Something seems amiss in the process of generating the errormessage:
f <- function(x){}
f(y = print("foo"))
[1] "foo"
Error in f(y = print("foo")) : unused argument(s) (y = "foo")
The argument seems to be getting evaluated and its value is being used.
luke
On Thu, 16 Apr 2009, William Dunlap wrote:
Note that Kieren's example labelled the first
argument to try() with an improper label res30=,
not expr= (or is that a mailer turning something
into '30='?). If it really is an improper argument
tag then this could be showing a buglet in reporting
on wrongly named arguments:
> invisible(rm(x,y))
> x<-try(silent=TRUE, badTag=stop("Oops"))
Error in try(silent = TRUE, badTag = stop("Oops")) : Oops
> x
Error: object "x" not found
> y<-try(silent=TRUE, expr=stop("Oops"))
> y
[1] "Error in try(silent = TRUE, expr = stop(\"Oops\")) : Oops\n"
attr(,"class")
[1] "try-error"
In the first example I would expect an error message like
unused argument(s) (badTag = stop("Oops"))
but it is appropriate that try() would abort if it
is called in a bad way. Perhaps it is trying to make that
error message and that triggered the evaluation of the argument,
as in
> grep(mypattern=stop("Oops"), "wxyz")
Error in grep(mypattern = stop("Oops"), "wxyz") : Oops
where one might expect an error message regarding the wrongly
named argument, as in:
> grep(mypattern="x", "wxyz")
Error in grep(mypattern = "x", "wxyz") :
unused argument(s) (mypattern = "x")
Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
-----Original Message-----
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Dirk Eddelbuettel
Sent: Wednesday, April 15, 2009 7:14 PM
To: Kieran O'Neill
Cc: r-devel@r-project.org
Subject: Re: [Rd] How can I catch errors thrown from c via
the Rcpperror() function?
Kieran,
On 15 April 2009 at 18:03, Kieran O'Neill wrote:
| I am using the flowClust package from BioConductor, which
is largely
| implemented in c. For some of my data, the package
occasionally (and
| quite stochastically) encounters a particular condition
which halts its
| operation. At this point, it calls the error() function
defined by Rcpp,
| and halts.
|
| What I would like to be able to do is to catch the error
thrown, and
| retry the operation a few times before giving up.
|
| However, when I wrap the call to flowClust in try() or
tryCatch(), the
| error seems to completely bypass them:
|
| Examples:
|
| 1. This is a trivial example just to test the try() function, and
| correctly assigns the error to the variable x:
|
| > x <- try(stop(simpleError('blah')))
| Error : blah
| > x
| [1] "Error : blah\n"
| attr(,"class")
| [1] "try-error"
|
| 2. This is an example using flowClust (using real data, set up to
| guarantee that the error is thrown):
|
| > x <- try(res30 = flowClust(tFrame, K=30, B=1000,
varNames=c('CD4',
| 'CD8','KI67', 'CD45RO', 'CD28', 'CD57', 'CCR5', 'CD19',
'CD27', 'CCR7',
| 'CD127')))
| Error in flowClust(tFrame, K = 30, B = 1000, varNames =
c("CD4", "CD8", :
|
| The covariance matrix is near singular!
| Try running the program with a different initial
configuration or less
| clusters
| > x
| Error: object "x" not found
|
|
| The c code throwing the error is as follows (from flowClust.c):
|
| if(status!=0)
| {
| error("\n The covariance matrix is near singular! \n
Try running
| the program with a different initial configuration or less clusters
| \n"); }
|
|
| I looked up the error() function in Writing R Extensions
and it states:
| "The basic error handling routines are the equivalents of stop and
| warning in R code, and use the same interface."
|
| Yet, it seems that they are not caught by R's error handling code.
|
| So:
|
| 1. Is this the general case (that Rcpp error()s are not
handled by try()
| and related methods in R)? (I'm sure this could be tested
with a trivial
| example, but I'm not yet familiar enough with wrapping c
code in R to do
| so.)
Allow me to take the narrow view here as Rcpp maintainer.
What you can do
with Rcpp is to provide a C++ layer of try/catch around inner
code which may
throw C++ exception. This will usually be caught, and (as
shown in the Rcpp
docs and examples) we can pass the exception message back up to R as a
regular error message. This is very useful as it gives you
control back at
the R prompt rather than just going belly-up.
Now, R's try() and tryCatch() are completely separate and not
tied into the
exception mechanism Rcpp deals with, which is at a much lower level.
Likewise, you may be out of luck with flowClust if it is C
program. You
could try to add a C++ layer that tried to catch error and
allows you do
continue your loops. I did something like that 15 years ago in my
dissertation research to ensure I survived the occassional
numerical error
from Fortran during longer Monte Carlo runs,
| 2. If so, what is the correct way to handle them in R?
Tricky. See 1. :)
| 3. If not, do you have any suggestions as to what may have caused
| flowClust to behave in this way? (So that I can contact the package
| maintainers and report the bug.)
You could always contact them anyway and ask for advice.
Hth, Dirk
--
Three out of two people have difficulties with fractions.
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--
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics and Fax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: l...@stat.uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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