@@ -199,7 +199,7 @@ static void printTime(const std::string &message, unsigned totalSeconds)

     int minutes = totalSeconds / 60;

     totalSeconds -= minutes * 60;

     int seconds = totalSeconds;

-    printf("%s: %02d:%02d:%02d\n", message.c_str(), hours, minutes, seconds);

+    Rprintf("%s: %02d:%02d:%02d\n", message.c_str(), hours, minutes, seconds);

 }

 // need to call storeSamplerInfo before calling this function

@@ -70,7 +70,7 @@ RowMatrix::RowMatrix(const std::string &path)

     while (csv.hasNext())

     {

         MatrixElement e(csv.getNext());

-        this->operator(e.row, e.col) = e.value;

+        this->operator()(e.row, e.col) = e.value;

     }

 }

@@ -1,38 +1,39 @@

 #include "CsvParser.h"

 #include "../math/Algorithms.h"

+#include <fstream>

 #include <iostream>

 // get the number of rows and cols in a csv file

-MatrixDimension CsvParser::getDimensions(const std::string &path)

+MatrixDimensions CsvParser::getDimensions(const std::string &path)

 {

     // initialize struct that holds dimensions

-    MatrixDimension dim(0,0);

+    MatrixDimensions dim(0,0);

     // open file stream

-    std::ifstream str(path);

+    std::ifstream file_str(path.c_str());

     // read first entry (blank)

     std::string line;

-    std::getline(mFile, line, ',');

+    std::getline(file_str, line, ',');

     // get col size

     std::size_t pos;

     do

     {

-        std::getline(mFile, line, ',');

+        std::getline(file_str, line, ',');

         dim.nCol++;

     }

     while ((pos = line.find('\n')) == std::string::npos);

     // get row size

     dim.nRow++; // acount for current row

-    while (mFile.peek() != EOF)

+    while (file_str.peek() != EOF)

     {

         // throw away data

         do

         {

-            std::getline(mFile, line, ',');

+            std::getline(file_str, line, ',');

         }

         while ((pos = line.find('\n')) == std::string::npos);

@@ -49,7 +50,7 @@ MatrixDimension CsvParser::getDimensions(const std::string &path)

 // open file, read column names

 CsvParser::CsvParser(const std::string &path) : mCurrentRow(0), mCurrentCol(0)

 {

-    mFile.open(path);

+    mFile.open(path.c_str());

 }

 bool CsvParser::hasNext()

@@ -23,7 +23,7 @@ public:

     bool hasNext();

     MatrixElement getNext();

-    static MatrixDimension getDimensions(const std::string &path);

+    static MatrixDimensions getDimensions(const std::string &path);

 };

 #endif

\ No newline at end of file

@@ -22,12 +22,12 @@ struct MatrixElement

     }

 };

-struct MatrixDimension

+struct MatrixDimensions

 {

     unsigned nRow;

     unsigned nCol;

-    MatrixDimension(unsigned nr, unsigned nc) : nRow(nr), nCol(nc) {}

+    MatrixDimensions(unsigned nr, unsigned nc) : nRow(nr), nCol(nc) {}

 };

 #endif

\ No newline at end of file