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.an...@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.an...@gmail.com > >> <mailto:mario.an...@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.mich...@gene.com > >> <mailto:lawrence.mich...@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 < > >> > > maech...@lynne.stat.math.ethz.ch > >> <mailto:maech...@lynne.stat.math.ethz.ch>> wrote: > >> > > >> > >> >>>>> Michael Lawrence <lawrence.mich...@gene.com > >> <mailto:lawrence.mich...@gene.com>> >>>>> > >> > >> on Sat, 24 Jan 2015 06:39:37 -0800 writes: > >> > >> > >> > >> > On Sat, Jan 24, 2015 at 12:58 AM, Mario Annau > > >> > >> <mario.an...@gmail.com <mailto:mario.an...@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@r-project.org <mailto:R-devel@r-project.org> > >> mailing list >> > >> > >> https://stat.ethz.ch/mailman/listinfo/r-devel > >> > >> > >> > >> > ______________________________________________ > > >> > >> R-devel@r-project.org <mailto:R-devel@r-project.org> > >> mailing list > > >> > >> https://stat.ethz.ch/mailman/listinfo/r-devel > >> > >> > >> > > >> > >> > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
