From MEC at stowers.org  Wed Nov 28 14:47:37 2012
From: MEC at stowers.org (Cook, Malcolm)
Date: Wed, 28 Nov 2012 07:47:37 -0600
Subject: [Rd] bug with mapply() on an S4 object
In-Reply-To: <20661.60229.635742.917114@stat.math.ethz.ch>
References: <50A480AF.1030901@fhcrc.org> <50B5615B.90303@fhcrc.org>
	<50B562C9.3090108@fhcrc.org>,
	<20661.60229.635742.917114@stat.math.ethz.ch>
Message-ID: <2C40E43D1F7A56408C4463FD245DDDF9079088BFCE@EXCHMB-02.stowers-institute.org>

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.  

~malcolm_cook at stowers.org


>>>>> Herv? Pag?s <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, Herv?.

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, Herv? Pag?s 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, Herv?!
Martin


    >> On 11/14/2012 09:42 PM, Herv? Pag?s 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.
    >>>
    >>

    > --
    > Herv? Pag?s

    > 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]

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[Rd] bug with mapply() on an S4 object
Cook, Malcolm