Skip to content

Avoid out-of-bounds access in overlaps #7598

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
aitap wants to merge 4 commits into
base: master
Choose a base branch
from
+22 −7
Open

Avoid out-of-bounds access in overlaps #7598

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
327849e
Add tests
aitap Jan 15, 2026
e2b19ea
overlaps: avoid accessing length-0 vectors in ux
aitap Jan 15, 2026
354c3db
overlaps: avoid 'lookup' list overflow
aitap Jan 15, 2026
9688a35
NEWS entry
aitap Jan 15, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions NEWS.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,8 @@

8. When fixing duplicate factor levels, `setattr()` no longer crashes upon encountering missing factor values, [#7595](https://github.com/Rdatatable/data.table/issues/7595). Thanks to @sindribaldur for the report and @aitap for the fix.

9. `foverlaps()` no longer crashes due to out-of-bounds access to list and integer vectors when `y` has no rows or the non-range part of the join fails, [#7597](https://github.com/Rdatatable/data.table/issues/7597). Thanks to @nextpagesoft for the report and @aitap for the fix.

### Notes

1. {data.table} now depends on R 3.5.0 (2018).
Expand Down
11 changes: 11 additions & 0 deletions inst/tests/tests.Rraw
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21484,3 +21484,14 @@ dt = data.table(a=1:4, b=1:2)
test(2362.51, optimize=0:2, dt[, c(list()), b, verbose=TRUE], data.table(b=integer(0L)), output="GForce FALSE")
test(2362.52, optimize=0:2, dt[, c(lapply(.SD, sum), list()), b, verbose=TRUE], output=out)
test(2362.53, optimize=0:2, dt[, list(lapply(.SD, sum), list()), b, verbose=TRUE], output="GForce FALSE")

# foverlaps shouldn't segfault on 0-row 'y', #7597
x = data.table(Id = "A", StartX = 1L, EndX = 2L)
y = data.table(Id = character(), StartY = integer(), EndY = integer())
by.x = c("Id", "StartX", "EndX")
by.y = c("Id", "StartY", "EndY")
setkeyv(y, by.y)
y2 = data.table(Id = "none", StartY = integer(1), EndY = integer(1))
setkeyv(y2, by.y)
test(2363, foverlaps(x, y, by.x, by.y), foverlaps(x, y2, by.x, by.y))
rm(x, y, y2)
16 changes: 9 additions & 7 deletions src/ijoin.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -223,7 +223,7 @@ SEXP lookup(SEXP ux, SEXP xlen, SEXP indices, SEXP gaps, SEXP overlaps, SEXP mul

SEXP overlaps(SEXP ux, SEXP imatches, SEXP multArg, SEXP typeArg, SEXP nomatchArg, SEXP verbose) {

R_len_t uxcols=LENGTH(ux),rows=length(VECTOR_ELT(imatches,0));
R_len_t uxcols=LENGTH(ux), rows=length(VECTOR_ELT(imatches,0)), xrows=length(VECTOR_ELT(ux,0));
int nomatch = INTEGER(nomatchArg)[0], totlen=0, thislen;
int *from = INTEGER(VECTOR_ELT(imatches, 0));
int *to = INTEGER(VECTOR_ELT(imatches, 1));
Expand Down Expand Up @@ -252,7 +252,7 @@ SEXP overlaps(SEXP ux, SEXP imatches, SEXP multArg, SEXP typeArg, SEXP nomatchAr
// As a first pass get the final length, so that we can allocate up-front and not deal with R_Calloc + R_Realloc + size calculation hassle
// Checked the time for this loop on realisitc data (81m reads) and took 0.27 seconds! No excuses ;).
start = clock();
if (mult == ALL) {
if (xrows && mult == ALL) {
totlen=0;
switch (type) {
case START: case END:
Expand Down Expand Up @@ -340,7 +340,7 @@ SEXP overlaps(SEXP ux, SEXP imatches, SEXP multArg, SEXP typeArg, SEXP nomatchAr
// switching mult=ALL,FIRST,LAST separately to
// - enhance performance for special cases, and
// - easy to fix any bugs in the future
switch (mult) {
if (xrows) switch (mult) {
case ALL:
switch (type) {
case START : case END :
Expand Down Expand Up @@ -402,8 +402,7 @@ SEXP overlaps(SEXP ux, SEXP imatches, SEXP multArg, SEXP typeArg, SEXP nomatchAr
case ANY :
for (int i=0; i<rows; ++i) {
const int len = thislen;
// k = (from[i]>0) ? from[i] : 1;
const int k = from[i];
const int k = (from[i]>0) ? from[i] : 1;
if (k<=to[i]) {
tmp1 = VECTOR_ELT(lookup, k-1);
for (int m=0; m<count[k-1]; ++m) {
Expand Down Expand Up @@ -659,8 +658,7 @@ SEXP overlaps(SEXP ux, SEXP imatches, SEXP multArg, SEXP typeArg, SEXP nomatchAr
for (int i=0; i<rows; ++i) {
const int len = thislen;
INTEGER(f1__)[thislen] = i+1;
// k = (from[i]>0) ? from[i] : 1;
const int k = from[i];
const int k = (from[i]>0) ? from[i] : 1;
if (k <= to[i]) {
if (k==to[i] && count[k-1]) {
tmp1 = VECTOR_ELT(lookup, k-1);
Expand Down Expand Up @@ -723,6 +721,10 @@ SEXP overlaps(SEXP ux, SEXP imatches, SEXP multArg, SEXP typeArg, SEXP nomatchAr
}
break;
default: internal_error(__func__, "unknown mult: %d", mult); // # nocov
} else if (totlen) {
int *f1i = INTEGER(f1__), *f2i = INTEGER(f2__);
for (R_len_t i = 0; i < totlen; ++i) f1i[i] = i+1;
for (R_len_t i = 0; i < totlen; ++i) f2i[i] = NA_INTEGER;
}
end2 = clock() - start;
if (LOGICAL(verbose)[0])
Expand Down
Loading