diff --git a/R-package/src/base.h b/R-package/src/base.h
index f8eacee20fe4..eb555193ec10 100644
--- a/R-package/src/base.h
+++ b/R-package/src/base.h
@@ -7,15 +7,20 @@
 #define MXNET_RCPP_BASE_H_
 
 #include <Rcpp.h>
+#include <dmlc/base.h>
 #include <mxnet/c_api.h>
-// to be removed
-#include <dmlc/logging.h>
 
 namespace mxnet {
 namespace R {
 
 // change to Rcpp::cerr later, for compatiblity of older version for now
-#define RLOG_FATAL LOG(FATAL)
+#define RLOG_FATAL ::Rcpp::Rcerr
+
+// checking macro for R side
+#define RCHECK(x)                                           \
+  if (!(x))                                                 \
+    RLOG_FATAL << "Check "                                  \
+        "failed: " #x << ' '
 
 /*!
  * \brief protected MXNet C API call, report R error if happens.
diff --git a/R-package/src/ndarray.cc b/R-package/src/ndarray.cc
index 0d1edcbda035..8cbfff3bfa6e 100644
--- a/R-package/src/ndarray.cc
+++ b/R-package/src/ndarray.cc
@@ -1,5 +1,4 @@
 #include <Rcpp.h>
-#include <dmlc/base.h>
 #include "./base.h"
 #include "./ndarray.h"
 
@@ -41,7 +40,7 @@ SEXP NDArray::Load(const std::string& filename) {
                         &out_name_size, &out_names));
   Rcpp::List out(out_size);
   for (mx_uint i = 0; i < out_size; ++i) {
-    out[i] = Rcpp::XPtr<NDArray>(new NDArray(out_arr[i]));
+    out[i] = NDArray::RObject(out_arr[i]);
   }
   if (out_name_size != 0) {
     std::vector<std::string> lst_names(out_size);
@@ -105,9 +104,8 @@ NDArrayFunction::NDArrayFunction(FunctionHandle handle)
 
 SEXP NDArrayFunction::operator() (SEXP* args) {
   BEGIN_RCPP;
-  if (!accept_empty_out_) {
-    RLOG_FATAL << "not yet support mutate target";
-  }
+  RCHECK(accept_empty_out_)
+      << "not yet support mutate target";
   NDArrayHandle ohandle;
   MX_CALL(MXNDArrayCreateNone(&ohandle));
   std::vector<mx_float> scalars(num_scalars_);
@@ -124,7 +122,7 @@ SEXP NDArrayFunction::operator() (SEXP* args) {
                        dmlc::BeginPtr(use_vars),
                        dmlc::BeginPtr(scalars),
                        &ohandle));
-  return Rcpp::XPtr<NDArray>(new NDArray(ohandle));
+  return NDArray::RObject(ohandle);
   END_RCPP;
 }
 
@@ -137,9 +135,8 @@ void NDArray::InitRcppModule() {
 
 void NDArrayFunction::InitRcppModule() {
   Rcpp::Module* scope = ::getCurrentScope();
-  if (scope == NULL) {
-    RLOG_FATAL << "Init Module need to be called inside scope";
-  }
+  RCHECK(scope != NULL)
+      << "Init Module need to be called inside scope";
   mx_uint out_size;
   FunctionHandle *arr;
   MX_CALL(MXListFunctions(&out_size, &arr));
diff --git a/R-package/src/ndarray.h b/R-package/src/ndarray.h
index 174d0568a316..269d2bdb5e4d 100644
--- a/R-package/src/ndarray.h
+++ b/R-package/src/ndarray.h
@@ -20,13 +20,17 @@ class NDArray {
   /*! \brief default constructor */
   NDArray() {}
   /*!
-   * \brief construct NDArray from handle
+   * \brief create a R object that correspond to the NDArray
    * \param handle the NDArrayHandle needed for output.
    * \param writable Whether the NDArray is writable or not.
    */
-  explicit NDArray(NDArrayHandle handle,
-                   bool writable = true)
-      : handle_(handle), writable_(writable) {}
+  static SEXP RObject(NDArrayHandle handle, bool writable = true) {
+    NDArray *nd = new NDArray();
+    nd->handle_ = handle;
+    nd->writable_ = writable;
+    // will call destructor after finalize
+    return Rcpp::XPtr<NDArray>(nd, true);
+  }
   /*!
    * \brief Load a list of ndarray from the file.
    * \param filename the name of the file.
@@ -42,6 +46,12 @@ class NDArray {
   /*! \brief static function to initialize the Rcpp functions */
   static void InitRcppModule();
 
+  /*! \brief destructor */
+  ~NDArray() {
+    // free the handle
+    MX_CALL(MXNDArrayFree(handle_));
+  }
+
  private:
   // declare friend class
   friend class NDArrayFunction;