Add local patch of changes sent upstream

coatless-rpkg · Nov 30, 2024 · 33a2b63 · 33a2b63
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commit 33a2b63
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diff --git a/ChangeLog b/ChangeLog
@@ -1,5 +1,14 @@
 2024-11-29  James Balamuta  <[email protected]>
 
+    * inst/include/ensmallen_bits/agemoea/agemoea.hpp: removed unused private field variable
+    * inst/include/problems/dtlz/dtlz2_function.hpp: removed unused variable.
+    * inst/include/problems/dtlz/dtlz4_function.hpp: ditto
+    * inst/include/problems/dtlz/dtlz5_function.hpp: ditto
+    * inst/include/problems/dtlz/dtlz6_function.hpp: ditto
+    * inst/include/problems/dtlz/dtlz7_function.hpp: ditto
+    * inst/include/problems/maf/maf5_function.hpp: ditto
+    * inst/include/problems/maf/maf6_function.hpp: ditto
+
 	* DESCRIPTION (Version): Release 2.22.0
 	* NEWS.md: Update for Ensmallen release 2.22.0
 	* inst/include/ensmallen_bits: Upgraded to Ensmallen 2.22.0

diff --git a/NEWS.md b/NEWS.md
@@ -9,6 +9,8 @@
     ([#409](https://github.com/mlpack/ensmallen/pull/409)).
   - Added IPOP and BIPOP restart mechanisms for CMA-ES.
     ([#403](https://github.com/mlpack/ensmallen/pull/403)).
+- Addressed uninitialized variable and private field warnings 
+    ([#65](https://github.com/coatless-rpkg/rcppensmallen/pull/65))
 
 # RcppEnsmallen 0.2.21.1.1
 

diff --git a/inst/include/ensmallen_bits/agemoea/agemoea.hpp b/inst/include/ensmallen_bits/agemoea/agemoea.hpp
@@ -347,7 +347,7 @@ class AGEMOEA
       size_t idxQ,
       const std::vector<size_t>& ranks,
       const std::vector<typename MatType::elem_type>& survivalScore);
-  
+
  /**
   * Normalizes the front given the extreme points in the current front.
   *
@@ -363,7 +363,7 @@ class AGEMOEA
      arma::Col<typename MatType::elem_type>& normalization,
      const std::vector<size_t>& front,
      const arma::Row<size_t>& extreme);
- 
+
  /**
   * Get the geometry information p of Lp norm (p > 0).
   *
@@ -377,7 +377,7 @@ class AGEMOEA
       std::vector<arma::Col<typename MatType::elem_type> >& calculatedObjectives,
       const std::vector<size_t>& front,
       const arma::Row<size_t>& extreme);
-  
+
   /**
    * Finds the pairwise Lp distance between all the points in the front.
    *
@@ -395,7 +395,7 @@ class AGEMOEA
 
   /**
    * Finding the indexes of the extreme points in the front.
-   *  
+   *
    * @param indexes vector containing the slected indexes.
    * @param calculatedObjectives The current population objectives.
    * @param front The front of the current generation.
@@ -405,11 +405,11 @@ class AGEMOEA
       arma::Row<size_t>& indexes,
       std::vector<arma::Col<typename MatType::elem_type> >& calculatedObjectives,
       const std::vector<size_t>& front);
-  
+
   /**
    * Finding the distance of each point in the front from the line formed
    * by pointA and pointB.
-   * 
+   *
    * @param distance The vector containing the distances of the points in the fron from the line.
    * @param calculatedObjectives Reference to the current population evaluated Objectives.
    * @param front The front of the current generation(indices of population).
@@ -423,10 +423,10 @@ class AGEMOEA
       const std::vector<size_t>& front,
       const arma::Col<typename MatType::elem_type>& pointA,
       const arma::Col<typename MatType::elem_type>& pointB);
-  
+
   /**
    * Find the Diversity score corresponding the solution S using the selected set.
-   * 
+   *
    * @param selected The current selected set.
    * @param pairwiseDistance The current pairwise distance for the whole front.
    * @param S The relative index of S being considered within the front.
@@ -452,12 +452,6 @@ class AGEMOEA
   //! Probability that crossover will occur.
   double crossoverProb;
 
-  //! Probability that mutation will occur.
-  double mutationProb;
-
-  //! Strength of the mutation.
-  double mutationStrength;
-
   //! The crowding degree of the mutation. Higher value produces a mutant
   //! resembling its parent.
   double distributionIndex;

diff --git a/inst/include/ensmallen_bits/problems/dtlz/dtlz2_function.hpp b/inst/include/ensmallen_bits/problems/dtlz/dtlz2_function.hpp
@@ -23,8 +23,8 @@ namespace test {
  * \f[
  * x_M = [x_i, n - M + 1 <= i <= n]
  * g(x) = \Sigma{i = n - M + 1}^n (x_i - 0.5)^2
- * 
- * f_1(x) = 0.5 * cos(x_1 * pi * 0.5) * cos(x_2 * pi * 0.5) * ... cos(x_2 * pi * 0.5) * (1 + g(x_M)) 
+ *
+ * f_1(x) = 0.5 * cos(x_1 * pi * 0.5) * cos(x_2 * pi * 0.5) * ... cos(x_2 * pi * 0.5) * (1 + g(x_M))
  * f_2(x) = 0.5 * cos(x_1 * pi * 0.5) * cos(x_2 * pi * 0.5) * ... sin(x_M-1 * pi * 0.5) * (1 + g(x_M))
  * .
  * .
@@ -35,9 +35,9 @@ namespace test {
  * 0 <= x_i <= 1 for i = 1,...,n.
  *
  * This should be optimized to x_i = 0.5 (for all x_i in x_M), at:
- * 
+ *
  * For more information, please refer to:
- * 
+ *
  * @code
  * @incollection{deb2005scalable,
  * title={Scalable test problems for evolutionary multiobjective optimization},
@@ -62,7 +62,7 @@ namespace test {
     size_t numParetoPoints;
 
     public:
-      
+
       /**
        * Object Constructor.
        * Initializes the individual objective functions.
@@ -82,10 +82,10 @@ namespace test {
         // Convenience typedef.
         typedef typename MatType::elem_type ElemType;
         return arma::Col<ElemType>(numVariables, 1, arma::fill::zeros);
-      } 
-      
+      }
+
       // Get the private variables.
-      
+
       // Get the number of objectives.
       size_t GetNumObjectives ()
       { return this -> numObjectives; }
@@ -110,20 +110,19 @@ namespace test {
        */
       arma::Row<typename MatType::elem_type> g(const MatType& coords)
       {
-        size_t k = numVariables - numObjectives + 1;
 
         // Convenience typedef.
         typedef typename MatType::elem_type ElemType;
-        
+
         arma::Row<ElemType> innerSum(size(coords)[1], arma::fill::zeros);
-        
+
         for(size_t i = numObjectives - 1; i < numVariables; i++)
         {
-          innerSum += arma::pow((coords.row(i) - 0.5), 2); 
-        } 
-        
+          innerSum += arma::pow((coords.row(i) - 0.5), 2);
+        }
+
         return innerSum;
-      }    
+      }
 
       /**
        * Evaluate the objectives with the given coordinate.
@@ -141,21 +140,21 @@ namespace test {
         arma::Row<ElemType> value = 0.5 * (1.0 + G);
         for(size_t i = 0; i < numObjectives - 1; i++)
         {
-          objectives.row(i) =  value %  
+          objectives.row(i) =  value %
               arma::sin(coords.row(i) * arma::datum::pi * 0.5);
-          value = value % arma::cos(coords.row(i) * arma::datum::pi * 0.5); 
+          value = value % arma::cos(coords.row(i) * arma::datum::pi * 0.5);
         }
         objectives.row(numObjectives - 1) = value;
-        return objectives;    
+        return objectives;
       }
-      
+
       // Individual Objective function.
-      // Changes based on stop variable provided. 
+      // Changes based on stop variable provided.
       struct DTLZ2Objective
       {
         DTLZ2Objective(size_t stop, DTLZ2& dtlz): stop(stop), dtlz(dtlz)
-        {/* Nothing to do here. */}  
-        
+        {/* Nothing to do here. */}
+
         /**
          * Evaluate one objective with the given coordinate.
          *
@@ -182,8 +181,8 @@ namespace test {
           }
 
           value = value * (1.0 + dtlz.g(coords)[0]);
-          return value;  
-        }        
+          return value;
+        }
 
         DTLZ2& dtlz;
         size_t stop;
@@ -193,12 +192,12 @@ namespace test {
       std::tuple<DTLZ2Objective, DTLZ2Objective, DTLZ2Objective> GetObjectives()
       {
           return std::make_tuple(objectiveF1, objectiveF2, objectiveF3);
-      } 
+      }
 
       //! Get the Reference Front.
       //! Front. The implementation has been taken from pymoo.
       arma::mat GetReferenceFront()
-      { 
+      {
       	Uniform refGenerator;
         arma::mat refDirs = refGenerator.Generate<arma::mat>(3, this -> numParetoPoints, 0);
         arma::colvec x = arma::normalise(refDirs, 2, 1);
@@ -214,4 +213,4 @@ namespace test {
   } //namespace test
   } //namespace ens
 
-#endif
+#endif
diff --git a/inst/include/ensmallen_bits/problems/dtlz/dtlz4_function.hpp b/inst/include/ensmallen_bits/problems/dtlz/dtlz4_function.hpp
@@ -23,8 +23,8 @@ namespace test {
  * \f[
  * x_M = [x_i, n - M + 1 <= i <= n]
  * g(x) = \Sigma{i = n - M + 1}^n (x_i - 0.5)^2
- * 
- * f_1(x) = 0.5 * cos(x_1^alpha * pi * 0.5) * cos(x_2^alpha * pi * 0.5) * ... cos(x_2^alpha * pi * 0.5) * (1 + g(x_M)) 
+ *
+ * f_1(x) = 0.5 * cos(x_1^alpha * pi * 0.5) * cos(x_2^alpha * pi * 0.5) * ... cos(x_2^alpha * pi * 0.5) * (1 + g(x_M))
  * f_2(x) = 0.5 * cos(x_1^alpha * pi * 0.5) * cos(x_2^alpha * pi * 0.5) * ... sin(x_M-1^alpha * pi * 0.5) * (1 + g(x_M))
  * .
  * .
@@ -35,9 +35,9 @@ namespace test {
  * 0 <= x_i <= 1 for i = 1,...,n.
  *
  * This should be optimized to x_i = 0.5 (for all x_i in x_M), at:
- * 
+ *
  * For more information, please refer to:
- * 
+ *
  * @code
  * @incollection{deb2005scalable,
  * title={Scalable test problems for evolutionary multiobjective optimization},
@@ -85,8 +85,8 @@ namespace test {
         // Convenience typedef.
         typedef typename MatType::elem_type ElemType;
         return arma::Col<ElemType>(numVariables, 1, arma::fill::zeros);
-      } 
-      
+      }
+
       // Get the private variables.
 
       // Get the number of objectives.
@@ -113,20 +113,19 @@ namespace test {
        */
       arma::Row<typename MatType::elem_type> g(const MatType& coords)
       {
-        size_t k = numVariables - numObjectives + 1;
 
         // Convenience typedef.
         typedef typename MatType::elem_type ElemType;
-        
+
         arma::Row<ElemType> innerSum(size(coords)[1], arma::fill::zeros);
-        
+
         for(size_t i = numObjectives - 1; i < numVariables; i++)
         {
-          innerSum += arma::pow((coords.row(i) - 0.5), 2); 
-        } 
-        
+          innerSum += arma::pow((coords.row(i) - 0.5), 2);
+        }
+
         return innerSum;
-      }    
+      }
 
       /**
        * Evaluate the objectives with the given coordinate.
@@ -144,21 +143,21 @@ namespace test {
         arma::Row<ElemType> value = 0.5 * (1.0 + G);
         for(size_t i = 0; i < numObjectives - 1; i++)
         {
-          objectives.row(i) =  value %  
+          objectives.row(i) =  value %
               arma::sin(arma::pow(coords.row(i), alpha) * arma::datum::pi * 0.5);
-          value = value % arma::cos(arma::pow(coords.row(i), alpha) * arma::datum::pi * 0.5); 
+          value = value % arma::cos(arma::pow(coords.row(i), alpha) * arma::datum::pi * 0.5);
         }
         objectives.row(numObjectives - 1) = value;
-        return objectives;    
+        return objectives;
       }
-      
+
       // Individual Objective function.
-      // Changes based on stop variable provided. 
+      // Changes based on stop variable provided.
       struct DTLZ4Objective
       {
         DTLZ4Objective(size_t stop, DTLZ4& dtlz): stop(stop), dtlz(dtlz)
-        {/* Nothing to do here.*/}  
-        
+        {/* Nothing to do here.*/}
+
         /**
          * Evaluate one objective with the given coordinate.
          *
@@ -185,8 +184,8 @@ namespace test {
           }
 
           value = value * (1 + dtlz.g(coords)[0]);
-          return value;  
-        }        
+          return value;
+        }
 
         DTLZ4& dtlz;
         size_t stop;
@@ -196,12 +195,12 @@ namespace test {
       std::tuple<DTLZ4Objective, DTLZ4Objective, DTLZ4Objective> GetObjectives()
       {
           return std::make_tuple(objectiveF1, objectiveF2, objectiveF3);
-      } 
+      }
 
       //! Get the Reference Front.
       //! Front. The implementation has been taken from pymoo.
       arma::mat GetReferenceFront()
-      { 
+      {
       	Uniform refGenerator;
         arma::mat refDirs = refGenerator.Generate<arma::mat>(3, this -> numParetoPoints, 0);
         arma::colvec x = arma::normalise(refDirs, 2, 1);
@@ -217,4 +216,4 @@ namespace test {
   } //namespace test
   } //namespace ens
 
-#endif
+#endif