Commit 2d7b5503 authored by arq5x's avatar arq5x
Browse files

resolve conflict

parents b1e3d8de 833bd238
......@@ -134,8 +134,8 @@ INCLUDES = -I$(SRC_DIR)/utils/bedFile \
all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
@echo "- Building main bedtools binary."
@$(CXX) $(CXXFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
@$(CXX) $(CXXFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
@$(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)
@echo "done."
@echo "- Creating executables for old CLI."
......
......@@ -26,7 +26,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
......
......@@ -28,7 +28,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -24,7 +24,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -30,7 +30,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -28,7 +28,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -33,7 +33,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
......
......@@ -39,7 +39,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -25,7 +25,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -30,7 +30,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -51,7 +51,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -26,7 +26,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -26,7 +26,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
......
......@@ -25,7 +25,7 @@ INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
-I$(UTILITIES_DIR)/version/ \
-I$(UTILITIES_DIR)/ToolBase/ \
-I$(TOOL_DIR)/intersectFile/
# ----------------------------------
# define our source and object files
......@@ -41,7 +41,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -38,7 +38,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -42,7 +42,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -25,7 +25,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -37,7 +37,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -25,7 +25,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -39,7 +39,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -26,7 +26,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -35,7 +35,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
......
......@@ -23,7 +23,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -32,15 +32,15 @@ PROGRAM= regressTest
all: #$(BUILT_OBJECTS)
@echo "compiling RegressTest.cpp"
@$(CXX) -c -o $(OBJ_DIR)/RegressTest.o RegressTest.cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(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) $(INCLUDES)
@$(CXX) -c -o $(OBJ_DIR)/regressTestMain.o regressTestMain.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
.PHONY: all
#$(BUILT_OBJECTS): $(SOURCES)
# @echo " * compiling" $(*F).cpp
# @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
# @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
......
......@@ -30,7 +30,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -36,7 +36,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -28,7 +28,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -26,7 +26,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -26,7 +26,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -36,7 +36,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -25,7 +25,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -28,7 +28,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -27,7 +27,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -21,7 +21,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
clean:
@echo "Cleaning up."
......
......@@ -61,7 +61,7 @@ $(LIBRARY): $(OBJECTS)
$(OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) -o $(*D)/$(*F).o
@$(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o
.PHONY: api
api:
......
......@@ -27,7 +27,7 @@ BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(INCLUDES)
......
......@@ -23,7 +23,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(INCLUDES)
......
......@@ -35,7 +35,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -19,7 +19,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS)
clean:
@echo "Cleaning up."
......
......@@ -31,7 +31,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -31,7 +31,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -33,9 +33,9 @@ all: $(BUILT_OBJECTS) $(SUBDIRS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling FileRecordMgr.cpp"
@$(CXX) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
@echo " * compiling FileRecordMergeMgr.cpp"
@$(CXX) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
......
......@@ -36,7 +36,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -20,9 +20,9 @@ BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
$(BUILT_OBJECTS): $(SOURCES) $(SUBDIRS)
@echo " * compiling GenomeFile.cpp"
@$(CXX) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
@echo " * compiling NewGenomeFile.cpp"
@$(CXX) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
#$(EXT_OBJECTS):
# @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
......
......@@ -30,7 +30,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
......
......@@ -33,7 +33,7 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -28,7 +28,7 @@ BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(INCLUDES)
......
......@@ -11,7 +11,7 @@ BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
clean:
@echo "Cleaning up."
......
......@@ -20,7 +20,7 @@ BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C -W $(INCLUDES)
......
......@@ -17,7 +17,7 @@ BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))