A possible fix for this is to filter the 'unsused' list before
printing the error message and replacing the promises with
their PRCODE expressions.
Index: match.c
===================================================================
--- match.c (revision 48329)
+++ match.c (working copy)
@@ -355,9 +355,28 @@
}
if(last != R_NilValue) {
+ /* show bad arguments in call without evaluating them */
+ SEXP unusedForError = R_NilValue, last = R_NilValue ;
+ for(b=unused ; b!=R_NilValue ; b=CDR(b)) {
+ SEXP tagB = TAG(b) ;
+ SEXP carB = CAR(b) ;
+ if (TYPEOF(carB)==PROMSXP) {
+ carB = PRCODE(carB) ;
+ }
+ if (last==R_NilValue) {
+ PROTECT(last = CONS(carB, R_NilValue));
+ SET_TAG(last, tagB);
+ unusedForError = last ;
+ } else {
+ SETCDR(last, CONS(carB, R_NilValue));
+ last = CDR(last) ;
+ SET_TAG(last, tagB);
+ }
+ }
errorcall(R_GlobalContext->call,
_("unused argument(s) %s"),
- CHAR(STRING_ELT(deparse1line(unused, 0), 0)) + 4);
+ CHAR(STRING_ELT(deparse1line(unusedForError, 0),
0)) + 4);
+ /* '+4' is to remove 'list' from
'list(badTag1,...)' */
}
}
UNPROTECT(1);
E.g.,
> f<-function(x,y)x+y
> f(print(1),y=print(2),x=print(3),stop("oops"))
Error in f(print(1), y = print(2), x = print(3), stop("oops")) :
unused argument(s) (print(1), stop("oops"))
> f(print(1),y=print(2),x=print(3),z=stop("oops"))
Error in f(print(1), y = print(2), x = print(3), z = stop("oops")) :
unused argument(s) (print(1), z = stop("oops"))
> f(print(1),y=print(2),z=print(3),x=stop("oops"))
Error in f(print(1), y = print(2), z = print(3), x = stop("oops")) :
unused argument(s) (print(1), z = print(3))
These calls used to give:
> f(print(1),y=print(2),x=print(3),stop("oops"))
[1] 1
Error in f(print(1), y = print(2), x = print(3), stop("oops")) : oops
> f(print(1),y=print(2),x=print(3),z=stop("oops"))
[1] 1
Error in f(print(1), y = print(2), x = print(3), z = stop("oops")) :
oops
> f(print(1),y=print(2),z=print(3),x=stop("oops"))
[1] 1
[1] 3
Error in f(print(1), y = print(2), z = print(3), x = stop("oops")) :
unused argument(s) (1, z = 3)
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 William Dunlap
> Sent: Thursday, April 16, 2009 10:05 AM
> To: l...@stat.uiowa.edu
> Cc: r-devel@r-project.org; Dirk Eddelbuettel
> Subject: Re: [Rd] How can I catch errors thrown from c via
> the Rcpperror()function?
>
> > -----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
> >
>
> ______________________________________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
Property changes on: .
___________________________________________________________________
Name: svn:ignore
+ *.d
Index: match.c
===================================================================
--- match.c (revision 48329)
+++ match.c (working copy)
@@ -355,9 +355,28 @@
}
if(last != R_NilValue) {
+ /* show bad arguments in call without evaluating them */
+ SEXP unusedForError = R_NilValue, last = R_NilValue ;
+ for(b=unused ; b!=R_NilValue ; b=CDR(b)) {
+ SEXP tagB = TAG(b) ;
+ SEXP carB = CAR(b) ;
+ if (TYPEOF(carB)==PROMSXP) {
+ carB = PRCODE(carB) ;
+ }
+ if (last==R_NilValue) {
+ PROTECT(last = CONS(carB, R_NilValue));
+ SET_TAG(last, tagB);
+ unusedForError = last ;
+ } else {
+ SETCDR(last, CONS(carB, R_NilValue));
+ last = CDR(last) ;
+ SET_TAG(last, tagB);
+ }
+ }
errorcall(R_GlobalContext->call,
_("unused argument(s) %s"),
- CHAR(STRING_ELT(deparse1line(unused, 0), 0)) + 4);
+ CHAR(STRING_ELT(deparse1line(unusedForError, 0), 0)) + 4);
+ /* '+4' is to remove 'list' from 'list(badTag1,...)' */
}
}
UNPROTECT(1);
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
