From lawrence.michael at gene.com  Tue Jun  6 20:48:36 2017
From: lawrence.michael at gene.com (Michael Lawrence)
Date: Tue, 6 Jun 2017 11:48:36 -0700
Subject: [Rd] surprisingly,
 S4 classes with a "dim" or "dimnames" slot are final (in the Java
 sense)
In-Reply-To: <CAOQ5NyfV+Ga2_e2gg2VCdoAR6zFsS2GZYLM3V1m9gb4J10XwUQ@mail.gmail.com>
References: <59360088.2060800@fredhutch.org>
 <CAOQ5NyfV+Ga2_e2gg2VCdoAR6zFsS2GZYLM3V1m9gb4J10XwUQ@mail.gmail.com>
Message-ID: <CAOQ5NycTo42rLtRyh_Xpu78exP7eLnKt2_eDuKWrG5OrQGpiiQ@mail.gmail.com>

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> 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, Herv? Pag?s <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.
>>
>> --
>> Herv? Pag?s
>>
>> 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
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
>

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