Avoid potential protection stack overflow in bboxCalcR_c

[anashen]

Hello,

Thank you for your work on this package. I understand that it is in the process of being deprecated / is in maintenance mode; I'm hoping this PR can be considered as part of a patch update. It includes a fix for regression in behavior that seems to have been introduced in the latest version on CRAN, v2.2-3.

I was made aware of this issue via satijalab/seurat#10527.

For context: we currently use the SpatialPolygons class from your package to handle certain types of single-cell spatial transcriptomics data (and also hope to transition fully to sf soon). Recently, users with sp version v2.2-3 have reported Error: protect(): protection stack overflow on object-creation functions that use the SpatialPolygons constructor.

I looked into this by going through the changes introduced in v2.2-3, and I think the culprit is the bboxCalcR_c function. There are calls to PROTECT each polygon during the loop to go through all vertex coordinates to calculate the bounding box...

sp/src/sp_xports.c

Lines 468 to 479 in a4624aa

	for (j=0; j<npl; j++) {
	crds = PROTECT(GET_SLOT(VECTOR_ELT(Pl, j), Rf_install("coords"))); pc++;
	n = INTEGER_POINTER(Rf_getAttrib(crds, R_DimSymbol))[0];
	for (k=0; k<n; k++) {
	x = NUMERIC_POINTER(crds)[k];
	y = NUMERIC_POINTER(crds)[k+n];
	if (x > UX) UX = x;
	if (y > UY) UY = y;
	if (x < LX) LX = x;
	if (y < LY) LY = y;
	}
	}

...but when the number of polygons exceeds the default protection stack size, it can produce a protection stack overflow error.

This PR proposes to simply add a call to UNPROTECT crds, and decrement pc, after accessing the coordinates of all vertices for the given polygon.

Example

I've included a reprex of the error below. It runs successfully loading a checkout of this branch.

library(sp)

packageVersion("sp")
#> [1] '2.2.3'

# small triangle
polygon <- Polygons(
  list(Polygon(rbind(c(0, 0), c(1, 0), c(0, 1), c(0, 0)))),
  ID = "template"
)

# "large" object, 55k polygons
polygons <- lapply(seq_len(55000L), function(i) {
  slot(polygon, "ID") <- paste0("cell", i)
  polygon
})

# object creation succeeds for a smaller number of polygons
small <- SpatialPolygons(polygons[seq_len(40000L)])

# large input fails on object creation
large <- SpatialPolygons(polygons)
#> Error:
#> ! protect(): protection stack overflow

sessioninfo::session_info(pkgs = "attached")
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.5.2 (2025-10-31)
#>  os       Ubuntu 20.04.6 LTS
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2026-10-09
#>  pandoc   3.1.1 @ /opt/quarto/bin/tools/ (via rmarkdown)
#>  quarto   1.3.353 @ /usr/local/bin/quarto
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package * version date (UTC) lib source
#>  sp      * 2.2-3   2026-07-19 [1] CRAN (R 4.5.2)
#> 
#>  [1] /home/shenoya/R/x86_64-pc-linux-gnu-library/4.5
#>  [2] /usr/local/lib/R/site-library
#>  [3] /usr/lib/R/site-library
#>  [4] /usr/lib/R/library
#>  * ── Packages attached to the search path.
#> 
#> ──────────────────────────────────────────────────────────────────────────────

^{Created on 2026-10-09 with reprex v2.1.1}

Tests

With this edit, all package tests pass (run locally under Ubuntu 20.04.6 LTS).

[edzer]

Nice catch - thanks!