@@ -25,4 +25,10 @@

     #define GAPS_ASSERT_MSG(cond, msg) ((void)sizeof(cond))

 #endif 

+#define GAPS_ERROR(msg)                             \

+    do {                                            \

+        Rcpp::Rcout << "error: " << msg << '\n';    \

+        Rcpp::stop("CoGAPS aborted");                              \

+    } while(0)

+

 #endif

\ No newline at end of file

@@ -9,9 +9,14 @@

 TEST_CASE("Test Parsers")

 {

+    Rcpp::Environment env = Rcpp::Environment::global_env();

+    std::string csvPath = Rcpp::as<std::string>(env["gistCsvPath"]);

+    std::string tsvPath = Rcpp::as<std::string>(env["gistTsvPath"]);

+    std::string mtxPath = Rcpp::as<std::string>(env["gistMtxPath"]);

+

     SECTION("Test CsvParser")

     {

-        CsvParser p("../../inst/extdata/GIST.csv");

+        CsvParser p(csvPath);

         REQUIRE(p.nRow() == 1363);

         REQUIRE(p.nCol() == 9);

@@ -36,7 +41,7 @@ TEST_CASE("Test Parsers")

     SECTION("Test TsvParser")

     {

-        TsvParser p("../../inst/extdata/GIST.tsv");

+        TsvParser p(tsvPath);

         REQUIRE(p.nRow() == 1363);

         REQUIRE(p.nCol() == 9);

@@ -61,25 +66,21 @@ TEST_CASE("Test Parsers")

     SECTION("Test MtxParser")

     {

-        MtxParser p("../../inst/extdata/GIST.mtx");

+        MtxParser p(mtxPath);

         REQUIRE(p.nRow() == 1363);

         REQUIRE(p.nCol() == 9);

-        unsigned row = 0;

-        unsigned col = 0;

         unsigned count = 0;

         while (p.hasNext())

         {

             MatrixElement e(p.getNext());

-            REQUIRE(e.row() == row);

-            REQUIRE(e.col() == col);

+

+            REQUIRE(e.row() < 1363);

+            REQUIRE(e.row() >= 0);

+            REQUIRE(e.col() < 9);

+            REQUIRE(e.col() >= 0);

             ++count;

-            ++row;

-            if (row == 1363) {

-                ++col;

-                row = 0;

-            }

         }

         REQUIRE(count == 12267);

     }

@@ -51,410 +51,90 @@ TEST_CASE("Test Matrix.h")

         REQUIRE(cmS.nRow() == 1363);

         REQUIRE(cmS.nCol() == 9);

     }

+}

-    SECTION("Matrix Initialization from .tsv file")

+static void populateSequential(std::vector<unsigned> &vec, unsigned n)

+{

+    for (unsigned i = 0; i < n; ++i)

     {

-        std::vector<unsigned> whichRows;

-        std::vector<unsigned> whichCols;

-        for (unsigned i = 0; i < 1363; ++i)

-        {

-            whichRows.push_back(i);

-        }

-        for (unsigned i = 0; i < 9; ++i)

-        {

-            whichCols.push_back(i);

-        }

-        TsvParser p1("../../inst/extdata/GIST.tsv");

-        RowMatrix tsvRowMatrix(p1, true, whichRows);

-        REQUIRE(tsvRowMatrix.nRow() == 1363);

-        REQUIRE(tsvRowMatrix.nCol() == 9);

-

-        TsvParser p2("../../inst/extdata/GIST.tsv");

-        ColMatrix tsvColMatrix(p2, true, whichRows);

-        REQUIRE(tsvColMatrix.nRow() == 1363);

-        REQUIRE(tsvColMatrix.nCol() == 9);

-

-        TsvParser p3("../../inst/extdata/GIST.tsv");

-        RowMatrix tsvRowMatrixT(p3, false, whichCols);

-        REQUIRE(tsvRowMatrixT.nRow() == 9);

-        REQUIRE(tsvRowMatrixT.nCol() == 1363);

-

-        TsvParser p4("../../inst/extdata/GIST.tsv");

-        ColMatrix tsvColMatrixT(p4, false, whichCols);

-        REQUIRE(tsvColMatrixT.nRow() == 9);

-        REQUIRE(tsvColMatrixT.nCol() == 1363);

-

-        float sum = 0;

-        for (unsigned i = 0; i < tsvRowMatrix.nCol(); ++i)

-        {

-            sum += tsvRowMatrix.getRow(0)[i];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 97);

-

-        sum = 0;

-        for (unsigned i = 0; i < tsvColMatrix.nCol(); ++i)

-        {

-            sum += tsvColMatrix.getCol(i)[0];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 97);

-

-        sum = 0;

-        for (unsigned i = 0; i < tsvRowMatrixT.nRow(); ++i)

-        {

-            sum += tsvRowMatrixT.getRow(i)[0];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 97);

-

-        sum = 0;

-        for (unsigned i = 0; i < tsvRowMatrixT.nRow(); ++i)

-        {

-            sum += tsvColMatrixT.getCol(0)[i];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 97);

-

-        for (unsigned i = 0; i < 1000; ++i)

-        {

-            whichRows.pop_back();

-        }

-

-        for (unsigned i = 0; i < 7; ++i)

-        {

-            whichCols.pop_back();

-        }

-

-        TsvParser p5("../../inst/extdata/GIST.tsv");

-        tsvRowMatrix = RowMatrix(p5, true, whichRows);

-        REQUIRE(tsvRowMatrix.nRow() == 363);

-        REQUIRE(tsvRowMatrix.nCol() == 9);

-

-        TsvParser p6("../../inst/extdata/GIST.tsv");

-        tsvColMatrix = ColMatrix(p6, true, whichRows);

-        REQUIRE(tsvColMatrix.nRow() == 363);

-        REQUIRE(tsvColMatrix.nCol() == 9);

-

-        TsvParser p7("../../inst/extdata/GIST.tsv");

-        tsvRowMatrixT = RowMatrix(p7, false, whichCols);

-        REQUIRE(tsvRowMatrixT.nRow() == 2);

-        REQUIRE(tsvRowMatrixT.nCol() == 1363);

-

-        TsvParser p8("../../inst/extdata/GIST.tsv");

-        tsvColMatrixT = ColMatrix(p8, false, whichCols);

-        REQUIRE(tsvColMatrixT.nRow() == 2);

-        REQUIRE(tsvColMatrixT.nCol() == 1363);

-

-        sum = 0;

-        for (unsigned i = 0; i < tsvRowMatrix.nCol(); ++i)

-        {

-            sum += tsvRowMatrix.getRow(0)[i];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 97);

-

-        sum = 0;

-        for (unsigned i = 0; i < tsvColMatrix.nCol(); ++i)

-        {

-            sum += tsvColMatrix.getCol(i)[0];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 97);

-

-        sum = 0;

-        for (unsigned i = 0; i < tsvRowMatrixT.nRow(); ++i)

-        {

-            sum += tsvRowMatrixT.getRow(i)[0];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 20);

-

-        sum = 0;

-        for (unsigned i = 0; i < tsvRowMatrixT.nRow(); ++i)

-        {

-            sum += tsvColMatrixT.getCol(0)[i];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 20);

+        vec.push_back(i);

     }

+}

-    SECTION("Matrix Initialization from .mtx file")

+template <class Parser>

+static void testMatrixConstruction(const std::string &path)

+{

+    std::vector<unsigned> allRows, allCols;

+    std::vector<unsigned> someRows, someCols;

+

+    populateSequential(allRows, 1363);

+    populateSequential(allCols, 9);

+    populateSequential(someRows, 363);

+    populateSequential(someCols, 2);

+

+    Parser p1(path);

+    RowMatrix allRowMat(p1, true, allRows);

+    REQUIRE(allRowMat.nRow() == 1363);

+    REQUIRE(allRowMat.nCol() == 9);

+

+    Parser p2(path);

+    ColMatrix allColMat(p2, true, allRows);

+    REQUIRE(allColMat.nRow() == 1363);

+    REQUIRE(allColMat.nCol() == 9);

+

+    Parser p3(path);

+    RowMatrix allRowMatT(p3, false, allCols);

+    REQUIRE(allRowMatT.nRow() == 9);

+    REQUIRE(allRowMatT.nCol() == 1363);

+

+    Parser p4(path);

+    ColMatrix allColMatT(p4, false, allCols);

+    REQUIRE(allColMatT.nRow() == 9);

+    REQUIRE(allColMatT.nCol() == 1363);

+

+    for (unsigned i = 0; i < 1363; ++i)

     {

-        std::vector<unsigned> whichRows;

-        std::vector<unsigned> whichCols;

-        for (unsigned i = 0; i < 1363; ++i)

-        {

-            whichRows.push_back(i);

-        }

-        for (unsigned i = 0; i < 9; ++i)

-        {

-            whichCols.push_back(i);

-        }

-

-        MtxParser p1("../../inst/extdata/GIST.mtx");

-        RowMatrix mtxRowMatrix(p1, true, whichRows);

-        REQUIRE(mtxRowMatrix.nRow() == 1363);

-        REQUIRE(mtxRowMatrix.nCol() == 9);

-

-        MtxParser p2("../../inst/extdata/GIST.mtx");

-        ColMatrix mtxColMatrix(p2, true, whichRows);

-        REQUIRE(mtxColMatrix.nRow() == 1363);

-        REQUIRE(mtxColMatrix.nCol() == 9);

-

-        MtxParser p3("../../inst/extdata/GIST.mtx");

-        RowMatrix mtxRowMatrixT = RowMatrix(p3, false, whichCols);

-        REQUIRE(mtxRowMatrixT.nRow() == 9);

-        REQUIRE(mtxRowMatrixT.nCol() == 1363);

-

-        MtxParser p4("../../inst/extdata/GIST.mtx");

-        ColMatrix mtxColMatrixT = ColMatrix(p4, false, whichCols);

-        REQUIRE(mtxColMatrixT.nRow() == 9);

-        REQUIRE(mtxColMatrixT.nCol() == 1363);

-

-        float sum = 0;

-        for (unsigned i = 0; i < mtxRowMatrix.nCol(); ++i)

-        {

-            sum += mtxRowMatrix.getRow(0)[i];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 97);

-

-        sum = 0;

-        for (unsigned i = 0; i < mtxColMatrix.nCol(); ++i)

-        {

-            sum += mtxColMatrix.getCol(i)[0];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 97);

-

-        sum = 0;

-        for (unsigned i = 0; i < mtxRowMatrixT.nRow(); ++i)

-        {

-            sum += mtxRowMatrixT.getRow(i)[0];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 97);

-

-        sum = 0;

-        for (unsigned i = 0; i < mtxRowMatrixT.nRow(); ++i)

-        {

-            sum += mtxColMatrixT.getCol(0)[i];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 97);

-

-        for (unsigned i = 0; i < 1000; ++i)

-        {

-            whichRows.pop_back();

-        }

-

-        for (unsigned i = 0; i < 7; ++i)

-        {

-            whichCols.pop_back();

-        }

-

-        MtxParser p5("../../inst/extdata/GIST.mtx");

-        mtxRowMatrix = RowMatrix(p5, true, whichRows);

-        REQUIRE(mtxRowMatrix.nRow() == 363);

-        REQUIRE(mtxRowMatrix.nCol() == 9);

-

-        MtxParser p6("../../inst/extdata/GIST.mtx");

-        mtxColMatrix = ColMatrix(p6, true, whichRows);

-        REQUIRE(mtxColMatrix.nRow() == 363);

-        REQUIRE(mtxColMatrix.nCol() == 9);

-

-        MtxParser p7("../../inst/extdata/GIST.mtx");

-        mtxRowMatrixT = RowMatrix(p7, false, whichCols);

-        REQUIRE(mtxRowMatrixT.nRow() == 2);

-        REQUIRE(mtxRowMatrixT.nCol() == 1363);

-

-        MtxParser p8("../../inst/extdata/GIST.mtx");

-        mtxColMatrixT = ColMatrix(p8, false, whichCols);

-        REQUIRE(mtxColMatrixT.nRow() == 2);

-        REQUIRE(mtxColMatrixT.nCol() == 1363);

-

-        sum = 0;

-        for (unsigned i = 0; i < mtxRowMatrix.nCol(); ++i)

-        {

-            sum += mtxRowMatrix.getRow(0)[i];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 97);

-

-        sum = 0;

-        for (unsigned i = 0; i < mtxColMatrix.nCol(); ++i)

-        {

-            sum += mtxColMatrix.getCol(i)[0];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 97);

-

-        sum = 0;

-        for (unsigned i = 0; i < mtxRowMatrixT.nRow(); ++i)

-        {

-            sum += mtxRowMatrixT.getRow(i)[0];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 20);

-

-        sum = 0;

-        for (unsigned i = 0; i < mtxRowMatrixT.nRow(); ++i)

-        {

-            sum += mtxColMatrixT.getCol(0)[i];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 20);

+        REQUIRE(allRowMat(i, 3) == allColMat(i, 3));

+        REQUIRE(allRowMat(i, 3) == allRowMatT(3, i));

+        REQUIRE(allRowMat(i, 3) == allColMatT(3, i));

     }

-    SECTION("Matrix Initialization from .csv file")

-    {

-        std::vector<unsigned> whichRows;

-        std::vector<unsigned> whichCols;

-        for (unsigned i = 0; i < 1363; ++i)

-        {

-            whichRows.push_back(i);

-        }

-        for (unsigned i = 0; i < 9; ++i)

-        {

-            whichCols.push_back(i);

-        }

-        CsvParser p1("../../inst/extdata/GIST.csv");

-        RowMatrix csvRowMatrix(p1, true, whichRows);

-        REQUIRE(csvRowMatrix.nRow() == 1363);

-        REQUIRE(csvRowMatrix.nCol() == 9);

-

-        CsvParser p2("../../inst/extdata/GIST.csv");

-        ColMatrix csvColMatrix(p2, true, whichRows);

-        REQUIRE(csvColMatrix.nRow() == 1363);

-        REQUIRE(csvColMatrix.nCol() == 9);

-

-        CsvParser p3("../../inst/extdata/GIST.csv");

-        RowMatrix csvRowMatrixT = RowMatrix(p3, false, whichCols);

-        REQUIRE(csvRowMatrixT.nRow() == 9);

-        REQUIRE(csvRowMatrixT.nCol() == 1363);

+    Parser p5(path);

+    RowMatrix someRowMat(p1, true, someRows);

+    REQUIRE(someRowMat.nRow() == 363);

+    REQUIRE(someRowMat.nCol() == 9);

-        CsvParser p4("../../inst/extdata/GIST.csv");

-        ColMatrix csvColMatrixT = ColMatrix(p4, false, whichCols);

-        REQUIRE(csvColMatrixT.nRow() == 9);

-        REQUIRE(csvColMatrixT.nCol() == 1363);

+    Parser p6(path);

+    ColMatrix someColMat(p2, true, someRows);

+    REQUIRE(someColMat.nRow() == 363);

+    REQUIRE(someColMat.nCol() == 9);

-        float sum = 0;

-        for (unsigned i = 0; i < csvRowMatrix.nCol(); ++i)

-        {

-            sum += csvRowMatrix.getRow(0)[i];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 97);

+    Parser p7(path);

+    RowMatrix someRowMatT(p3, false, someCols);

+    REQUIRE(someRowMatT.nRow() == 2);

+    REQUIRE(someRowMatT.nCol() == 1363);

-        sum = 0;

-        for (unsigned i = 0; i < csvColMatrix.nCol(); ++i)

-        {

-            sum += csvColMatrix.getCol(i)[0];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 97);

+    Parser p8(path);

+    ColMatrix someColMatT(p4, false, someCols);

+    REQUIRE(someColMatT.nRow() == 2);

+    REQUIRE(someColMatT.nCol() == 1363);

-        sum = 0;

-        for (unsigned i = 0; i < csvRowMatrixT.nRow(); ++i)

-        {

-            sum += csvRowMatrixT.getRow(i)[0];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 97);

-

-        sum = 0;

-        for (unsigned i = 0; i < csvRowMatrixT.nRow(); ++i)

-        {

-            sum += csvColMatrixT.getCol(0)[i];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 97);

-

-        for (unsigned i = 0; i < 1000; ++i)

-        {

-            whichRows.pop_back();

-        }

-

-        for (unsigned i = 0; i < 7; ++i)

-        {

-            whichCols.pop_back();

-        }

-

-        CsvParser p5("../../inst/extdata/GIST.csv");

-        csvRowMatrix = RowMatrix(p5, true, whichRows);

-        REQUIRE(csvRowMatrix.nRow() == 363);

-        REQUIRE(csvRowMatrix.nCol() == 9);

-

-        CsvParser p6("../../inst/extdata/GIST.csv");

-        csvColMatrix = ColMatrix(p6, true, whichRows);

-        REQUIRE(csvColMatrix.nRow() == 363);

-        REQUIRE(csvColMatrix.nCol() == 9);

-

-        CsvParser p7("../../inst/extdata/GIST.csv");

-        csvRowMatrixT = RowMatrix(p7, false, whichCols);

-        REQUIRE(csvRowMatrixT.nRow() == 2);

-        REQUIRE(csvRowMatrixT.nCol() == 1363);

-

-        CsvParser p8("../../inst/extdata/GIST.csv");

-        csvColMatrixT = ColMatrix(p8, false, whichCols);

-        REQUIRE(csvColMatrixT.nRow() == 2);

-        REQUIRE(csvColMatrixT.nCol() == 1363);

-

-        sum = 0;

-        for (unsigned i = 0; i < csvRowMatrix.nCol(); ++i)

-        {

-            sum += csvRowMatrix.getRow(0)[i];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 97);

-

-        sum = 0;

-        for (unsigned i = 0; i < csvColMatrix.nCol(); ++i)

-        {

-            sum += csvColMatrix.getCol(i)[0];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 97);

-

-        sum = 0;

-        for (unsigned i = 0; i < csvRowMatrixT.nRow(); ++i)

-        {

-            sum += csvRowMatrixT.getRow(i)[0];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 20);

-

-        sum = 0;

-        for (unsigned i = 0; i < csvRowMatrixT.nRow(); ++i)

-        {

-            sum += csvColMatrixT.getCol(0)[i];

-        }

-        sum *= 10;

-        sum = (int) sum;

-        REQUIRE(sum == 20);

+    for (unsigned i = 0; i < 363; ++i)

+    {

+        REQUIRE(someRowMat(i, 1) == someColMat(i, 1));

+        REQUIRE(someRowMat(i, 1) == someRowMatT(1, i));

+        REQUIRE(someRowMat(i, 1) == someColMatT(1, i));

     }

 }

+

+TEST_CASE("Test Matrix Construction from file")

+{

+    Rcpp::Environment env = Rcpp::Environment::global_env();

+    std::string csvPath = Rcpp::as<std::string>(env["gistCsvPath"]);

+    std::string tsvPath = Rcpp::as<std::string>(env["gistTsvPath"]);

+    std::string mtxPath = Rcpp::as<std::string>(env["gistMtxPath"]);

+

+    testMatrixConstruction<CsvParser>(csvPath);

+    testMatrixConstruction<TsvParser>(tsvPath);

+    testMatrixConstruction<MtxParser>(mtxPath);

+}

\ No newline at end of file

@@ -103,7 +103,8 @@ inline void fill(Matrix &mat, Parser &p, bool partitionRows, std::vector<unsigne

         std::vector<unsigned>::iterator newRowIndex = std::find(whichIndices.begin(), whichIndices.end(), e[rowSelect]);

         if (newRowIndex != whichIndices.end())

         {

-            mat.operator()(std::distance(whichIndices.begin(), newRowIndex), e[colSelect]) = e.value;

+            unsigned row = std::distance(whichIndices.begin(), newRowIndex);

+            mat.operator()(row, e[colSelect]) = e.value;

         }

     }

 }

@@ -1,4 +1,5 @@

 #include "CsvParser.h"

+#include "../GapsAssert.h"

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

 #include <fstream>

@@ -15,12 +16,20 @@ mCurrentRow(0), mCurrentCol(0)

     // read first entry (blank)

     std::string line;

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

+    if (file_str.eof() || file_str.fail())

+    {

+        GAPS_ERROR("Invalid CSV file");

+    }

     // get col size

     std::size_t pos;

     do

     {

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

+        if (file_str.eof() || file_str.fail())

+        {

+            GAPS_ERROR("Invalid CSV file");

+        }

         ++mNumCols;

     }

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

@@ -50,6 +59,7 @@ mCurrentRow(0), mCurrentCol(0)

 bool CsvParser::hasNext()

 {

+    mFile >> std::ws;

     return mFile.peek() != EOF;

 }

@@ -1,17 +1,30 @@

 #include "MtxParser.h"

 #include "MatrixElement.h"

+#include "../GapsAssert.h"

 #include <sstream>

+#include <Rcpp.h>

 MtxParser::MtxParser(const std::string &path) : mNumRows(0), mNumCols(0)

 {

     mFile.open(path.c_str());

+    // read first line

+    std::string line;

+    std::getline(mFile, line);

+    if (mFile.eof() || mFile.fail())

+    {

+        GAPS_ERROR("Invalid MTX file");

+    }

+

     // skip over comments

-    std::string line = "%";

     while (line.find('%') != std::string::npos)

     {

         std::getline(mFile, line);

+        if (mFile.eof() || mFile.fail())

+        {

+            GAPS_ERROR("Invalid MTX file");

+        }

     }

     std::stringstream ss(line); // this line contains dimensions

@@ -21,17 +34,18 @@ MtxParser::MtxParser(const std::string &path) : mNumRows(0), mNumCols(0)

 bool MtxParser::hasNext()

 {

+    mFile >> std::ws; // get rid of whitespace

     return mFile.peek() != EOF;

 }

 MatrixElement MtxParser::getNext()

 {

-    MatrixElement e(0, 0, 0.f);

-    unsigned buff;

-    mFile >> buff;

-    e.dim[0] = buff - 1;

-    mFile >> buff;

-    e.dim[1] = buff - 1;

-    mFile >> e.value;

-    return e;

+    unsigned row = 0, col = 0;

+    float val = 0.f;

+

+    mFile >> row;

+    mFile >> col;

+    mFile >> val;

+

+    return MatrixElement(row - 1, col - 1, val);

 }

@@ -1,4 +1,5 @@

 #include "TsvParser.h"

+#include "../GapsAssert.h"

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

 #include <fstream>

@@ -15,12 +16,21 @@ mCurrentRow(0), mCurrentCol(0)

     // read first entry (blank)

     std::string line;

     std::getline(file_str, line, '\t');

+    if (file_str.eof() || file_str.fail())

+    {

+        GAPS_ERROR("Invalid TSV file");

+    }

     // get col size

     std::size_t pos;

     do

     {

         std::getline(file_str, line, '\t');

+        if (file_str.eof() || file_str.fail())

+        {

+            GAPS_ERROR("Invalid TSV file");

+        }

+

         ++mNumCols;

     }

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

@@ -50,6 +60,7 @@ mCurrentRow(0), mCurrentCol(0)

 bool TsvParser::hasNext()

 {

+    mFile >> std::ws;

     return mFile.peek() != EOF;

 }

@@ -5,7 +5,9 @@ test_that("Catch unit tests pass",

     data(SimpSim)

     data(GIST)

-    gistMtxPath <- system.file("data/GIST.mtx", package="CoGAPS")

+    gistCsvPath <<- system.file("extdata/GIST.csv", package="CoGAPS")

+    gistTsvPath <<- system.file("extdata/GIST.tsv", package="CoGAPS")

+    gistMtxPath <<- system.file("extdata/GIST.mtx", package="CoGAPS")

     run_catch_unit_tests()

 })