diff --git a/src/gbm/gblinear-inl.hpp b/src/gbm/gblinear-inl.hpp
index a9d4c8d62..624f15c28 100644
--- a/src/gbm/gblinear-inl.hpp
+++ b/src/gbm/gblinear-inl.hpp
@@ -24,6 +24,7 @@ class GBLinear : public IGradBooster {
   }
   // set model parameters
   virtual void SetParam(const char *name, const char *val) {
+    using namespace std;
     if (!strncmp(name, "bst:", 4)) {
       param.SetParam(name + 4, val);
     }
@@ -166,6 +167,7 @@ class GBLinear : public IGradBooster {
       learning_rate = 1.0f;
     }
     inline void SetParam(const char *name, const char *val) {
+      using namespace std;
       // sync-names
       if (!strcmp("eta", name)) learning_rate = static_cast<float>(atof(val));
       if (!strcmp("lambda", name)) reg_lambda = static_cast<float>(atof(val));
@@ -207,9 +209,10 @@ class GBLinear : public IGradBooster {
       Param(void) {
         num_feature = 0;
         num_output_group = 1;
-        memset(reserved, 0, sizeof(reserved));
+        std::memset(reserved, 0, sizeof(reserved));
       }
       inline void SetParam(const char *name, const char *val) {
+        using namespace std;
         if (!strcmp(name, "bst:num_feature")) num_feature = atoi(val);
         if (!strcmp(name, "num_output_group")) num_output_group = atoi(val);
       }
diff --git a/src/gbm/gbm.cpp b/src/gbm/gbm.cpp
index 4713838e9..e280fdd4a 100644
--- a/src/gbm/gbm.cpp
+++ b/src/gbm/gbm.cpp
@@ -1,7 +1,6 @@
 #define _CRT_SECURE_NO_WARNINGS
 #define _CRT_SECURE_NO_DEPRECATE
 #include <cstring>
-using namespace std;
 #include "./gbm.h"
 #include "./gbtree-inl.hpp"
 #include "./gblinear-inl.hpp"
@@ -9,6 +8,7 @@ using namespace std;
 namespace xgboost {
 namespace gbm {
 IGradBooster* CreateGradBooster(const char *name) {
+  using namespace std;
   if (!strcmp("gbtree", name)) return new GBTree();
   if (!strcmp("gblinear", name)) return new GBLinear();
   utils::Error("unknown booster type: %s", name);
diff --git a/src/gbm/gbtree-inl.hpp b/src/gbm/gbtree-inl.hpp
index 8fea28727..ed52afa7d 100644
--- a/src/gbm/gbtree-inl.hpp
+++ b/src/gbm/gbtree-inl.hpp
@@ -23,6 +23,7 @@ class GBTree : public IGradBooster {
     this->Clear();
   }
   virtual void SetParam(const char *name, const char *val) {
+    using namespace std;
     if (!strncmp(name, "bst:", 4)) {
       cfg.push_back(std::make_pair(std::string(name+4), std::string(val)));
       // set into updaters, if already intialized
@@ -171,14 +172,14 @@ class GBTree : public IGradBooster {
     updaters.clear();
     std::string tval = tparam.updater_seq;
     char *pstr;
-    pstr = strtok(&tval[0], ",");
+    pstr = std::strtok(&tval[0], ",");
     while (pstr != NULL) {
       updaters.push_back(tree::CreateUpdater(pstr));
       for (size_t j = 0; j < cfg.size(); ++j) {
         // set parameters
         updaters.back()->SetParam(cfg[j].first.c_str(), cfg[j].second.c_str());
       }
-      pstr = strtok(NULL, ",");
+      pstr = std::strtok(NULL, ",");
     }
     tparam.updater_initialized = 1;
   }
@@ -279,6 +280,7 @@ class GBTree : public IGradBooster {
       updater_initialized = 0;
     }
     inline void SetParam(const char *name, const char *val){
+      using namespace std;
       if (!strcmp(name, "updater") &&
           strcmp(updater_seq.c_str(), val) != 0) {
         updater_seq = val;
@@ -319,7 +321,7 @@ class GBTree : public IGradBooster {
       num_pbuffer = 0;
       num_output_group = 1;
       size_leaf_vector = 0;
-      memset(reserved, 0, sizeof(reserved));
+      std::memset(reserved, 0, sizeof(reserved));
     }
     /*!
      * \brief set parameters from outside
@@ -327,6 +329,7 @@ class GBTree : public IGradBooster {
      * \param val  value of the parameter
      */
     inline void SetParam(const char *name, const char *val) {
+      using namespace std;
       if (!strcmp("num_pbuffer", name)) num_pbuffer = atol(val);
       if (!strcmp("num_output_group", name)) num_output_group = atol(val);
       if (!strcmp("bst:num_roots", name)) num_roots = atoi(val);
diff --git a/src/io/io.cpp b/src/io/io.cpp
index dead398f7..d251d7a96 100644
--- a/src/io/io.cpp
+++ b/src/io/io.cpp
@@ -1,7 +1,6 @@
 #define _CRT_SECURE_NO_WARNINGS
 #define _CRT_SECURE_NO_DEPRECATE
 #include <string>
-using namespace std;
 #include "./io.h"
 #include "../utils/io.h"
 #include "../utils/utils.h"
diff --git a/src/io/simple_dmatrix-inl.hpp b/src/io/simple_dmatrix-inl.hpp
index 9a88a6bfa..374d621e9 100644
--- a/src/io/simple_dmatrix-inl.hpp
+++ b/src/io/simple_dmatrix-inl.hpp
@@ -55,8 +55,8 @@ class DMatrixSimple : public DataMatrix {
         RowBatch::Inst inst = batch[i];
         row_data_.resize(row_data_.size() + inst.length);
         if (inst.length != 0) {
-          memcpy(&row_data_[row_ptr_.back()], inst.data,
-                 sizeof(RowBatch::Entry) * inst.length);
+          std::memcpy(&row_data_[row_ptr_.back()], inst.data,
+                      sizeof(RowBatch::Entry) * inst.length);
         }
         row_ptr_.push_back(row_ptr_.back() + inst.length);
       }
@@ -82,6 +82,7 @@ class DMatrixSimple : public DataMatrix {
    * \param silent whether print information or not
    */
   inline void LoadText(const char* fname, bool silent = false) {
+    using namespace std;
     this->Clear();
     FILE* file = utils::FopenCheck(fname, "r");
     float label; bool init = true;
@@ -135,7 +136,7 @@ class DMatrixSimple : public DataMatrix {
    * \return whether loading is success
    */
   inline bool LoadBinary(const char* fname, bool silent = false) {
-    FILE *fp = fopen64(fname, "rb");
+    std::FILE *fp = fopen64(fname, "rb");
     if (fp == NULL) return false;
     utils::FileStream fs(fp);
     this->LoadBinary(fs, silent, fname);
@@ -208,6 +209,7 @@ class DMatrixSimple : public DataMatrix {
    * \param savebuffer whether do save binary buffer if it is text
    */
   inline void CacheLoad(const char *fname, bool silent = false, bool savebuffer = true) {
+    using namespace std;
     size_t len = strlen(fname);
     if (len > 8 && !strcmp(fname + len - 7, ".buffer")) {
       if (!this->LoadBinary(fname, silent)) {
diff --git a/src/learner/dmatrix.h b/src/learner/dmatrix.h
index bef84900a..b58f7b2bb 100644
--- a/src/learner/dmatrix.h
+++ b/src/learner/dmatrix.h
@@ -90,6 +90,7 @@ struct MetaInfo {
   }
   // try to load group information from file, if exists
   inline bool TryLoadGroup(const char* fname, bool silent = false) {
+    using namespace std;
     FILE *fi = fopen64(fname, "r");
     if (fi == NULL) return false;
     group_ptr.push_back(0);
@@ -105,6 +106,7 @@ struct MetaInfo {
     return true;
   }
   inline std::vector<float>& GetFloatInfo(const char *field) {
+    using namespace std;
     if (!strcmp(field, "label")) return labels;
     if (!strcmp(field, "weight")) return weights;
     if (!strcmp(field, "base_margin")) return base_margin;
@@ -115,6 +117,7 @@ struct MetaInfo {
     return ((MetaInfo*)this)->GetFloatInfo(field);
   }
   inline std::vector<unsigned> &GetUIntInfo(const char *field) {
+    using namespace std;
     if (!strcmp(field, "root_index")) return info.root_index;
     if (!strcmp(field, "fold_index")) return info.fold_index;
     utils::Error("unknown field %s", field);
@@ -125,6 +128,7 @@ struct MetaInfo {
   }
   // try to load weight information from file, if exists
   inline bool TryLoadFloatInfo(const char *field, const char* fname, bool silent = false) {
+    using namespace std;
     std::vector<float> &data = this->GetFloatInfo(field);
     FILE *fi = fopen64(fname, "r");
     if (fi == NULL) return false;
diff --git a/src/learner/evaluation-inl.hpp b/src/learner/evaluation-inl.hpp
index 52877e17b..fb0b8953d 100644
--- a/src/learner/evaluation-inl.hpp
+++ b/src/learner/evaluation-inl.hpp
@@ -147,10 +147,11 @@ struct EvalAMS : public IEvaluator {
   explicit EvalAMS(const char *name) {
     name_ = name;
     // note: ams@0 will automatically select which ratio to go
-    utils::Check(sscanf(name, "ams@%f", &ratio_) == 1, "invalid ams format");
+    utils::Check(std::sscanf(name, "ams@%f", &ratio_) == 1, "invalid ams format");
   }
   virtual float Eval(const std::vector<float> &preds,
                      const MetaInfo &info) const {
+    using namespace std;
     const bst_omp_uint ndata = static_cast<bst_omp_uint>(info.labels.size());
 
     utils::Check(info.weights.size() == ndata, "we need weight to evaluate ams");
@@ -202,6 +203,7 @@ struct EvalAMS : public IEvaluator {
 struct EvalPrecisionRatio : public IEvaluator{
  public:
   explicit EvalPrecisionRatio(const char *name) : name_(name) {
+    using namespace std;
     if (sscanf(name, "apratio@%f", &ratio_) == 1) {
       use_ap = 1;
     } else {
@@ -342,6 +344,7 @@ struct EvalRankList : public IEvaluator {
 
  protected:
   explicit EvalRankList(const char *name) {
+    using namespace std;
     name_ = name;
     minus_ = false;
     if (sscanf(name, "%*[^@]@%u[-]?", &topn_) != 1) {
@@ -388,7 +391,7 @@ struct EvalNDCG : public EvalRankList{
     for (size_t i = 0; i < rec.size() && i < this->topn_; ++i) {
       const unsigned rel = rec[i].second;
       if (rel != 0) { 
-        sumdcg += ((1 << rel) - 1) / log(i + 2.0);
+        sumdcg += ((1 << rel) - 1) / std::log(i + 2.0);
       }
     }
     return static_cast<float>(sumdcg);
diff --git a/src/learner/evaluation.h b/src/learner/evaluation.h
index ec37e1f4a..f34d832c8 100644
--- a/src/learner/evaluation.h
+++ b/src/learner/evaluation.h
@@ -36,6 +36,7 @@ struct IEvaluator{
 namespace xgboost {
 namespace learner {
 inline IEvaluator* CreateEvaluator(const char *name) {
+  using namespace std;
   if (!strcmp(name, "rmse")) return new EvalRMSE();
   if (!strcmp(name, "error")) return new EvalError();
   if (!strcmp(name, "merror")) return new EvalMatchError();
@@ -56,6 +57,7 @@ inline IEvaluator* CreateEvaluator(const char *name) {
 class EvalSet{
  public:
   inline void AddEval(const char *name) {
+    using namespace std;
     for (size_t i = 0; i < evals_.size(); ++i) {
       if (!strcmp(name, evals_[i]->Name())) return;
     }
diff --git a/src/learner/learner-inl.hpp b/src/learner/learner-inl.hpp
index 5d7c9d06a..05519de8b 100644
--- a/src/learner/learner-inl.hpp
+++ b/src/learner/learner-inl.hpp
@@ -79,6 +79,7 @@ class BoostLearner {
    * \param val  value of the parameter
    */
   inline void SetParam(const char *name, const char *val) {
+    using namespace std;
     // in this version, bst: prefix is no longer required 
     if (strncmp(name, "bst:", 4) != 0) {
       std::string n = "bst:"; n += name;
@@ -290,7 +291,7 @@ class BoostLearner {
       base_score = 0.5f;
       num_feature = 0;
       num_class = 0;
-      memset(reserved, 0, sizeof(reserved));
+      std::memset(reserved, 0, sizeof(reserved));
     }
     /*!
      * \brief set parameters from outside
@@ -298,6 +299,7 @@ class BoostLearner {
      * \param val value of the parameter
      */
     inline void SetParam(const char *name, const char *val) {
+      using namespace std;
       if (!strcmp("base_score", name)) base_score = static_cast<float>(atof(val));
       if (!strcmp("num_class", name)) num_class = atoi(val);
       if (!strcmp("bst:num_feature", name)) num_feature = atoi(val);
diff --git a/src/learner/objective-inl.hpp b/src/learner/objective-inl.hpp
index 576549eac..96aacf12d 100644
--- a/src/learner/objective-inl.hpp
+++ b/src/learner/objective-inl.hpp
@@ -101,6 +101,7 @@ class RegLossObj : public IObjFunction{
   }
   virtual ~RegLossObj(void) {}
   virtual void SetParam(const char *name, const char *val) {
+    using namespace std;
     if (!strcmp("scale_pos_weight", name)) {
       scale_pos_weight = static_cast<float>(atof(val));
     }
@@ -156,6 +157,7 @@ class SoftmaxMultiClassObj : public IObjFunction {
   }
   virtual ~SoftmaxMultiClassObj(void) {}
   virtual void SetParam(const char *name, const char *val) {
+    using namespace std;
     if (!strcmp( "num_class", name )) nclass = atoi(val);
   }
   virtual void GetGradient(const std::vector<float> &preds,
@@ -247,6 +249,7 @@ class LambdaRankObj : public IObjFunction {
   }
   virtual ~LambdaRankObj(void) {}
   virtual void SetParam(const char *name, const char *val) {
+    using namespace std;
     if (!strcmp( "loss_type", name )) loss.loss_type = atoi(val);
     if (!strcmp( "fix_list_weight", name)) fix_list_weight = static_cast<float>(atof(val));
     if (!strcmp( "num_pairsample", name)) num_pairsample = atoi(val);
diff --git a/src/learner/objective.h b/src/learner/objective.h
index d741ba61f..6b11b7d18 100644
--- a/src/learner/objective.h
+++ b/src/learner/objective.h
@@ -67,6 +67,7 @@ namespace xgboost {
 namespace learner {
 /*! \brief factory funciton to create objective function by name */
 inline IObjFunction* CreateObjFunction(const char *name) {
+  using namespace std;
   if (!strcmp("reg:linear", name)) return new RegLossObj(LossType::kLinearSquare);
   if (!strcmp("reg:logistic", name)) return new RegLossObj(LossType::kLogisticNeglik);
   if (!strcmp("binary:logistic", name)) return new RegLossObj(LossType::kLogisticClassify);
diff --git a/src/tree/model.h b/src/tree/model.h
index 6d885faa7..8049a1608 100644
--- a/src/tree/model.h
+++ b/src/tree/model.h
@@ -53,7 +53,7 @@ class TreeModel {
     Param(void) {
       max_depth = 0;
       size_leaf_vector = 0;
-      memset(reserved, 0, sizeof(reserved));
+      std::memset(reserved, 0, sizeof(reserved));
     }
     /*! 
      * \brief set parameters from outside 
@@ -61,6 +61,7 @@ class TreeModel {
      * \param val  value of the parameter
      */
     inline void SetParam(const char *name, const char *val) {
+      using namespace std;
       if (!strcmp("num_roots", name)) num_roots = atoi(val);
       if (!strcmp("num_feature", name)) num_feature = atoi(val);
       if (!strcmp("size_leaf_vector", name)) size_leaf_vector = atoi(val);
diff --git a/src/tree/param.h b/src/tree/param.h
index 79bc162c3..04ea5277f 100644
--- a/src/tree/param.h
+++ b/src/tree/param.h
@@ -62,6 +62,7 @@ struct TrainParam{
    * \param val  value of the parameter
    */            
   inline void SetParam(const char *name, const char *val) {
+    using namespace std;
     // sync-names
     if (!strcmp(name, "gamma")) min_split_loss = static_cast<float>(atof(val));
     if (!strcmp(name, "eta")) learning_rate = static_cast<float>(atof(val));
diff --git a/src/tree/updater.cpp b/src/tree/updater.cpp
index 09b63eb49..2cb6552fe 100644
--- a/src/tree/updater.cpp
+++ b/src/tree/updater.cpp
@@ -1,7 +1,6 @@
 #define _CRT_SECURE_NO_WARNINGS
 #define _CRT_SECURE_NO_DEPRECATE
 #include <cstring>
-using namespace std;
 #include "./updater.h"
 #include "./updater_prune-inl.hpp"
 #include "./updater_refresh-inl.hpp"
@@ -10,6 +9,7 @@ using namespace std;
 namespace xgboost {
 namespace tree {
 IUpdater* CreateUpdater(const char *name) {
+  using namespace std;
   if (!strcmp(name, "prune")) return new TreePruner();
   if (!strcmp(name, "refresh")) return new TreeRefresher<GradStats>();
   if (!strcmp(name, "grow_colmaker")) return new ColMaker<GradStats>();
diff --git a/src/tree/updater_prune-inl.hpp b/src/tree/updater_prune-inl.hpp
index 98fdf5ee4..726999f55 100644
--- a/src/tree/updater_prune-inl.hpp
+++ b/src/tree/updater_prune-inl.hpp
@@ -17,6 +17,7 @@ class TreePruner: public IUpdater {
   virtual ~TreePruner(void) {}
   // set training parameter
   virtual void SetParam(const char *name, const char *val) {
+    using namespace std;
     param.SetParam(name, val);
     if (!strcmp(name, "silent")) silent = atoi(val);
   }
diff --git a/src/utils/fmap.h b/src/utils/fmap.h
index f9437cc6c..607f37013 100644
--- a/src/utils/fmap.h
+++ b/src/utils/fmap.h
@@ -24,15 +24,15 @@ class FeatMap {
   // function definitions
   /*! \brief load feature map from text format */
   inline void LoadText(const char *fname) {
-    FILE *fi = utils::FopenCheck(fname, "r");
+    std::FILE *fi = utils::FopenCheck(fname, "r");
     this->LoadText(fi);
-    fclose(fi);
+    std::fclose(fi);
   }
   /*! \brief load feature map from text format */
-  inline void LoadText(FILE *fi) {
+  inline void LoadText(std::FILE *fi) {
     int fid;
     char fname[1256], ftype[1256];
-    while (fscanf(fi, "%d\t%[^\t]\t%s\n", &fid, fname, ftype) == 3) {
+    while (std::fscanf(fi, "%d\t%[^\t]\t%s\n", &fid, fname, ftype) == 3) {
       this->PushBack(fid, fname, ftype);
     }
   }
@@ -62,6 +62,7 @@ class FeatMap {
 
  private:
   inline static Type GetType(const char *tname) {
+    using namespace std;
     if (!strcmp("i", tname)) return kIndicator;
     if (!strcmp("q", tname)) return kQuantitive;
     if (!strcmp("int", tname)) return kInteger;
diff --git a/src/utils/io.h b/src/utils/io.h
index a15e2f0ce..026e3fec7 100644
--- a/src/utils/io.h
+++ b/src/utils/io.h
@@ -91,21 +91,21 @@ class IStream {
 /*! \brief implementation of file i/o stream */
 class FileStream : public IStream {
  private:
-  FILE *fp;
+  std::FILE *fp;
  public:
-  explicit FileStream(FILE *fp) : fp(fp) {
+  explicit FileStream(std::FILE *fp) : fp(fp) {
   }
   virtual size_t Read(void *ptr, size_t size) {
-    return fread(ptr, size, 1, fp);
+    return std::fread(ptr, size, 1, fp);
   }
   virtual void Write(const void *ptr, size_t size) {
-    fwrite(ptr, size, 1, fp);
+    std::fwrite(ptr, size, 1, fp);
   }
   inline void Seek(size_t pos) {
-    fseek(fp, 0, SEEK_SET);
+    std::fseek(fp, 0, SEEK_SET);
   }
   inline void Close(void) {
-    fclose(fp);
+    std::fclose(fp);
   }
 };
 
diff --git a/src/utils/random.h b/src/utils/random.h
index 57e1f243d..1e3e617f9 100644
--- a/src/utils/random.h
+++ b/src/utils/random.h
@@ -53,7 +53,7 @@ inline double NextDouble(void) {
 }
 /*! \brief return a random number in n */
 inline uint32_t NextUInt32(uint32_t n) {
-  return (uint32_t)floor(NextDouble() * n);
+  return (uint32_t)std::floor(NextDouble() * n);
 }
 /*! \brief return  x~N(mu,sigma^2) */
 inline double SampleNormal(double mu, double sigma) {
diff --git a/src/utils/utils.h b/src/utils/utils.h
index c319c5ab7..afe17f64c 100644
--- a/src/utils/utils.h
+++ b/src/utils/utils.h
@@ -149,8 +149,8 @@ inline void Error(const char *fmt, ...) {
 #endif
 
 /*! \brief replace fopen, report error when the file open fails */
-inline FILE *FopenCheck(const char *fname, const char *flag) {
-  FILE *fp = fopen64(fname, flag);
+inline std::FILE *FopenCheck(const char *fname, const char *flag) {
+  std::FILE *fp = fopen64(fname, flag);
   Check(fp != NULL, "can not open file \"%s\"\n", fname);
   return fp;
 }