[Rd] External pointers and an apparent memory leak

From: James Bullard <jbullard_at_pacificbiosciences.com>
Date: Wed, 14 Sep 2011 21:21:25 +0000


I'm using external pointers and seemingly leaking memory. My determination of a memory leak is that the R process continually creeps up in memory as seen by top while the usage as reported by gc() stays flat. I have isolated the C code:

void h5R_allocate_finalizer(SEXP eptr) {

    Rprintf("Calling the finalizer\n");
    void* vector = R_ExternalPtrAddr(eptr);     free(vector);
    R_ClearExternalPtr(eptr);
}

SEXP h5R_allocate(SEXP size) {

    int i = INTEGER(size)[0];
    char* vector = (char*) malloc(i*sizeof(char));     SEXP e_ptr = R_MakeExternalPtr(vector, R_NilValue, R_NilValue);     R_RegisterCFinalizerEx(e_ptr, h5R_allocate_finalizer, TRUE);     return e_ptr;

}

If I run an R program like this:

v <- replicate(100000, {
  .Call("h5R_allocate", as.integer(1000000))
})


rm(v)
gc()

Then you can see the problem (top reports that R still has a bunch of memory, but R doesn't think it does). I have tried using valgrind and it says I have memory left on the table at the end lest you think it is because top. Also, I have tried Free/Calloc as well and this doesn't make a difference. Finally, I see this in both R-2-12 (patched) and R-2-13 - I think it is more an understanding issue on my part.

thanks much in advance, to me it really resembles the connection.c code, but what am I missing?

thanks, jim

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