R devel - Feb 2015 - Proper way to define cbind, rbind for s4 classes in package

>>>>> 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
    >>

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
>     >> 
>

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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