How to catch both warnings and errors?

Sun, Dec 5, 2010 6:13 PM

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

David Winsemius, MD
West Hartford, CT

How to catch both warnings and errors?

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