Merge pull request #644 from nlmixr2/m1mac

Add forder and rxInv string fixes as requested by CRAN

NEWS.md

@@ -3,6 +3,7 @@
 ## Other changes
 
 - `rxUi` compression now defaults to fast compression
+- Fixes String literal formatting issues as identified by CRAN (#643)
 
 # rxode2 2.1.0
 

src/forder.cpp

@@ -100,10 +100,10 @@ extern "C" int getRxThreads(const int64_t n, const bool throttle) {
 
 extern "C" SEXP getRxThreads_R(SEXP verbose) {
   if (!isLogical(verbose) || LENGTH(verbose)!=1 || INTEGER(verbose)[0]==NA_LOGICAL)
-    Rf_errorcall(R_NilValue, _("'verbose' must be TRUE or FALSE"));
+    Rf_errorcall(R_NilValue, "%s", _("'verbose' must be TRUE or FALSE"));
   if (LOGICAL(verbose)[0]) {
 #ifndef _OPENMP
-    Rprintf(_("This installation of data.table has not been compiled with OpenMP support.\n"));
+    Rprintf("%s", _("This installation of data.table has not been compiled with OpenMP support.\n"));
 #endif
     // this output is captured, paste0(collapse="; ")'d, and placed at the end of test.data.table() for display in the last 13 lines of CRAN check logs
     // it is also printed at the start of test.data.table() so that we can trace any Killed events on CRAN before the end is reached
@@ -125,7 +125,7 @@ extern "C" SEXP getRxThreads_R(SEXP verbose) {
 extern "C" SEXP setRxthreads(SEXP threads, SEXP percent, SEXP throttle) {
   if (length(throttle)) {
     if (!isInteger(throttle) || LENGTH(throttle)!=1 || INTEGER(throttle)[0]<1)
-      error(_("'throttle' must be a single number, non-NA, and >=1"));
+      error("%s", _("'throttle' must be a single number, non-NA, and >=1"));
     rxThrottle = INTEGER(throttle)[0];
   }
   int old = rxThreads;
@@ -139,11 +139,11 @@ extern "C" SEXP setRxthreads(SEXP threads, SEXP percent, SEXP throttle) {
   } else if (length(threads)) {
     int n=0;
     if (length(threads)!=1 || !isInteger(threads) || (n=INTEGER(threads)[0]) < 0) {  // <0 catches NA too since NA is negative (INT_MIN)
-      Rf_errorcall(R_NilValue, _("threads= must be either NULL or a single number >= 0 See ?setRxthreads"));
+      Rf_errorcall(R_NilValue, "%s", _("threads= must be either NULL or a single number >= 0 See ?setRxthreads"));
     }
     int num_procs = imax(omp_get_num_procs(), 1); // max just in case omp_get_num_procs() returns <= 0 (perhaps error, or unsupported)
     if (!isLogical(percent) || length(percent)!=1 || LOGICAL(percent)[0]==NA_LOGICAL) {
-      Rf_errorcall(R_NilValue, _("internal error: percent= must be TRUE or FALSE at C level"));  // # nocov
+      Rf_errorcall(R_NilValue, "%s", _("internal error: percent= must be TRUE or FALSE at C level"));  // # nocov
     }
     if (LOGICAL(percent)[0]) {
       if (n<2 || n>100) error(_("internal error: threads==%d should be between 2 and 100 (percent=TRUE at C level)"), n);  // # nocov

src/rxInv.cpp

@@ -18,12 +18,12 @@ using namespace R;
 using namespace arma;
 extern "C" SEXP _rxCholInv(SEXP dms, SEXP theta, SEXP tn);
 
-//' Invert matrix using RcppArmadillo.  
+//' Invert matrix using RcppArmadillo.
 //'
 //' @param matrix matrix to be inverted.
-//' 
+//'
 //' @return inverse or pseudo inverse of matrix.
-//' 
+//'
 //' @export
 // [[Rcpp::export]]
 NumericVector rxInv(SEXP matrix){
@@ -33,7 +33,7 @@ NumericVector rxInv(SEXP matrix){
   success = inv(imat, smatrix);
   if (!success){
     imat = pinv(smatrix);
-    Rprintf(_("matrix seems singular; Using pseudo-inverse\n"));
+    Rprintf("%s", _("matrix seems singular; Using pseudo-inverse\n"));
   }
   NumericVector ret;
   ret = wrap(imat);
@@ -71,15 +71,15 @@ arma::mat rxToCholOmega(arma::mat cholMat){
 //'   [rxSymInvCholCreate()] with the default arguments and return a
 //'   reactive s3 object.  Otherwise, use the inversion object to
 //'   calculate the requested derivative/inverse.
-//' 
+//'
 //' @param theta Thetas to be used for calculation.  If missing (`NULL`), a
 //'     special s3 class is created and returned to access `Omega^1`
 //'     objects as needed and cache them based on the theta that is
 //'     used.
-//' 
+//'
 //' @param type The type of object.  Currently the following types are
 //'     supported:
-//' 
+//'
 //' * `cholOmegaInv` gives the
 //'     Cholesky decomposition of the Omega Inverse matrix.
 //' * `omegaInv` gives the Omega Inverse matrix.
@@ -88,18 +88,18 @@ arma::mat rxToCholOmega(arma::mat cholMat){
 //' * `d(D)` gives the `d(diagonal(Omega^-1))` with respect to
 //'     the theta parameter specified in the `thetaNumber`
 //'     parameter
-//' 
+//'
 //' @param thetaNumber For types `d(omegaInv)` and `d(D)`,
 //'     the theta number that the derivative is taken against.  This
 //'     must be positive from 1 to the number of thetas defining the
 //'     Omega matrix.
-//' 
+//'
 //' @return Matrix based on parameters or environment with all the
 //'     matrixes calculated in variables `omega`, `omegaInv`, `dOmega`,
 //'     `dOmegaInv`.
-//' 
+//'
 //' @author Matthew L. Fidler
-//' 
+//'
 //' @export
 // [[Rcpp::export]]
 RObject rxSymInvChol(RObject invObjOrMatrix, Nullable<NumericVector> theta = R_NilValue, std::string type = "cholOmegaInv", int thetaNumber = 0){
@@ -200,7 +200,7 @@ RObject rxSymInvCholEnvCalculate(List obj, std::string what, Nullable<NumericVec
       } else if (what == "chol.omega1"){
         rxSymInvCholEnvCalculate(obj, "chol.omegaInv", R_NilValue);
         arma::mat ret = rxToCholOmega(as<arma::mat>(e["chol.omegaInv"]));
-        e["chol.omega1"] = ret; 
+        e["chol.omega1"] = ret;
       } else if (what == "omega"){
         rxSymInvCholEnvCalculate(obj, "chol.omega1", R_NilValue);
         arma::mat U1 = as<mat>(e["chol.omega1"]);

src/rxode2_df.cpp

@@ -215,7 +215,7 @@ extern "C" SEXP rxode2_df(int doDose0, int doTBS) {
   if (op->badSolve){
     if (op->naTime){
       rxSolveFreeC();
-      Rf_errorcall(R_NilValue, _("'alag(.)'/'rate(.)'/'dur(.)' cannot depend on the state values"));
+      Rf_errorcall(R_NilValue, "%s", _("'alag(.)'/'rate(.)'/'dur(.)' cannot depend on the state values"));
     }
     if (nidCols == 0){
       for (int solveid = 0; solveid < rx->nsub * rx->nsim; solveid++){
@@ -225,7 +225,7 @@ extern "C" SEXP rxode2_df(int doDose0, int doTBS) {
         }
       }
       rxSolveFreeC();
-      Rf_errorcall(R_NilValue, _("could not solve the system"));
+      Rf_errorcall(R_NilValue, "%s", _("could not solve the system"));
     } else {
       warning(_("some ID(s) could not solve the ODEs correctly; These values are replaced with 'NA'"));
     }