diff --git a/R-package/src/Makevars b/R-package/src/Makevars
index 995dc4379..a13d40a31 100644
--- a/R-package/src/Makevars
+++ b/R-package/src/Makevars
@@ -2,7 +2,6 @@
 PKGROOT=../../
 # _*_ mode: Makefile; _*_
 CXX=`"${R_HOME}/bin/R" CMD config CXX`
-CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
 CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXXFLAGS`
 # expose these flags to R CMD SHLIB
 PKG_CPPFLAGS= -DXGBOOST_CUSTOMIZE_MSG_ -I$(PKGROOT)  $(SHLIB_OPENMP_CFLAGS)
diff --git a/R-package/src/Makevars.win b/R-package/src/Makevars.win
index e4bd42d37..00ed5017c 100644
--- a/R-package/src/Makevars.win
+++ b/R-package/src/Makevars.win
@@ -2,7 +2,6 @@
 PKGROOT=../../
 # _*_ mode: Makefile; _*_
 CXX=`"${R_HOME}/bin/Rcmd" config CXX`
-CFLAGS=`"${R_HOME}/bin/Rcmd" config CFLAGS`
 CXXFLAGS=`"${R_HOME}/bin/Rcmd" config CXXFLAGS`
 # expose these flags to R CMD SHLIB
 PKG_CPPFLAGS= -DXGBOOST_CUSTOMIZE_MSG_ -I$(PKGROOT)  $(SHLIB_OPENMP_CFLAGS)