as.data.table() recurses without end on a survival::Surv object (or any data.frame carrying one)

[amaltawfik]

Summary

as.data.table() never terminates on a Surv object, or on any data.frame that
carries a Surv column. It exhausts a stack limit instead. A Surv column is the
normal way survival data is carried, so this is reachable by an ordinary
as.data.table(df) on a survival dataset.

Reproducer

library(data.table)   # 1.18.4
library(survival)     # 3.8.11

s <- Surv(c(5, 10, 15), c(1, 0, 1))

as.data.table(s)
#> Error: node stack overflow

d <- data.frame(a = 1:3)
d$y <- s
as.data.table(d)
#> Error: node stack overflow

A plain matrix column is fine; the trigger is specifically a classed matrix whose
as.data.frame method returns a data.frame that still contains it:

d2 <- data.frame(a = 1:3); d2$m <- matrix(1:6, nrow = 3)
as.data.table(d2)     # OK, 3 x 3

Cause

Surv is a matrix carrying class(x) == "Surv", so S3 dispatch selects
as.data.table.default, not as.data.table.matrix:

# R/as.data.table.R#9-11
as.data.table.default = function(x, ...){
  as.data.table(as.data.frame(x, ...), ...)
}

as.data.frame(<Surv>) returns a one-column data.frame whose column is still a
Surv (survival keeps the class deliberately, as emmeans does in #6874):

str(as.data.frame(s))
#> 'data.frame':	3 obs. of  1 variable:
#>  $ x: 'Surv' num [1:3, 1:2]  5  10+ 15
#>   ..- attr(*, "dimnames")=List of 2
#>   .. ..$ : NULL
#>   .. ..$ : chr [1:2] "time" "status"
#>   ..- attr(*, "type")= chr "right"

That data.frame's class is exactly "data.frame", so the guard added for #6874
at R/as.data.table.R#256-260 does not apply. Control then reaches

# R/as.data.table.R#271-275
if (any(cols_with_dims(x))) {
  # a data.frame with a column that is data.frame needs to be expanded; test 2013.4
  # x may be a class with [[ method that behaves differently, so as.list first for default [[, #4526
  return(as.data.table.list(as.list(x), keep.rownames=keep.rownames, key = key,...))
}

and in as.data.table.list:

# R/as.data.table.R#169
xi = x[[i]] = as.data.table(xi, keep.rownames=keep.rownames)  # we will never allow a matrix to be a column; always unpack the columns

which dispatches the Surv column straight back to as.data.table.default. Closed
loop.

Suggested patch

The atomic-vector methods (one chained definition, integer through ITime) already
carry an is.matrix() short-circuit at R/as.data.table.R#14-19;
as.data.table.default is the one method that lacks it:

 as.data.table.default = function(x, ...){
+  if (is.matrix(x)) return(as.data.table.matrix(x, ...))
   as.data.table(as.data.frame(x, ...), ...) # we cannot assume as.data.frame will do copy, thus setDT changed to as.data.table #3230
 }

Applied to 1.18.4 and tested. The recursion is gone and the result is what the
matrix method would have produced all along:

as.data.table(s)
#     time status
#    <num>  <num>
# 1:     5      1
# 2:    10      0
# 3:    15      1

as.data.table(d)
#        a y.time y.status
#    <int>  <num>    <num>
# 1:     1      5        1
# 2:     2     10        0
# 3:     3     15        1

Regression checks with the patch in place, all OK: data.frame, matrix, integer,
character, factor, list, table, Date, ts, NULL.

Related

• data.table fails with emmeans objects #6874 (emmeans) — same family, different shape. Its guard covers
  as.data.frame(x) returning an object with the same class; here as.data.frame
  returns a genuine data.frame and it is the column that keeps the class, so the
  guard is never reached.
• Infinite recursion in as.data.table() #6878 — closed as a duplicate of data.table fails with emmeans objects #6874.
• Ability to have a "Surv" class data column in a data.table object #1204 (open since 2015, labelled bug / non-atomic column) — Surv columns in
  data.table. Different symptom ([.Surv error), same underlying "non-atomic column"
  area; linked for cross-reference.

I am aware of the position taken in #6874 that a looping as.data.frame method is the
downstream package's problem. Two reasons this one is worth guarding anyway: Surv
comes from a Recommended package, and its class-preserving as.data.frame is
deliberate and long-standing; and data.table's own vector methods already carry the
one-line guard that would prevent it.

Session info

R version 4.6.1 (2026-06-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

packages: data.table 1.18.4, survival 3.8.11