some strict cxx98 check

src/io/dmlc_simple.cpp

@@ -141,7 +141,7 @@ class SingleFileSplit : public dmlc::InputSplit {
 
 class StdFile : public dmlc::Stream {
  public:
-  explicit StdFile(FILE *fp, bool use_stdio)
+  explicit StdFile(std::FILE *fp, bool use_stdio)
       : fp(fp), use_stdio(use_stdio) {
   }  
   virtual ~StdFile(void) {
@@ -180,6 +180,7 @@ InputSplit* InputSplit::Create(const char *uri,
                                unsigned part,
                                unsigned nsplit,
                                const char *type) {
+  using namespace std;
   using namespace xgboost;
   const char *msg = "xgboost is compiled in local mode\n"\
       "to use hdfs, s3 or distributed version, compile with make dmlc=1";
@@ -190,13 +191,14 @@ InputSplit* InputSplit::Create(const char *uri,
 }
 
 Stream *Stream::Create(const char *fname, const char * const mode, bool allow_null) {
+  using namespace std;
   using namespace xgboost;
   const char *msg = "xgboost is compiled in local mode\n"\
       "to use hdfs, s3 or distributed version, compile with make dmlc=1";
   utils::Check(strncmp(fname, "s3://", 5) != 0, msg);
   utils::Check(strncmp(fname, "hdfs://", 7) != 0, msg);
   
-  FILE *fp = NULL;
+  std::FILE *fp = NULL;
   bool use_stdio = false;
   using namespace std;
 #ifndef XGBOOST_STRICT_CXX98_

src/io/io.cpp

@@ -15,6 +15,7 @@ DataMatrix* LoadDataMatrix(const char *fname,
                            bool savebuffer,
                            bool loadsplit,
                            const char *cache_file) {
+  using namespace std;
   std::string fname_ = fname;
   
   const char *dlm = strchr(fname, '#');

src/io/libsvm_parser.h

@@ -111,7 +111,8 @@ class LibSVMPageFactory  {
    */
   inline void ParseBlock(char *begin,
                          char *end,
-                         LibSVMPage *out) {    
+                         LibSVMPage *out) {
+    using namespace std;
     out->Clear();
     char *p = begin;
     while (p != end) {

src/io/page_fmatrix-inl.hpp

@@ -255,7 +255,7 @@ class FMatrixPage : public IFMatrix {
 
  protected:
   inline bool TryLoadColData(void) {
-    FILE *fi = fopen64(col_meta_name_.c_str(), "rb");
+    std::FILE *fi = fopen64(col_meta_name_.c_str(), "rb");
     if (fi == NULL) return false;    
     utils::FileStream fs(fi);
     LoadMeta(&fs);

src/utils/thread.h

@@ -55,8 +55,10 @@ inline void ThreadExit(void *status) {
 }  // namespace xgboost
 #else
 // thread interface using g++     
+extern "C" {
 #include <semaphore.h>
 #include <pthread.h>
+}
 namespace xgboost {
 namespace utils {
 /*!\brief semaphore class */
@@ -120,6 +122,7 @@ class Semaphore {
   }
   #endif  
 };
+
 /*!\brief simple thread class */
 class Thread {
  private:
@@ -130,7 +133,7 @@ class Thread {
     pthread_attr_init(&attr);
     pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
     pthread_create(&thread, &attr, entry, param);
-  }  
+  }
   inline int Join(void) {
     void *status;
     return pthread_join(thread, &status);

src/utils/thread_buffer.h

@@ -31,7 +31,8 @@ class ThreadBuffer {
   }
   /*!\brief set parameter, will also pass the parameter to factory */
   inline void SetParam(const char *name, const char *val) {
-    if (!std::strcmp( name, "buffer_size")) buf_size = atoi(val);
+    using namespace std;
+    if (!strcmp( name, "buffer_size")) buf_size = atoi(val);
     factory.SetParam(name, val);
   }
   /*!