@@ -4266,41 +4266,6 @@ else

   :

 fi

-    { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether C++ compiler accepts -Wno-unused-function" >&5

-$as_echo_n "checking whether C++ compiler accepts -Wno-unused-function... " >&6; }

-if ${ax_cv_check_cxxflags___Wno_unused_function+:} false; then :

-  $as_echo_n "(cached) " >&6

-else

-

-  ax_check_save_flags=$CXXFLAGS

-  CXXFLAGS="$CXXFLAGS  -Wno-unused-function"

-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext

-/* end confdefs.h.  */

-

-int

-main ()

-{

-

-  ;

-  return 0;

-}

-_ACEOF

-if ac_fn_cxx_try_compile "$LINENO"; then :

-  ax_cv_check_cxxflags___Wno_unused_function=yes

-else

-  ax_cv_check_cxxflags___Wno_unused_function=no

-fi

-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext

-  CXXFLAGS=$ax_check_save_flags

-fi

-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_cv_check_cxxflags___Wno_unused_function" >&5

-$as_echo "$ax_cv_check_cxxflags___Wno_unused_function" >&6; }

-if test "x$ax_cv_check_cxxflags___Wno_unused_function" = xyes; then :

-  GAPS_CXX_FLAGS+=" -Wno-unused-function "

-else

-  :

-fi

-

 fi

 # set compile flags for SIMD

@@ -49,8 +49,8 @@ if test "x$warnings" = "xyes" ; then

     AX_CHECK_COMPILE_FLAG([-Wall], [GAPS_CXX_FLAGS+=" -Wall "])

     AX_CHECK_COMPILE_FLAG([-Wextra], [GAPS_CXX_FLAGS+=" -Wextra "])

     AX_CHECK_COMPILE_FLAG([-Werror], [GAPS_CXX_FLAGS+=" -Werror "])

-    AX_CHECK_COMPILE_FLAG([-Wno-unused-parameter], [GAPS_CXX_FLAGS+=" -Wno-unused-parameter "])

-    AX_CHECK_COMPILE_FLAG([-Wno-unused-function], [GAPS_CXX_FLAGS+=" -Wno-unused-function "])

+    AX_CHECK_COMPILE_FLAG([-Wno-unused-parameter],

+        [GAPS_CXX_FLAGS+=" -Wno-unused-parameter "])

 fi

 # set compile flags for SIMD

@@ -6,9 +6,9 @@

 static RowMatrix convertRMatrix(const Rcpp::NumericMatrix &rmat)

 {

     RowMatrix mat(rmat.nrow(), rmat.ncol());

-    for (unsigned i = 0; i < rmat.nrow(); ++i)

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

     {

-        for (unsigned j = 0; j < rmat.ncol(); ++j)

+        for (unsigned j = 0; j < mat.nCol(); ++j)

         {

             mat(i,j) = rmat(i,j);

         }

@@ -13,20 +13,20 @@

 #endif

 #ifdef GAPS_DEBUG

-    #define GAPS_ASSERT(cond)                                           \

-        do {                                                            \

-            if (!(cond))                                                \

-            {                                                           \

-                gaps_printf("assert failed %s %d\n", __FILE__, __LINE__);   \

-                std::exit(0);                                           \

-            }                                                           \

+    #define GAPS_ASSERT(cond)                                             \

+        do {                                                              \

+            if (!(cond))                                                  \

+            {                                                             \

+                gaps_printf("assert failed %s %d\n", __FILE__, __LINE__); \

+                std::exit(0);                                             \

+            }                                                             \

         } while(0)

     #define GAPS_ASSERT_MSG(cond, msg)                                  \

         do {                                                            \

             if (!(cond))                                                \

             {                                                           \

-                gaps_cout << "assert failed " << __FILE__ << " " <<   \

+                gaps_cout << "assert failed " << __FILE__ << " " <<     \

                     __LINE__ << " , " << msg << '\n';                   \

                 std::exit(0);                                           \

             }                                                           \

@@ -42,10 +42,7 @@

 #define gaps_stop std::exit(0)

 #endif

-#define GAPS_ERROR(msg)                             \

-    do {                                            \

-        gaps_cout << "error: " << msg << '\n';    \

-        gaps_stop;                              \

-    } while(0)

+// NOLINTNEXTLINE

+#define GAPS_ERROR(msg) do {gaps_cout << "error: " << msg << '\n'; gaps_stop;} while(0)

 #endif

\ No newline at end of file

@@ -6,6 +6,7 @@

     #include <omp.h>

 #endif

+/*

 static std::vector< std::vector<unsigned> > sampleIndices(unsigned n, unsigned nSets)

 {

     unsigned setSize = n / nSets;

@@ -26,6 +27,7 @@ static std::vector< std::vector<unsigned> > sampleIndices(unsigned n, unsigned n

     sampleIndices.push_back(toBeSampled);

     return sampleIndices;

 }

+*/

 void GapsDispatcher::runOneCycle(unsigned k)

 {

@@ -52,13 +52,16 @@ private:

     void runOneCycle(unsigned k);

+    GapsDispatcher(const GapsDispatcher &p); // don't allow copies

+    GapsDispatcher& operator=(const GapsDispatcher &p); // don't allow copies

+

 public:

-    GapsDispatcher(uint32_t seed=0) : mNumPatterns(3), mMaxIterations(1000),

-        mOutputFrequency(250), mSeed(seed), mAlphaA(0.01), mAlphaP(0.01),

-        mMaxGibbsMassA(100.f), mMaxGibbsMassP(100.f), mPrintMessages(true),

-        mSingleCell(false), mDataIsLoaded(false), mNumCoresPerSet(1),

-        mFixedMatrix('N')

+    explicit GapsDispatcher(uint32_t seed=0) : mNumPatterns(3),

+        mMaxIterations(1000), mOutputFrequency(250), mSeed(seed), mAlphaA(0.01),

+        mAlphaP(0.01), mMaxGibbsMassA(100.f), mMaxGibbsMassP(100.f),

+        mPrintMessages(true), mSingleCell(false), mDataIsLoaded(false),

+        mNumCoresPerSet(1), mFixedMatrix('N')

     {

         gaps::random::setSeed(mSeed);

     }

@@ -22,9 +22,9 @@ private:

 public:

     RowMatrix(unsigned nrow, unsigned ncol);

+    explicit RowMatrix(const ColMatrix &mat);

-    RowMatrix(const std::string &p);

-    RowMatrix(const ColMatrix &mat);

+    explicit RowMatrix(const std::string &path);

     //RowMatrix(const std::string &p, bool parseRows, std::vector<unsigned> whichIndices);

     unsigned nRow() const {return mNumRows;}

@@ -58,9 +58,9 @@ private:

 public:

     ColMatrix(unsigned nrow, unsigned ncol);

-    ColMatrix(const RowMatrix &mat);

+    explicit ColMatrix(const RowMatrix &mat);

-    ColMatrix(const std::string &p);

+    explicit ColMatrix(const std::string &path);

     //ColMatrix(const std::string &p, bool parseRows, std::vector<unsigned> whichIndices);

     unsigned nRow() const {return mNumRows;}

@@ -19,6 +19,9 @@ private:

     unsigned mCurrentRow;

     unsigned mCurrentCol;

+    CsvParser(const CsvParser &p); // don't allow copies

+    CsvParser& operator=(const CsvParser &p); // don't allow copies

+

 public:

     explicit CsvParser(const std::string &path);

@@ -1,7 +1,7 @@

 #include "../GapsAssert.h"

+#include "CsvParser.h"

 #include "FileParser.h"

 #include "MtxParser.h"

-#include "CsvParser.h"

 #include "TsvParser.h"

 #include <string>

@@ -16,14 +16,15 @@ enum GapsFileType

 static GapsFileType fileType(const std::string &path)

 {

-    std::size_t pos = path.find_last_of(".");

+    std::size_t pos = path.find_last_of('.');

     std::string ext = path.substr(pos);

-    if (ext.find("/") != std::string::npos) { return GAPS_INVALID_FILE_TYPE; }

-    else if (ext == ".mtx") { return GAPS_MTX; }

-    else if (ext == ".csv") { return GAPS_CSV; }

-    else if (ext == ".tsv") { return GAPS_TSV; }

-    else { return GAPS_INVALID_FILE_TYPE; }

+    if (ext.find('/') != std::string::npos) { return GAPS_INVALID_FILE_TYPE; }

+    if (ext == ".mtx") { return GAPS_MTX; }

+    if (ext == ".csv") { return GAPS_CSV; }

+    if (ext == ".tsv") { return GAPS_TSV; }

+

+    return GAPS_INVALID_FILE_TYPE;

 }

 AbstractFileParser* AbstractFileParser::create(const std::string &path)

@@ -6,8 +6,15 @@

 // file parser interface

 class AbstractFileParser

 {

+private:

+

+    AbstractFileParser(const AbstractFileParser &p); // don't allow copies

+    AbstractFileParser& operator=(const AbstractFileParser &p); // don't allow copies

+

 public:

+    AbstractFileParser() {}

+

     static AbstractFileParser* create(const std::string &path);

     virtual ~AbstractFileParser() = 0;

@@ -16,6 +16,9 @@ private:

     unsigned mNumRows;

     unsigned mNumCols;

+    MtxParser(const MtxParser &p); // don't allow copies

+    MtxParser& operator=(const MtxParser &p); // don't allow copies

+

 public:

     explicit MtxParser(const std::string &path);

@@ -19,6 +19,9 @@ private:

     unsigned mCurrentRow;

     unsigned mCurrentCol;

+    TsvParser(const TsvParser &p); // don't allow copies

+    TsvParser& operator=(const TsvParser &p); // don't allow copies

+

 public:

     explicit TsvParser(const std::string &path);

new file mode 100644

Binary files /dev/null and b/tests/testthat/test_ar.temp differ