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#### Formal classes & methods
#### - Started by moving checks from ./reg-S4.R:
### all "Matrix" + "late_and_no-relevant-print" now here
#### - No *.Rout.save <==> use stopifnot() etc for testing
#### - Recommended packages allowed, e.g., "Matrix"
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)),
is.function(Matrix::crossprod), # needed Matrix 1.6-1.1 for R-devel, Sep.2023
##
TRUE)
## R's internal C R_check_class_and_super() was not good enough
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)
show(mC <- as(m, "dgCMatrix"))
show(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))
## classUnion <--> class hierarchy :
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")
## 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))
## 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
## Error message of "unable to find .. method" now lists signature argument names:
setGeneric("BaseGeneric", \(x, y, ...) standardGeneric("BaseGeneric"))
setMethod("BaseGeneric", signature(x = "numeric", y = "numeric"), \(x,y, ...) x + y)
errXY <- try(BaseGeneric(X = 1, Y = 2))
err1 <- try(BaseGeneric(1))
err1Y <- try(BaseGeneric(1, Y = 2))
stopifnot(exprs = {
identical(3, BaseGeneric(1, 2))
inherits(errXY, "try-error")
grepl('x = "missing", y = "missing"', attr(errXY,"condition")$message)
inherits(err1, "try-error")
grepl('x = "numeric", y = "missing"', attr(err1, "condition")$message)
identical(err1, err1Y) # (as $call is empty)
})
## PR#17496: sealClass()
setClass("foo", slots = c(name = "character"), sealed = TRUE)
stopifnot(isSealedClass("foo"))
tools::assertError(setClass("foo"))
stopifnot(removeClass("foo"))
setClass("foo")
sealClass("foo") # failed in R < 4.5.0
stopifnot(isSealedClass("foo"))
stopifnot(removeClass("foo"))
## show(<non-syntactic name>) should recommend backticks for showMethods()
stopifnot(any(grepl("showMethods(`body<-`)", capture.output(show(`body<-`)), fixed=TRUE)))
## show( <genericFunction>) should use correct " Use showMethods(.....) for ...."
pkg <- "Matrix"
if(length(P <- grep(pkg, search(), fixed=TRUE, value=TRUE)))
detach(P, character.only=TRUE, force=TRUE)
(hasME <- requireNamespace(pkg, quietly=TRUE, lib.loc = .Library))
if(hasME) {
capture.output( show(Matrix::"diag<-") ) |> tail(1) -> out1
stopifnot(grepl("showMethods(Matrix::`diag<-`)", out1, fixed=TRUE))
##
if(require(pkg, character.only=TRUE)) {
capture.output( show(Matrix::"diag<-") ) |> tail(1) -> out1
stopifnot(grepl("showMethods(`diag<-`)", out1, fixed=TRUE))
detach(paste0("package:", pkg), character.only=TRUE, unload=TRUE)
} else
unloadNamespace(pkg)
}
## trace(), debug() etc for coerce methods -- PR#18823
trr <- quote(list(.Generic, .Method, .defined, .target))
sig <- c("ANY", "logical")
m0 <- selectMethod(coerce, signature = sig)
a0 <- as(0, "logical") # just `FALSE`
trace(coerce, tracer = trr, signature = sig)
m1 <- selectMethod(coerce, signature = sig)
a1 <- as(0, "logical") # error "object '.Generic' not found" in R <= 4.4.3
untrace(coerce, signature = sig)
m2 <- selectMethod(coerce, signature = sig)
stopifnot( is(m0, "MethodDefinition"),
!is(m0, "MethodDefinitionWithTrace"),
is(m1, "MethodDefinitionWithTrace"),
identical(m0, m2), identical(a0, a1))
## Checking that "simple" as() still works:
setClass("A", slots = c(x = "NULL"))
setClass("B", slots = c(x = "NULL"))
setIs("A", "B",
test = function(.) { TRUE },
coerce = function(.) new("B"),
replace = function(., value) new("B"))
B <- as(new("A"), "B") ## gave Error in asMethod@generic : ... `@` applied to ... "function"
stopifnot(identical(B, new("B")))
cat('Time elapsed: ', proc.time(),'\n')
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