From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: Print compilation commands
--- bedtools.orig/src/annotateBed/Makefile
+++ bedtools/src/annotateBed/Makefile
@@ -26,7 +26,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 		
 clean:
--- bedtools.orig/src/bamToBed/Makefile
+++ bedtools/src/bamToBed/Makefile
@@ -28,7 +28,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) 
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) 
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/bamToFastq/Makefile
+++ bedtools/src/bamToFastq/Makefile
@@ -24,7 +24,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) 
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) 
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/bed12ToBed6/Makefile
+++ bedtools/src/bed12ToBed6/Makefile
@@ -27,7 +27,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/bedToBam/Makefile
+++ bedtools/src/bedToBam/Makefile
@@ -30,7 +30,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/bedToIgv/Makefile
+++ bedtools/src/bedToIgv/Makefile
@@ -28,7 +28,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/bedpeToBam/Makefile
+++ bedtools/src/bedpeToBam/Makefile
@@ -33,7 +33,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/	
--- bedtools.orig/src/closestFile/Makefile
+++ bedtools/src/closestFile/Makefile
@@ -40,7 +40,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/clusterBed/Makefile
+++ bedtools/src/clusterBed/Makefile
@@ -25,10 +25,10 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/clusterMain.o $(OBJ_DIR)/clusterBed.o
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- bedtools.orig/src/complementFile/Makefile
+++ bedtools/src/complementFile/Makefile
@@ -42,7 +42,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/coverageFile/Makefile
+++ bedtools/src/coverageFile/Makefile
@@ -38,7 +38,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/expand/Makefile
+++ bedtools/src/expand/Makefile
@@ -27,7 +27,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/fastaFromBed/Makefile
+++ bedtools/src/fastaFromBed/Makefile
@@ -30,7 +30,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/fisher/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/flankBed/Makefile
+++ bedtools/src/flankBed/Makefile
@@ -26,7 +26,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 		
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/genomeCoverageBed/Makefile
+++ bedtools/src/genomeCoverageBed/Makefile
@@ -27,7 +27,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/getOverlap/Makefile
+++ bedtools/src/getOverlap/Makefile
@@ -26,7 +26,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 	
 clean:
--- bedtools.orig/src/groupBy/Makefile
+++ bedtools/src/groupBy/Makefile
@@ -43,7 +43,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/intersectFile/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/jaccard/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/linksBed/Makefile
+++ bedtools/src/linksBed/Makefile
@@ -25,10 +25,10 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/linksMain.o $(OBJ_DIR)/linksBed.o
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- bedtools.orig/src/mapFile/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/maskFastaFromBed/Makefile
+++ bedtools/src/maskFastaFromBed/Makefile
@@ -26,7 +26,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/mergeFile/Makefile
+++ bedtools/src/mergeFile/Makefile
@@ -40,10 +40,10 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/mergeHelp.o $(OBJ_DIR)/mergeFile.o
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- bedtools.orig/src/multiBamCov/Makefile
+++ bedtools/src/multiBamCov/Makefile
@@ -26,7 +26,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/multiIntersectBed/Makefile
+++ bedtools/src/multiIntersectBed/Makefile
@@ -27,7 +27,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/nekSandbox1/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/nucBed/Makefile
+++ bedtools/src/nucBed/Makefile
@@ -27,10 +27,10 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/nucBedMain.o $(OBJ_DIR)/nucBed.o
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- bedtools.orig/src/pairToBed/Makefile
+++ bedtools/src/pairToBed/Makefile
@@ -27,7 +27,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/pairToPair/Makefile
+++ bedtools/src/pairToPair/Makefile
@@ -27,7 +27,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 
 clean:
--- bedtools.orig/src/randomBed/Makefile
+++ bedtools/src/randomBed/Makefile
@@ -23,7 +23,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/regressTest/Makefile
+++ bedtools/src/regressTest/Makefile
@@ -32,9 +32,9 @@
 
 all: #$(BUILT_OBJECTS)
 	@echo "compiling RegressTest.cpp"
-	@$(CXX) -c -o $(OBJ_DIR)/RegressTest.o RegressTest.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(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) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $(OBJ_DIR)/regressTestMain.o regressTestMain.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 	
 .PHONY: all
 
--- bedtools.orig/src/reldist/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/sampleFile/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/shiftBed/Makefile
+++ bedtools/src/shiftBed/Makefile
@@ -26,7 +26,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/shuffleBed/Makefile
+++ bedtools/src/shuffleBed/Makefile
@@ -28,7 +28,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/slopBed/Makefile
+++ bedtools/src/slopBed/Makefile
@@ -26,7 +26,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/sortBed/Makefile
+++ bedtools/src/sortBed/Makefile
@@ -26,10 +26,10 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/sortMain.o $(OBJ_DIR)/sortBed.o
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- bedtools.orig/src/spacingFile/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/split/Makefile
+++ bedtools/src/split/Makefile
@@ -25,7 +25,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/subtractFile/Makefile
+++ bedtools/src/subtractFile/Makefile
@@ -40,7 +40,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/tagBam/Makefile
+++ bedtools/src/tagBam/Makefile
@@ -28,7 +28,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/unionBedGraphs/Makefile
+++ bedtools/src/unionBedGraphs/Makefile
@@ -27,7 +27,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/utils/BamTools-Ancillary/Makefile
+++ bedtools/src/utils/BamTools-Ancillary/Makefile
@@ -21,10 +21,10 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
 
 clean:
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- bedtools.orig/src/utils/BamTools/Makefile
+++ bedtools/src/utils/BamTools/Makefile
@@ -61,7 +61,7 @@
 
 $(OBJECTS): $(SOURCES)
 	@echo " * compiling" $(*F).cpp
-	@$(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o
+	$(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o
 
 .PHONY: api
 api:
--- bedtools.orig/src/utils/BinTree/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(INCLUDES)
@@ -37,4 +37,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/BinTree.o
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- bedtools.orig/src/utils/BlockedIntervals/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(INCLUDES)
--- bedtools.orig/src/utils/Contexts/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/utils/Fasta/Makefile
+++ bedtools/src/utils/Fasta/Makefile
@@ -19,7 +19,7 @@
 	
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/utils/FileRecordTools/FileReaders/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/utils/FileRecordTools/Makefile
+++ bedtools/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) -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) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 	
 	
 
--- bedtools.orig/src/utils/FileRecordTools/Records/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
@@ -46,4 +46,4 @@
 		$(OBJ_DIR)/BedPlusInterval.o $(OBJ_DIR)/Bed12Interval.o $(OBJ_DIR)/BamRecord.o $(OBJ_DIR)/VcfRecord.o $(OBJ_DIR)/GffRecord.o $(OBJ_DIR)/BlockMgr.o $(OBJ_DIR)/StrandQueue.o \
 		$(OBJ_DIR)/RecordKeyList.o $(OBJ_DIR)/RecordKeyVector.o
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- bedtools.orig/src/utils/GenomeFile/Makefile
+++ bedtools/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) -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) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 #$(EXT_OBJECTS):
 #	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
--- bedtools.orig/src/utils/KeyListOps/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 
 $(EXT_OBJECTS):
@@ -41,4 +41,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/KeyListOps.o $(OBJ_DIR)/KeyListOpsMethods.o
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- bedtools.orig/src/utils/NewChromsweep/Makefile
+++ bedtools/src/utils/NewChromsweep/Makefile
@@ -34,10 +34,10 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/NewChromsweep.o $(BIN_DIR)/CloseSweep.o
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- bedtools.orig/src/utils/RecordOutputMgr/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(INCLUDES)
@@ -38,4 +38,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/RecordOutputMgr.o 
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- bedtools.orig/src/utils/ToolBase/Makefile
+++ bedtools/src/utils/ToolBase/Makefile
@@ -30,7 +30,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(INCLUDES)
@@ -39,4 +39,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/ToolBase.o 
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- bedtools.orig/src/utils/VectorOps/Makefile
+++ bedtools/src/utils/VectorOps/Makefile
@@ -11,10 +11,10 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- bedtools.orig/src/utils/bedFile/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C -W $(INCLUDES)
@@ -29,4 +29,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- bedtools.orig/src/utils/bedFilePE/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(INCLUDES)
@@ -26,4 +26,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- bedtools.orig/src/utils/bedGraphFile/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C -W $(INCLUDES)
--- bedtools.orig/src/utils/chromsweep/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(INCLUDES)
@@ -29,4 +29,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- bedtools.orig/src/utils/driver/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
 	
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/utils/fileType/Makefile
+++ bedtools/src/utils/fileType/Makefile
@@ -22,10 +22,10 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/fileType.o $(OBJ_DIR)/FileRecordTypeChecker.o
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- bedtools.orig/src/utils/general/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/utils/sequenceUtilities/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(INCLUDES)
@@ -26,4 +26,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- bedtools.orig/src/utils/tabFile/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C -W $(INCLUDES)
@@ -28,4 +28,4 @@
 	@echo "Cleaning up."
 	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
 
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
--- bedtools.orig/src/utils/version/Makefile
+++ bedtools/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) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/windowBed/Makefile
+++ bedtools/src/windowBed/Makefile
@@ -27,7 +27,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 clean:
 	@echo "Cleaning up."
--- bedtools.orig/src/windowMaker/Makefile
+++ bedtools/src/windowMaker/Makefile
@@ -26,7 +26,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+	$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/
