The R Project SVN R

####--- S4 Methods (and Classes)  --- see also ../src/library/methods/tests/
options(useFancyQuotes=FALSE)
require(methods)
##too fragile: showMethods(where = "package:methods")

##-- S4 classes with S3 slots [moved from ./reg-tests-1.R]
setClass("test1", representation(date="POSIXct"))
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)
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")
setMethod("f", c("character", "character"), function(x,  y) paste(x,y))

## trace the generic
trace("f", quote(x <- c("A", x)), exit = quote(xy <<- c(x, "Z")), print = FALSE)

## 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)

stopifnot(identical(f("B", "C"), paste(c("A","B","D"), "C")))
stopifnot(identical(xyy, c("A", "B", "D", "W")))
# got broken by Luke's lexical scoping fix:
#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")
## 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.
## (But most of this example is irrelevant if one avoids S3 methods for
## S4 classes, as one should.)
setClass("bar", representation(a="numeric"))
foo <- new("bar", a=pi)
foo
show(foo)
print(foo)

setMethod("show", "bar", function(object){cat("show method\n")})
show(foo)
foo
print(foo)
# suppressed because output depends on current choice of S4 type or
# not.  Can reinstate when S4 type is obligatory
# print(foo, digits = 4)

## DON'T DO THIS:  S3 methods for S4 classes are a design error JMC iii.9.09
## print.bar <- function(x, ...) cat("print method\n")
## foo
## print(foo)
## show(foo)

setMethod("print", "bar", function(x, ...){cat("S4 print method\n")})
foo
print(foo)
show(foo)
## 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)

setClassUnion("integer or NULL", members = c("integer","NULL"))
setClass("c1", representation(x = "integer", code = "integer or NULL"))
nc <- new("c1", x = 1:2)
str(nc)# gave ^ANULL^A in 2.0.0
##


library(stats4)
showMethods("coerce", classes=c("matrix", "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,]
stopifnot(identical(d2[-1,], d2[2:3,]))
## Now make "[" into S4 generic by defining a trivial method
setClass("Mat", representation(Dim = "integer", "VIRTUAL"))
setMethod("[", signature(x = "Mat",
             i = "missing", j = "missing", drop = "ANY"),
      function (x, i, j, drop) x)
## Can even remove the method: it doesn't help
removeMethod("[", signature(x = "Mat",
                            i = "missing", j = "missing", drop = "ANY"))
d2[1:2,] ## used to fail badly; now okay
stopifnot(identical(d2[-1,], d2[2:3,]))
## failed in R <= 2.1.x


## Fritz' S4 "odditiy"
setClass("X", representation(bar="numeric"))
setClass("Y", contains="X")
## 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"))
setMethod("foo", signature(object= "X", arg="missing"),
          function(object, arg) cat("an X object with bar =", object@bar, "\n"))
setMethod("foo", signature(object= "Y", arg="missing"),
          function(object, arg) cat("a Y object with bar =", object@bar, "\n"))
## 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") )
## now create objects and call methods:
y <- new("Y", bar=2)
## showMethods("foo")
foo(y)
foo(y, arg=TRUE)## Hello World!
## OK, inheritance worked, and we have
## showMethods("foo")
foo(y)
## still 'Y' -- was 'X object' in R < 2.3


## Multiple inheritance
setClass("A", representation(x = "numeric"))
setClass("B", representation(y = "character"))
setClass("C", contains = c("A", "B"), representation(z = "logical"))
new("C")
setClass("C", contains = c("A", "B"), representation(z = "logical"),
         prototype = prototype(x = 1.5, y = "test", z = TRUE))
(cc <- new("C"))
## failed reconcilePropertiesAndPrototype(..) after svn r37018
stopifnot(identical(selectSuperClasses("C", dropVirtual = TRUE), c("A", "B")),
      0 == length(.selectSuperClasses(getClass("B")@contains)))

## "Logic" group -- was missing in R <= 2.4.0
stopifnot(all(getGroupMembers("Logic") %in% c("&", "|")),
      any(getGroupMembers("Ops") == "Logic"))
setClass("brob", contains="numeric")
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)
setMethod("Logic", signature("ANY", "brob"), logic2)
## Now ensure that using group members gives error:
assertError <- function(expr)
    stopifnot(inherits(try(expr, silent = TRUE), "try-error"))
assertWarning <- function(expr)
    stopifnot(inherits(tryCatch(expr, warning = function(w)w), "warning"))
assertWarning_atleast <- function(expr) {
    r <- tryCatch(expr, warning = function(w)w, error = function(e)e)
    stopifnot(inherits(r, "warning") || inherits(r, "error"))
}

assertError(b & b)
assertError(b | 1)
assertError(TRUE & b)


## methods' hidden cbind() / rbind:
cBind <- methods:::cbind
setClass("myMat", representation(x = "numeric"))
setMethod("cbind2", signature(x = "myMat", y = "missing"), function(x,y) x)
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")
(f <- new("Foo", name="Sam", matrix()))
f2 <- new("Foo", .Data = diag(2), name="Diag")# explicit .Data
(m <- as(f, "matrix"))
## this has no longer (2.7.0) an S4 bit: set it explicitly just for testing:
stopifnot(isS4(m. <- asS4(m)),
          identical(m, f@.Data))
show(m.)
print(m.)
## 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, ...))
setClass("myMat", contains="matrix")
setClass("mmat2", contains="matrix")
setClass("mmat3", contains="mmat2")
setMethod(Gfun, signature(x = "myMat"),
      function(x, extrarg = TRUE) {
          cat("in 'myMat' method for 'Gfun() : extrarg=", extrarg, "\n")
          Gfun(unclass(x))
      })
setMethod(Gfun, signature(x = "mmat2"),
      function(x, extrarg = TRUE) {
          cat("in 'mmat2' method for 'Gfun() : extrarg=", extrarg, "\n")
          x <- unclass(x)
          callGeneric()
      })
setMethod(Gfun, signature(x = "mmat3"),
      function(x, extrarg = TRUE) {
          cat("in 'mmat3' method for 'Gfun() : extrarg=", extrarg, "\n")
          x <- as(x, "mmat2")
          callGeneric()
      })
wrapG <- function(x, a1, a2) {
    myextra <- missing(a1) && missing(a2)
    Gfun(x, extrarg = myextra)
}

(mm <- new("myMat", diag(3)))
Gfun(mm)
stopifnot(identical(wrapG(mm),    Gfun(mm, TRUE)),
          identical(wrapG(mm,,2), Gfun(mm, FALSE)))

Gfun(mm, extrarg = FALSE)
m2 <- new("mmat2", diag(3))
Gfun(m2)
Gfun(m2, extrarg = FALSE)
## The last two gave Error ...... variable ".local" was not found
(m3 <- new("mmat3", diag(3)))
Gfun(m3)
Gfun(m3, extrarg = FALSE) # used to not pass 'extrarg'

## -- a variant of the above which failed in version <= 2.5.1 :
setGeneric("Gf", function(x, ...) standardGeneric("Gf"))
setMethod(Gf, signature(x = "mmat2"),
          function(x, ...) {
              cat("in 'mmat2' method for 'Gf()\n")
              x <- unclass(x)
              callGeneric()
          })
setMethod(Gf, signature(x = "mmat3"),
          function(x, ...) {
              cat("in 'mmat3' method for 'Gf()\n")
              x <- as(x, "mmat2")
              callGeneric()
          })
setMethod(Gf, signature(x = "matrix"),
      function(x, a1, ...) {
              cat(sprintf("matrix %d x %d ...\n", nrow(x), ncol(x)))
              list(x=x, a1=a1, ...)
          })

wrap2 <- function(x, a1, ...) {
    A1 <- if(missing(a1)) "A1" else as.character(a1)
    Gf(x, ..., a1 = A1)
}
## Gave errors in R 2.5.1 :
wrap2(m2, foo = 3.14)
wrap2(m2, 10, answer.all = 42)


## regression tests of dispatch: most of these became primitive in 2.6.0
setClass("c1", "numeric")
setClass("c2", "numeric")
x_c1 <- new("c1")
# the next failed < 2.5.0 as the signature in .BasicFunsList was wrong
setMethod("as.character", "c1", function(x, ...) "fn test")
as.character(x_c1)

setMethod("as.integer", "c1", function(x, ...) 42)
as.integer(x_c1)

setMethod("as.logical", "c1", function(x, ...) NA)
as.logical(x_c1)

setMethod("as.complex", "c1", function(x, ...) pi+0i)
as.complex(x_c1)

setMethod("as.raw", "c1", function(x) as.raw(10))
as.raw(x_c1)

# as.double, as.real use as.numeric for their methods to maintain equivalence
setMethod("as.numeric", "c1", function(x, ...) 42+pi)
identical(as.numeric(x_c1),as.double(x_c1))
identical(as.numeric(x_c1),as.real(x_c1))


setMethod(as.double, "c2", function(x, ...) x@.Data+pi)
x_c2 <- new("c2", pi)
identical(as.numeric(x_c2),as.double(x_c2))
identical(as.numeric(x_c2),as.real(x_c2))

## '!' changed signature from 'e1' to 'x' in 2.6.0
setClass("foo", "logical")
setMethod("!", "foo", function(e1) e1+NA)
selectMethod("!", "foo")
xx <- new("foo", FALSE)
!xx

## This failed for about one day -- as.vector(x, mode) :
setMethod("as.vector", signature(x = "foo", mode = "missing"),
          function(x) unclass(x))
## whereas this fails in R versions earlier than 2.6.0:
setMethod("as.vector", "foo", function(x) unclass(x))
stopifnot(removeClass("foo"))

## stats4::AIC in R < 2.7.0 used to clobber stats::AIC
pfit <- function(data) {
    m <- mean(data)
    loglik <- sum(dpois(data, m))
    ans <- list(par = m, loglik = loglik)
    class(ans) <- "pfit"
    ans
}
AIC.pfit <- function(object, ..., k = 2) -2*object$loglik + k
AIC(pfit(1:10))
library(stats4) # and keep on search() for tests below
AIC(pfit(1:10)) # failed in R < 2.7.0

## For a few days (~ 2008-01-30), this failed to work without any notice:
setClass("Mat",  representation(Dim = "integer","VIRTUAL"))
setClass("dMat", representation(x = "numeric",  "VIRTUAL"), contains = "Mat")
setClass("CMat", representation(dnames = "list","VIRTUAL"), contains = "Mat")
setClass("dCMat", contains = c("dMat", "CMat"))
stopifnot(!isVirtualClass("dCMat"),
      length(slotNames(new("dCMat"))) == 3)


## Passing "..." arguments in nested callGeneric()s
setClass("m1", contains="matrix")
setClass("m2", contains="m1")
setClass("m3", contains="m2")
##
setGeneric("foo", function(x, ...) standardGeneric("foo"))
setMethod("foo", signature(x = "m1"),
      function(x, ...) cat(" <m1> ", format(match.call()),"\n"))
setMethod("foo", signature(x = "m2"),
      function(x, ...) {
          cat(" <m2> ", format(match.call()),"\n")
          x <- as(x, "m1"); callGeneric()
      })
setMethod("foo", signature(x = "m3"),
      function(x, ...) {
          cat(" <m3> ", format(match.call()),"\n")
          x <- as(x, "m2"); callGeneric()
      })
foo(new("m1"), bla = TRUE)
foo(new("m2"), bla = TRUE)
foo(new("m3"), bla = TRUE)
## The last one used to loose 'bla = TRUE' {the "..."} when it got to m1

## is() for S3 objects with multiple class strings
setClassUnion("OptionalPOSIXct",   c("POSIXct",   "NULL"))
stopifnot(is(Sys.time(), "OptionalPOSIXct"))
## failed in R 2.7.0

## getGeneric() / getGenerics() "problems" related to 'tools' usage:
e4 <- as.environment("package:stats4")
gg4 <- getGenerics(e4)
stopifnot(c("BIC", "coef", "confint", "logLik", "plot", "profile",
            "show", "summary", "update", "vcov") %in% gg4, # %in% : "future proof"
          unlist(lapply(gg4, function(g) !is.null(getGeneric(g, where = e4)))),
          unlist(lapply(gg4, function(g) !is.null(getGeneric(g)))))
em <- as.environment("package:methods")
ggm <- getGenerics(em)
gms <- c("addNextMethod", "body<-", "cbind2", "initialize",
     "loadMethod", "Ops", "rbind2", "show")
stopifnot(unlist(lapply(ggm, function(g) !is.null(getGeneric(g, where = em)))),
      unlist(lapply(ggm, function(g) !is.null(getGeneric(g)))),
      gms %in% ggm,
      gms %in% tools:::get_S4_generics_with_methods(em), # with "message"
      ## all above worked in 2.7.0, however:
      isGeneric("show",  where=e4),
      hasMethods("show", where=e4), hasMethods("show", where=em),
      ## isGeneric("dim", where=as.environment("package:Matrix"))
      identical(as.character(gg4), #gg4 has packages attr.; tools::: doesn't
            tools:::get_S4_generics_with_methods(e4))
      )
## the last failed in R 2.7.0 : was not showing  "show"
## TODO: use "Matrix" checks once that is >= 1.0

## containing "array" ("matrix", "ts", ..)
t. <- ts(1:10, frequency = 4, start = c(1959, 2))
setClass("Arr", contains= "array"); x <- new("Arr", cbind(17))
setClass("Ts",  contains= "ts");   tt <- new("Ts", t.); t2 <- as(t., "Ts")
setClass("ts2", representation(x = "Ts", y = "ts"))
tt2 <- new("ts2", x=t2, y=t.)
stopifnot(dim(x) == c(1,1), is(tt, "ts"), is(t2, "ts"),
          ## FIXME:  identical(tt, t2)
          length(tt) == length(t.),
          identical(tt2@x, t2), identical(tt2@y, t.))
## new(..) failed in R 2.7.0

## Method with wrong argument order :
setGeneric("test1", function(x, printit = TRUE, name = "tmp")
           standardGeneric("test1"))
assertWarning_atleast(
setMethod("test1", "numeric", function(x, name, printit) match.call())
)## did not warn or error in R 2.7.0 and earlier

library(stats4)
c1 <- getClass("mle", where = "stats4")
c2 <- getClass("mle", where = "package:stats4")
s1 <- getMethod("summary", "mle", where = "stats4")
s2 <- getMethod("summary", "mle", where = "package:stats4")
stopifnot(is(c1, "classRepresentation"),
      is(s1, "MethodDefinition"),
      identical(c1,c2), identical(s1,s2))
## failed at times in the past

## Extending "matrix", the .Data slot etc:
setClass("moo", representation("matrix"))
m <- matrix(1:4, 2, dimnames= list(NULL, c("A","B")))
nf <- new("moo", .Data = m)
n2 <- new("moo", 3:1, 3,2)
n3 <- new("moo", 1:6, ncol=2)
stopifnot(identical(m,          as(nf, "matrix")),
      identical(matrix(3:1,3,2),    as(n2, "matrix")),
      identical(matrix(1:6,ncol=2), as(n3, "matrix")))
## partly failed at times in pre-2.8.0

## From "Michael Lawrence" <....@fhcrc.org>  To r-devel@r-project, 25 Nov 2008:
## NB: setting a generic on order() is *not* the approved method
## -- set xtfrm() methods instead
setGeneric("order", signature="...",
       function (..., na.last=TRUE, decreasing=FALSE)
       standardGeneric("order"))
stopifnot(identical(rbind(1), matrix(1,1,1)))
setGeneric("rbind", function(..., deparse.level=1)
       standardGeneric("rbind"), signature = "...")
stopifnot(identical(rbind(1), matrix(1,1,1)))
## gave Error in .Method( .... in R 2.8.0

## median( <simple S4> )
## FIXME: if we use "C" instead of "L", this fails because of caching
setClass("L", contains = "list")
## {simplistic, just for the sake of testing here} :
setMethod("Compare", signature(e1="L", e2="ANY"),
          function(e1,e2) sapply(e1, .Generic, e2=e2))
## note the next does *not* return an object of the class.
setMethod("Summary", "L",
      function(x, ..., na.rm=FALSE) {x <- unlist(x); callNextMethod()})
setMethod("[", signature(x="L", i="ANY", j="missing",drop="missing"),
          function(x,i,j,drop) new(class(x), x@.Data[i]))
## defining S4 methods for sort() has no effect on calls to
## sort() from functions in a name space; e.g., median.default.
## but setting an xtfrm() method works.
setMethod("xtfrm", "L", function(x) xtfrm(unlist(x@.Data)))
## median is documented to use mean(), so we need an S3 mean method:
## An S4 method will not do because of the long-standing S4 scoping bug.
mean.L <- function(x, ...) new("L", mean(unlist(x@.Data), ...))
x <- new("L", 1:3); x2 <- x[-2]
stopifnot(unlist(x2) == (1:3)[-2],
      is(mx <- median(x), "L"), mx == 2,
      ## median of two
      median(x2) == x[2])
## NB: quantile() is not said to work on such an object, and only does so
## for order statistics (so should not be tested, but was in earlier versions).

## Buglet in as() generation for class without own slots
setClass("SIG", contains="signature")
stopifnot(packageSlot(class(S <- new("SIG"))) == ".GlobalEnv",
      packageSlot(class(ss <- new("signature"))) == "methods",
      packageSlot(class(as(S, "signature"))) == "methods")
## the 3rd did not have "methods"

## Invalid "factor"s -- now "caught" by  validity check :
 ok.f <- gl(3,5, labels = letters[1:3])
bad.f <- structure(rep(1:3, each=5), levels=c("a","a","b"), class="factor")
validObject(ok.f) ; assertError(validObject(bad.f))
setClass("myF", contains = "factor")
validObject(new("myF", ok.f))
assertError(validObject(new("myF", bad.f)))
removeClass("myF")
## no validity check in R <= 2.9.0

## as(x, .)   when x is from an "unregistered" S3 class :
as(structure(1:3, class = "foobar"), "vector")
## failed to work in R <= 2.9.0

## S4 dispatch in the internal generic xtfrm (added in 2.11.0)
setClass("numWithId", representation(id = "character"), contains = "numeric")
x <- new("numWithId", 1:3, id = "An Example")
xtfrm(x) # works as the base representation is numeric
setMethod('xtfrm', 'numWithId', function(x) x@.Data)
xtfrm(x)
stopifnot(identical(xtfrm(x), 1:3))
## new in 2.11.0

## [-dispatch using callNextMethod()
setClass("C1", representation(a = "numeric"))
setClass("C2", contains = "C1")
setMethod("[", "C1", function(x,i,j,...,drop=TRUE)
      cat("drop in C1-[ :", drop, "\n"))
setMethod("[", "C2", function(x,i,j,...,drop=TRUE) {
    cat("drop in C2-[ :", drop, "\n")
    callNextMethod()
})
x <- new("C1"); y <- new("C2")
x[1, drop=FALSE]
y[1, drop=FALSE]
## the last gave TRUE on C1-level in R 2.10.x;
## the value of drop was wrongly taken from the default.

## All slot names -- but "class" -- should work now
problNames <- c("names", "dimnames", "row.names",
                "class", "comment", "dim", "tsp")
myTry <- function(expr, ...) tryCatch(expr, error = function(e) e)
tstSlotname <- function(nm) {
    r <- myTry(setClass("foo", representation =
                        structure(list("character"), .Names = nm)))
    if(is(r, "error")) return(r$message)
    ## else
    ch <- LETTERS[1:5]
    ## instead of  new("foo", <...> = ch):
    x <- myTry(do.call(new, structure(list("foo", ch), .Names=c("", nm))))
    if(is(x, "error")) return(x$message)
    y <- myTry(new("foo"));      if(is(y, "error")) return(y$message)
    r <- myTry(capture.output(show(x))); if(is(r, "error")) return(r$message)
    r <- myTry(capture.output(show(y))); if(is(r, "error")) return(r$message)
    ## else
    slot(y, nm) <- slot(x, nm)
    stopifnot(validObject(x), identical(x,y), identical(slot(x, nm), ch))
    return(TRUE)
}
R <- sapply(problNames, tstSlotname, simplify = FALSE)
str(R) # just so ...
stopifnot(is.character(R[["class"]]),
          sapply(R[names(R) != "class"], isTRUE))
## only "class" (and ".Data", ...) is reserved as slot name

## implicit generics ..
setMethod("sample", "C2",
          function(x, size, replace=FALSE, prob=NULL) {"sample.C2"})
stopifnot(is(sample,"standardGeneric"),
      ## the signature must come from the implicit generic:
      identical(sample@signature, c("x", "size")),
      identical(packageSlot(sample), "base"),
      ## default method must still work:
      identical({set.seed(3); sample(3)}, 1:3))
## failed in R 2.11.0

## Still, signature is taken from "def"inition, if one is provided:
## (For test, qqplot must be a "simple" function:)
stopifnot(is.function(qqplot) && identical(class(qqplot), "function"))
setGeneric("qqplot", function(x, y, ...) standardGeneric("qqplot"))
stopifnot(is(qqplot, "standardGeneric"),
      identical(qqplot@signature, c("x","y")))
## failed for a day ~ 2005-05-26, for R-devel only