diff --git a/src/complementBed/Makefile b/src/complementBed/Makefile
index 61b56bf85728b8df7eb327db0ad500d4378230db..c35e2c873bcbca2c21866fb02d71b5473d2968d4 100755
--- a/src/complementBed/Makefile
+++ b/src/complementBed/Makefile
@@ -28,7 +28,6 @@ all: $(PROGRAM)
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $@ $^ $(LIBS)	
 	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
diff --git a/src/coverageBed/Makefile b/src/coverageBed/Makefile
index 61325a3f0f2045912eccfc4679b1c41998a6b834..da338ba3de54af8b56b0b39edfe73893780ad043 100644
--- a/src/coverageBed/Makefile
+++ b/src/coverageBed/Makefile
@@ -28,7 +28,6 @@ all: $(PROGRAM)
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $@ $^ $(LIBS)	
 	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
diff --git a/src/fastaFromBed/Makefile b/src/fastaFromBed/Makefile
index 7c6c8bda0ca8ce8ae2e21430fa7654d55987e34a..54f75713793b332c3222a52bc84f6ba12f611f3f 100755
--- a/src/fastaFromBed/Makefile
+++ b/src/fastaFromBed/Makefile
@@ -28,7 +28,6 @@ all: $(PROGRAM)
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $@ $^ $(LIBS)	
 	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
diff --git a/src/genomeCoverageBed/Makefile b/src/genomeCoverageBed/Makefile
index 992924d1bf29d9276b0fdb6ede33323fc1a2233a..cac145cd08b36b184cab0764a78156d19368f755 100755
--- a/src/genomeCoverageBed/Makefile
+++ b/src/genomeCoverageBed/Makefile
@@ -28,7 +28,6 @@ all: $(PROGRAM)
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $@ $^ $(LIBS)	
 	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
diff --git a/src/intersectBed/Makefile b/src/intersectBed/Makefile
index 53c03e010b3f58f79ddebb33ded0780ca6068652..0fb788a2fc244afc2792f899002d7a327bf7e22f 100644
--- a/src/intersectBed/Makefile
+++ b/src/intersectBed/Makefile
@@ -28,7 +28,6 @@ all: $(PROGRAM)
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $@ $^ $(LIBS)	
 	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
diff --git a/src/mergeBed/Makefile b/src/mergeBed/Makefile
index 3030a89f3151fa01a81b111d3e3c751ad5e92f13..f4401d20609bceefbae9fc6ee47613883447cc26 100755
--- a/src/mergeBed/Makefile
+++ b/src/mergeBed/Makefile
@@ -28,7 +28,6 @@ all: $(PROGRAM)
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $@ $^ $(LIBS)	
 	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
diff --git a/src/sortBed/Makefile b/src/sortBed/Makefile
index 54f390bad771e50e929af000af88d93ef2e1ab89..a0b8a27daeefe893ce4b5f3a7823ce44108d30da 100755
--- a/src/sortBed/Makefile
+++ b/src/sortBed/Makefile
@@ -28,7 +28,6 @@ all: $(PROGRAM)
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $@ $^ $(LIBS)	
 	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)