some fix to make it more c++

Makefile

@@ -2,7 +2,7 @@ export CC  = gcc
 export CXX = g++
 export LDFLAGS= -pthread -lm 
 
-export CFLAGS = -Wall -O3 -msse2  -Wno-unknown-pragmas -fPIC -pedantic -ansi
+export CFLAGS = -Wall -O3 -msse2  -Wno-unknown-pragmas -fPIC -pedantic -std=c++98 -Wpedantic -pedantic-errors
 
 ifeq ($(no_omp),1)
 	CFLAGS += -DDISABLE_OPENMP 

R-package/src/xgboost_R.cpp

@@ -8,6 +8,7 @@
 #include "src/utils/utils.h"
 #include "src/utils/omp.h"
 #include "src/utils/matrix_csr.h"
+using namespace std;
 using namespace xgboost;
 
 extern "C" {
@@ -18,10 +19,12 @@ extern "C" {
 // implements error handling
 namespace xgboost {
 namespace utils {
-void (*Printf)(const char *fmt, ...) = Rprintf;
+extern "C" {
-void (*Assert)(int exp, const char *fmt, ...) = XGBoostAssert_R;
+  void (*Printf)(const char *fmt, ...) = Rprintf;
-void (*Check)(int exp, const char *fmt, ...) = XGBoostCheck_R;
+  void (*Assert)(int exp, const char *fmt, ...) = XGBoostAssert_R;
-void (*Error)(const char *fmt, ...) = error;
+  void (*Check)(int exp, const char *fmt, ...) = XGBoostCheck_R;
+  void (*Error)(const char *fmt, ...) = error;
+}
 }  // namespace utils
 
 namespace random {

src/learner/evaluation-inl.hpp

@@ -8,8 +8,8 @@
 #include <vector>
 #include <utility>
 #include <string>
-#include <climits>
 #include <cmath>
+#include <climits>
 #include <algorithm>
 #include "./evaluation.h"
 #include "./helper_utils.h"

src/learner/helper_utils.h

@@ -7,6 +7,7 @@
  */
 #include <utility>
 #include <vector>
+#include <cmath>
 #include <algorithm>
 namespace xgboost {
 namespace learner {

src/learner/objective-inl.hpp

@@ -6,9 +6,9 @@
  * \author Tianqi Chen, Kailong Chen
  */
 #include <vector>
-#include <cmath>
 #include <algorithm>
 #include <utility>
+#include <cmath>
 #include <functional>
 #include "../data.h"
 #include "./objective.h"
@@ -37,7 +37,7 @@ struct LossType {
       case kLogisticRaw:
       case kLinearSquare: return x;
       case kLogisticClassify:
-      case kLogisticNeglik: return 1.0f / (1.0f + expf(-x));
+      case kLogisticNeglik: return 1.0f / (1.0f + std::exp(-x));
       default: utils::Error("unknown loss_type"); return 0.0f;
     }
   }
@@ -50,7 +50,7 @@ struct LossType {
   inline float FirstOrderGradient(float predt, float label) const {
     switch (loss_type) {
       case kLinearSquare: return predt - label;
-      case kLogisticRaw: predt = 1.0f / (1.0f + expf(-predt));
+      case kLogisticRaw: predt = 1.0f / (1.0f + std::exp(-predt));
       case kLogisticClassify:
       case kLogisticNeglik: return predt - label;
       default: utils::Error("unknown loss_type"); return 0.0f;
@@ -65,7 +65,7 @@ struct LossType {
   inline float SecondOrderGradient(float predt, float label) const {
     switch (loss_type) {
       case kLinearSquare: return 1.0f;
-      case kLogisticRaw: predt = 1.0f / (1.0f + expf(-predt));
+      case kLogisticRaw: predt = 1.0f / (1.0f + std::exp(-predt));
       case kLogisticClassify:
       case kLogisticNeglik: return predt * (1 - predt);
       default: utils::Error("unknown loss_type"); return 0.0f;
@@ -80,7 +80,7 @@ struct LossType {
         loss_type == kLogisticNeglik ) {
       utils::Check(base_score > 0.0f && base_score < 1.0f,
                    "base_score must be in (0,1) for logistic loss");
-      base_score = -logf(1.0f / base_score - 1.0f);
+      base_score = -std::log(1.0f / base_score - 1.0f);
     }
     return base_score;
   }
@@ -419,8 +419,8 @@ class LambdaRankObjNDCG : public LambdaRankObj {
       for (size_t i = 0; i < pairs.size(); ++i) {
         unsigned pos_idx = pairs[i].pos_index;
         unsigned neg_idx = pairs[i].neg_index;
-        float pos_loginv = 1.0f / logf(pos_idx + 2.0f);
+        float pos_loginv = 1.0f / std::log(pos_idx + 2.0f);
-        float neg_loginv = 1.0f / logf(neg_idx + 2.0f);
+        float neg_loginv = 1.0f / std::log(neg_idx + 2.0f);
         int pos_label = static_cast<int>(sorted_list[pos_idx].label);
         int neg_label = static_cast<int>(sorted_list[neg_idx].label);
         float original =
@@ -438,7 +438,7 @@ class LambdaRankObjNDCG : public LambdaRankObj {
     for (size_t i = 0; i < labels.size(); ++i) {
       const unsigned rel = static_cast<unsigned>(labels[i]);
       if (rel != 0) {
-        sumdcg += ((1 << rel) - 1) / logf(static_cast<float>(i + 2));
+        sumdcg += ((1 << rel) - 1) / std::log(static_cast<float>(i + 2));
       }
     }
     return static_cast<float>(sumdcg);

src/utils/random.h

@@ -91,7 +91,7 @@ struct Random{
 	// use rand instead of rand_r in windows, for MSVC it is fine since rand is threadsafe
 	// For cygwin and mingw, this can slows down parallelism, but rand_r is only used in objective-inl.hpp, won't affect speed in general
 	// todo, replace with another PRNG
-#if defined(_MSC_VER)||defined(_WIN32)
+#if defined(_MSC_VER)||defined(_WIN32)||defined(XGBOOST_STRICT_CXX98_)
     return Uniform();
 #else
     return static_cast<double>(rand_r(&rseed)) / (static_cast<double>(RAND_MAX) + 1.0);

src/utils/utils.h

@@ -15,7 +15,7 @@
 #endif
 
 #if !defined(__GNUC__)
-#define fopen64 fopen
+#define fopen64 std::fopen
 #endif
 #ifdef _MSC_VER
 // NOTE: sprintf_s is not equivalent to snprintf, 
@@ -31,7 +31,7 @@
 
 #ifdef __APPLE__ 
 #define off64_t off_t
-#define fopen64 fopen
+#define fopen64 std::fopen
 #endif
 
 extern "C" {
@@ -52,6 +52,7 @@ typedef long int64_t;
 namespace xgboost {
 /*! \brief namespace for helper utils of the project */
 namespace utils {
+
 /*! \brief error message buffer length */
 const int kPrintBuffer = 1 << 12;
 
@@ -86,10 +87,10 @@ void HandlePrint(const char *msg);
 
 #ifdef XGBOOST_STRICT_CXX98_
 // these function pointers are to be assigned 
-extern void (*Printf)(const char *fmt, ...);
+extern "C" void (*Printf)(const char *fmt, ...);
-extern void (*Assert)(int exp, const char *fmt, ...);
+extern "C" void (*Assert)(int exp, const char *fmt, ...);
-extern void (*Check)(int exp, const char *fmt, ...);
+extern "C" void (*Check)(int exp, const char *fmt, ...);
-extern void (*Error)(const char *fmt, ...);
+extern "C" void (*Error)(const char *fmt, ...);
 #else
 /*! \brief printf, print message to the console */
 inline void Printf(const char *fmt, ...) {