diff --git a/R-package/src/Makevars b/R-package/src/Makevars
index a13d40a31..d9f794589 100644
--- a/R-package/src/Makevars
+++ b/R-package/src/Makevars
@@ -2,10 +2,10 @@
 PKGROOT=../../
 # _*_ mode: Makefile; _*_
 CXX=`"${R_HOME}/bin/R" CMD config CXX`
-CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXXFLAGS`
+TCXXFLAGS=`"${R_HOME}/bin/R" CMD config CXXFLAGS`
 # expose these flags to R CMD SHLIB
 PKG_CPPFLAGS= -DXGBOOST_CUSTOMIZE_MSG_ -I$(PKGROOT)  $(SHLIB_OPENMP_CFLAGS)
-XGBFLAG= $(CXXFLAGS) -DXGBOOST_CUSTOMIZE_MSG_ -fPIC  $(SHLIB_OPENMP_CFLAGS)
+XGBFLAG= $(TCXXFLAGS) -DXGBOOST_CUSTOMIZE_MSG_ -fPIC  $(SHLIB_OPENMP_CFLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
 
 CXXOBJ= xgboost_wrapper.o xgboost_io.o xgboost_gbm.o xgboost_updater.o
diff --git a/R-package/src/Makevars.win b/R-package/src/Makevars.win
index 00ed5017c..2ba962895 100644
--- a/R-package/src/Makevars.win
+++ b/R-package/src/Makevars.win
@@ -2,10 +2,10 @@
 PKGROOT=../../
 # _*_ mode: Makefile; _*_
 CXX=`"${R_HOME}/bin/Rcmd" config CXX`
-CXXFLAGS=`"${R_HOME}/bin/Rcmd" config CXXFLAGS`
+TCXXFLAGS=`"${R_HOME}/bin/Rcmd" config CXXFLAGS`
 # expose these flags to R CMD SHLIB
 PKG_CPPFLAGS= -DXGBOOST_CUSTOMIZE_MSG_ -I$(PKGROOT)  $(SHLIB_OPENMP_CFLAGS)
-XGBFLAG= $(CXXFLAGS) -DXGBOOST_CUSTOMIZE_MSG_ -fPIC  $(SHLIB_OPENMP_CFLAGS)
+XGBFLAG= $(TCXXFLAGS) -DXGBOOST_CUSTOMIZE_MSG_ -fPIC  $(SHLIB_OPENMP_CFLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
 
 CXXOBJ= xgboost_wrapper.o xgboost_io.o xgboost_gbm.o xgboost_updater.o