From |@wrence@m|ch@e| @end|ng |rom gene@com  Wed Nov 27 12:57:39 2019
From: |@wrence@m|ch@e| @end|ng |rom gene@com (Michael Lawrence)
Date: Wed, 27 Nov 2019 03:57:39 -0800
Subject: [Rd] Troubles using numeric in s4 class union
In-Reply-To: <24030.25488.546854.295498@stat.math.ethz.ch>
References: <CAP0QTepYgET5x+5aAZGwXKCZ+fs8bhHH5aswL1s3oebv6feU9A@mail.gmail.com>
 <24030.25488.546854.295498@stat.math.ethz.ch>
Message-ID: <CAOQ5Nyf47MMXRtfr3Kgt6O35TfHCR0eqJ+42Y+YMguUG-uaB5A@mail.gmail.com>

I've been working on this and will hopefully get a fix checked in today.

On Wed, Nov 27, 2019 at 3:53 AM Martin Maechler
<maechler at stat.math.ethz.ch> wrote:
>
> >>>>> Ezra Tucker
> >>>>>     on Mon, 11 Nov 2019 21:47:41 +0000 writes:
>
> > Hi all,
> >
> > I came across an issue in using the Matrix package which made it that I
> > could only subset Matrices using the numeric class, but could not using
> > integers. Steps to reproduce the problem:
> >
> > library(Matrix)
> >
> > # this class has *nothing* to do with Matrix
> > setClass("MyClass",
> >     representation(myvalue = "numeric"),
> >     prototype(myvalue = NA_real_))
> > # this class also has nothing to do with Matrix
> > setClassUnion("NumOrMyClass", c("numeric", "MyClass"))
> >
> > # this is to demonstrate creating and subsetting a specific Matrix
> > m <- new("dgCMatrix", i = c(2L, 0L, 1L, 2L, 0L, 1L), p = c(0L, 1L, 2L, 4L,
> > 4L, 6L),
> >     Dim = c(3L, 5L), Dimnames = list(NULL, NULL), x = c(2, 1, 2, 1, 2, 1),
> > factors = list())
> > # this next line fails:
> > m[1:2, 1:2]
> >
> > The last line fails consistently with R 3.6.1 and Matrix 1.2-17 on a
> > variety of operating systems and computers (tested with ubuntu 19.10 &
> > windows 10). I'll note at this point that without the class union I defined
> > above, the rest of the code works perfectly fine.
> >
> > There are 2 workarounds I've come up with. Firstly, one could change the
> > last line to
> > m[as.numeric(1:2), as.numeric(1:2)]
> > or as.numeric(seq()) or c(1, 2), etc.
> >
> > The other workaround is to change setClassUnion("NumOrMyClass",
> > c("numeric", "MyClass")) to setClassUnion("NumOrMyClass", c("numeric",
> > "double", "integer", "MyClass")), which I believe should be the recommended
> > workaround here.
> >
> > The underlying issue, though, is that I would not have expected *anything*
> > that I write to get in the way of Matrix; in fact, the classes that I
> > defined have nothing to do with Matrix at all. So, I have some fears that
> > this might be a bigger problem, possibly either in Methods or in Base.
> >
> > 1. Can others confirm that this is in fact an issue as I believe it to be?
>
> yes, others have confirmed this is an issue .. (unfortunately
> not in this R-devel thread).
>
> Thank you, Ezra, very much for your helpful report, including a
> simple reproducible example.
>
> > 2. If it is a legitimate issue, have others seen it manifested working with
> > other packages that are not Matrix? In this case, I believe that the class
> > union I defied is somehow interfering with the "index" class union in
> > Matrix, R/AllClass.R, line 809
>
> > 3. Why should the class union I defined interfere with the inner workings
> > of a separate package?
>
> There is no good reason ...
>
> > 4. Is this a bug in Base or Methods?
>
> This is a bug in "base R", in package 'methods'.
>
> The R core team had taken the issue up, already two weeks ago,
> but unfortunately did not get to address this in a definitive
> way.  ==>  I'll remind us about it !
>
> Martin Maechler
> ETH Zurich and R Core
>
>
> > Thank you for your time!
> >
> > Sincerely,
> > Ezra
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



-- 
Michael Lawrence
Senior Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
michafla at gene.com

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[Rd] Troubles using numeric in s4 class union
Michael Lawrence