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: [EMAIL PROTECTED]
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
______________________________________________
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
