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

From: hadley wickham <h.wickham_at_gmail.com>
Date: Wed, 04 Feb 2009 16:28:29 -0600

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

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

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Received on Wed 04 Feb 2009 - 22:32:43 GMT

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