@ch,
A few functions only work with an atomic list and not all lists such as sort. The list is atomic when there is a single value at each position and no other R objects. This warning pops up for those functions that are used with nested lists.
> list(1,1:5,6)
[[1]]
[1] 1
[[2]]
[1] 1 2 3 4 5
[[3]]
[1] 6
> sort(list(1,1:5,6))
Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) :
'x' must be atomic