From lawrence.michael at gene.com  Mon Feb  9 23:38:29 2015
From: lawrence.michael at gene.com (Michael Lawrence)
Date: Mon, 9 Feb 2015 14:38:29 -0800
Subject: [Rd] Proper way to define cbind, rbind for s4 classes in package
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Are you able to create a reproducible example, somehow?

Thanks,
Michael

On Mon, Feb 9, 2015 at 2:28 PM, Mario Annau <mario.annau at gmail.com> wrote:

> Hi Michael,
> I've tested your change in r67699 (using r67773) and the function now
> correctly dispatches to r/cbind2 within the R-session without
> bind_activation(TRUE). However, running unit tests using R CMD check I
> figured out that the same function call delegates to r/cbind.matrix
> (function uses S4 class as first- and matrix as second argument). Is
> this a bug and/or how can I get function dispatch right (to r/cbind2)
> for my test cases?
> best,
> mario
>
>
> Am 02/02/15 um 12:32 schrieb Martin Maechler:
> >>>>>> Michael Lawrence <lawrence.michael at gene.com>
> >>>>>>     on Sun, 1 Feb 2015 19:23:06 -0800 writes:
> >
> >     > I've implemented the proposed changes in
> >     > R-devel. Minimally tested, so please try it. It should
> >     > delegate to r/cbind2 when there is at least one S4
> >     > argument and S3 dispatch fails (so you'll probably want to
> >     > add an S3 method for your class to introduce a conflict,
> >     > otherwise it will dispatch to cbind.data.frame if one of
> >     > the args is a data.frame). There may no longer be a need
> >     > for cBind() and rBind().
> >
> >     > Michael
> >
> > This sounds great!   Thank you very much, Michael!
> > :-) :-)
> >
> > ... but .... :-(  experiments with the Matrix package (and R
> > devel with your change), show a remaining buglet with treating of
> dimnames :
> >
> >    > M1 <- Matrix(m1 <- matrix(1:12, 3,4))
> >    > cbind(m1, MM = -1)
> >                MM
> >    [1,] 1 4 7 10 -1
> >    [2,] 2 5 8 11 -1
> >    [3,] 3 6 9 12 -1
> >    > cbind(M1, MM = -1)   ## ---- notice the "..."
> >    3 x 5 Matrix of class "dgeMatrix"
> >                ...
> >    [1,] 1 4 7 10  -1
> >    [2,] 2 5 8 11  -1
> >    [3,] 3 6 9 12  -1
> >    > rbind(R1 = 10:11, m1)
> >       [,1] [,2] [,3] [,4]
> >    R1   10   11   10   11
> >        1    4    7   10
> >        2    5    8   11
> >        3    6    9   12
> >    > rbind(R1 = 10:11, M1) ## --- notice the 'deparse.level'
> >    4 x 4 Matrix of class "dgeMatrix"
> >                [,1] [,2] [,3] [,4]
> >    deparse.level   10   11   10   11
> >                   1    4    7   10
> >                   2    5    8   11
> >                   3    6    9   12
> >    >
> >
> > Also, it seems you are not observing the 'deparse.level'
> > argument at all:
> > Looking at the last three lines of the example in  ?cbind,
> >
> >      rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 0) # middle 2
> rownames
> >      rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rownames
> (default)
> >      rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 2) # 4 rownames
> >
> > but using a Matrix matrix 'dd', we see that (row)names
> > construction needs to amended:
> >
> >   > (dd <- Matrix(rbind(c(0:1,0,0))))
> >   1 x 4 sparse Matrix of class "dgCMatrix"
> >
> >   [1,] . 1 . .
> >
> >   > rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 0) # middle 2
> rownames
> >   4 x 4 sparse Matrix of class "dgCMatrix"
> >
> >   deparse.level  1  2  3  4
> >   c              2  2  2  2
> >   a++           10 10 10 10
> >                .  1  .  .
> >   > rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rownames
> (default)
> >   4 x 4 sparse Matrix of class "dgCMatrix"
> >
> >   deparse.level  1  2  3  4
> >   c              2  2  2  2
> >   a++           10 10 10 10
> >                .  1  .  .
> >   > rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 2) # 4 rownames
> >   4 x 4 sparse Matrix of class "dgCMatrix"
> >
> >   deparse.level  1  2  3  4
> >   c              2  2  2  2
> >   a++           10 10 10 10
> >                .  1  .  .
> >   >
> >
> >
> >
> >     > On Mon, Jan 26, 2015 at 3:55 AM, Martin Maechler <
> >     > maechler at lynne.stat.math.ethz.ch> wrote:
> >
> >     >> >>>>> Michael Lawrence <lawrence.michael at gene.com> >>>>>
> >     >> on Sat, 24 Jan 2015 06:39:37 -0800 writes:
> >     >>
> >     >> > On Sat, Jan 24, 2015 at 12:58 AM, Mario Annau >
> >     >> <mario.annau at gmail.com> wrote: >> Hi all, this question
> >     >> has already been posted on >> stackoverflow, however
> >     >> without success, see also
> >     >> >>
> >     >>
> http://stackoverflow.com/questions/27886535/proper-way-to-use-cbind-rbind-with-s4-classes-in-package
> >     >> .
> >     >> >>
> >     >> >> I have written a package using S4 classes and would
> >     >> like >> to use the functions rbind, cbind with these
> >     >> defined >> classes.
> >     >> >>
> >     >> >> Since it does not seem to be possible to define rbind
> >     >> and >> cbind directly as S4 methods (see ?cBind) I
> >     >> defined >> rbind2 and cbind2 instead:
> >     >> >>
> >     >>
> >     >> > This needs some clarification. It certainly is possible
> >     >> to > define cbind and rbind methods. The BiocGenerics
> >     >> package > defines generics for those and many methods are
> >     >> defined by > e.g. S4Vectors, IRanges, etc.  The issue is
> >     >> that dispatch > on "..." is singular, i.e., you can only
> >     >> specify one class > that all args in "..." must share
> >     >> (potentially through > inheritance).
> >     >>
> >     >> > Thus, trying to combine objects from a > different
> >     >> hierarchy (or non-S4 objects) will not > work.
> >     >>
> >     >> Yes, indeed, that's the drawback
> >     >>
> >     >> I've been there almost surely before everyone else, with
> >     >> the Matrix package...  and I have been the author of
> >     >> cbind2(), rbind2(), and of course, of cBind(), and
> >     >> rBind().
> >     >>
> >     >> At the time when I introduced these, the above
> >     >> possibility of writing S4 methods for '...'  where not
> >     >> yet part of R.
> >     >>
> >     >> > This has not been a huge problem for us in >
> >     >> practice. For example, we have a DataFrame object that >
> >     >> mimics data.frame. To cbind a data.frame with a
> >     >> DataFrame, > the user can just call the DataFrame() >
> >     >> constructor. rbind() between different data structures is
> >     >> > much less common.
> >     >>
> >     >> well... yes and no.  Think of using the Matrix package,
> >     >> maybe with another package that defines another
> >     >> generalized matrix class...  It would be nice if things
> >     >> worked automatically / perfectly there.
> >     >>
> >     >> > The cBind and rBind functions in Matrix (and the
> >     >> r/cbind > that get installed by bind_activation, the code
> >     >> is shared) > work by recursing, dropping the first
> >     >> argument until two > are left, and then combining with
> >     >> r/cbind2(). The Biobase > package uses a similar strategy
> >     >> to mimic c() via its > non-standard combine()
> >     >> generic. The nice thing about the > combine() approach is
> >     >> the user entry point and the generic > are the same,
> >     >> instead of having methods on rbind2() and > the user
> >     >> calling rBind().
> >     >>
> >     >> > I would argue that bind_activation(TRUE) should be >
> >     >> discouraged,
> >     >>
> >     >> Yes, you are right Michael; it should be discouraged at
> >     >> least to be run in a *package*.  One could think of its
> >     >> use by an explicit user call.
> >     >>
> >     >> > because it replaces the native rbind and > cbind with
> >     >> recursive variants that are going to cause > problems,
> >     >> performance and otherwise. This is why it is >
> >     >> hidden. Perhaps a reasonable compromise would be for the
> >     >> > native cbind and rbind to check whether any arguments
> >     >> are > S4 and if so, resort to recursion. Recursion does
> >     >> seem to > be a clean way to implement "type promotion",
> >     >> i.e., to > answer the question "which type should the
> >     >> result be when > faced with mixed-type args?".
> >     >>
> >     >> Exactly.  That has been my idea at the time ..  ((yes,
> >     >> I'm also the author of the bind_activation()
> >     >> "(mis)functionality".))
> >     >>
> >     >> > Hopefully others have better ideas.
> >     >>
> >     >> that would be great.
> >     >>
> >     >> And even if not, it would be great if we could implement
> >     >> your idea > Perhaps a reasonable compromise would be for
> >     >> the > native cbind and rbind to check whether any
> >     >> arguments are > S4 and if so, resort to recursion.
> >     >>
> >     >> without a noticable performance penalty in the case of no
> >     >> S4 arguments.
> >     >>
> >     >> Martin
> >     >>
> >     >>
> >     >> > Michael
> >     >>
> >     >> >> setMethod("rbind2", signature(x="ClassA", y = "ANY"),
> >     >> >> function(x, y) { # Do stuff ...  })
> >     >> >>
> >     >> >> setMethod("cbind2", signature(x="ClassA", y = "ANY"),
> >     >> >> function(x, y) { # Do stuff ...  })
> >     >> >>
> >     >> >> >From ?cbind2 I learned that these functions need to
> >     >> be >> activated using methods:::bind_activation to
> >     >> replace >> rbind and cbind from base.
> >     >> >>
> >     >> >> I included the call in the package file R/zzz.R using
> >     >> the >> .onLoad function:
> >     >> >>
> >     >> >> .onLoad <- function(...) { # Bind activation of
> >     >> cbind(2) >> and rbind(2) for S4 classes >>
> >     >> methods:::bind_activation(TRUE) } This works as >>
> >     >> expected. However, running R CMD check I am now getting
> >     >> >> the following NOTE since I am using an unexported >>
> >     >> function in methods:
> >     >> >>
> >     >> >> * checking dependencies in R code ... NOTE Unexported
> >     >> >> object imported by a ':::' call: >>
> >     >> 'methods:::bind_activation' See the note in ?`:::` about
> >     >> >> the use of this operator.  How can I get rid of the
> >     >> NOTE >> and what is the proper way to define the methods
> >     >> cbind >> and rbind for S4 classes in a package?
> >     >> >>
> >     >> >> Best, mario
> >     >> >>
> >     >> >> ______________________________________________ >>
> >     >> R-devel at r-project.org mailing list >>
> >     >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >     >>
> >     >> > ______________________________________________ >
> >     >> R-devel at r-project.org mailing list >
> >     >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >     >>
> >
>

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[Rd] Proper way to define cbind, rbind for s4 classes in package
Michael Lawrence