILT_OBJECTS): $(SOURCES) ++ @echo " * compiling" $(*F).cpp ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/reldist/Makefile ++++ b/src/reldist/Makefile +@@ -30,7 +30,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/sampleFile/Makefile ++++ b/src/sampleFile/Makefile +@@ -37,7 +37,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/shiftBed/Makefile ++++ b/src/shiftBed/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/shuffleBed/Makefile ++++ b/src/shuffleBed/Makefile +@@ -28,7 +28,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/slopBed/Makefile ++++ b/src/slopBed/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/sortBed/Makefile ++++ b/src/sortBed/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/spacingFile/Makefile ++++ b/src/spacingFile/Makefile +@@ -37,7 +37,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/split/Makefile ++++ b/src/split/Makefile +@@ -25,7 +25,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/subtractFile/Makefile ++++ b/src/subtractFile/Makefile +@@ -40,7 +40,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/tagBam/Makefile ++++ b/src/tagBam/Makefile +@@ -28,7 +28,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/unionBedGraphs/Makefile ++++ b/src/unionBedGraphs/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/BamTools/Makefile ++++ b/src/utils/BamTools/Makefile +@@ -56,12 +56,12 @@ + + $(LIBRARY): $(OBJECTS) + @echo " * linking $(LIBRARY)" +- ar cr $@ $^ ++ $(AR) cr $@ $^ + -ranlib $@ + + $(OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o -c $(*D)/$(*F).cpp + + .PHONY: api + api: +--- a/src/utils/BamTools-Ancillary/Makefile ++++ b/src/utils/BamTools-Ancillary/Makefile +@@ -21,7 +21,7 @@ +
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/utils/bedFile/Makefile ++++ b/src/utils/bedFile/Makefile +@@ -20,7 +20,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C -W $(INCLUDES) +--- a/src/utils/bedFilePE/Makefile ++++ b/src/utils/bedFilePE/Makefile +@@ -17,7 +17,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) +--- a/src/utils/bedGraphFile/Makefile ++++ b/src/utils/bedGraphFile/Makefile +@@ -19,7 +19,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C -W $(INCLUDES) +--- a/src/utils/BinTree/Makefile ++++ b/src/utils/BinTree/Makefile +@@ -28,7 +28,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) +--- a/src/utils/BlockedIntervals/Makefile ++++ b/src/utils/BlockedIntervals/Makefile +@@ -23,7 +23,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) +--- a/src/utils/chromsweep/Makefile ++++ b/src/utils/chromsweep/Makefile +@@ -20,7 +20,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) +--- a/src/utils/Contexts/Makefile ++++ b/src/utils/Contexts/Makefile +@@ -36,7 +36,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/driver/Makefile ++++ b/src/utils/driver/Makefile +@@ -85,7 +85,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/Fasta/Makefile ++++ b/src/utils/Fasta/Makefile +@@ -19,7 +19,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/FileRecordTools/FileReaders/Makefile ++++ b/src/utils/FileRecordTools/FileReaders/Makefile +@@ -32,7 +32,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/FileRecordTools/FileReaders/Makefile~ ++++ b/src/utils/FileRecordTools/FileReaders/Makefile~ +@@ -31,7 +31,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/FileRecordTools/Makefile ++++ b/src/utils/FileRecordTools/Makefile +@@ -34,9 +34,9 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling FileRecordMgr.cpp" +- @$(CXX) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp + @echo " * compiling FileRecordMergeMgr.cpp" +- @$(CXX) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp + + + +--- a/src/utils/FileRecordTools/Records/Makefile ++++ b/src/utils/FileRecordTools/Records/Makefile +@@ -37,7 +37,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/fileType/Makefile ++++ b/src/utils/fileType/Makefile +@@ -22,7 +22,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/general/Makefile ++++ b/src/utils/general/Makefile +@@ -21,7 +21,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/GenomeFile/Makefile ++++ b/src/utils/GenomeFile/Makefile +@@ -20,9 +20,9 @@ + + $(BUILT_OBJECTS): $(SOURCES) $(SUBDIRS) + @echo " * compiling GenomeFile.cpp" +- @$(CXX) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp + @echo " * compiling NewGenomeFile.cpp" +- @$(CXX) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp + + #$(EXT_OBJECTS): + # @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ +--- a/src/utils/gzstream/Makefile ++++ b/src/utils/gzstream/Makefile +@@ -38,7 +38,7 @@ + UTILITIES_DIR = ../../utils/ + + ${OBJ_DIR}/gzstream.o : gzstream.C gzstream.h +- $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/gzstream.o gzstream.C $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/gzstream.o gzstream.C + + clean: + @echo "Cleaning up." +--- a/src/utils/KeyListOps/Makefile ++++ b/src/utils/KeyListOps/Makefile +@@ -31,7 +31,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + + $(EXT_OBJECTS): +--- a/src/utils/NewChromsweep/Makefile ++++ b/src/utils/NewChromsweep/Makefile +@@ -34,7 +34,7 @@ +
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/utils/RecordOutputMgr/Makefile ++++ b/src/utils/RecordOutputMgr/Makefile +@@ -29,7 +29,7 @@ +
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+--- a/src/utils/sequenceUtilities/Makefile ++++ b/src/utils/sequenceUtilities/Makefile +@@ -17,7 +17,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) +--- a/src/utils/tabFile/Makefile ++++ b/src/utils/tabFile/Makefile +@@ -19,7 +19,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C -W $(INCLUDES) +--- a/src/utils/ToolBase/Makefile ++++ b/src/utils/ToolBase/Makefile +@@ -30,7 +30,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(INCLUDES) +--- a/src/utils/VectorOps/Makefile ++++ b/src/utils/VectorOps/Makefile +@@ -11,7 +11,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/utils/version/Makefile ++++ b/src/utils/version/Makefile +@@ -20,7 +20,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) $(HEADERS) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/windowBed/Makefile ++++ b/src/windowBed/Makefile +@@ -27,7 +27,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + clean: + @echo "Cleaning up." +--- a/src/windowMaker/Makefile ++++ b/src/windowMaker/Makefile +@@ -26,7 +26,7 @@ + + $(BUILT_OBJECTS): $(SOURCES) + @echo " * compiling" $(*F).cpp +- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp + + $(EXT_OBJECTS): + @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/ |