Merge pull request #630 from nlmixr2/629-mem-issues

629 mem issues
nlmixr2 · Dec 6, 2023 · 5000367 · 5000367
2 parents dd99ee0 + d60cfeb
commit 5000367
Show file tree

Hide file tree

Showing 5 changed files with 31 additions and 10 deletions.
diff --git a/man/reexports.Rd b/man/reexports.Rd
diff --git a/src/approx.c b/src/approx.c
@@ -81,7 +81,7 @@ static inline double getValue(int idx, double *y, rx_solving_options_ind *ind, r
     if (op->f2 == 1.0 && op->f1 == 0.0) {
       // use nocb
       // Go forward
-      while (ISNA(ret) && i != ind->n_all_times){
+      while (ISNA(ret) && i != ind->n_all_times-1){
         i++; ret = y[ind->ix[i]];
       }
       if (ISNA(ret)){
@@ -309,4 +309,3 @@ void _update_par_ptr(double t, unsigned int id, rx_solve *rx, int idxIn) {
 
 /* void doSort(rx_solving_options_ind *ind); */
 void sortInd(rx_solving_options_ind *ind);
-
diff --git a/src/rxData.cpp b/src/rxData.cpp
@@ -42,7 +42,7 @@ void resetSolveLinB();
 using namespace Rcpp;
 using namespace arma;
 
-typedef void (*seedEng_t)(uint32_t ncores);
+typedef void (*seedEng_t)(int ncores);
 extern seedEng_t seedEng;
 
 #include "cbindThetaOmega.h"
@@ -2144,15 +2144,22 @@ List rxSimThetaOmega(const Nullable<NumericVector> &params    = R_NilValue,
       }
       if (_globals.gsigma != NULL) free(_globals.gsigma);
       rx->neps = sigma0.n_rows;
-      _globals.gsigma = (double*)malloc((rx->neps * rx->neps + 2 * rx->neps)* sizeof(double));
-      std::copy(&sigma0[0], &sigma0[0] + rx->neps * rx->neps, _globals.gsigma + 2 * rx->neps);
+      if (rx->neps > 0) {
+        _globals.gsigma = (double*)malloc((rx->neps * rx->neps + 2 * rx->neps)* sizeof(double));
+        std::copy(&sigma0[0], &sigma0[0] + rx->neps * rx->neps,
+                  _globals.gsigma + 2 * rx->neps);
+      } else {
+        _globals.gsigma = NULL;
+      }
       _globals.nSigma = 0;
     }
     arma::vec in = as<arma::vec>(sigmaLower);
     arma::vec lowerSigmaV = fillVec(in, sigma0.n_rows);
     arma::vec upperSigmaV = fillVec(in, sigma0.n_rows);
-    std::copy(&lowerSigmaV[0], &lowerSigmaV[0] + rx->neps, _globals.gsigma);
-    std::copy(&upperSigmaV[0], &upperSigmaV[0] + rx->neps, _globals.gsigma + rx->neps);
+    if (rx->neps > 0) {
+      std::copy(&lowerSigmaV[0], &lowerSigmaV[0] + rx->neps, _globals.gsigma);
+      std::copy(&upperSigmaV[0], &upperSigmaV[0] + rx->neps, _globals.gsigma + rx->neps);
+    }
     // structure of _globals.gsigma is
     // lower
     // upper
@@ -4886,7 +4893,7 @@ SEXP rxSolve_(const RObject &obj, const List &rxControl,
       warning(_("since throwing warning with NA time, change to single threaded"));
       op->cores=1;
     }
-    seedEng(op->cores);
+    seedEng((int)(op->cores));
     if (_globals.pendingDoses != NULL) {
       int i=0;
       while (_globals.pendingDoses[i] != NULL){

diff --git a/src/rxode2_df.cpp b/src/rxode2_df.cpp
@@ -24,6 +24,7 @@
 #include <unistd.h>
 #include <stdio.h>
 #include <climits>
+#include <cmath>
 #include "checkmate.h"
 #include <stdint.h>    // for uint64_t rather than unsigned long long
 #include "../inst/include/rxode2.h"
@@ -751,12 +752,22 @@ extern "C" SEXP rxode2_df(int doDose0, int doTBS) {
             } else if (TYPEOF(tmp) == LGLSXP) {
               // Everything here is double
               dfi = LOGICAL(tmp);
-              dfi[ii] = (int) (get_fkeep(j, curi + ind->ix[i], ind));
+              double curD = get_fkeep(j, curi + ind->ix[i], ind);
+              if (ISNA(curD) || std::isnan(curD)) {
+                dfi[ii] = NA_LOGICAL;
+              } else {
+                dfi[ii] = (int) (curD);
+              }
             } else {
               dfi = INTEGER(tmp);
               /* if (j == 0) RSprintf("j: %d, %d; %f\n", j, i, get_fkeep(j, curi + i)); */
               // is this ntimes = nAllTimes or nObs time for this subject...?
-              dfi[ii] = (int) (get_fkeep(j, curi + ind->ix[i], ind));
+              double curD = get_fkeep(j, curi + ind->ix[i], ind);
+              if (ISNA(curD) || std::isnan(curD)) {
+                dfi[ii] = NA_INTEGER;
+              } else {
+                dfi[ii] = (int) (curD);
+              }
             }
             jj++;
           }

diff --git a/src/rxode2parse.cpp b/src/rxode2parse.cpp
@@ -105,6 +105,9 @@ END_RCPP
 
 extern "C" SEXP _rxode2parse_udfEnvSet(SEXP udf) {
 BEGIN_RCPP
+  if (Rf_isNull(udf)) {
+    return R_NilValue;
+  }
   if (Rf_length(udf) == 0 || Rf_length(udf) == 1) {
     return R_NilValue;
   }