R version 2.5.0 Patched (2007-05-21 r41653)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> ##--- S4 Methods (and Classes)
> library(methods)
> ##too fragile: showMethods(where = "package:methods")
> 
> ##-- S4 classes with S3 slots [moved from ./reg-tests-1.R]
> setClass("test1", representation(date="POSIXct"))
[1] "test1"
> x <- new("test1", date=as.POSIXct("2003-10-09"))
> stopifnot(format(x @ date) == "2003-10-09")
> ## line 2 failed in 1.8.0 because of an extraneous space in "%in%"
> 
> stopifnot(all.equal(3:3, 3.), all.equal(1., 1:1))
> 
> ## trace (requiring methods):
> f <- function(x, y) { c(x,y)}
> xy <- 0
> trace(f, quote(x <- c(1, x)), exit = quote(xy <<- x), print = FALSE)
[1] "f"
> fxy <- f(2,3)
> stopifnot(identical(fxy, c(1,2,3)))
> stopifnot(identical(xy, c(1,2)))
> untrace(f)
> 
> ## a generic and its methods
> 
> setGeneric("f")
[1] "f"
> setMethod("f", c("character", "character"), function(x,	 y) paste(x,y))
[1] "f"
> 
> ## trace the generic
> trace("f", quote(x <- c("A", x)), exit = quote(xy <<- c(x, "Z")), print = FALSE)
[1] "f"
> 
> ## should work for any method
> 
> stopifnot(identical(f(4,5), c("A",4,5)),
+           identical(xy, c("A", 4, "Z")))
> 
> stopifnot(identical(f("B", "C"), paste(c("A","B"), "C")),
+           identical(xy, c("A", "B", "Z")))
> 
> ## trace a method
> trace("f", sig = c("character", "character"), quote(x <- c(x, "D")),
+       exit = quote(xy <<- xyy <<- c(x, "W")), print = FALSE)
[1] "f"
> 
> stopifnot(identical(f("B", "C"), paste(c("A","B","D"), "C")))
> # These two got broken by Luke's lexical scoping fix
> #stopifnot(identical(xy, c("A", "B", "D", "W")))
> #stopifnot(identical(xy, xyy))
> 
> ## but the default method is unchanged
> stopifnot(identical(f(4,5), c("A",4,5)),
+           identical(xy, c("A", 4, "Z")))
> 
> removeGeneric("f")
[1] TRUE
> ## end of moved from trace.Rd
> 
> 
> ## print/show dispatch  [moved from  ./reg-tests-2.R ]
> ## The results  have waffled back and forth.
> ## Currently (R 2.4.0) the intent is that automatic printing of S4
> ## objects should correspond to a call to show(), as per the green
> ## book, p. 332.  Therefore, the show() method is called, once defined,
> ## for auto-printing foo, regardless of the S3 or S4 print() method.
> setClass("bar", representation(a="numeric"))
[1] "bar"
> foo <- new("bar", a=pi)
> foo
An object of class "bar"
Slot "a":
[1] 3.141593

> show(foo)
An object of class "bar"
Slot "a":
[1] 3.141593

> print(foo)
An object of class "bar"
Slot "a":
[1] 3.141593

> 
> setMethod("show", "bar", function(object){cat("show method\n")})
[1] "show"
> show(foo)
show method
> foo
show method
> print(foo)
show method
> # suppressed because output depends on current choice of S4 type or
> # not.  Can reinstate when S4 type is obligatory
> # print(foo, digits = 4)
> 
> print.bar <- function(x, ...) cat("print method\n")
> foo
show method
> print(foo)
print method
> show(foo)
show method
> 
> setMethod("print", "bar", function(x, ...){cat("S4 print method\n")})
Creating a new generic function for "print" in ".GlobalEnv"
[1] "print"
> foo
show method
> print(foo)
S4 print method
> show(foo)
show method
> ## calling print() with more than one argument suppresses the show()
> ## method, largely to prevent an infinite loop if there is in fact no
> ## show() method for this class.  A better solution would be desirable.
> print(foo, digits = 4)
S4 print method
> 
> setClassUnion("integer or NULL", members = c("integer","NULL"))
[1] "integer or NULL"
> setClass("c1", representation(x = "integer", code = "integer or NULL"))
[1] "c1"
> nc <- new("c1", x = 1:2)
> str(nc)# gave ^ANULL^A in 2.0.0
Formal class 'c1' [package ".GlobalEnv"] with 2 slots
  ..@ x   : int [1:2] 1 2
  ..@ code: NULL
> ##
> 
> 
> library(stats4)
> showMethods("coerce", classes=c("matrix", "numeric"))
Function: coerce (package methods)
from="ANY", to="matrix"
from="ANY", to="numeric"

> ## {gave wrong result for a while in R 2.4.0}
> 
> ## the following showMethods() output tends to generate errors in the tests
> ## whenever the contents of the packages change. Searching in the
> ## diff's can easily mask real problems.  If there is a point
> ## to the printout, e.g., to verify that certain methods exist,
> ## hasMethod() would be a useful replacement
> 
> ## showMethods(where = "package:stats4")
> ## showMethods("show")
> ## showMethods("show")
> ## showMethods("plot") # (ANY,ANY) and (profile.mle, missing)
> ## showMethods(classes="mle")
> ## showMethods(classes="matrix")
> 
> 
> ##--- "[" fiasco before R 2.2.0 :
> d2 <- data.frame(b= I(matrix(1:6,3,2)))
> ## all is well:
> d2[2,]
     [,1] [,2]
[1,]    2    5
> stopifnot(identical(d2[-1,], d2[2:3,]))
> ## Now make "[" into S4 generic by defining a trivial method
> setClass("Mat", representation(Dim = "integer", "VIRTUAL"))
[1] "Mat"
> setMethod("[", signature(x = "Mat",
+ 			 i = "missing", j = "missing", drop = "ANY"),
+ 	  function (x, i, j, drop) x)
[1] "["
> ## Can even remove the method: it doesn't help
> removeMethod("[", signature(x = "Mat",
+                             i = "missing", j = "missing", drop = "ANY"))
[1] TRUE
> d2[1:2,] ## used to fail badly; now okay
     [,1] [,2]
[1,]    1    4
[2,]    2    5
> stopifnot(identical(d2[-1,], d2[2:3,]))
> ## failed in R <= 2.1.x
> 
> 
> ## Fritz' S4 "odditiy"
> setClass("X", representation(bar="numeric"))
[1] "X"
> setClass("Y", contains="X")
[1] "Y"
> ## Now we define a generic foo() and two different methods for "X" and
> ## "Y" objects for arg missing:
> setGeneric("foo", function(object, arg) standardGeneric("foo"))
[1] "foo"
> setMethod("foo", signature(object= "X", arg="missing"),
+           function(object, arg) cat("an X object with bar =", object@bar, "\n"))
[1] "foo"
> setMethod("foo", signature(object= "Y", arg="missing"),
+           function(object, arg) cat("a Y object with bar =", object@bar, "\n"))
[1] "foo"
> ## Finally we create a method where arg is "logical" only for class
> ## "X", hence class "Y" should inherit that:
> setMethod("foo", signature(object= "X", arg= "logical"),
+           function(object, arg) cat("Hello World!\n") )
[1] "foo"
> ## now create objects and call methods:
> y <- new("Y", bar=2)
> ## showMethods("foo")
> foo(y)
a Y object with bar = 2 
> foo(y, arg=TRUE)## Hello World!
Hello World!
> ## OK, inheritance worked, and we have
> ## showMethods("foo")
> foo(y)
a Y object with bar = 2 
> ## still 'Y' -- was 'X object' in R < 2.3
> 
> 
> ## Multiple inheritance
> setClass("A", representation(x = "numeric"))
[1] "A"
> setClass("B", representation(y = "character"))
[1] "B"
> setClass("C", contains = c("A", "B"), representation(z = "logical"))
[1] "C"
> new("C")
An object of class "C"
Slot "z":
logical(0)

Slot "x":
numeric(0)

Slot "y":
character(0)

> setClass("C", contains = c("A", "B"), representation(z = "logical"),
+          prototype = prototype(x = 1.5, y = "test", z = TRUE))
[1] "C"
> (cc <- new("C"))
An object of class "C"
Slot "z":
[1] TRUE

Slot "x":
[1] 1.5

Slot "y":
[1] "test"

> ## failed reconcilePropertiesAndPrototype(..) after svn r37018
> 
> ## "Logic" group -- was missing in R <= 2.4.0
> stopifnot(all(getGroupMembers("Logic") %in% c("&", "|")),
+ 	  any(getGroupMembers("Ops") == "Logic"))
> setClass("brob", contains="numeric")
[1] "brob"
> b <- new("brob", 3.14)
> logic.brob.error <- function(nm)
+     stop("logic operator '", nm, "' not applicable to brobs")
> logic2 <- function(e1,e2) logic.brob.error(.Generic)
> setMethod("Logic", signature("brob", "ANY"), logic2)
[1] "Logic"
> setMethod("Logic", signature("ANY", "brob"), logic2)
[1] "Logic"
> ## Now ensure that using group members gives error:
> assertError <- function(expr)
+     stopifnot(inherits(try(expr, silent = TRUE), "try-error"))
> assertError(b & b)
Warning message:
Ambiguous method selection for "&", target "brob#brob" (the first of the signatures shown will be used)
    brob#ANY
    ANY#brob
 in: .findInheritedMethods(classes, fdef, mtable) 
> assertError(b | 1)
> assertError(TRUE & b)
> 
> ## methods' hidden cbind() / rbind:
> cBind <- methods:::cbind
> setClass("myMat", representation(x = "numeric"))
[1] "myMat"
> setMethod("cbind2", signature(x = "myMat", y = "missing"), function(x,y) x)
[1] "cbind2"
> m <- new("myMat", x = c(1, pi))
> stopifnot(identical(m, cBind(m)))
> 
> 
> ## explicit print or show on a basic class with an S4 bit
> ## caused infinite recursion
> setClass("Foo", representation(name="character"), contains="matrix")
[1] "Foo"
> (f <- new("Foo", name="Sam", matrix()))
An object of class "Foo"
     [,1]
[1,]   NA
Slot "name":
[1] "Sam"

> (m <- as(f, "matrix"))
     [,1]
[1,]   NA
> show(m)
     [,1]
[1,]   NA
> print(m)
     [,1]
[1,]   NA
> ## fixed in 2.5.0 patched
> 
> ## callGeneric inside a method with new arguments {hence using .local()}:
> setGeneric("Gfun", function(x, ...) standardGeneric("Gfun"),
+ 	   useAsDefault = function(x, ...) sum(x, ...))
[1] "Gfun"
> setClass("myMat", contains="matrix")
[1] "myMat"
> setClass("mmat2", contains="matrix")
[1] "mmat2"
> setClass("mmat3", contains="mmat2")
[1] "mmat3"
> setMethod(Gfun, signature(x = "myMat"),
+ 	  function(x, extrarg = TRUE) {
+ 	      cat("in 'myMat' method for 'Gfun() : extrarg=", extrarg, "\n")
+ 	      Gfun(unclass(x))
+ 	  })
[1] "Gfun"
attr(,"package")
[1] ".GlobalEnv"
> setMethod(Gfun, signature(x = "mmat2"),
+ 	  function(x, extrarg = TRUE) {
+ 	      cat("in 'mmat2' method for 'Gfun() : extrarg=", extrarg, "\n")
+ 	      x <- unclass(x)
+ 	      callGeneric()
+ 	  })
[1] "Gfun"
attr(,"package")
[1] ".GlobalEnv"
> setMethod(Gfun, signature(x = "mmat3"),
+ 	  function(x, extrarg = TRUE) {
+ 	      cat("in 'mmat3' method for 'Gfun() : extrarg=", extrarg, "\n")
+ 	      x <- as(x, "mmat2")
+ 	      callGeneric()
+ 	  })
[1] "Gfun"
attr(,"package")
[1] ".GlobalEnv"
> (mm <- new("myMat", diag(3)))
An object of class "myMat"
     [,1] [,2] [,3]
[1,]    1    0    0
[2,]    0    1    0
[3,]    0    0    1
> Gfun(mm)
in 'myMat' method for 'Gfun() : extrarg= TRUE 
[1] 3
> Gfun(mm, extrarg = FALSE)
in 'myMat' method for 'Gfun() : extrarg= FALSE 
[1] 3
> m2 <- new("mmat2", diag(3))
> Gfun(m2)
in 'mmat2' method for 'Gfun() : extrarg= TRUE 
[1] 3
> Gfun(m2, extrarg = FALSE)
in 'mmat2' method for 'Gfun() : extrarg= FALSE 
[1] 3
> ## The last two gave Error ...... variable ".local" was not found
> (m3 <- new("mmat3", diag(3)))
An object of class "mmat3"
     [,1] [,2] [,3]
[1,]    1    0    0
[2,]    0    1    0
[3,]    0    0    1
> Gfun(m3)
in 'mmat3' method for 'Gfun() : extrarg= TRUE 
in 'mmat2' method for 'Gfun() : extrarg= TRUE 
[1] 3
> Gfun(m3, extrarg = FALSE) # used to not pass 'extrarg'
in 'mmat3' method for 'Gfun() : extrarg= FALSE 
in 'mmat2' method for 'Gfun() : extrarg= FALSE 
[1] 3
> 
>