Capturing all warnings (with messages)

Jon Clayden wrote on 02/04/2009 12:11 PM:

Dear Jeff,

Many thanks for the suggestion, but I don't think tryCatch() is the
answer, mainly because it causes code to stop executing when a warning
is signalled:

f <- function(w) print(w$message)
tryCatch({warning("Test"); print(3)},warning=f)

[1] "Test"

(The "print(3)" call is not run.) In this regard,
withCallingHandlers() is preferable. But either way it is untidy, at
best, to routinely put code inside one of these functions when I know
I always want to handle warnings my way. If I could set an appropriate
option when a package is loaded, or in an .Rprofile, then I should
never need to worry about whether a bit of code might generate
warnings and so should be wrapped.

So you want your program to handle all warnings your way, but you want 
to continue execution after you have trapped the warnings. What 
specifically do you want your program to do with a warning once you know 
what it is?

(I'd like to help you work through your problem to a solution because I 
selfishly want to learn more about R's condition and restart system for 
rapache's sake, my personal project. Right now, the way rapache notifies 
users of R warnings and errors is crude but works.)

Jeff

Regards,
Jon

2009/2/4 Jeffrey Horner <jeff.horner at vanderbilt.edu>:

Jon Clayden wrote on 02/04/2009 06:59 AM:

Dear all,

For an open-source project that I'm working on (1), which uses R for 
all
its heavy lifting but includes a wrapper shell script, I was hoping 
to find
a way to capture all warnings (and, in fact, errors too), and handle 
them in
my own way. I realise I can do this for a single expression using 
something
like:

 > f <- function(w) print(w$message)
 > withCallingHandlers(warning("Test"),warning=f)

[1] "Test"
Warning message:
In withCallingHandlers(warning("Test"), warning = f) : Test

But I would like to capture all warnings, globally. The
"warning.expression" option doesn't seem to allow an argument, and I 
can't
seem to use "last.warning" to get at the message either:

 > g <- function() print(last.warning$message)
 > options(warning.expression=quote(g()))
 > warning("Test2")

NULL

Could anyone tell me whether there's a way to do this, please? An old
thread on this topic seemed to go unresolved (2), and I've skimmed 
RNEWS and
I don't see anything about this since then.

In fact, the thread did have the answer: tryCatch(). The help page is 
a bear
to read and comprehend, but if you do invest the time it should 
convince you
that you will want to use it. I find that I have to read and reread many
sections of R documentation before I can reconcile what I want to 
know with
what the authors are trying to tell me.

I don't comprehend everything about R's condition system, but let me 
see if
I can convince you that you need tryCatch() to do what you want.

Consider:

x <- function() warning("warning message")
y <- function() call_unknown_fun()
z <- function() message('message message')

Each of these functions signal conditions of a particular condition 
class:
simpleWarning, simpleError, and simpleMessage, respectively.

w <- function(e) str(e)

I'm going to use w  to trap the simpleWarning condition:

tryCatch(x(),simpleWarning=w)

List of 2
 $ message: chr "warning message"
 $ call   : language x()
 - attr(*, "class")= chr [1:3] "simpleWarning" "warning" "condition"

So tryCatch returned a list with two elements, the message and the 
call that
signaled the condition. In fact the list is actually an S3 object of 
class
simpleWarning, which inherits from warning and condition. Reading the 
help
page for tryCatch(), I can actually do this:

tryCatch(x(),condition=w)

List of 2
 $ message: chr "warning message"
 $ call   : language x()
 - attr(*, "class")= chr [1:3] "simpleWarning" "warning" "condition"

since simpleWarning inherits from condition. And in fact I can use the
condition class to trap everything I want.

tryCatch(y(),condition=w)

List of 2
 $ message: chr "could not find function \"call_unknown_fun\""
 $ call   : language y()
 - attr(*, "class")= chr [1:3] "simpleError" "error" "condition"

tryCatch(z(),condition=w)

List of 2
 $ message: chr "message message\n"
 $ call   : language message("message message")
 - attr(*, "class")= chr [1:3] "condition" "message" "simpleMessage"

(Side note: is the class hierarchy actually correct for this 
simpleMessage
object?)

So in summary, wrap every R expression you want to run within a single
tryCatch() call and trap all conditions with one handler for the 
abstract
class named 'condition'. I think that's what you want...

Jeff

 > sessionInfo()

R version 2.8.1 (2008-12-22)
i386-apple-darwin8.11.1

locale:
en_GB.UTF-8/en_US.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  splines   methods
[8] base

other attached packages:
[1] tractor.session_1.0.0   tractor.base_1.0.3      tractor.nt_1.0.2

loaded via a namespace (and not attached):
[1] tools_2.8.1

Regards,
Jon


(1) http://code.google.com/p/tractor/
(2) http://finzi.psych.upenn.edu/R/Rhelp02/archive/61872.html


-- 
Jonathan D. Clayden, Ph.D.
Research Fellow
Radiology and Physics Unit
UCL Institute of Child Health
30 Guilford Street
LONDON  WC1N 1EH
United Kingdom

t | +44 (0)20 7905 2708
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-- 
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