[Rd] surprisingly, S4 classes with a "dim" or "dimnames" slot are final (in the Java sense)

[Hervé Pagès]

Thanks Michael for taking care of this.  H.

On 06/06/2017 11:48 AM, Michael Lawrence wrote:
> I've fixed this and will commit soon.
>
> Disregard my dim<-() example; that behaves as expected (the class needs
> a dim<-() method).
>
> Michael
>
> On Tue, Jun 6, 2017 at 5:16 AM, Michael Lawrence <michafla at gene.com
> <mailto:michafla at gene.com>> wrote:
>
>     Thanks for the report. The issue is that one cannot set special
>     attributes like names, dim, dimnames, etc on S4 objects. I was
>     aready working on this and will have a fix soon.
>
>      > a2 <- new("A2")
>      > dim(a2) <- c(2, 3)
>     Error in dim(a2) <- c(2, 3) : invalid first argument
>
>
>     On Mon, Jun 5, 2017 at 6:08 PM, Hervé Pagès <hpages at fredhutch.org
>     <mailto:hpages at fredhutch.org>> wrote:
>
>         Hi,
>
>         It's nice to be able to define S4 classes with slots that correspond
>         to standard attributes:
>
>            setClass("A1", slots=c(names="character"))
>            setClass("A2", slots=c(dim="integer"))
>            setClass("A3", slots=c(dimnames="list"))
>
>         By doing this, one gets a few methods for free:
>
>            a1 <- new("A1", names=letters[1:3])
>            names(a1)     # "a" "b" "c"
>            a2 <- new("A2", dim=4:3)
>            nrow(a2)      # 4
>            a3 <- new("A3", dimnames=list(NULL, letters[1:3]))
>            colnames(a3)  # "a" "b" "c"
>
>         However, when it comes to subclassing, some of these slots cause
>         problems. I can extend A1:
>
>            setClass("B1", contains="A1")
>
>         but trying to extend A2 or A3 produces an error (with a
>         non-informative
>         message in the 1st case and a somewhat obscure one in the 2nd):
>
>            setClass("B2", contains="A2")
>            # Error in attr(prototype, slotName) <- attr(pri, slotName) :
>            #   invalid first argument
>
>            setClass("B3", contains="A3")
>            # Error in attr(prototype, slotName) <- attr(pri, slotName) :
>            #   'dimnames' applied to non-array
>
>         So it seems that the presence of a "dim" or "dimnames" slot
>         prevents a
>         class from being extended. Is this expected? I couldn't find
>         anything
>         in TFM about this. Sorry if I missed it.
>
>         Thanks,
>         H.
>
>         --
>         Hervé Pagès
>
>         Program in Computational Biology
>         Division of Public Health Sciences
>         Fred Hutchinson Cancer Research Center
>         1100 Fairview Ave. N, M1-B514
>         P.O. Box 19024
>         Seattle, WA 98109-1024
>
>         E-mail: hpages at fredhutch.org <mailto:hpages at fredhutch.org>
>         Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>         Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>
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>
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319