--- a/Makefile.gcc
+++ b/Makefile.gcc
@@ -1,7 +1,6 @@
 # Makefile August 2006 by Alexandros Stamatakis
 # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca>
 
-CC = gcc 
 
 ARCH := $(shell uname -m)
 ifeq ($(ARCH), x86_64)
@@ -10,7 +9,7 @@
 ARCH_CFLAGS=
 endif
 
-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 $(ARCH_CFLAGS) #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+CFLAGS += -D_GNU_SOURCE #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
 
 LIBRARIES = -lm
 
@@ -23,7 +22,7 @@
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h
 
 raxmlHPC : $(objs)
-	$(CC) -o raxmlHPC $(objs) $(LIBRARIES) $(LDFLAGS) 
+	$(CC) $(CFLAGS) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES)
 
 rmqs.o : rmqs.c $(GLOBAL_DEPS)
 classify.o : classify.c $(GLOBAL_DEPS)
@@ -51,8 +50,6 @@
 
 
 
-eigen.o : eigen.c $(GLOBAL_DEPS)
-	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC