R help - Dec 2010 - How to catch both warnings and errors?

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 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.

The function should *always* return the list with the three components.

How can I achieve this?

Cheers,

Marius

Ps: How can I get the warning/error message in a nice string (as it is printed
in a normal warning/error message)? The approach shown below is somehow ugly. 
Basically, I had trouble converting the call w$call to a string.

## based on http://tolstoy.newcastle.edu.au/R/help/04/06/0217.html
## and http://www.mail-archive.com/r-help at r-project.org/msg81380.html
f <- function(x){
    ## warnings
    w.list <- NULL # init warning
    w.handler <- function(w){ # warning handler
	warn <- simpleWarning(w$message, w$call) # build warning
        w.list <<- c(w.list, paste(warn, collapse = " ")) # save
warning
        invokeRestart("muffleWarning")
    }
    ## errors
    e.list <- NULL # init errors
    e.handler <- function(e){ # error handler
	err <- simpleError(e$message, e$call)
	e.list <<- c(e.list, paste(err, collapse = " ")) # save error 
    }
    ## execute command   
    res <- withCallingHandlers(log(x), warning = w.handler, error =
e.handler)
    ## return result with warnings and errors
    list(result = res, warning = w.list, error = e.list)
}

f(1) 
f(-1) 
f("a")

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)
}

> The function should *always* return the list with the three  
> components.
>
> How can I achieve this?
>
> Cheers,
>
> Marius
>
> Ps: How can I get the warning/error message in a nice string (as it  
> is printed
> in a normal warning/error message)? The approach shown below is  
> somehow ugly.
> Basically, I had trouble converting the call w$call to a string.
>
> ## based on http://tolstoy.newcastle.edu.au/R/help/04/06/0217.html
> ## and http://www.mail-archive.com/r-help at r-project.org/msg81380.html
> f <- function(x){
>    ## warnings
>    w.list <- NULL # init warning
>    w.handler <- function(w){ # warning handler
> 	warn <- simpleWarning(w$message, w$call) # build warning
>        w.list <<- c(w.list, paste(warn, collapse = " ")) #
save
> warning
>        invokeRestart("muffleWarning")
>    }
>    ## errors
>    e.list <- NULL # init errors
>    e.handler <- function(e){ # error handler
> 	err <- simpleError(e$message, e$call)
> 	e.list <<- c(e.list, paste(err, collapse = " ")) # save
error
>    }
>    ## execute command
>    res <- withCallingHandlers(log(x), warning = w.handler, error =  
> e.handler)
>    ## return result with warnings and errors
>    list(result = res, warning = w.list, error = e.list)
> }
>
> f(1)
> f(-1)
> f("a")
>
> ______________________________________________
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT