Merge branch 'main' into 68-use-new-steady-state-for-lincmt

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 2.0.13
-Date: 2022-11-10 14:23:39 UTC
-SHA: edb38d156f0c2a631d4bde9283133ac9e2d4d936
+Version: 2.0.17
+Date: 2023-12-09 14:16:33 UTC
+SHA: 322bf8f43bd079b336d33cd4e3af1f7a6a91648c

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rxode2parse
 Title: Parsing and Code Generation Functions for 'rxode2'
-Version: 2.0.16.9000
+Version: 2.0.17.9000
 Authors@R: c(
     person("Matthew L.", "Fidler", , "matthew.fidler@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8538-6691")),
@@ -57,4 +57,3 @@ Language: en-US
 NeedsCompilation: yes
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-VignetteBuilder: knitr

NEWS.md

@@ -1,18 +1,21 @@
 # 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 +28,12 @@
 * 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
+
+* `etTrans` now supports keeping logical vectors (with the appropriate
+  version of `rxode2`).
+
+* Security fixes were applied as requested by CRAN
 
 # rxode2parse 2.0.16
 

cran-comments.md

@@ -1,6 +1,6 @@
 # Cran comments
 
-- Explicitly use data.table in the R code (already used in C/C++)
-  - This fixes the note that we are not using data.table in our package (though we were)
-
-
+- Fixes the issues requested flagged by CRAN
+- Also changes solving structure; The reverse dependencies
+  rxode2random rxode2et and rxode2 need updates after this
+- Once updated the rxode2 reverse dependencies all successfully check

inst/include/rxode2_model_shared.h

@@ -14,7 +14,7 @@
 #define _safe_log(a) (&_solveData->safeZero ? (((a) <= 0) ? log(DBL_EPSILON) : log(a)) : log(a))
 #define safe_zero(a) (&_solveData->safeZero ? ((a) == 0 ? DBL_EPSILON : ((double)(a))) : ((double)(a)))
 #define _as_zero(a) (&_solveData->safeZero && fabs((double)(a)) < sqrt(DBL_EPSILON) ? 0.0 : ((double)(a)))
-#define _as_dbleps(a) (&_solveData->safeZero && fabs(a) < sqrt(DBL_EPSILON) ? (((double)(a)) < 0 ? -sqrt(DBL_EPSILON)  : sqrt(DBL_EPSILON)) : ((double)(a)))
+#define _as_dbleps(a) (&_solveData->safeZero && fabs((double)a) < sqrt(DBL_EPSILON) ? (((double)(a)) < 0 ? -sqrt(DBL_EPSILON)  : sqrt(DBL_EPSILON)) : ((double)(a)))
 #define _as_dbleps2(a) (&_solveData->safeZero && fabs((double)(a)) < sqrt(DBL_EPSILON) ? sqrt(DBL_EPSILON) : ((double)(a)))
 #define factorial(a) exp(lgamma1p(a))
 #define sign_exp(sgn, x)(((sgn) > 0.0) ? exp(x) : (((sgn) < 0.0) ? -exp(x) : 0.0))

src/codegen.c

@@ -152,7 +152,7 @@ void codegen(char *model, int show_ode, const char *prefix, const char *libname,
         // Hence CMT = 4 could translate in data to 44 with sensi=10
         // Then cmt=44 translates back to cmt-10 or 4.
         // This makes the sensitivity equations insensitive to CMT changes that occur in FOCEi
-        sAppend(&sbOut,"#define _CMT ((abs(CMT)<=%d) ? CMT : ((CMT<0) ? CMT+%d: CMT-%d))\n",
+        sAppend(&sbOut,"#define _CMT ((fabs(CMT)<=%d) ? CMT : ((CMT<0) ? CMT+%d: CMT-%d))\n",
                 baseSize, tb.sensi, tb.sensi);
       } else {
         sAppendN(&sbOut,"#define _CMT CMT\n", 17);

src/etTran.cpp

@@ -317,10 +317,10 @@ 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 {
@@ -455,6 +455,33 @@ bool rxode2parseIsIntegerish(SEXP in) {
   return as<bool>(isIntegerish(in));
 }
 
+RObject etTranGetAttrKeep(SEXP in) {
+  RObject cur = as<RObject>(in);
+  std::vector<std::string> attr = cur.attributeNames();
+  if (cur.hasAttribute("levels")) {
+    List ret(attr.size()-1);
+    CharacterVector retN(attr.size()-1);
+    unsigned int j = 0;
+    for (unsigned int i = 0; i < attr.size(); ++i) {
+      if (attr[i] != "levels") {
+        retN[j] = attr[i];
+        ret[j] = cur.attr(attr[i]);
+        j++;
+      }
+    }
+    ret.attr("names") = retN;
+    return as<RObject>(ret);
+  }
+  List ret(attr.size());
+  CharacterVector retN(attr.size());
+  for (unsigned int i = 0; i < attr.size(); ++i) {
+    retN[i] = attr[i];
+    ret[i] = cur.attr(attr[i]);
+  }
+  ret.attr("names") = retN;
+  return as<RObject>(ret);
+}
+
 //' Event translation for rxode2
 //'
 //' @param inData Data frame to translate
@@ -651,7 +678,7 @@ 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());
@@ -1249,7 +1276,7 @@ List etTransParse(List inData, List mv, bool addCmt=false,
         obsId.push_back(cid);
       }
       if (caddl > 0){
-        Rf_warningcall(R_NilValue, _("'addl' is ignored with observations"));
+        Rf_warningcall(R_NilValue, "%s", _("'addl' is ignored with observations"));
       }
       if (flg != 1){
         flg=1;
@@ -1370,10 +1397,10 @@ List etTransParse(List inData, List mv, bool addCmt=false,
         if (rateI == 0) allInf=false;
         else allBolus=false;
         if (caddl > 0){
-          Rf_warningcall(R_NilValue, _("'addl' is ignored with 'EVID=2'"));
+          Rf_warningcall(R_NilValue, "%s", _("'addl' is ignored with 'EVID=2'"));
         }
         if (flg != 1){
-          Rf_warningcall(R_NilValue, _("'ss' is ignored with 'EVID=2'"));
+          Rf_warningcall(R_NilValue, "%s", _("'ss' is ignored with 'EVID=2'"));
         }
         id.push_back(cid);
         evid.push_back(2);
@@ -1415,10 +1442,10 @@ List etTransParse(List inData, List mv, bool addCmt=false,
     case 3:
       cevid = 3;
       if (caddl > 0){
-        Rf_warningcall(R_NilValue, _("'addl' is ignored with 'EVID=3'"));
+        Rf_warningcall(R_NilValue, "%s", _("'addl' is ignored with 'EVID=3'"));
       }
       if (flg != 1){
-        Rf_warningcall(R_NilValue, _("'ss' is ignored with 'EVID=3'"));
+        Rf_warningcall(R_NilValue, "%s", _("'ss' is ignored with 'EVID=3'"));
       }
       id.push_back(cid);
       evid.push_back(3);
@@ -1496,11 +1523,11 @@ List etTransParse(List inData, List mv, bool addCmt=false,
         continue;
       }
       if (rateI != 0 && hasEvid){
-        Rf_warningcall(R_NilValue, _("'rate' or 'dur' is ignored with classic rxode2 'EVID's"));
+        Rf_warningcall(R_NilValue, "%s", _("'rate' or 'dur' is ignored with classic rxode2 'EVID's"));
         rateI = 0;
       }
       if (flg!=1 && hasEvid){ // ss=1 is the same as ss=0 for NONMEM
-        Rf_warningcall(R_NilValue, _("'ss' is ignored with classic rxode2 'EVID's"));
+        Rf_warningcall(R_NilValue, "%s", _("'ss' is ignored with classic rxode2 'EVID's"));
         flg=1;
       }
     }
@@ -1861,7 +1888,7 @@ 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;
     }
   }
@@ -1899,10 +1926,10 @@ 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)"));
+  if (warnCensNA) Rf_warningcall(R_NilValue, "%s", _("censoring missing 'DV' values do not make sense"));
+  if (warnNaTime) Rf_warningcall(R_NilValue, "%s", _("missing 'TIME' values do not make sense (ignored)"));
 #ifdef rxSolveT
   REprintf("  Time7: %f\n", ((double)(clock() - _lastT0))/CLOCKS_PER_SEC);
   _lastT0 = clock();
@@ -1994,11 +2021,11 @@ List etTransParse(List inData, List mv, bool addCmt=false,
   int censAdd = 0;
   if (censCol != -1) censAdd=1;
   if (censAdd && censNone) {
-    Rf_warningcall(R_NilValue, _("while censoring is included in dataset, no observations are censored"));
+    Rf_warningcall(R_NilValue, "%s", _("while censoring is included in dataset, no observations are censored"));
     censAdd=0;
   }
   if (swapDvLimit){
-    Rf_warningcall(R_NilValue, _("'dv' and 'limit' swapped since 'limit' > 'dv'"));
+    Rf_warningcall(R_NilValue, "%s", _("'dv' and 'limit' swapped since 'limit' > 'dv'"));
   }
   int limitAdd = 0;
   if (limitCol != -1) limitAdd=1;
@@ -2104,36 +2131,48 @@ List etTransParse(List inData, List mv, bool addCmt=false,
   for (j = 0; j < (int)(keepCol.size()); j++){
     SEXP cur = inData[keepCol[j]];
     RObject calc;
-    List curType(2);
+    List curType(3);
     if (TYPEOF(cur) == STRSXP){
       calc = convertId_(cur);
       curType[0] = IntegerVector::create(1);
       curType[1] = calc.attr("levels");
+      curType[2] = etTranGetAttrKeep(cur);
       calc.attr("levels") = R_NilValue;
       calc.attr("class") = R_NilValue;
       inDataFK[j] = as<NumericVector>(calc);
       inDataFKL[j] = curType;
     } else if (TYPEOF(cur) == INTSXP){
       calc = cur;
       if (calc.hasAttribute("levels")) {
+        // need to check type
+        calc = clone(cur); // make sure they don't affect changes
         curType[0] = IntegerVector::create(2);
         curType[1] = calc.attr("levels");
+        curType[2] = etTranGetAttrKeep(cur);
         calc.attr("levels") = R_NilValue;
         calc.attr("class") = R_NilValue;
         inDataFK[j] = as<NumericVector>(calc);
       } else {
         curType[0] = IntegerVector::create(3);
         curType[1] = R_NilValue;
+        curType[2] = etTranGetAttrKeep(cur);
         inDataFK[j] = as<NumericVector>(calc);
       }
       inDataFKL[j] = curType;
     } else if (TYPEOF(cur) == REALSXP) {
       curType[0] = IntegerVector::create(4);
       curType[1] = R_NilValue;
+      curType[2] = etTranGetAttrKeep(cur);
       inDataFK[j] = cur;
       inDataFKL[j] = curType;
+    } else if (TYPEOF(cur) == LGLSXP) {
+      curType[0]  = IntegerVector::create(5);
+      curType[1]  = R_NilValue;
+      curType[2] = etTranGetAttrKeep(cur);
+      inDataFK[j] = as<NumericVector>(cur);
+      inDataFKL[j] = curType;
     } else {
-      stop("the columns that are kept must be either a string, a factor, an integer number, or a real number");
+      stop(_("the columns that are kept must be either an underlying logical, string, factor, integer number, or real number"));
     }
   }
   int maxItemsPerId = 0;
@@ -2450,7 +2489,7 @@ List etTransParse(List inData, List mv, bool addCmt=false,
   Rf_setAttrib(lstF, R_RowNamesSymbol, IntegerVector::create(NA_INTEGER,-idxOutput.size()+rmAmt));
   if (doWarnNeg){
     if (!warnedNeg){
-      Rf_warningcall(R_NilValue, _("\nwith negative times, compartments initialize at first negative observed time\nwith positive times, compartments initialize at time zero\nuse 'rxSetIni0(FALSE)' to initialize at first observed time\nthis warning is displayed once per session"));
+      Rf_warningcall(R_NilValue, "%s", _("\nwith negative times, compartments initialize at first negative observed time\nwith positive times, compartments initialize at time zero\nuse 'rxSetIni0(FALSE)' to initialize at first observed time\nthis warning is displayed once per session"));
       warnedNeg=true;
     }
   }

src/tran.c

@@ -297,7 +297,7 @@ char *f1LinCmtLine = NULL;
 char *rate1LinCmtLine = NULL;
 char *dur1LinCmtLine = NULL;
 
-SEXP _rxode2parse_resetUdf();
+SEXP _rxode2parse_resetUdf(void);
 
 void reset(void) {
   // Reset sb/sbt string buffers

src/tran.h

@@ -333,7 +333,7 @@ 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);