From mario.annau at gmail.com  Mon Feb  9 23:28:03 2015
From: mario.annau at gmail.com (Mario Annau)
Date: Mon, 09 Feb 2015 23:28:03 +0100
Subject: [Rd] Proper way to define cbind, rbind for s4 classes in package
In-Reply-To: <21711.24672.449563.817210@stat.math.ethz.ch>
References: <54C35EB5.3060402@gmail.com>	<CAOQ5NyeRprfmr+RyUxnoz3JCy9jsz+hasWZN0A=KBrRbdkykRw@mail.gmail.com>	<21702.11046.319866.816795@stat.math.ethz.ch>	<CAOQ5Nye8A7gkmrP_VROs6h59zo8Ts20_RpLMf0F=aPCxUhKX4w@mail.gmail.com>
	<21711.24672.449563.817210@stat.math.ethz.ch>
Message-ID: <54D93473.2040609@gmail.com>

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
>     >> 
>



[Rd] Proper way to define cbind, rbind for s4 classes in package
Mario Annau