R devel - Jun 2009 - validObject throws non-caught error when slot doesn't exist

I have been retooling an S4 class definition to include another slot and 
have found that the methods::validObject function (defined in 
methods/R/SClasses.R) in R-devel throws an error that isn't caught 
internally (and thus not controllable by 'test' argument) when 
retrieving a non-existent slot. The offending line of code is shown below:

 > validObject
function (object, test = FALSE, complete = FALSE)
{
...
    for (i in seq_along(slotTypes)) {
        classi <- slotTypes[[i]]
        sloti <- slot(object, slotNames[[i]]) # offending line of code

One potential patch is to substitute the offending line with

        sloti <- try(slot(object, slotNames[[i]]), silent = TRUE)
        if (class(sloti) == "try-error") {
            errors <- c(errors, paste("missing slot \"",
slotNames[[i]],
                "\"", sep = ""))
            next
        }

Here is a reproduce and an example using vaildObject2 that substitutes 
the offending line with the code given above:

 > setClass("Foo", representation(bar = "character"))
[1] "Foo"
 > a <- new("Foo", bar = letters)
 > setClass("Foo", representation(bar = "character", star
= "numeric"))
[1] "Foo"
 > validObject(a, test = TRUE)
Error in slot(object, slotNames[[i]]) :
  no slot of name "star" for this object of class "Foo"
 > validObject2(a, test = TRUE)
[1] "missing slot \"star\""
 > sessionInfo()
R version 2.10.0 Under development (unstable) (2009-06-12 r48755)
i386-apple-darwin9.6.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     



Patrick

Patrick,

Thanks for the bug report and the proposed patch.

There are some related ways that validObject can fail (e.g., if the 
revised class definition extends one of the object types or if the 
object is an S3 object), so the patch needs to be a little more general, 
but I will commit something to the 2.10 development version and send mail).

John

Patrick Aboyoun wrote:
> I have been retooling an S4 class definition to include another slot 
> and have found that the methods::validObject function (defined in 
> methods/R/SClasses.R) in R-devel throws an error that isn't caught 
> internally (and thus not controllable by 'test' argument) when 
> retrieving a non-existent slot. The offending line of code is shown 
> below:
>
> > validObject
> function (object, test = FALSE, complete = FALSE)
> {
> ...
>    for (i in seq_along(slotTypes)) {
>        classi <- slotTypes[[i]]
>        sloti <- slot(object, slotNames[[i]]) # offending line of code
>
> One potential patch is to substitute the offending line with
>
>        sloti <- try(slot(object, slotNames[[i]]), silent = TRUE)
>        if (class(sloti) == "try-error") {
>            errors <- c(errors, paste("missing slot \"",
slotNames[[i]],
>                "\"", sep = ""))
>            next
>        }
>
> Here is a reproduce and an example using vaildObject2 that substitutes 
> the offending line with the code given above:
>
> > setClass("Foo", representation(bar = "character"))
> [1] "Foo"
> > a <- new("Foo", bar = letters)
> > setClass("Foo", representation(bar = "character",
star = "numeric"))
> [1] "Foo"
> > validObject(a, test = TRUE)
> Error in slot(object, slotNames[[i]]) :
>  no slot of name "star" for this object of class "Foo"
> > validObject2(a, test = TRUE)
> [1] "missing slot \"star\""
> > sessionInfo()
> R version 2.10.0 Under development (unstable) (2009-06-12 r48755)
> i386-apple-darwin9.6.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base    
>
>
> Patrick
>
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