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
f | +44 (0)20 7905 2358
w | www.homepages.ucl.ac.uk/~sejjjd2/
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--
http://biostat.mc.vanderbilt.edu/JeffreyHorner
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