[Rd] bug with mapply() on an S4 object
Hervé Pagès
hpages at fhcrc.org
Wed Nov 28 19:00:02 CET 2012
Hi Martin, Malcolm,
Thanks Martin for applying the fix.
On 11/28/2012 05:47 AM, Cook, Malcolm wrote:
> Yes, yes, excellent and great , I am tracking this development with great interest.
>
> Am I correct that the implications for BioConductor is the tearing out of the Xapply from generics and the expecations that List and descendents would now "just work" with {t,mc,mcl,...}apply? That would be a grand outcome.
Yes it's nice to have more things work out-of-the-box on
list-like or vector-like S4 objects. It makes implementation of
new List or Vector concrete subclasses easier and the overall code
for the 100+ subclasses currently defined in Bioconductor simpler,
cleaner, and easier to maintain (less code duplication).
In the particular case of base::mapply(), it's true that, with this
fix, we don't need to explicitly turn mapply() into a generic anymore
(in BiocGenerics), at least in theory, because now it works on objects
with length and [[ methods. However, we might want to keep the generic
in BiocGenerics anyway, because a BioC developer might still want to
override the default method (i.e. the mapply,ANY method, pointing to
base::mapply) with a method for particular objects that is semantically
equivalent but more efficient on those objects.
Cheers,
H.
>
> ~malcolm_cook at stowers.org
>
>
>>>>>> Hervé Pagès <hpages at fhcrc.org>
>>>>>> on Tue, 27 Nov 2012 17:03:05 -0800 writes:
>
> > Some formatting issues when copy/pasting the patch in the
> > body of the email so I've attached the diff file.
>
> Thank you, Hervé.
>
> I have committed (a slightly simplified version of) your patch
> to R-devel (to become 2.16.0).
> Backporting to '2.15.2 patched' would be a bit of work
> -- mapply's C interface is not .Internal() there --
> so I've kept it in R-devel.
>
> > On 11/27/2012 04:56 PM, Hervé Pagès wrote:
> >> Hi,
> >>
> >> Here is a patch for this (against current R-devel). The "caching" of
> >> the .Primitive for 'length' is taken from seq_along() C code (in
> >> R-devel/src/main/seq.c).
> >>
> >> hpages at thinkpad:~/svn/R$ svn diff R-devel
> >> Index: R-devel/src/main/mapply.c
> >> ===================================================================
> >> --- R-devel/src/main/mapply.c (revision 61172)
> >> +++ R-devel/src/main/mapply.c (working copy)
>
> [.............]
>
> >> lengths = (R_xlen_t *) R_alloc(m, sizeof(R_xlen_t));
> >> for(i = 0; i < m; i++){
> >> - lengths[i] = xlength(VECTOR_ELT(varyingArgs, i));
> >> + int dispatch_ok = 0;
> >> + tmp1 = VECTOR_ELT(varyingArgs, i);
> >> + if (isObject(tmp1)) {
> >> + /* Looks like DispatchOrEval() needs a pairlist. We reproduce what
> >> + pairlist(tmp1) would do i.e. tmp2 <- as.pairlist(list(tmp1)).
> >> + Is there a more direct way to go from tmp1 to tmp2? */
>
> indeed, there is a more direct way:
>
> tmp2 = lang1(tmp1)
>
> and that's what I've used in the commit.
>
> >> + PROTECT(tmp2 = allocVector(VECSXP, 1));
> >> + SET_VECTOR_ELT(tmp2, 0, tmp1);
> >> + PROTECT(tmp2 = coerceVector(tmp2, LISTSXP));
> >> + dispatch_ok = DispatchOrEval(call, length_op, "length",
> >> + tmp2, rho, &ans, 0, 1);
> >> + UNPROTECT(2);
> >> + }
> >> + lengths[i] = dispatch_ok ? asInteger(ans) : xlength(tmp1);
> >> if(lengths[i] == 0) zero++;
> >> if (lengths[i] > longest) longest = lengths[i];
> >> }
> >>
> >> Hopefully the bug can be fixed. Thanks!
>
> Many thanks to you, Hervé!
> Martin
>
>
> >> On 11/14/2012 09:42 PM, Hervé Pagès wrote:
> >>> Hi,
> >>>
> >>> Starting with ordinary vectors, so we know what to expect:
> >>>
> >>> > mapply(function(x, y) {x * y}, 101:106, rep(1:3, 2))
> >>> [1] 101 204 309 104 210 318
> >>>
> >>> > mapply(function(x, y) {x * y}, 101:106, 1:3)
> >>> [1] 101 204 309 104 210 318
> >>>
> >>> Now with an S4 object:
> >>>
> >>> setClass("A", representation(aa="integer"))
> >>> a <- new("A", aa=101:106)
> >>>
> >>> > length(a)
> >>> [1] 1
> >>>
> >>> Implementing length():
> >>>
> >>> setMethod("length", "A", function(x) length(x at aa))
> >>>
> >>> Testing length():
> >>>
> >>> > length(a) # sanity check
> >>> [1] 6
> >>>
> >>> No [[ yet for those objects so the following error is expected:
> >>>
> >>> > mapply(function(x, y) {x * y}, a, rep(1:3, 2))
> >>> Error in dots[[1L]][[1L]] : this S4 class is not subsettable
> >>>
> >>> Implementing [[:
> >>>
> >>> setMethod("[[", "A", function(x, i, j, ...) x at aa[[i]])
> >>>
> >>> Testing [[:
> >>>
> >>> > a[[1]]
> >>> [1] 101
> >>> > a[[5]]
> >>> [1] 105
> >>>
> >>> Trying mapply again:
> >>>
> >>> > mapply(function(x, y) {x * y}, a, rep(1:3, 2))
> >>> [1] 101 202 303 101 202 303
> >>>
> >>> Wrong. It looks like internally a[[1]] is always used instead of a[[i]].
> >>>
> >>> The real problem it seems is that 'a' is treated as if it was of
> >>> length 1:
> >>>
> >>> > mapply(function(x, y) {x * y}, a, 1:3)
> >>> [1] 101 202 303
> >>> > mapply(function(x, y) {x * y}, a, 5)
> >>> [1] 505
> >>>
> >>> In other words, internal dispatch works for [[ but not for length().
> >>>
> >>> Thanks,
> >>> H.
> >>>
> >>
>
> > --
> > Hervé Pagès
>
> > Program in Computational Biology
> > Division of Public Health Sciences
> > Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N, M1-B514
> > P.O. Box 19024
> > Seattle, WA 98109-1024
>
> > E-mail: hpages at fhcrc.org
> > Phone: (206) 667-5791
> > Fax: (206) 667-1319
>
> > [DELETED ATTACHMENT external: mapply.diff, text/x-patch]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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