On Dec 5, 2010, at 7:35 PM, Marius Hofert wrote:
On 2010-12-06, at 01:07 , David Winsemius wrote:
On Dec 5, 2010, at 3:13 PM, Marius Hofert wrote:
Dear expeRts,
I am struggling with warning/error handling.
I would like to call a function which can produce either
a) normal output
b) a warning
c) an error
Since the function is called several (thousand) times in a loop, I
would like
to proceed "quietly" and collect the warnings and errors [to deal
with them at a
later point].
I do not see the function warnings() being used below:
?warnings
It delivers the stored warnings with different default behavior for
interactive and non-interactive sessions.
I have seen constructs with tryCatch (which can deal with errors)
and with
withCallingHandlers (which can deal with warnings), but I cannot
figure out how
to catch *both* warnings and errors. Below is a minimal example of
the function
that is called several times in a large loop. The function should
catch warnings
and errors; the former work fine, but with the latter I do not
know how to proceed.
Made some changes in you code but don't know if it is what you were
hoping for:
f <- function(x){
## warnings
w.list <- NULL # init warning
w.handler <- function(w){ # warning handler
warn <- simpleWarning(w$message, w$call) # build warning
# first change here
w.list <<- c(w.list, paste(warnings(), collapse = " ")) # save
warning
invokeRestart("muffleWarning")
}
## errors
e.list <- NULL # init errors # not sure this is good idea
e.handler <- function(e){ # error handler
err <- c(e.list, e$message, e$call) # save error
return( err)
}
## execute command
# wrapped cal in try()
res <- withCallingHandlers(try(log(x)), warning = w.handler, error
= e.handler)
## return result with warnings and errors
list(result = res, warning = w.list, error = e.list)
}
Dear David,
many thanks for your help.
If I call your code with f(-1) and f("a"), I obtain:
f(-1)
$result
[1] NaN
$warning
[1] ""
$error
NULL
=> The problem is that the warning is not given.
f("a")
Error in log(x) : Non-numeric argument to mathematical function
$result
[1] "Error in log(x) : Non-numeric argument to mathematical function
\n"
attr(,"class")
[1] "try-error"
$warning
NULL
$error
NULL
=> The problem is that the error message is printed to the R console
instead of suppressed (setting silent = TRUE didn't help either).
Further, the $error component is empty (the error message should
appear there -- if possible)
Sorry. I was being misled by warnings that existed at my global level
into thinking i had succeeded. This modification will suppress warning
and error but will not populate the lists as we had hoped:
f <- function(expr){
## warnings
w.list <- NULL # init warning
w.handler <- function(w){ # warning handler
warn <- c(w$message, w$call) # build warning
# first change here
muffleWarning <<- c(w.list, warn, collapse = " ") # save warning
invokeRestart("muffleWarning")}
## errors
e.list <- NULL # init errors # not sure this is good idea
e.handler <- function(e){ # error handler
e.list <<- c(e.list, e$message, e$call) # save error
return( e.list)
}
## execute command
# wrapped cal in try()
res <- withCallingHandlers(try(expr, silent=TRUE), warning =
w.handler, error = e.handler)
## return result with warnings and errors
list(result = res, warning = w.list, error = e.list)
}
> test <- f(log(-1))
> test
$result
[1] NaN
$warning
NULL
$error
NULL
> test <- f(log("a"))
> test
$result
[1] "Error in log(\"a\") : Non-numeric argument to mathematical
function\n"
attr(,"class")
[1] "try-error"
$warning
NULL
$error
NULL
Do you know a solution?
Cheers,
Marius
David Winsemius, MD
West Hartford, CT
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