Garbage collection of seemingly PROTECTed pairlist

[rorynolan]

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 (beause 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 PROTECT ed 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 GitHub - rorynolan/testpkg: Minimal package to display my PROTECTion problem 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.

I really want to know what my mistake is.

I should add that 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.

[EconomiCurtis]

This topic appears to be cross-posted on stack overflow three days ago,

Garbage collection of seemingly PROTECTed pairlist

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[rorynolan]

A few nice solutions found here

Garbage collection of seemingly PROTECTed pairlist