[R] How to properly finalize external pointers?

[Luke Tierney]

On Fri, 3 Aug 2007, "Jens Oehlschlägel" wrote:

> Dear R .Call() insiders,
>
> Can someone enlighten me how to properly finalize external pointers in C code (R-2.5.1 win)? What is the relation between R_ClearExternalPtr and the finalizer set in R_RegisterCFinalizer?

There is none.  R_ClearExternalPtr(s) is equivalent to
R_SetExternalPtrAddr(s, NULL);

> I succeeded registering a finalizer that works when an R object containing an external pointer is garbage collected. However, I have some difficulties figuring out how to do that in an explicit closing function.
>
> I observed that
> - calling R_ClearExternalPtr does not trigger the finalizer and is dangerous because it removes the pointer before the finalizer needs it at garbage-collection-time (no finalization = memory leak)
> - calling the finalizer directly ensures finalization but now the finalizer is called twice (once again at garbage collection time, and I did not find documentation how to unregister the finalizer)
> - It works to delete the SEXP external pointer object but only if not calling R_ClearExternalPtr (but why then do we need it?) Furthermore it is unfortunate to delay freeing the external pointers memory if I know during runtime that it can be done immediately.
>
> Shouldn't R_ClearExternalPtr call the finalizer and then unregister it? (this would also work when removing the SEXP external pointer object is difficult because it was handed over to the closing function directly as a parameter)

No.  External pointers are often used without finalization.  Usually
one would chose either an explicit release or finalization via GC but
not both.  If you want to use explicit release with finalization as a
backup you need to write your C code accordingly.  I would do this by
setting the pointer to NULL with R_ClearExternalPtr in the explicit
close routine and checking whether it has already been set to NULL in
the finalizer.

Best,

luke

>
> Best regards
>
>
> Jens Oehlschlägel
>
>
> // C-code
>
> static void rindex_finalize(SEXP extPtr){
>  pINT ptr = R_ExternalPtrAddr(extPtr);
>  if(ptr){
>    Free(ptr);
>    Rprintf("finalized\n");
>  }else{
>    Rprintf("nothing to finalize\n");
>  }
>  return;
> }
>
>
> SEXP rindex_open(
>  SEXP Sn
> ){
>  int i,n = INTEGER(Sn)[0];
>  pINT ptr = Calloc(sizeof(INT)*n, INT);
>  SEXP extPtr, ret;
>  for (i=0;i<n;i++){
>    ptr[i] = i;
>  }
>  extPtr = R_MakeExternalPtr(ptr, install("Rindex_extPtr"), R_NilValue);
>  R_RegisterCFinalizer(extPtr, rindex_finalize);
>
>  PROTECT(ret = allocVector(VECSXP, 1));
>  SET_VECTOR_ELT(ret,0,extPtr);
>  UNPROTECT(1);
>  return ret;
> }
>
> SEXP rindex_close(
>  SEXP obj
> ){
>  int i, n= 10;
>  SEXP ret, extPtr=VECTOR_ELT(obj, 0);
>  pINT p, ptr = R_ExternalPtrAddr(extPtr);
>
>  PROTECT(ret = allocVector(INTSXP, n));
>  p = INTEGER(ret);
>  for (i=0;i<n;i++){
>    Rprintf("ptri=%d\n",ptr[i]);
>    p[i] = ptr[i];
>  }
>
>  /* this does finalize immediately but at next garbage collection again
>  rindex_finalize(extPtr);
>  */
>
>  /* this must not called otherwise the pointer is gone at garbage collection time
>  R_ClearExternalPtr(extPtr);
>  */
>
>  /* this triggers the finalizer but only at next garbage collection */
>  SET_VECTOR_ELT(obj,0,R_NilValue);
>
>  UNPROTECT(1);
>  return ret;
> }
>
>
> # R-Code
> initRindex <- function(){
>  dyn.load(file.path(.libPaths(), "rindex", "libs", paste("rindex", .Platform$dynlib.ext, sep = "")))
> }
>
> doneRindex <- function(){
>  dyn.unload(file.path(.libPaths(), "rindex", "libs", paste("rindex", .Platform$dynlib.ext, sep = "")))
> }
>
>
> openRindex <- function(n=10){
>  .Call("rindex_open", as.integer(n))
> }
>
> closeRindex <- function(extPtr){
>  .Call("rindex_close", extPtr)
> }
>
> if (FALSE){
>  # now try it
>  require(rindex)
>
>  initRindex()
>
>  extPtr <- openRindex()
>  extPtr
>  extPtr2 <- closeRindex(extPtr)
>  extPtr2
>  gc()
>
>  extPtr <- openRindex()
>  extPtr2 <- extPtr
>  extPtr2
>  rm(extPtr)
>  gc()
>  extPtr2
>  rm(extPtr2)
>  gc()
>  extPtr2
>
>  doneRindex()
> }
>
>
>> version
>               _
> platform       i386-pc-mingw32
> arch           i386
> os             mingw32
> system         i386, mingw32
> status
> major          2
> minor          5.1
> year           2007
> month          06
> day            27
> svn rev        42083
> language       R
> version.string R version 2.5.1 (2007-06-27)
>
>
>
>

-- 
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:      luke at stat.uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu