diff --git a/NEWS.md b/NEWS.md
index 84eea6cfe..da512f4b1 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -6,6 +6,8 @@ This file records the changes in xgboost library in reverse chronological order.
 ## in progress version
 * Refactored gbm to allow more friendly cache strategy
   - Specialized some prediction routine
+* Automatically remove nan from input data when it is sparse.
+  - This can solve some of user reported problem of istart != hist.size
 
 ## v0.6 (2016.07.29)
 * Version 0.5 is skipped due to major improvements in the core
diff --git a/src/c_api/c_api.cc b/src/c_api/c_api.cc
index 0f535b250..f1c02188f 100644
--- a/src/c_api/c_api.cc
+++ b/src/c_api/c_api.cc
@@ -238,22 +238,31 @@ XGB_DLL int XGDMatrixCreateFromCSREx(const size_t* indptr,
 
   API_BEGIN();
   data::SimpleCSRSource& mat = *source;
-  mat.row_ptr_.resize(nindptr);
-  for (size_t i = 0; i < nindptr; ++i) {
-    mat.row_ptr_[i] = indptr[i];
-  }
-  mat.row_data_.resize(nelem);
-  for (size_t i = 0; i < nelem; ++i) {
-    mat.row_data_[i] = RowBatch::Entry(indices[i], data[i]);
-    mat.info.num_col = std::max(mat.info.num_col,
-                                static_cast<uint64_t>(indices[i] + 1));
+  mat.row_ptr_.reserve(nindptr);
+  mat.row_data_.reserve(nelem);
+  mat.row_ptr_.resize(1);
+  mat.row_ptr_[0] = 0;
+  size_t num_column = 0;
+  for (size_t i = 1; i < nindptr; ++i) {
+    for (size_t j = indptr[i - 1]; j < indptr[i]; ++j) {
+      if (!common::CheckNAN(data[j])) {
+        // automatically skip nan.
+        mat.row_data_.emplace_back(RowBatch::Entry(indices[j], data[j]));
+        num_column = std::max(num_column, static_cast<size_t>(indices[j] + 1));
+      }
+    }
+    mat.row_ptr_.push_back(mat.row_data_.size());
   }
+
+  mat.info.num_col = num_column;
   if (num_col > 0) {
-    CHECK_LE(mat.info.num_col, num_col);
+    CHECK_LE(mat.info.num_col, num_col)
+        << "num_col=" << num_col << " vs " << mat.info.num_col;
     mat.info.num_col = num_col;
   }
   mat.info.num_row = nindptr - 1;
-  mat.info.num_nonzero = nelem;
+  LOG(INFO) << "num_row=" << mat.info.num_row;
+  mat.info.num_nonzero = mat.row_data_.size();
   *out = new std::shared_ptr<DMatrix>(DMatrix::Create(std::move(source)));
   API_END();
 }
@@ -291,7 +300,9 @@ XGB_DLL int XGDMatrixCreateFromCSCEx(const size_t* col_ptr,
   for (omp_ulong i = 0; i < static_cast<omp_ulong>(ncol); ++i) {  // NOLINT(*)
     int tid = omp_get_thread_num();
     for (size_t j = col_ptr[i]; j < col_ptr[i+1]; ++j) {
-      builder.AddBudget(indices[j], tid);
+      if (!common::CheckNAN(data[j])) {
+        builder.AddBudget(indices[j], tid);
+      }
     }
   }
   builder.InitStorage();
@@ -299,9 +310,11 @@ XGB_DLL int XGDMatrixCreateFromCSCEx(const size_t* col_ptr,
   for (omp_ulong i = 0; i < static_cast<omp_ulong>(ncol); ++i) {  // NOLINT(*)
     int tid = omp_get_thread_num();
     for (size_t j = col_ptr[i]; j < col_ptr[i+1]; ++j) {
-      builder.Push(indices[j],
-                   RowBatch::Entry(static_cast<bst_uint>(i), data[j]),
-                   tid);
+      if (!common::CheckNAN(data[j])) {
+        builder.Push(indices[j],
+                     RowBatch::Entry(static_cast<bst_uint>(i), data[j]),
+                     tid);
+      }
     }
   }
   mat.info.num_row = mat.row_ptr_.size() - 1;
diff --git a/src/tree/updater_colmaker.cc b/src/tree/updater_colmaker.cc
index 5c4126702..60a8eb75b 100644
--- a/src/tree/updater_colmaker.cc
+++ b/src/tree/updater_colmaker.cc
@@ -670,9 +670,8 @@ class ColMaker: public TreeUpdater {
       #pragma omp parallel for schedule(static)
       for (bst_omp_uint i = 0; i < ndata; ++i) {
         const bst_uint ridx = rowset[i];
-        if (ridx >= position.size()) {
-          LOG(INFO) << "ridx exceed bound\n";
-        }
+        CHECK_LT(ridx, position.size())
+            << "ridx exceed bound " << "ridx="<<  ridx << " pos=" << position.size();
         const int nid = this->DecodePosition(ridx);
         if (tree[nid].is_leaf()) {
           // mark finish when it is not a fresh leaf
diff --git a/src/tree/updater_histmaker.cc b/src/tree/updater_histmaker.cc
index c8fe5c7a3..87c73e9f8 100644
--- a/src/tree/updater_histmaker.cc
+++ b/src/tree/updater_histmaker.cc
@@ -298,8 +298,15 @@ class CQHistMaker: public HistMaker<TStats> {
         hist.data[istart].Add(gstats);
       } else {
         while (istart < hist.size && !(fv < hist.cut[istart])) ++istart;
-        CHECK_NE(istart, hist.size);
-        hist.data[istart].Add(gstats);
+        if (istart != hist.size) {
+          hist.data[istart].Add(gstats);
+        } else {
+          LOG(INFO) << "fv=" << fv << ", hist.size=" << hist.size;
+          for (size_t i = 0; i < hist.size; ++i) {
+            LOG(INFO) << "hist[" << i << "]=" << hist.cut[i];
+          }
+          LOG(FATAL) << "fv=" << fv << ", hist.last=" << hist.cut[hist.size - 1];
+        }
       }
     }
   };