[FIXED] How do I save warnings and errors as output from a function?

Issue

I'm using lapply to run a complex function on a large number of items, and I'd like to save the output from each item (if any) together with any warnings/errors that were produced so that I can tell which item produced which warning/error.

I found a way to catch warnings using withCallingHandlers (described here). However, I need to catch errors as well. I can do it by wrapping it in a tryCatch (as in the code below), but is there a better way to do it?

catchToList <- function(expr) {
  val <- NULL
  myWarnings <- NULL
  wHandler <- function(w) {
    myWarnings <<- c(myWarnings, w$message)
    invokeRestart("muffleWarning")
  }
  myError <- NULL
  eHandler <- function(e) {
    myError <<- e$message
    NULL
  }
  val <- tryCatch(withCallingHandlers(expr, warning = wHandler), error = eHandler)
  list(value = val, warnings = myWarnings, error=myError)
} 

Sample output of this function is:

> catchToList({warning("warning 1");warning("warning 2");1})
$value
[1] 1

$warnings
[1] "warning 1" "warning 2"

$error
NULL

> catchToList({warning("my warning");stop("my error")})
$value
NULL

$warnings
[1] "my warning"

$error
[1] "my error"

There are several questions here on SO that discuss tryCatch and error handling, but none that I found that address this particular issue. See How can I check whether a function call results in a warning?, warnings() does not work within a function? How can one work around this?, and How to tell lapply to ignore an error and process the next thing in the list? for the most relevant ones.

Solution

Maybe this is the same as your solution, but I wrote a factory to convert plain old functions into functions that capture their values, errors, and warnings, so I can

test <- function(i)
    switch(i, "1"=stop("oops"), "2"={ warning("hmm"); i }, i)
res <- lapply(1:3, factory(test))

with each element of the result containing the value, error, and / or warnings. This would work with user functions, system functions, or anonymous functions (factory(function(i) ...)). Here's the factory

factory <- function(fun)
    function(...) {
        warn <- err <- NULL
        res <- withCallingHandlers(
            tryCatch(fun(...), error=function(e) {
                err <<- conditionMessage(e)
                NULL
            }), warning=function(w) {
                warn <<- append(warn, conditionMessage(w))
                invokeRestart("muffleWarning")
            })
        list(res, warn=warn, err=err)
    }

and some helpers for dealing with the result list

.has <- function(x, what)
    !sapply(lapply(x, "[[", what), is.null)
hasWarning <- function(x) .has(x, "warn")
hasError <- function(x) .has(x, "err")
isClean <- function(x) !(hasError(x) | hasWarning(x))
value <- function(x) sapply(x, "[[", 1)
cleanv <- function(x) sapply(x[isClean(x)], "[[", 1)

Answered By - Martin Morgan

Answer Checked By - Willingham (PHPFixing Volunteer)