Merge pull request #466 from nlmixr2/466-no-binary

Stop requiring binary linkage
nlmixr2 · Aug 21, 2024 · 21c4721 · 21c4721
2 parents 9e66956 + 0ec16dd
commit 21c4721
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Showing 13 changed files with 452 additions and 555 deletions.
diff --git a/R/onLoad.R b/R/onLoad.R
@@ -20,9 +20,29 @@
         PACKAGE = "nlmixr2est")
 }
 
+# This will be saved when compiled
+rxode2.api <- names(rxode2::.rxode2ptrs())
+
+.iniRxode2Ptr <- function() {
+  .ptr <- rxode2::.rxode2ptrs()
+  .nptr <- names(.ptr)
+  if (length(rxode2.api) > length(.nptr)) {
+    stop("nlmixr2est requires a newer version of rxode2 api, cannot run nlmixr2est\ntry `install.packages(\"rxode2\")` to get a newer version of rxode2", call.=FALSE)
+  } else {
+    .nptr <- .nptr[seq_along(rxode2.api)]
+    if (!identical(rxode2.api, .nptr)) {
+      .bad <- TRUE
+      stop("nlmixr2est needs a different version of rxode2 api, cannot run nlmixr2est\ntry `install.packages(\"rxode2\")` to get a newer version of rxode2, or update both packages", call.=FALSE)
+    }
+  }
+  .Call(`_nlmixr2est_iniRxodePtrs`, .ptr,
+        PACKAGE = "nlmixr2est")
+}
+
 .onLoad <- function(libname, pkgname) {
   backports::import(pkgname)
   .iniLotriPtr()
+  .iniRxode2Ptr()
   if (requireNamespace("generics", quietly = TRUE)) {
     rxode2::.s3register("generics::tidy", "nlmixr2FitCore")
     rxode2::.s3register("generics::tidy", "nlmixr2FitCoreSilent")
@@ -42,13 +62,12 @@
 
 compiled.rxode2.md5 <- rxode2::rxMd5()
 
+
 .onAttach <- function(libname, pkgname) {
   ## nocov start
   ## Setup rxode2.prefer.tbl
   .iniLotriPtr()
-  if (compiled.rxode2.md5 != rxode2::rxMd5()) {
-    stop("nlmixr2 compiled against different version of rxode2, cannot run nlmixr2est\ntry `install.packages(\"nlmixr2est\", type = \"source\")` to recompile", call.=FALSE)
-  }
+  .iniRxode2Ptr()
   ## nlmixr2SetupMemoize()
   ## options(keep.source = TRUE)
   ## nocov end

diff --git a/README.Rmd b/README.Rmd
@@ -34,10 +34,6 @@ You can install the development version of nlmixr2est from [GitHub](https://gith
 
 ``` r
 # install.packages("remotes")
-remotes::install_github("nlmixr2/rxode2parse")
-remotes::install_github("nlmixr2/rxode2random")
-remotes::install_github("nlmixr2/rxode2et")
-remotes::install_github("nlmixr2/rxode2ll")
 remotes::install_github("nlmixr2/rxode2")
 remotes::install_github("nlmixr2/nlmixr2data")
 remotes::install_github("nlmixr2/lotri")

diff --git a/src/armahead.h b/src/armahead.h
@@ -10,7 +10,7 @@
 #include <time.h>
 #include <Rmath.h>
 #include <RcppArmadillo.h>
-#include <rxode2.h>
+#include <rxode2ptr.h>
 
 
 #ifndef rxDistributionNorm

diff --git a/src/censResid.h b/src/censResid.h
@@ -10,27 +10,24 @@
 
 #if defined(__cplusplus)
 
-extern "C" {
-  typedef SEXP (*_rxode2random_rxRmvnSEXP_t)(SEXP nSSEXP, SEXP muSSEXP, SEXP sigmaSSEXP, SEXP lowerSSEXP, SEXP upperSSEXP, SEXP ncoresSSEXP, SEXP isCholSSEXP, SEXP keepNamesSSEXP, SEXP aSSEXP, SEXP tolSSEXP, SEXP nlTolSSEXP, SEXP nlMaxiterSSEXP);
-  extern _rxode2random_rxRmvnSEXP_t rxRmvnSEXPnlmixrEst;
-}
+#include <rxode2ptr.h>
 
 static inline double truncnorm(double mean, double sd, double low, double hi){
   if (R_finite(mean) && R_finite(sd)) {
     NumericMatrix sigma(1,1);
     sigma(0,0)=sd;
-    SEXP ret = rxRmvnSEXPnlmixrEst(wrap(IntegerVector::create(1)),
-                                       wrap(NumericVector::create(mean)),
-                                       wrap(sigma),
-                                       wrap(NumericVector::create(low)),
-                                       wrap(NumericVector::create(hi)),
-                                       wrap(IntegerVector::create(1)),
-                                       wrap(LogicalVector::create(false)),
-                                       wrap(LogicalVector::create(false)),
-                                       wrap(NumericVector::create(0.4)),
-                                       wrap(NumericVector::create(2.05)),
-                                       wrap(NumericVector::create(1e-10)),
-                                       wrap(IntegerVector::create(100)));
+    SEXP ret = _rxode2_rxRmvnSEXP_(wrap(IntegerVector::create(1)),
+                                   wrap(NumericVector::create(mean)),
+                                   wrap(sigma),
+                                   wrap(NumericVector::create(low)),
+                                   wrap(NumericVector::create(hi)),
+                                   wrap(IntegerVector::create(1)),
+                                   wrap(LogicalVector::create(false)),
+                                   wrap(LogicalVector::create(false)),
+                                   wrap(NumericVector::create(0.4)),
+                                   wrap(NumericVector::create(2.05)),
+                                   wrap(NumericVector::create(1e-10)),
+                                   wrap(IntegerVector::create(100)));
     return REAL(ret)[0];
   }
   return NA_REAL;

diff --git a/src/init.c b/src/init.c
@@ -89,8 +89,6 @@ SEXP _nlmixr2est_filterNormalLikeAndDoses(SEXP, SEXP, SEXP);
 
 SEXP _nlmixr2est_rxode2hasLlik(void);
 
-typedef SEXP (*_rxode2random_rxRmvnSEXP_t)(SEXP nSSEXP, SEXP muSSEXP, SEXP sigmaSSEXP, SEXP lowerSSEXP, SEXP upperSSEXP, SEXP ncoresSSEXP, SEXP isCholSSEXP, SEXP keepNamesSSEXP, SEXP aSSEXP, SEXP tolSSEXP, SEXP nlTolSSEXP, SEXP nlMaxiterSSEXP);
-_rxode2random_rxRmvnSEXP_t rxRmvnSEXPnlmixrEst;
 SEXP _nlmixr2est_RcppExport_registerCCallable(void);
 
 SEXP _nlmixr2est_nlmSetup(SEXP);
@@ -127,7 +125,10 @@ SEXP _nlmixr2est_popedSolveIdME2(SEXP, SEXP, SEXP, SEXP, SEXP,
 
 SEXP _nlmixr2est_iniLotriPtr(SEXP ptr);
 
+SEXP _nlmixr2est_iniRxodePtrs(SEXP ptr);
+
 static const R_CallMethodDef CallEntries[] = {
+  {"_nlmixr2est_iniRxodePtrs", (DL_FUNC) &_nlmixr2est_iniRxodePtrs, 1},
   {"_nlmixr2est_iniLotriPtr", (DL_FUNC) &_nlmixr2est_iniLotriPtr, 1},
   {"_nlmixr2est_uninformativeEta", (DL_FUNC) &_nlmixr2est_uninformativeEta, 1},
   {"_nlmixr2est_popedSolveIdME2", (DL_FUNC) &_nlmixr2est_popedSolveIdME2, 7},
@@ -207,7 +208,6 @@ void R_init_nlmixr2est(DllInfo *dll)
   R_registerRoutines(dll, CEntries, CallEntries, NULL, NULL);
   R_useDynamicSymbols(dll, TRUE);
   R_forceSymbols(dll,FALSE);
-  rxRmvnSEXPnlmixrEst = (_rxode2random_rxRmvnSEXP_t)R_GetCCallable("rxode2","_rxode2_rxRmvnSEXP");
 }
 
 void rxOptionsFreeFocei(void);