R help - Jul 2005 - Redirecting Messages and Errors to a file

Hello all,
I'm trying to setup a simple construct that will email me all errors,
warnings, and output of a sample R script. My initial thought was to use
sink() and tryCatch around the script such that at the end of the script
any output would be mailed to me, i.e.:

sinkFile <- tempfile()
sink(sinkFile)
tryCatch({
	[R script]},
	finally = {
		sink()
		if (length(readLines(sinkFile)))
			mailOutput(readLines(sinkFile))
	})

However, the sink() does not seem to be capturing the error messages as
I would have hoped. That is, if the R-script is {print("abc");
stop("def")}, the print output is captured to the file, the stop error
message is not, and instead sent to the screen.

Any thoughts on how to do this such that everything is sent to the file
for emailing? Perhaps something different all together?

Thanks,
Robert


This e-mail, and any attachments hereto, are intended for us...{{dropped}}

On Wed, 27 Jul 2005, McGehee, Robert wrote:
>
> However, the sink() does not seem to be capturing the error messages as
> I would have hoped. That is, if the R-script is {print("abc");
> stop("def")}, the print output is captured to the file, the stop
error
> message is not, and instead sent to the screen.
>
> Any thoughts on how to do this such that everything is sent to the file
> for emailing? Perhaps something different all together?
There is a separate output connection for errors.  The help page for 
sink() describes how to divert it, and warns of risks in doing so.

 	-thomas

Ahh, I misunderstood the help page. I took that since the default values
for type were c("output", "message"), that both the output
_and_ the
messages were simultaneously being redirected (else why not just make
the default "output"). I see that this is not the case (as noted in
the
details). 

After specifying type = "message", I was also able to successfully
send
off the error messages to a file, but not at the same time as sending
the output. That is, do I need to have two sink files, one for errors,
one for output and then append them before mailing? I'd prefer a way of
sending all output/messages to the same file to preserve the order of
the messages/output, if this is possible.

Robert

-----Original Message-----
From: Thomas Lumley [mailto:tlumley at u.washington.edu] 
Sent: Wednesday, July 27, 2005 10:37 AM
To: McGehee, Robert
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] Redirecting Messages and Errors to a file


On Wed, 27 Jul 2005, McGehee, Robert wrote:
>
> However, the sink() does not seem to be capturing the error messages
as
> I would have hoped. That is, if the R-script is {print("abc");
> stop("def")}, the print output is captured to the file, the stop
error
> message is not, and instead sent to the screen.
>
> Any thoughts on how to do this such that everything is sent to the
file
> for emailing? Perhaps something different all together?
There is a separate output connection for errors.  The help page for 
sink() describes how to divert it, and warns of risks in doing so.

 	-thomas