From jeff.horner at vanderbilt.edu  Wed Feb  4 17:52:58 2009
From: jeff.horner at vanderbilt.edu (Jeffrey Horner)
Date: Wed, 04 Feb 2009 10:52:58 -0600
Subject: [Rd] Capturing all warnings (with messages)
In-Reply-To: <1F999E4C-B39B-46B4-92BC-074EFEE4B1E8@ucl.ac.uk>
References: <1F999E4C-B39B-46B4-92BC-074EFEE4B1E8@ucl.ac.uk>
Message-ID: <4989C7EA.1090700@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
> 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



[Rd] Capturing all warnings (with messages)
Jeffrey Horner