####--- S4 Methods (and Classes) --- see also ../src/library/methods/tests/ options(useFancyQuotes=FALSE) require(methods) assertCondition <- tools::assertCondition # "import" ##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: assertCondition(b & b, "error") assertCondition(b | 1, "error") assertCondition(TRUE & b, "error") ## 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), .hasSlot(f, "name"))# failed in R <= 2.13.1 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)) setMethod(as.double, "c2", function(x, ...) x@.Data+pi) x_c2 <- new("c2", pi) identical(as.numeric(x_c2),as.double(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(" ", format(match.call()),"\n")) setMethod("foo", signature(x = "m2"), function(x, ...) { cat(" ", format(match.call()),"\n") x <- as(x, "m1"); callGeneric() }) setMethod("foo", signature(x = "m3"), function(x, ...) { cat(" ", 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")) assertCondition( setMethod("test1", "numeric", function(x, name, printit) match.call()), "warning", "error")## 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( ) ## 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 namespace; 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) ; assertCondition(validObject(bad.f), "error") setClass("myF", contains = "factor") validObject(new("myF", ok.f)) assertCondition(validObject(new("myF", bad.f)), "error") 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 ## 'L$A@x <- ..' setClass("foo", representation(x = "numeric")) f <- new("foo", x = pi*1:2) L <- list() L$A <- f L$A@x[] <- 7 if( identical(f, L$A) ) stop("Oops! f is identical to L$A, even though not touched!") ## did not duplicate in 2.0.0 <= Rversion <= 2.11.1 ## prototypes for virtual classes: NULL if legal, otherwise 1st member ## OptionalPosixct above includes NULL stopifnot(is.null(getClass("OptionalPOSIXct")@prototype)) ## "IntOrChar" had invalid NULL prototype < 2.15.0 setClassUnion("IntOrChar", c("integer", "character")) stopifnot(is.integer(getClass("IntOrChar")@prototype)) ## produced an error < 2.15.0 stopifnot(identical(isGeneric("&&"), FALSE)) ## mapply() on S4 objects with a "non-primitive" length() method setClass("A", representation(aa="integer")) aa <- 11:16 a <- new("A", aa=aa) setMethod(length, "A", function(x) length(x@aa)) setMethod(`[[`, "A", function(x, i, j, ...) x@aa[[i]]) stopifnot(length(a) == 6, identical(a[[5]], aa[[5]]), identical(mapply(`*`, aa, rep(1:3, 2)), mapply(`*`, a, rep(1:3, 2)))) ## Up to R 2.15.2, internally 'a' is treated as if it was of length 1 ## because internal dispatch did not work for length().