diff --git a/R-package/src/Makevars b/R-package/src/Makevars
index 1e77150db..7dfda4d57 100644
--- a/R-package/src/Makevars
+++ b/R-package/src/Makevars
@@ -1,13 +1,12 @@
 # package root
 PKGROOT=../../
 # _*_ mode: Makefile; _*_
-export CC  = gcc
-export CXX = g++
-
-
+CXX=`R CMD config CXX`
+CFLAGS=`R CMD config CFLAGS` 
 # expose these flags to R CMD SHLIB
-PKG_CPPFLAGS = -O3 -Wno-unknown-pragmas  -DXGBOOST_CUSTOMIZE_ERROR_  -fPIC  $(SHLIB_OPENMP_CFLAGS)
-PKG_CPPFLAGS += -I$(PKGROOT)
+PKG_CPPFLAGS= -DXGBOOST_CUSTOMIZE_ERROR_ -I$(PKGROOT)  $(SHLIB_OPENMP_CFLAGS)
+XGBFLAG= $(CFLAGS) -DXGBOOST_CUSTOMIZE_ERROR_ -fPIC  $(SHLIB_OPENMP_CFLAGS)
+
 PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
 
 ifeq ($(no_omp),1)
@@ -27,7 +26,7 @@ xgboost_gbm.o: $(PKGROOT)/src/gbm/gbm.cpp
 xgboost_updater.o: $(PKGROOT)/src/tree/updater.cpp
 
 $(CXXOBJ) : 
-	$(CXX) -c $(PKG_CPPFLAGS) -o $@ $(firstword $(filter %.cpp %.c, $^) )
+	$(CXX) -c $(XGBFLAG) -o $@ $(firstword $(filter %.cpp %.c, $^) )
 
 clean:
 	rm -rf *.so *.o *~ *.dll
diff --git a/R-package/src/Makevars.win b/R-package/src/Makevars.win
index c6d10bf1c..3df9891fc 100644
--- a/R-package/src/Makevars.win
+++ b/R-package/src/Makevars.win
@@ -1,20 +1,13 @@
 # package root
 PKGROOT=../../
 # _*_ mode: Makefile; _*_
-export CC  = gcc
-export CXX = g++
-
-
+CXX=`Rcmd config CXX`
+CFLAGS=`Rcmd config CFLAGS` 
 # expose these flags to R CMD SHLIB
-PKG_CPPFLAGS = -O3 -Wno-unknown-pragmas  -DXGBOOST_CUSTOMIZE_ERROR_ -fopenmp -fPIC  $(SHLIB_OPENMP_CFLAGS)
-PKG_CPPFLAGS += -I$(PKGROOT)
+PKG_CPPFLAGS= -DXGBOOST_CUSTOMIZE_ERROR_ -I$(PKGROOT)  $(SHLIB_OPENMP_CFLAGS)
+XGBFLAG= $(CFLAGS) -DXGBOOST_CUSTOMIZE_ERROR_ -fPIC  $(SHLIB_OPENMP_CFLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
 
-# add flag to build native code even in cross compiler
-ifeq "$(WIN)" "64"
-	PKG_CPPFLAGS += -m64
-endif
-
 ifeq ($(no_omp),1)
 	PKG_CPPFLAGS += -DDISABLE_OPENMP 
 endif