finish refactor, need debug

Makefile

@@ -1,19 +1,19 @@
 export CC  = gcc
 export CXX = g++
 export LDFLAGS= -pthread -lm 
-# note for R module
-# add include path to Rinternals.h here
+
+export CFLAGS = -Wall -O3 -msse2  -Wno-unknown-pragmas -fPIC
 
 ifeq ($(no_omp),1)
-	export CFLAGS = -Wall -O3 -msse2  -Wno-unknown-pragmas -DDISABLE_OPENMP -funroll-loops 
-else
-	export CFLAGS = -Wall -O3 -msse2 -Wno-unknown-pragmas -fopenmp  -funroll-loops 
+	CFLAGS += -DDISABLE_OPENMP 
+else 
+	CFLAGS += -fopenmp
 endif
 
 # specify tensor path
-BIN =
-OBJ = updater.o gbm.o xgboost_main.o
-#SLIB = wrapper/libxgboostwrapper.so 
+BIN = xgboost
+OBJ = updater.o gbm.o io.o
+SLIB = wrapper/libxgboostwrapper.so 
 #RLIB = wrapper/libxgboostR.so 
 .PHONY: clean all R python
 
@@ -22,10 +22,11 @@ all: $(BIN) $(OBJ)
 #xgboost: src/xgboost_main.cpp src/io/io.cpp src/data.h src/tree/*.h src/tree/*.hpp src/gbm/*.h src/gbm/*.hpp src/utils/*.h src/learner/*.h src/learner/*.hpp 
 
 # now the wrapper takes in two files. io and wrapper part
-#wrapper/libxgboostwrapper.so: wrapper/xgboost_wrapper.cpp src/io/io.cpp src/*.h src/*/*.hpp src/*/*.h
+wrapper/libxgboostwrapper.so: wrapper/xgboost_wrapper.cpp $(OBJ)
 updater.o: src/tree/updater.cpp 
 gbm.o: src/gbm/gbm.cpp 
-xgboost_main.o: src/xgboost_main.cpp
+io.o: src/io/io.cpp
+xgboost: src/xgboost_main.cpp $(OBJ)
 
 $(BIN) : 
 	$(CXX) $(CFLAGS) $(LDFLAGS) -o $@ $(filter %.cpp %.o %.c, $^)