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Jon Clayden

2009-Feb-04 12:59 UTC

[Rd] Capturing all warnings (with messages)

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/

Jeffrey Horner

2009-Feb-04 16:52 UTC

head link

[Rd] Capturing all warnings (with messages)

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

hadley wickham

2009-Feb-04 22:28 UTC

head link

[Rd] Capturing all warnings (with messages)

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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