[Rd] bug with mapply() on an S4 object
Hervé Pagès
hpages at fhcrc.org
Wed Nov 28 02:03:05 CET 2012
Some formatting issues when copy/pasting the patch in the body of the
email so I've attached the diff file.
Cheers,
H.
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)
> @@ -32,14 +32,39 @@
> int i, j, m, named, zero = 0;
> R_xlen_t *lengths, *counters, longest = 0;
> SEXP vnames, fcall = R_NilValue, mindex, nindex, tmp1, tmp2, ans;
> + static SEXP length_op = NULL;
>
> + /* Store the .Primitive for 'length' for DispatchOrEval to use. */
> + if (length_op == NULL) {
> + SEXP R_lengthSymbol = install("length");
> + length_op = eval(R_lengthSymbol, R_BaseEnv);
> + if (TYPEOF(length_op) != BUILTINSXP) {
> + length_op = NULL;
> + error("'length' is not a BUILTIN");
> + }
> + R_PreserveObject(length_op);
> + }
> +
> m = length(varyingArgs);
> vnames = PROTECT(getAttrib(varyingArgs, R_NamesSymbol));
> named = vnames != R_NilValue;
>
> 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? */
> + 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!
> H.
>
>
> 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
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