From pd@|gd @end|ng |rom gm@||@com  Sat Sep 12 09:22:14 2020
From: pd@|gd @end|ng |rom gm@||@com (peter dalgaard)
Date: Sat, 12 Sep 2020 09:22:14 +0200
Subject: [Rd] Garbage collection of seemingly PROTECTed pairlist
In-Reply-To: <CAFyhwT9LD8_UTRN1r-KGEQAw_RYODLvhwYCRFPxqjDi5dDaMAg@mail.gmail.com>
References: <CAFyhwT9LD8_UTRN1r-KGEQAw_RYODLvhwYCRFPxqjDi5dDaMAg@mail.gmail.com>
Message-ID: <B81F5C47-737E-451E-98CF-94708660795B@gmail.com>

Hm, I'm getting rusty on my C skills, but you repeatedly use a pattern like

>  while (row_num <= nr) {
>    Rprintf("row_num: %i\n", row_num);
>    SEXP row = PROTECT(C_int_mat_nth_row_nrnc(int_mat_int, nr, 2, row_num));

I wonder if there is a subtle difference between assignments and initialized declarations.

I.e. would it help to write it as

>  while (row_num <= nr) {
    SEXP row;
    Rprintf("row_num: %i\n", row_num);
    row = PROTECT(C_int_mat_nth_row_nrnc(int_mat_int, nr, 2, row_num));

?

-pd

> On 12 Sep 2020, at 00:35 , Rory Nolan <rorynoolan at gmail.com> wrote:
> 
> I want to write an R function using R's C interface that takes a 2-column
> matrix of increasing, non-overlapping integer intervals and returns a list
> with those intervals plus some added intervals, such that there are no
> gaps. For example, it should take the matrix rbind(c(5L, 6L), c(7L, 10L),
> c(20L, 30L)) and return list(c(5L, 6L), c(7L, 10L), c(11L, 19L), c(20L,
> 30L)). Because the output is of variable length, I use a pairlist (because
> it is growable) and then I call Rf_PairToVectorList() at the end to make it
> into a regular list.
> 
> I'm getting a strange garbage collection error. My PROTECTed pairlist prlst
> gets garbage collected away and causes a memory leak error when I try to
> access it.
> 
> Here's my code.
> 
> #include <Rinternals.h>
> 
> 
> SEXP C_int_mat_nth_row_nrnc(int *int_mat_int, int nr, int nc, int n) {
>  SEXP out = PROTECT(Rf_allocVector(INTSXP, nc));
>  int *out_int = INTEGER(out);
>  if (n <= 0 | n > nr) {
>    for (int i = 0; i != nc; ++i) {
>      out_int[i] = NA_INTEGER;
>    }
>  } else {
>    for (int i = 0; i != nr; ++i) {
>      out_int[i] = int_mat_int[n - 1 + i * nr];
>    }
>  }
>  UNPROTECT(1);
>  return out;}
> 
> SEXP C_make_len2_int_vec(int first, int second) {
>  SEXP out = PROTECT(Rf_allocVector(INTSXP, 2));
>  int *out_int = INTEGER(out);
>  out_int[0] = first;
>  out_int[1] = second;
>  UNPROTECT(1);
>  return out;}
> 
> SEXP C_fullocate(SEXP int_mat) {
>  int nr = Rf_nrows(int_mat), *int_mat_int = INTEGER(int_mat);
>  int last, row_num;  // row_num will be 1-indexed
>  SEXP prlst0cdr = PROTECT(C_int_mat_nth_row_nrnc(int_mat_int, nr, 2, 1));
>  SEXP prlst = PROTECT(Rf_list1(prlst0cdr));
>  SEXP prlst_tail = prlst;
>  last = INTEGER(prlst0cdr)[1];
>  row_num = 2;
>  while (row_num <= nr) {
>    Rprintf("row_num: %i\n", row_num);
>    SEXP row = PROTECT(C_int_mat_nth_row_nrnc(int_mat_int, nr, 2, row_num));
>    Rf_PrintValue(prlst);  // This is where the error occurs
>    int *row_int = INTEGER(row);
>    if (row_int[0] == last + 1) {
>      Rprintf("here1");
>      SEXP next = PROTECT(Rf_list1(row));
>      prlst_tail = SETCDR(prlst_tail, next);
>      last = row_int[1];
>      UNPROTECT(1);
>      ++row_num;
>    } else {
>      Rprintf("here2");
>      SEXP next_car = PROTECT(C_make_len2_int_vec(last + 1, row_int[0] - 1));
>      SEXP next = PROTECT(Rf_list1(next_car));
>      prlst_tail = SETCDR(prlst_tail, next);
>      last = row_int[0] - 1;
>      UNPROTECT(2);
>    }
>    UNPROTECT(1);
>  }
>  SEXP out = PROTECT(Rf_PairToVectorList(prlst));
>  UNPROTECT(3);
>  return out;}
> 
> As you can see, I have some diagnostic print statements in there. The
> offending line is line 40, which I have marked with a comment of // This is
> where the error occurs. I have a minimal reproducible package at
> https://github.com/rorynolan/testpkg and I have run R CMD CHECK with
> valgrind using GitHub actions, the results of which are at
> https://github.com/rorynolan/testpkg/runs/1076595757?check_suite_focus=true.
> That's where I found out which line is causing the error. This function
> works as expected sometimes, and then sometimes this issue appears. This
> lends weight to the suspicion that it's a garbage collection issue.
> 
> I really want to know what my mistake is. I'm not that interested in
> alternative implementations; I want to understand the mistake that I'm
> making so that I can avoid making it in future.
> 
> I have asked the question on stackoverflow to little avail, but the
> discussion there may prove helpful.
> https://stackoverflow.com/questions/63759604/garbage-collection-of-seemingly-protected-pairlist.
> 
> 
> 
> Thanks,
> 
> Rory
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com



[Rd] Garbage collection of seemingly PROTECTed pairlist
peter dalgaard