Clean up warnings.

src/mlpack/methods/kernel_pca/kernel_pca_impl.hpp

@@ -55,9 +55,9 @@ void KernelPCA<KernelType>::Apply(const arma::mat& data,
 
   arma::mat kernelMat(centeredData.n_rows, centeredData.n_rows);
 
-  for(int i = 0; i < centeredData.n_rows; i++)
+  for (size_t i = 0; i < centeredData.n_rows; i++)
   {
-    for(int j = 0; j < centeredData.n_rows; j++)
+    for (size_t j = 0; j < centeredData.n_rows; j++)
     {
       arma::vec v1 = trans(centeredData.row(i));
       arma::vec v2 = trans(centeredData.row(j));

src/mlpack/methods/neighbor_search/allkfn_main.cpp

@@ -64,7 +64,7 @@ int main(int argc, char *argv[])
   string distancesFile = CLI::GetParam<string>("distances_file");
   string neighborsFile = CLI::GetParam<string>("neighbors_file");
 
-  int leafSize = CLI::GetParam<int>("leaf_size");
+  int lsInt = CLI::GetParam<int>("leaf_size");
 
   size_t k = CLI::GetParam<int>("k");
 
@@ -87,11 +87,12 @@ int main(int argc, char *argv[])
   }
 
   // Sanity check on leaf size.
-  if (leafSize < 0)
+  if (lsInt < 0)
   {
-    Log::Fatal << "Invalid leaf size: " << leafSize << ".  Must be greater "
+    Log::Fatal << "Invalid leaf size: " << lsInt << ".  Must be greater "
         "than or equal to 0." << endl;
   }
+  size_t leafSize = lsInt;
 
   // Naive mode overrides single mode.
   if (singleMode && naive)

src/mlpack/methods/neighbor_search/allknn_main.cpp

@@ -65,7 +65,7 @@ int main(int argc, char *argv[])
   string distancesFile = CLI::GetParam<string>("distances_file");
   string neighborsFile = CLI::GetParam<string>("neighbors_file");
 
-  int leafSize = CLI::GetParam<int>("leaf_size");
+  int lsInt = CLI::GetParam<int>("leaf_size");
 
   size_t k = CLI::GetParam<int>("k");
 
@@ -88,11 +88,12 @@ int main(int argc, char *argv[])
   }
 
   // Sanity check on leaf size.
-  if (leafSize < 0)
+  if (lsInt < 0)
   {
-    Log::Fatal << "Invalid leaf size: " << leafSize << ".  Must be greater "
+    Log::Fatal << "Invalid leaf size: " << lsInt << ".  Must be greater "
         "than or equal to 0." << endl;
   }
+  size_t leafSize = lsInt;
 
   // Naive mode overrides single mode.
   if (singleMode && naive)

src/mlpack/methods/neighbor_search/neighbor_search.hpp

@@ -317,11 +317,6 @@ class NeighborSearch
   //! Query dataset (may not be given).
   const arma::mat& querySet;
 
-  //! Indicates if O(n^2) naive search is being used.
-  bool naive;
-  //! Indicates if single-tree search is being used (opposed to dual-tree).
-  bool singleMode;
-
   //! Pointer to the root of the reference tree.
   TreeType* referenceTree;
   //! Pointer to the root of the query tree (might not exist).
@@ -332,6 +327,11 @@ class NeighborSearch
   //! Indicates if we should free the query tree at deletion time.
   bool ownQueryTree;
 
+  //! Indicates if O(n^2) naive search is being used.
+  bool naive;
+  //! Indicates if single-tree search is being used (opposed to dual-tree).
+  bool singleMode;
+
   //! Instantiation of kernel.
   MetricType metric;
 

src/mlpack/methods/neighbor_search/neighbor_search_impl.hpp

@@ -25,12 +25,12 @@ NeighborSearch(const typename TreeType::Mat& referenceSet,
     queryCopy(querySet),
     referenceSet(referenceCopy),
     querySet(queryCopy),
-    naive(naive),
-    singleMode(!naive && singleMode), // No single mode if naive.
     referenceTree(NULL),
     queryTree(NULL),
     ownReferenceTree(true), // False if a tree was passed.
     ownQueryTree(true), // False if a tree was passed.
+    naive(naive),
+    singleMode(!naive && singleMode), // No single mode if naive.
     metric(metric),
     numberOfPrunes(0)
 {
@@ -64,12 +64,12 @@ NeighborSearch(const typename TreeType::Mat& referenceSet,
     referenceCopy(referenceSet),
     referenceSet(referenceCopy),
     querySet(referenceCopy),
-    naive(naive),
-    singleMode(!naive && singleMode), // No single mode if naive.
     referenceTree(NULL),
     queryTree(NULL),
     ownReferenceTree(true),
     ownQueryTree(false), // Since it will be the same as referenceTree.
+    naive(naive),
+    singleMode(!naive && singleMode), // No single mode if naive.
     metric(metric),
     numberOfPrunes(0)
 {

src/mlpack/methods/pca/pca.cpp

@@ -84,14 +84,14 @@ void PCA::Apply(const arma::mat& data,
  * from data matrix onto the basis vectors contained in the columns of
  * coeff/eigen vector matrix with only newDimension number of columns chosen.
  */
-void PCA::Apply(arma::mat& data, const int newDimension) const
+void PCA::Apply(arma::mat& data, const size_t newDimension) const
 {
   arma::mat coeffs;
   arma::vec eigVal;
 
   Apply(data, data, eigVal, coeffs);
 
-  if(newDimension < coeffs.n_rows && newDimension > 0)
+  if (newDimension < coeffs.n_rows && newDimension > 0)
     data.shed_rows(newDimension, data.n_rows - 1);
 }
 

src/mlpack/methods/pca/pca.hpp

@@ -49,7 +49,7 @@ class PCA
    * from data matrix onto the basis vectors contained in the columns of
    * coeff/eigen vector matrix with only newDimension number of columns chosen.
    */
-  void Apply(arma::mat& data, const int newDimension) const;
+  void Apply(arma::mat& data, const size_t newDimension) const;
 
   /**
    * Delete PCA object