Merge pull request #769 from nlmixr2/769-no-bin-dparser

No binary linkage to dparser
nlmixr2 · Aug 14, 2024 · 6296051 · 6296051
2 parents 4614144 + da82e61
commit 6296051
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Showing 5 changed files with 33 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -90,7 +90,7 @@ Imports:
     sys,
     tools,
     utils,
-    dparser,
+    dparser (>= 1.3.1-12),
     rxode2ll(>= 2.0.9),
     data.table (>= 1.12.4),
     qs (>= 0.26.3)
@@ -124,7 +124,7 @@ LinkingTo:
     RcppParallel,
     RcppEigen (>= 0.3.3.9.2),
     StanHeaders (>= 2.21.0.7),
-    dparser
+    dparser (>= 1.3.1-12)
 Encoding: UTF-8
 LazyData: true
 Language: en-US

diff --git a/NEWS.md b/NEWS.md
@@ -74,6 +74,12 @@
   changes in the `lotri` package will not require `rxode2` to be
   recompiled (in most cases) and will not crash the system.
 
+- `rxode2` also has no more binary linkage to `PreciseSums`
+
+- The binary linkage for `dparser` is reduced to C structures only,
+  making changes in dparser less likely to cause segmentation faults
+  in `rxode2` if it wasn't recompiled.
+
 ## Bug fixes
 
 - Fix `ui$props$endpoint` when the ui endpoint is defined in terms of the ode instead of lhs. See #754

diff --git a/R/rxode-options.R b/R/rxode-options.R
@@ -59,6 +59,7 @@
     setProgSupported(0)
   }
   .ggplot2Fix()
+  .linkAll()
 } ## nocov end
 
 .iniLotriPtrs <- function() {
@@ -69,6 +70,16 @@
   .Call(`_iniPreciseSumsPtr`, PreciseSums::.preciseSumsPtr())
 }
 
+.iniDparserPtr <- function() {
+  .Call(`_rxode2_iniDparserPtr`, dparser::.dparsePtr())
+}
+
+.linkAll <- function() {
+  .iniLotriPtrs()
+  .iniPreciseSumsPtr()
+  .iniDparserPtr()
+}
+
 
 .onAttach <- function(libname, pkgname) {
   ## For some strange reason, mvnfast needs to be loaded before rxode2 to work correctly
@@ -77,10 +88,8 @@
   if (!interactive()) {
     setProgSupported(0)
   }
-  # Setup lotri C linkages using function pointers
-  .iniLotriPtrs()
-  # Setup PreciseSums linkage with function pointers
-  .iniPreciseSumsPtr()
+  .linkAll()
+
   rxTempDir()
   .ggplot2Fix()
   v <- utils::packageVersion("rxode2")

diff --git a/src/init.c b/src/init.c
@@ -360,8 +360,11 @@ SEXP _rxode2_rxQs(SEXP);
 SEXP iniLotriPtr(SEXP ptr);
 SEXP iniPreciseSumsPtr(SEXP ptr);
 
+SEXP _rxode2_iniDparserPtr(SEXP ptr);
+
 void R_init_rxode2(DllInfo *info){
   R_CallMethodDef callMethods[]  = {
+    {"_rxode2_iniDparserPtr", (DL_FUNC) &_rxode2_iniDparserPtr, 1},
     {"_iniPreciseSumsPtr", (DL_FUNC) &iniPreciseSumsPtr, 1},
     {"_iniLotriPtr", (DL_FUNC) &iniLotriPtr, 1},
     {"_rxode2_rxode2parseSetRstudio", (DL_FUNC) &_rxode2_rxode2parseSetRstudio, 1},

diff --git a/src/tran.c b/src/tran.c
@@ -14,7 +14,6 @@
 #include "genModelVars.h"
 #include "print_node.h"
 #include <errno.h>
-#include <dparser.h>
 #include <R.h>
 #include <Rinternals.h>
 #include <R_ext/Rdynload.h>
@@ -26,6 +25,15 @@
 #else
 #define _(String) (String)
 #endif
+
+// change the name of the iniDparser pointer
+#define iniDparserPtr _rxode2_iniDparserPtr
+
+#include <dparserPtr.h>
+
+dparserPtrIni;
+
+
 #include "tran.g.d_parser.h"
 
 #define MXSYM 50000