[Rd] Proper way to define cbind, rbind for s4 classes in package
Mario Annau
mario.annau at gmail.com
Sat Feb 21 08:56:59 CET 2015
Thank you very much for your effort! I can confirm that *bind S4 method
dispatching now works for my use cases as expected (tested using r67856).
Cheers,
mario
Am 20/02/15 um 12:40 schrieb Martin Maechler:
>>>>>> Mario Annau <mario.annau at gmail.com>
>>>>>> on Wed, 11 Feb 2015 20:18:53 +0100 writes:
>
> > sorry - I just got irritated by my different R-versions.
> > The behaviour I described in the previous mail was discovered using R
> > 3.1.2 without bind_activation(TRUE). In r67773 all calls are delegated
> > to r/cbind.matrix and not r/cbind2.
> > As a workaround I have now implemented an S3 method for my S4 class
> > which correctly dispatches for both versions (3.1.2 and r67699+) - see
> > also the commit for the h5 package on github:
> > https://github.com/mannau/h5/commit/20daea37ade1a317458c8a1d03928f579e457f93.
> > Any better ideas are welcome.
>
> and in the mean time there have been a few off-list e-mails,
>
> {"No, using an S3 method was definitely not the idea of
> Michael's changes!" .. }
>
> and many hours of work by me.
> R-devel svn rev 67852 and later now has cbind() / rbind()
> working in a better way, dipatching to either cbind2(), rbind2()
> S4 methods for "your" classes, or to S4 rbind() or cbind()
> methods for your classes.
>
> Notably the new code now should create column / rownames
> analogously to base::cbind / rbind, influenced by deparse.level
> in the case of non-matrix arguments.
>
> Small changes in some outputs may occur, notably as the hidden
> methods:::cbind and rbind functions (think of "S4 default method")
> now do obey deparse.level and also otherwise should create row
> and column names in the same way as base::[cr]bind().
>
> Martin Maechler
> ETH Zurich and R Core Team
>
> > br,
> > mario
>
>
> > Am 09/02/15 um 23:38 schrieb Michael Lawrence:
> >> 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
> >> <mailto: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
> >> <mailto: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
> >> <mailto:maechler at lynne.stat.math.ethz.ch>> wrote:
> >> >
> >> > >> >>>>> Michael Lawrence <lawrence.michael at gene.com
> >> <mailto: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 <mailto: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 <mailto:R-devel at r-project.org>
> >> mailing list >>
> >> > >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >> > >>
> >> > >> > ______________________________________________ >
> >> > >> R-devel at r-project.org <mailto:R-devel at r-project.org>
> >> mailing list >
> >> > >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >> > >>
> >> >
> >>
> >>
>
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