Merge pull request #74 from nlmixr2/73-cran

73 cran

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rxode2parse
 Title: Parsing and Code Generation Functions for 'rxode2'
-Version: 2.0.16.9000
+Version: 2.0.17
 Authors@R: c(
     person("Matthew L.", "Fidler", , "matthew.fidler@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8538-6691")),

NEWS.md

@@ -1,18 +1,19 @@
-# rxode2parse (development version)
+# rxode2parse 2.0.17
 
 * Added ability to query R user functions in a rxode2 model (will
   force single threaded solve)
 
 * Moved core `rxFunParse` and `rxRmFunParse` here so that C and R user
   function clashes can be handled
 
-* Model variables now tracks which compartments have a lag-time defined
+* Model variables now tracks which compartments have a lag-time
+  defined
 
 * For compartment with steady state doses (NONMEM equivalent SS=1,
   SS=2), an additional tracking time-point is added at to track the
   time when the lagged dose is given.  As an upshot, the lagged dose
   will start at the steady state concentration shifted by + ii - lag
-  in `rxode2`
+  in `rxode2` (currently for ode systems only)
 
 * This release calculates non bio-availability adjusted duration for
   all rates instead of trying to figure the rate duration during
@@ -25,7 +26,9 @@
 * Steady state bolus doses with `addl` are treated as non steady state
   events (like what is observed in `NONMEM`)
 
-* Timsort was upgraded; drop radix support in rxode2 struct
+* Timsort was upgraded; drop radix support in rxode2 structure
+
+* Security fixes were applied as requested by CRAN
 
 # rxode2parse 2.0.16
 

src/etTran.cpp

@@ -313,10 +313,10 @@ IntegerVector toCmt(RObject inCmt, CharacterVector& state, const bool isDvid,
             warn = warn + std::to_string(warnDvid[i]) + ", ";
           }
           warn = warn + std::to_string(warnDvid[warnDvid.size()-1]);
-          Rf_warningcall(R_NilValue, warn.c_str());
+          Rf_warningcall(R_NilValue, "%s", warn.c_str());
         }
         if (warnConvertDvid.size() > 0){
-          Rf_warningcall(R_NilValue, warnC.c_str());
+          Rf_warningcall(R_NilValue, "%s", warnC.c_str());
         }
         return out;
       } else {
@@ -647,7 +647,7 @@ List etTransParse(List inData, List mv, bool addCmt=false,
         wKeep += " " + as<std::string>(keep[j]);
       }
     }
-    Rf_warningcall(R_NilValue, wKeep.c_str());
+    Rf_warningcall(R_NilValue, "%s", wKeep.c_str());
   }
   List covUnits(covCol.size());
   CharacterVector covUnitsN(covCol.size());
@@ -1857,7 +1857,7 @@ List etTransParse(List inData, List mv, bool addCmt=false,
           doseId.push_back(allId[j]);
         }
       }
-      Rf_warningcall(R_NilValue, idWarn.c_str());
+      Rf_warningcall(R_NilValue, "%s", idWarn.c_str());
       redoId=true;
     }
   }
@@ -1895,7 +1895,7 @@ List etTransParse(List inData, List mv, bool addCmt=false,
         }
       }
     }
-    if (!_ini0) Rf_warningcall(R_NilValue, idWarn.c_str());
+    if (!_ini0) Rf_warningcall(R_NilValue, "%s", idWarn.c_str());
   }
   if (warnCensNA) Rf_warningcall(R_NilValue, _("censoring missing 'DV' values do not make sense"));
   if (warnNaTime) Rf_warningcall(R_NilValue, _("missing 'TIME' values do not make sense (ignored)"));

src/tran.h

@@ -331,7 +331,7 @@ static inline int allSpaces(char *v2) {
 
 void parseFree(int last);
 
-#define err_trans(chr) Rf_errorcall(R_NilValue, _(chr));
+#define err_trans(chr) Rf_errorcall(R_NilValue, "%s", _(chr));
 
 void _rxode2parse_unprotect(void);