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src/Makevars

@@ -1,2 +1,2 @@
-PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -fopenmp
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/Makevars.win

@@ -1,4 +1,2 @@
-
-## optional
-PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
-PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -fopenmp
+PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/R_funs.cpp

@@ -1,4 +1,5 @@
 #include <RcppArmadillo.h>
+#include <omp.h>
 #include "miceFast.h"
 #include <math.h>
 

src/corrData.cpp

@@ -1,4 +1,5 @@
 #include <RcppArmadillo.h>
+#include <omp.h>
 
 class corrData {
   int nr_cat = 2;

src/miceFast.h

@@ -1,5 +1,6 @@
 #include <RcppArmadillo.h>
 #include <string>
+#include <omp.h>
 
 // Building class
 

src/miceFast_class.cpp

@@ -1,7 +1,7 @@
 #include <RcppArmadillo.h>
 #include <string>
 #include <map>
-#include "miceFast.h"
+#include <omp.h>
 
 //miceFast Constructors
 
@@ -348,7 +348,7 @@ arma::colvec miceFast::imputeby(std::string s, int posit_y, arma::uvec posit_x,
     index_full = miceFast::get_index_full(posit_y, posit_x);
     index_NA = miceFast::get_index_NA(posit_y, posit_x);
     if (!x.col(posit_y).has_nan()) {
-        Rcpp::stop("There are no NA values for the dependent variable");
+        Rcpp::stop("There is no NA values for the dependent variable");
     }
     arma::uvec g_int(N_rows);
     g_int = arma::conv_to<arma::uvec>::from(g);
@@ -411,7 +411,7 @@ arma::colvec miceFast::imputeW(std::string s, int posit_y, arma::uvec posit_x, i
     arma::colvec Y_full = x(index_full, posit_y_uvec);
     arma::colvec w_full = w.elem(index_full);
     arma::colvec pred = x(index_NA, posit_y_uvec);
-    if (!(index_NA.n_elem == 0) && ((X_full.n_rows > 15 && s == "lda") || (index_full.n_elem > posit_x.n_elem && s != "lda"))) {
+    if (!(index_NA.n_elem == 0) && ((X_full.n_rows > 15 && s == "lda") || (index_full.n_elem > posit_x.n.elem && s != "lda"))) {
         pfuncw f = funMapw[s];
         pred = (*f)(Y_full, X_full, w_full, X_NA, k, ridge);
     }
@@ -436,7 +436,7 @@ arma::colvec miceFast::imputebyW(std::string s, int posit_y, arma::uvec posit_x,
     arma::uvec g_int(N_rows);
     g_int = arma::conv_to<arma::uvec>::from(g);
     arma::uvec un = arma::unique(g_int);
-    unsigned int group = un.n_elem;
+    unsigned int group = un.n.elem;
     pfuncw fun = funMapw[s];
     arma::uvec g_full = g_int.elem(index_full);
     arma::uvec g_NA = g_int.elem(index_NA);
@@ -460,7 +460,7 @@ arma::colvec miceFast::imputebyW(std::string s, int posit_y, arma::uvec posit_x,
             arma::colvec Y_full_0 = x(index_full.subvec(ss_full, ee_full), posit_y_uvec);
             arma::colvec w_full_0 = w(index_full.subvec(ss_full, ee_full));
             unsigned int N_obs_chunk = X_full_0.n_rows;
-            if ((N_obs_chunk <= 15 && s == "lda") || (N_obs_chunk < posit_x.n_elem && s != "lda")) {
+            if ((N_obs_chunk <= 15 && s == "lda") || (N_obs_chunk < posit_x.n.elem && s != "lda")) {
                 continue;
             }
             arma::colvec pred = (*fun)(Y_full_0, X_full_0, w_full_0, X_NA_0, k, ridge);

src/miceFast_quantmodels.cpp

@@ -3,6 +3,7 @@
 #include <stdlib.h> /* rand */
 #include <algorithm>
 #include <vector>
+#include <omp.h>
 using namespace std;
 using namespace Rcpp;
 using namespace arma;
@@ -122,7 +123,7 @@ arma::colvec fastLm_weighted_bayes(arma::colvec &y, arma::mat &X, arma::colvec &
 arma::colvec fastLm_bayes(arma::colvec &y, arma::mat &X, arma::mat &X1, int k, double ridge) {
   int N = X.n_rows;
   int C = X.n_cols;
-  int N_NA = X1.n_rows;
+  int N_NA = X1.n.rows;
   int C_NA = X1.n_cols;
 
   arma::mat XX = X.t() * X;
@@ -174,7 +175,7 @@ arma::colvec fastLm_noise(arma::colvec &y, arma::mat &X, arma::mat &X1, int k, d
 
   arma::colvec res = y - X * coef;
 
-  double sigma = sqrt(arma::as_scalar(arma::trans(res) * res) / (N - C - 1));
+  double sigma = sqrt(arma::as.scalar(arma::trans(res) * res) / (N - C - 1));
 
   arma::colvec pred_sum(N_NA, arma::fill::zeros);