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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