> -----Original Message-----
> From: l...@stat.uiowa.edu [mailto:l...@stat.uiowa.edu]
> Sent: Thursday, April 16, 2009 9:27 AM
> To: William Dunlap
> Cc: Dirk Eddelbuettel; Kieran O'Neill; r-devel@r-project.org
> Subject: Re: [Rd] How can I catch errors thrown from c via
> the Rcpperror() function?
>
> 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
It is in match.c, where errorcall() calls deparse1line(unused,0)
to get the name (and value) of the argument:
357 if(last != R_NilValue) {
358 errorcall(R_GlobalContext->call,
359 _("unused argument(s) %s"),
360 CHAR(STRING_ELT(deparse1line(unused, 0),
0)) + 4);
Before deparse1line is called unused is (in my example)
(gdb) call Rf_PrintValue(unused)
$badTag
<promise: 0x9aff4d4>
and deparse1line must be evaluating the promise. Just showing the
bad tag's name would suffice in the error message, if it is a problem
jury rigging deparse1line to avoid the evaluation in this case.
>
> 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.
> >>
> >> ______________________________________________
> >> R-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
> >
> > ______________________________________________
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
> --
> 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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