Evaluate an R expression and interrupts it if it takes too long

Evaluate an R expression and interrupts it if it takes too long.

withTimeout(expr, substitute=TRUE, envir=parent.frame(), timeout, cpu=timeout,
  elapsed=timeout, onTimeout=c("error", "warning", "silent"), ...)

Arguments

expr: The R expression to be evaluated.
substitute: If TRUE, argument expr is substitute():ed, otherwise not.
envir: The environment in which the expression should be evaluated.
timeout, cpu, elapsed: A numeric specifying the maximum number of seconds the expression is allowed to run before being interrupted by the timeout. The cpu and elapsed arguments can be used to specify whether time should be measured in CPU time or in wall time.
onTimeout: A character specifying what action to take if a timeout event occurs.
...: Not used.

Value

Returns the results of the expression evaluated. If timed out, NULL is returned if onTimeout was

"warning" or "silent". If "error" a TimeoutException is thrown.

Details

This method utilizes setTimeLimit() by first setting the timeout limits, then evaluating the expression that may or may not timeout. The method is guaranteed to reset the timeout limits to be infinitely long upon exiting, regardless whether it returns normally or preemptively due to a timeout or an error.

Known limitation: Not everything can be timed out

In order to understand when this function works and when it does not, it is useful to know that it utilizes R's built-in time-out mechanism, which sets the limits on what is possible and not. From setTimeLimit(), we learn that:

"Time limits are checked whenever a user interrupt could occur. This will happen frequently in R code and during Sys.sleep(*), but only at points in compiled C and Fortran code identified by the code author."

More precisely, if a function is implemented in native code (e.g. C) and the developer of that function does not check for user interrupts, then you cannot interrupt that function neither via a user interrupt (e.g. Ctrl-C) nor via the built-in time out mechanism. To change this, you need to contact the developer of that piece of code and ask them to check for R user interrupts in their native code.

Furthermore, it is not possible to interrupt/break out of a "readline" prompt (e.g. readline() and readLines()) using timeouts; the timeout exception will not be thrown until after the user completes the prompt (i.e. after pressing ENTER).

System calls via system() and system2() cannot be timed out via the above mechanisms. However, in R (>= 3.5.0) these functions have argument timeout providing their own independent timeout mechanism.

Other examples of calls that do not support timeout are "atomic" calls that may take very long such as large object allocation and rnorm(n) where n is very large.

(*) Note that on Unix and macOS, Sys.sleep(time) will signal a timeout error only after time seconds passed, regardless of timeout limit (< time).

Known limitation: May fail when temporarily switching language

withTimeout() does not handle the case when the expression evaluated temporarily switches the language used by R, e.g. assume we run in a non-French locale and call:


 withTimeout({
   olang <- Sys.getenv("LANGUAGE")
   on.exit(Sys.setenv(LANGUAGE=olang))
   Sys.setenv(LANGUAGE="fr")
   repeat Sys.sleep(0.1)
 }, timeout = 1.0, onTimeout = "warning")

In this case, the error message produced by setTimeLimit() is in French, i.e. `la limite de temps est atteinte`. However, when withTimeout() inspects this message, it can not know that French was used, and will therefore not check against the French template message for timeout errors. Because of this, withTimeout() fails to detect the timeout error (and therefore also deescalate it to a warning in this example).

Comment: This appears to only fail on MS Windows and macOS, whereas on Linux, withTimeout() appears to work, but it is unknown why there is a difference between operating systems in this case.

Author

Henrik Bengtsson

References

[1] R help thread 'Time out for a R Function' on 2010-12-07. https://stat.ethz.ch/pipermail/r-help/2010-December/262316.html

Examples

# - - - - - - - - - - - - - - - - - - - - - - - - -
# Function that takes "a long" time to run
# - - - - - - - - - - - - - - - - - - - - - - - - -
foo <- function() {
  print("Tic")
  for (kk in 1:100) {
    print(kk)
    Sys.sleep(0.1)
  }
  print("Tac")
}


# - - - - - - - - - - - - - - - - - - - - - - - - -
# Evaluate code, if it takes too long, generate
# a timeout by throwing a TimeoutException.
# - - - - - - - - - - - - - - - - - - - - - - - - -
res <- NULL
tryCatch({
  res <- withTimeout({
    foo()
  }, timeout = 0.75)
}, TimeoutException = function(ex) {
  message("Timeout. Skipping.")
})
#> [1] "Tic"
#> [1] 1
#> [1] 2
#> [1] 3
#> [1] 4
#> [1] 5
#> [1] 6
#> [1] 7
#> [1] 8
#> [1] 9
#> [1] 10
#> [1] 11
#> Timeout. Skipping.


# - - - - - - - - - - - - - - - - - - - - - - - - -
# Evaluate code, if it takes too long, generate
# a timeout returning NULL and generate a warning.
# - - - - - - - - - - - - - - - - - - - - - - - - -
res <- withTimeout({
  foo()
}, timeout = 0.75, onTimeout = "warning")
#> [1] "Tic"
#> [1] 1
#> [1] 2
#> [1] 3
#> [1] 4
#> [1] 5
#> [1] 6
#> [1] 7
#> [1] 8
#> [1] 9
#> Warning: reached elapsed time limit [cpu=0.75s, elapsed=0.75s]


# The same using an expression object
expr <- quote(foo())
res <- withTimeout(expr, substitute = FALSE,
                   timeout = 0.75, onTimeout = "warning")
#> [1] "Tic"
#> [1] 1
#> [1] 2
#> [1] 3
#> [1] 4
#> [1] 5
#> [1] 6
#> [1] 7
#> [1] 8
#> [1] 9
#> [1] 10
#> [1] 11
#> Warning: reached elapsed time limit [cpu=0.75s, elapsed=0.75s]


# - - - - - - - - - - - - - - - - - - - - - - - - -
# Evaluate code, if it takes too long, generate
# a timeout, and return silently NULL.
# - - - - - - - - - - - - - - - - - - - - - - - - -
res <- withTimeout({
  foo()
}, timeout = 0.75, onTimeout = "silent")
#> [1] "Tic"
#> [1] 1
#> [1] 2
#> [1] 3
#> [1] 4
#> [1] 5
#> [1] 6
#> [1] 7
#> [1] 8
#> [1] 9
#> [1] 10
#> [1] 11