Capturing all warnings (with messages)

Kurt Hornik and I have discussed off an on a mechanism for setting
default condition handlers.  So far we haven't come up with anything
satisfactory but we may yet.  In some ways this would be easier if the
top level was written in R, along the lines of .Program, so I've
played around with that a bit, but not to the point where it is usable
in production yet.

luke

On Wed, 4 Feb 2009, William Dunlap wrote:

In SV3 (or Splus prior to 5.0) one could redefine
the .Program expression, which
by default was close to print(eval(parse(stdin())) along
with some extras like printing warnings and errors in
certain ways and recording input in a .Audit file.   I
once wrote toy .Programs that used select() to
listen for data arriving on a socket and for commands
from stdin.  The data would be appended to a certain
dataset as it arrived and the user could ask to replot
it whenever he wanted.  You could use options("warning.expression")
and try() to present warnings and errors to the user in
whatever way you wanted.  I think it was used in old
versions of Splus on Windows to implement the connection
to the GUI.

Is this the sort of functionality you are looking for?

If you are writing a front-end for R the .Program is not
needed, as your front end can easily wrap boilerplate,
like eval.with.details, around whatever text the user types in.


Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com

-----Original Message-----
From: r-devel-bounces at r-project.org
[mailto:r-devel-bounces at r-project.org] On Behalf Of Jon Clayden
Sent: Wednesday, February 04, 2009 4:31 PM
To: hadley wickham
Cc: R-devel at r-project.org
Subject: Re: [Rd] Capturing all warnings (with messages)

Jeff, Hadley,

Many thanks for your responses. The eval.with.details package sounds
interesting and I'll certainly take a closer look, but it still seems
to me that these approaches are focussed on trapping warnings within
specific snippets of code rather than changing the way all warnings
(including those in standard packages) are reported.

This ability would surely be useful anytime that you wish to change
the reporting of warnings from the default. Say, for example, that you
wanted to include a timestamp with each warning message. You'd do it,
I would expect, by writing a function that checks the time and formats
the message appropriately. This is the kind of thing I'm after -- I
hope this clarifies things a bit more.

The warn.expression option *appears* to provide a way to do what I
want, but because the warning is not passed to the expression (or so
it seems), and last.warning is not set before the expression is
evaluated, the expression can only know that *some* warning condition
has been raised, not *which* one. Perhaps there is a reason that
last.warning cannot be set first (?), but this limits the usefulness
of the option.

Jon

2009/2/4 hadley wickham <h.wickham at gmail.com>:

Hi Jon,

I have an in-development package that attempts to do this.  It's
called eval.with.details and is available from
http://github.com/hadley/eval.with.details.  As you might

guess, it's

a version of eval that captures all details like messages, warnings,
errors and output so you can do whatever you want with them.  It
captures them in the way Jeff Horner describes - but there are a lot
of fiddly details to get right.

Unfortunately there isn't any documentation yet, but the majority of
what you're interested in is present in eval.r.  The code has been
fairly well tested - I'm using it in my own implementation

of a sweave

like system.

Hadley

On Wed, Feb 4, 2009 at 6:59 AM, Jon Clayden

<j.clayden at ucl.ac.uk> wrote:

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.

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/

-- 
http://had.co.nz/