[R] How to properly finalize external pointers?

["Jens Oehlschlägel"]

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?

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)

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)



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