@r-universe/webr 2023.6.11 → 2023.6.21

package/dist/vfs/usr/lib/R/tests/reg-S4.R

@@ -0,0 +1,1024 @@
+####--- S4 Methods (and Classes)  --- see also ../src/library/methods/tests/
+
+#### Instead of adding more tests depending on recommended packages,
+#### re-facror into a separate script and treat like eval-etc-2.R
+
+options(useFancyQuotes=FALSE)
+require(methods)
+assertError <- tools::assertError # "import"
+##too fragile: showMethods(where = "package:methods")
+
+## When this test comes too late, it failed too early in R <= 3.2.2
+require(stats4)
+detach("package:methods")
+require("methods")
+cc <- methods::getClassDef("standardGeneric")
+cc ## (auto) print failed here, in R <= 3.2.2
+stopifnot(.isMethodsDispatchOn()) ## was FALSE in R <= 3.2.2
+
+
+## Needs cached primitive generic for '$'
+new("envRefClass")# failed in R <= 3.2.0
+
+##-- 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)
+
+cn <- "integer or NULL"
+setClassUnion(cn, members = c("integer", "NULL"))
+setClass("c1", representation(x = "integer", code = cn))
+stopifnot(exprs = {
+    cn %in% extends(getClass("NULL"))
+    cn %in% extends(getClass(".NULL"))
+    cn %in% extends(getClass("integer"))
+})
+nc <- new("c1", x = 1:2)
+str(nc)# gave ^ANULL^A in 2.0.0
+##
+
+showMethods("coerce", classes=c("matrix", "numeric"))
+## {gave wrong result for a while in R 2.4.0}
+
+## Most for "mle" in stats4:
+for(f in c("coef", "confint", "logLik", "plot", "profile",
+	   "show", "summary", "update", "vcov"))
+    if(!hasMethods(f)) stop("no S4 methods found for ", f)
+
+
+##--- "[" 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(b & b)
+assertError(b | 1)
+assertError(TRUE & b)
+
+
+## methods' hidden cbind() / rbind:
+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, methods:::cbind(m)), 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 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),
+	  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"
+
+if(require("Matrix", lib.loc = .Library, quietly = TRUE)) {
+    D5. <- Diagonal(x = 5:1)
+    D5N <- D5.; D5N[5,5] <- NA
+    stopifnot(isGeneric("dim", where=as.environment("package:Matrix")),
+	      identical(D5., pmin(D5.)),
+	      identical(D5., pmax(D5.)),
+	      identical(D5., pmax(D5., -1)),
+	      identical(D5., pmin(D5., 7)),
+	      inherits((D5.3 <- pmin(D5.+2, 3)), "Matrix"),
+	      identical(as.matrix(pmin(D5.+2 , 3)),
+			pmin(as.matrix(D5.+2), 3)),
+	      identical(pmin(1, D5.), pmin(1, as.matrix(D5.))),
+	      identical(D5N, pmax(D5N, -1)),
+	      identical(D5N, pmin(D5N, 5)),
+	      identical(as.matrix(pmin(D5N +1, 3)),
+			pmin(as.matrix(D5N)+1, 3)),
+	      ##
+	      TRUE)
+} else
+    message("skipping tests requiring the Matrix package")
+
+
+## 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"))
+tools::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( <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 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) ; 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))# "integer" is "numeric"
+## 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
+## "IntOrChar" had invalid NULL prototype < 2.15.0
+setClassUnion("IntOrChar", c("integer", "character"))
+stopifnot(exprs = {
+    ## OptionalPosixct above includes NULL
+    is.null   (getClass("OptionalPOSIXct")@prototype)
+    is.integer(getClass("IntOrChar")      @prototype) ## produced an error < 2.15.0
+    "IntOrChar" %in% extends(getClass("character"))
+    "IntOrChar" %in% extends(getClass("integer"))
+    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]])
+setMethod(`[`,    "A", function(x, i, j, ...) new("A", aa = x@aa[i]))
+setMethod("is.na","A", function(x) is.na(x@aa))
+stopifnot(length(a) == 6, identical(a[[5]], aa[[5]]),
+          identical(a, rev(rev(a))), # using '['
+	  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().
+
+setMethod("is.unsorted", "A", function(x, na.rm, strictly)
+    is.unsorted(x@aa, na.rm=na.rm, strictly=strictly))
+
+stopifnot(!is.unsorted(a), # 11:16 *is* sorted
+	  is.unsorted(rev(a)))
+
+# getSrcref failed when rematchDefinition was used
+text <- '
+setClass("MyClass", representation(val = "numeric"))
+setMethod("plot", signature(x = "MyClass"),
+    function(x, y, ...) {
+        # comment
+	NULL
+    })
+setMethod("initialize", signature = "MyClass",
+    function(.Object, value) {
+	# comment
+	.Object@val <- value
+	return(.Object)
+    })
+'
+source(textConnection(text), keep.source = TRUE)
+getSrcref(getMethod("plot", "MyClass"))
+getSrcref(getMethod("initialize", "MyClass"))
+
+
+## PR#15691
+setGeneric("fun", function(x, ...) standardGeneric("fun"))
+setMethod("fun", "character", identity)
+setMethod("fun", "numeric", function(x) {
+  x <- as.character(x)
+  callGeneric()
+})
+
+stopifnot(identical(fun(1), do.call(fun, list(1))))
+## failed in R < 3.1.0
+
+
+## PR#15680
+setGeneric("f", function(x, y) standardGeneric("f"))
+setMethod("f", c("numeric", "missing"), function(x, y) x)
+try(?f(1))
+
+## "..." is not handled
+setGeneric("f", function(...) standardGeneric("f"))
+setMethod("f", "numeric", function(...) c(...))
+try(?f(1,2))
+
+## defaults in the generic formal arguments are not considered
+setGeneric("f", function(x, y=0) standardGeneric("f"))
+setMethod("f", c("numeric", "numeric"), function(x, y) x+y)
+try(?f(1))
+
+## Objects with S3 classes fail earlier
+setGeneric("f", function(x) standardGeneric("f"))
+setMethod("f", "numeric", function(x) x)
+setOldClass(c("foo", "numeric"))
+n <- structure(1, class=c("foo", "numeric"))
+try(?f(n))
+## different failures in R < 3.1.0.
+
+
+## identical() did not look at S4 bit:
+a <- 1:5
+b <- setClass("B", "integer")(a)
+stopifnot(is.character(all.equal(a, b)))
+attributes(a) <- attributes(b)
+if(!isS4(a)) { # still (unfortunately)
+    message("'a' is not S4 yet")
+    if(identical(a,b)) stop("identical() not looking at S4 bit")
+    ## set S4 bit manually:
+    a <- asS4(a)
+}
+stopifnot(identical(a, b), isS4(a))
+## failed in R <= 3.1.1
+
+
+### cbind(), rbind() now work both via rbind2(), cbind2() and rbind.
+##__ 1) __
+setClass("A", representation(a = "matrix"))
+setMethod("initialize", signature(.Object = "A"),
+    function(.Object, y) {
+      .Object@a <- y
+      .Object
+    })
+setMethod("rbind2", signature(x = "A", y = "matrix"),
+    function(x, y, ...) {
+      cat("rbind2(<A>, <matrix>) : ")
+      x@a <- rbind(x@a, y)
+      cat(" x@a done\n")
+      x
+    })
+setMethod("dim", "A", function(x) dim(x@a))
+mat1 <- matrix(1:9, nrow = 3)
+obj1 <- new("A", 10*mat1)
+om1 <- rbind(obj1, mat1)## now does work {it does need a working "dim" method!}
+stopifnot(identical(om1, rbind2(obj1, mat1)))
+rm(obj1,om1); removeClass("A")
+##
+##
+###__ 2) --- Matrix --- via cbind2(), rbind2()
+## this has its output checked strictly, so test depending on Matrix
+## has been moved to reg-tests-3.R
+##
+###__ 3) --- package 'its' like
+setClass("its",representation("matrix", dates="POSIXt"))
+m <- outer(1:3, setNames(1:5,LETTERS[1:5]))
+im <- new("its", m, dates=as.POSIXct(Sys.Date()))
+stopifnot(identical(m, im@.Data))
+ii  <- rbind(im, im-1)
+i.i <- cbind(im, im-7)
+stopifnot(identical(m, rbind(im)),
+          identical(m, cbind(im)),
+          identical(ii , rbind(m, m-1)),
+          identical(i.i, cbind(m, m-7)))
+rm(im, ii, i.i)
+removeClass("its")
+##
+##
+###__ 4) --- pkg 'mondate' like --
+setClass("mondate",
+         slots = c(timeunits = "character"), contains = "numeric")
+three <- 3
+m1 <- new("mondate", 1:4, timeunits = "hrs")
+m2 <- new("mondate", 7:8, timeunits = "min")
+stopifnot(identical(colnames(cbind(m1+1, deparse.level=2)), "m1 + 1"),
+          is.null  (colnames(cbind(m1+1, deparse.level=0))),
+          is.null  (colnames(cbind(m1+1, deparse.level=1))),
+          identical(colnames(cbind(m1)), "m1"),
+          colnames(cbind(m1  , M2 = 2, deparse.level=0)) == c(""  , "M2"),
+          colnames(cbind(m1  , M2 = 2))                  == c("m1", "M2"),
+          colnames(cbind(m1  , M2 = 2, deparse.level=2)) == c("m1", "M2"),
+          colnames(cbind(m1+1, M2 = 2, deparse.level=2)) == c("m1 + 1", "M2"),
+          colnames(cbind(m1+1, M2 = 2, deparse.level=1)) == c("",       "M2"))
+cbind(m1, three, m2)
+cbind(m1, three, m2,   deparse.level = 0) # none
+cbind(m1, three, m2+3, deparse.level = 1) # "m1" "three"
+cbind(m1, three, m2+3, deparse.level = 2) -> m3
+m3 #    ....  and "m2 + 3"
+stopifnot(identical(t(m3), rbind(m1, three, m2+3, deparse.level = 2)),
+          identical(cbind(m1, m2) -> m12,
+                    cbind(m1=m1@.Data, m2=m2@.Data)),
+          identical(rbind(m1, m2), t(m12)),
+          identical(cbind(m1, m2, T=T, deparse.level=0),
+                    cbind(m1@.Data, m2@.Data, T=T) -> mm),
+          identical(colnames(mm), c("", "", "T")),
+          identical(cbind(m1, m2, deparse.level=0),
+                    cbind(m1@.Data, m2@.Data)))
+##
+## Cleanup all class definitions etc -- seems necessary for the following "re"-definitions:
+invisible(lapply(getClasses(globalenv()), removeClass))
+nn <- names(globalenv())
+rm(list = c("nn", nn))
+
+## Using "data.frame" in a slot -- all have worked for long:
+setClass("A", representation(slot1="numeric", slot2="logical"))
+setClass("D1", contains="A", representation(design="data.frame"))
+setClass("D2", contains="D1")
+validObject(a <- new("A", slot1=77, slot2=TRUE))
+validObject(D. <- new("D2", a, design = data.frame(x = 1)))
+## using "formula" in a slot -- from Hervé Pages :
+setClass("B", contains="A", representation(design="formula"))
+setClass("C", contains="B")
+##
+a <- new("A", slot1=77, slot2=TRUE)
+validObject(C1 <- new("C", a, design = x ~ y))# failed for R <= 3.2.0
+C2 <- new("C", slot1=a@slot1, slot2=a@slot2, design=x ~ y)
+stopifnot(identical(C1, C2),
+	  identical(formula(), formula(NULL)),
+	  length(N <- new("formula")) == 0, inherits(N, "formula"),
+	  length(N <- new("table")  ) == 0, is.table(N),
+	  validObject(N <- new("summary.table")),
+	  length(N <- new("ordered")) == 0, is.ordered(N))
+## formula() and new("formula"), new("..") also failed  in R <= 3.2.0
+
+require("stats4")# -> "mle" class
+validObject(sig <- new("signature", obj = "mle"))
+stopifnot(c("package", "names") %in% slotNames(sig))
+str(sig) # failed, too
+
+cl4 <- getClasses("package:stats4")
+stopifnot(identical(getClasses(which(search() == "package:stats4")), cl4),
+	  c("mle", "profile.mle", "summary.mle") %in% cl4)
+## failed after an optimization patch
+
+detach("package:methods", force=TRUE)
+C1@slot1 <- pi
+stopifnot(identical(C1@slot1, pi))
+stopifnot(require("methods"))
+## Slot assignment failed in R <= 3.2.2, C code calling checkAtAssignment()
+
+## Error in argument evaluation of S4 generic - PR#16111
+f <- function() {
+    signal <- FALSE
+    withCallingHandlers({ g(sqrt(-1)) }, warning = function(w) {
+        signal <<- TRUE
+        invokeRestart("muffleWarning")
+    })
+    signal
+}
+g <- function(x) x
+op <- options(warn = 2)# warnings give errors
+stopifnot(isTRUE( f() ))
+setGeneric("g")
+stopifnot(isTRUE( f() ))
+options(op)
+## the second  f()  gave a warning and FALSE in  R versions  2.12.0 <= . <= 3.2.3
+
+
+stopifnot(
+    identical(formals(getGeneric("as.vector")), formals(base::as.vector)),
+    identical(formals(getGeneric("unlist")),    formals(base::unlist)))
+## failed for a while in R-devel (3.3.0)
+
+setClass("myInteger", contains=c("integer", "VIRTUAL"))
+setClass("mySubInteger", contains="myInteger")
+new("mySubInteger", 1L)
+## caused infinite recursion in R 3.3.0
+new("mySubInteger")
+## failed due to lack of prototype in R 3.6.0
+
+detach("package:methods", force=TRUE)
+methods::setClass("test1", methods::representation(date="POSIXct"))
+methods::setClass("test2", contains="test1")
+test <- function(x) UseMethod('test', x)
+test.test1 <- function(x) 'Hi'
+test(methods::new("test2", date=as.POSIXct("2003-10-09")))
+stopifnot(require("methods"))
+## S3 dispatch to superclass methods failed on S4 objects when
+## methods package was not attached
+
+
+## Tests for class fetching and conflict resolution
+setClass("htest1", slots=c(a="numeric",b="data.frame"), package="package1")
+setClass("htest2", slots=c(a="logical"), package="package2")
+class.list = list(
+    package1=getClassDef("htest1", where=class_env1),
+    package2=getClassDef("htest2", where=class_env2)
+)
+
+firstclass  <- methods:::.resolveClassList(class.list,.GlobalEnv,
+                                           package="package1")
+secondclass <- methods:::.resolveClassList(class.list,.GlobalEnv,
+                                           package="package2")
+alsofirstclass <- methods:::.resolveClassList(class.list,.GlobalEnv,
+                                              package="package3")
+stopifnot(!identical(firstclass, secondclass))
+stopifnot(identical(firstclass, class.list[[1]]))
+stopifnot(identical(secondclass, class.list[[2]]))
+stopifnot(identical(alsofirstclass, class.list[[1]]))
+
+## implicit coercion of S4 object to vector via as.vector() in sub-assignment
+setClass("A", representation(stuff="numeric"))
+as.vector.A <- function (x, mode="any") x@stuff
+v <- c(3.5, 0.1)
+a <- new("A", stuff=v)
+x <- y <- numeric(10)
+x[3:4] <- a
+y[3:4] <- v
+stopifnot(identical(x, y))
+
+## callNextMethod() was broken when augmenting args of primitive generics
+foo <- setClass("foo")
+bar <- setClass("bar", contains = "foo")
+
+setMethod("[", "foo",  function(x, i, j, ..., flag = FALSE, drop = FALSE) {
+    flag
+})
+
+setMethod("[", "bar", function(x, i, j, ..., flag = FALSE, drop = FALSE) {
+    callNextMethod()
+})
+
+BAR <- new("bar")
+stopifnot(identical(BAR[1L], FALSE))
+stopifnot(identical(BAR[1L, , flag=TRUE], TRUE))
+
+## avoid infinite recursion on Ops,structure methods
+setClass("MyInteger",
+         representation("integer")
+         )
+i <- new("MyInteger", 1L)
+m <- matrix(rnorm(300), 30,10)
+stopifnot(identical(i*m, m))
+
+## when rematching, do not drop arg with NULL default
+setGeneric("genericExtraArg",
+           function(x, y, extra) standardGeneric("genericExtraArg"),
+           signature="x")
+
+setMethod("genericExtraArg", "ANY", function(x, y=NULL) y)
+
+stopifnot(identical(genericExtraArg("foo", 1L), 1L))
+
+## callNextMethod() was broken for ... dispatch
+f <- function(...) length(list(...))
+setGeneric("f")
+setMethod("f", "character", function(...){ callNextMethod() })
+stopifnot(identical(f(1, 2, 3), 3L))
+stopifnot(identical(f("a", "b", "c"), 3L))
+
+## ... dispatch was evaluating missing arguments in the generic frame
+f <- function(x, ..., a = b) {
+    b <- "a"
+    a
+}
+setGeneric("f", signature = "...")
+stopifnot(identical(f(a=1), 1))
+stopifnot(identical(f(), "a"))
+
+## ensure forwarding works correctly for dots dispatch
+f2 <- function(...) f(...)
+stopifnot(identical(f2(a=1), 1))
+
+
+## R's internal C  R_check_class_and_super()  was not good enough
+if(require("Matrix", lib.loc = .Library, quietly = TRUE)) { withAutoprint({
+    setClass("Z", representation(zz = "list"))
+    setClass("C", contains = c("Z", "dgCMatrix"))
+    setClass("C2", contains = "C")
+    setClass("C3", contains = "C2")
+    m <- matrix(c(0,0,2:0), 3,5, dimnames = list(NULL,NULL))
+    m2 <- matrix(c(0,0,2:0), 3,5)
+    (mC <- as(m, "dgCMatrix"))
+    (cc <- as(mC, "C"))
+     c2 <- as(mC, "C2")
+     c3 <- as(mC, "C3")
+    stopifnot(
+        identical(capture.output(c2),
+                  sub("C3","C2", capture.output(c3)))
+      , identical(as(cc, "matrix"), m2) # changed for Matrix 1.5-x
+      , identical(as(c2, "matrix"), m2)
+      , identical(as(c3, "matrix"), m2)
+    )
+    invisible(lapply(c("Z","C","C2","C3"), removeClass))
+ })
+} else
+    message("skipping tests requiring the Matrix package")
+
+
+## Automatic coerce method creation:
+setClass("A", slots = c(foo = "numeric"))
+setClass("Ap", contains = "A", slots = c(p = "character"))
+cd <- getClassDef("Ap")
+body(cd@contains[["A"]]@coerce)[[2]] ## >>   value <- new("A")
+## was ... <-  new(structure("A", package = ".GlobalEnv"))
+## for a few days in R-devel (Nov.2017)
+
+
+## Error messages occurring during method selection are forwarded
+f <- function(x) x
+setGeneric("f")
+setMethod("f", signature("NULL"), function(x) NULL)
+err <- tryCatch(f(stop("this is mentioned")), error = identity)
+stopifnot(identical(err$message, "error in evaluating the argument 'x' in selecting a method for function 'f': this is mentioned"))
+
+
+## canCoerce(obj, .)  when length(class(obj)) > 1 :
+setOldClass("foo")
+setAs("foo", "A", function(from) new("A", foo=from))
+o3 <- structure(1:7, class = c("foo", "bar"))
+stopifnot( canCoerce(o3, "A") )
+## failed in R <= 3.6.1
+
+if(require("Matrix", lib.loc = .Library, quietly = TRUE)) { withAutoprint({
+    sci <- names(getClass("integer")@contains)
+    # These 2 classes have *nothing* to do with Matrix:
+    setClass("MyClass")
+    ncl <- "NumOrMyClass"
+    setClassUnion(ncl, c("numeric", "MyClass"))
+    nsci <- names(getClass("integer")@contains)
+    ## failed in R <= 3.6.2
+    stopifnot(sci %in% nsci, identical(setdiff(nsci, sci), ncl))
+
+    setClassUnion('dMatrixOrMatrix', members = c('dMatrix', 'matrix'))
+    ## failed in R <= 3.6.2
+    stopifnot("dMatrixOrMatrix" %in% names(getClass("dgCMatrix")@contains))
+
+    invisible(lapply(c("NumOrMyClass", "MyClass", "dMatrixOrMatrix"),
+                     removeClass))
+})
+} else
+    message("skipping tests requiring the Matrix package")
+
+setClass("foo", slots = c(y = "numeric"))
+setClass("bar", contains = "foo")
+body(getClass("bar")@contains[[1]]@coerce)[[2]]