From hpages at fhcrc.org  Wed Nov 28 01:56:59 2012
From: hpages at fhcrc.org (=?ISO-8859-1?Q?Herv=E9_Pag=E8s?=)
Date: Tue, 27 Nov 2012 16:56:59 -0800
Subject: [Rd] bug with mapply() on an S4 object
In-Reply-To: <50A480AF.1030901@fhcrc.org>
References: <50A480AF.1030901@fhcrc.org>
Message-ID: <50B5615B.90303@fhcrc.org>

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, 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



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