Re: [Rd] Capturing all warnings (with messages)

From: Jeffrey Horner <jeff.horner_at_vanderbilt.edu>
Date: Wed, 04 Feb 2009 10:52:58 -0600

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()

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()

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()

 > tryCatch(z(),condition=w)
List of 2
  $ message: chr "message message\n"
  $ call : language message("message message")

(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/
>
> ______________________________________________
> R-devel_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

-- 
http://biostat.mc.vanderbilt.edu/JeffreyHorner

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