| |
| R version 3.6.2 Patched (2020-02-12 r77795) -- "Dark and Stormy Night" |
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| |
| > ####--- S4 Methods (and Classes) --- see also ../src/library/methods/tests/ |
| > options(useFancyQuotes=FALSE) |
| > require(methods) |
| > assertError <- tools::assertError # "import" |
| > ##too fragile: showMethods(where = "package:methods") |
| > |
| > ## When this test comes too late, it fails too early in R <= 3.2.2 |
| > require(stats4) |
| Loading required package: stats4 |
| > detach("package:methods") |
| > require("methods") |
| Loading required package: methods |
| > cc <- methods::getClassDef("standardGeneric") |
| > cc ## (auto) print failed here, in R <= 3.2.2 |
| Class "standardGeneric" [package "methods"] |
| |
| Slots: |
| |
| Name: .Data generic package group |
| Class: function character character list |
| |
| Name: valueClass signature default skeleton |
| Class: character character optionalMethod call |
| |
| Extends: |
| Class "genericFunction", directly |
| Class "function", by class "genericFunction", distance 2 |
| Class "OptionalFunction", by class "function", distance 3 |
| Class "PossibleMethod", by class "function", distance 3 |
| Class "optionalMethod", by class "genericFunction", distance 4 |
| |
| Known Subclasses: "standardGenericWithTrace" |
| > stopifnot(.isMethodsDispatchOn()) ## was FALSE in R <= 3.2.2 |
| > |
| > |
| > ## Needs cached primitive generic for '$' |
| > new("envRefClass")# failed in R <= 3.2.0 |
| Reference class object of class "envRefClass" |
| > |
| > ##-- 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) |
| [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)) |
| > |
| > ## 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"))) |
| > 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") |
| [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. |
| > ## (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 |
| 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")}) |
| > 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) |
| > |
| > ## 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 |
| 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 |
| > |
| > 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 |
| Formal class 'c1' [package ".GlobalEnv"] with 2 slots |
| ..@ x : int [1:2] 1 2 |
| ..@ code: NULL |
| > ## |
| > |
| > 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} |
| > |
| > ## 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,] |
| [,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")) |
| > 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")) |
| [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")) |
| > 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")) |
| [1] "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) |
| 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")) |
| > setClass("B", representation(y = "character")) |
| > setClass("C", contains = c("A", "B"), representation(z = "logical")) |
| > 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)) |
| > (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 |
| > 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) |
| Note: method with signature 'brob#ANY' chosen for function '&', |
| target signature 'brob#brob'. |
| "ANY#brob" would also be valid |
| > 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())) |
| An object of class "Foo" |
| [,1] |
| [1,] NA |
| Slot "name": |
| [1] "Sam" |
| |
| > f2 <- new("Foo", .Data = diag(2), name="Diag")# explicit .Data |
| > (m <- as(f, "matrix")) |
| [,1] |
| [1,] NA |
| > ## 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.) |
| [,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") |
| > 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))) |
| 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 |
| > stopifnot(identical(wrapG(mm), Gfun(mm, TRUE)), |
| + identical(wrapG(mm,,2), Gfun(mm, FALSE))) |
| in 'myMat' method for 'Gfun() : extrarg= TRUE |
| in 'myMat' method for 'Gfun() : extrarg= TRUE |
| in 'myMat' method for 'Gfun() : extrarg= FALSE |
| in 'myMat' method for 'Gfun() : extrarg= FALSE |
| > |
| > 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 |
| > |
| > ## -- a variant of the above which failed in version <= 2.5.1 : |
| > setGeneric("Gf", function(x, ...) standardGeneric("Gf")) |
| [1] "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) |
| in 'mmat2' method for 'Gf() |
| matrix 3 x 3 ... |
| $x |
| [,1] [,2] [,3] |
| [1,] 1 0 0 |
| [2,] 0 1 0 |
| [3,] 0 0 1 |
| |
| $a1 |
| [1] "A1" |
| |
| $foo |
| [1] 3.14 |
| |
| > wrap2(m2, 10, answer.all = 42) |
| in 'mmat2' method for 'Gf() |
| matrix 3 x 3 ... |
| $x |
| [,1] [,2] [,3] |
| [1,] 1 0 0 |
| [2,] 0 1 0 |
| [3,] 0 0 1 |
| |
| $a1 |
| [1] "10" |
| |
| $answer.all |
| [1] 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) |
| [1] "fn test" |
| > |
| > setMethod("as.integer", "c1", function(x, ...) 42) |
| > as.integer(x_c1) |
| [1] 42 |
| > |
| > setMethod("as.logical", "c1", function(x, ...) NA) |
| > as.logical(x_c1) |
| [1] NA |
| > |
| > setMethod("as.complex", "c1", function(x, ...) pi+0i) |
| > as.complex(x_c1) |
| [1] 3.141593+0i |
| > |
| > setMethod("as.raw", "c1", function(x) as.raw(10)) |
| > as.raw(x_c1) |
| [1] 0a |
| > |
| > # 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)) |
| [1] TRUE |
| > |
| > |
| > setMethod(as.double, "c2", function(x, ...) x@.Data+pi) |
| > x_c2 <- new("c2", pi) |
| > identical(as.numeric(x_c2),as.double(x_c2)) |
| [1] TRUE |
| > |
| > ## '!' changed signature from 'e1' to 'x' in 2.6.0 |
| > setClass("foo", "logical") |
| > setMethod("!", "foo", function(e1) e1+NA) |
| Warning message: |
| For function '!', signature 'foo': argument in method definition changed from (e1) to (x) |
| > selectMethod("!", "foo") |
| Method Definition: |
| |
| function (x) |
| x + NA |
| |
| Signatures: |
| x |
| target "foo" |
| defined "foo" |
| > xx <- new("foo", FALSE) |
| > !xx |
| An object of class "foo" |
| [1] NA |
| > |
| > ## 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)) |
| [1] 0.05867604 |
| > library(stats4) # and keep on search() for tests below |
| > AIC(pfit(1:10)) # failed in R < 2.7.0 |
| [1] 0.05867604 |
| > |
| > ## 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")) |
| [1] "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) |
| <m1> foo(x = new("m1"), bla = TRUE) |
| > foo(new("m2"), bla = TRUE) |
| <m2> foo(x = new("m2"), bla = TRUE) |
| <m1> foo(x = x, bla = TRUE) |
| > foo(new("m3"), bla = TRUE) |
| <m3> foo(x = new("m3"), bla = TRUE) |
| <m2> foo(x = x, bla = TRUE) |
| <m1> foo(x = x, 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")) { |
| + 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(unname(as.matrix(pmin(D5N+1, 3))), |
| + pmin(as.matrix(D5N)+1, 3)), |
| + ## |
| + TRUE) |
| + } |
| Loading required package: Matrix |
| <sparse>[ <logic> ] : .M.sub.i.logical() maybe inefficient |
| > |
| > |
| > ## 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")) |
| [1] "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")) |
| Creating a new generic function for 'order' in the global environment |
| [1] "order" |
| > stopifnot(identical(rbind(1), matrix(1,1,1))) |
| > setGeneric("rbind", function(..., deparse.level=1) |
| + standardGeneric("rbind"), signature = "...") |
| Creating a new generic function for 'rbind' in the global environment |
| [1] "rbind" |
| > 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)) |
| [1] TRUE |
| > setClass("myF", contains = "factor") |
| > validObject(new("myF", ok.f)) |
| [1] TRUE |
| > assertError(validObject(new("myF", bad.f))) |
| > removeClass("myF") |
| [1] TRUE |
| > ## 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") |
| [1] 1 2 3 |
| > ## 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 |
| [1] 1 2 3 |
| attr(,"id") |
| [1] "An Example" |
| > setMethod('xtfrm', 'numWithId', function(x) x@.Data) |
| > xtfrm(x) |
| [1] 1 2 3 |
| > 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] |
| drop in C1-[ : FALSE |
| NULL |
| > y[1, drop=FALSE] |
| drop in C2-[ : FALSE |
| drop in C1-[ : FALSE |
| NULL |
| > ## 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 ... |
| List of 7 |
| $ names : logi TRUE |
| $ dimnames : logi TRUE |
| $ row.names: logi TRUE |
| $ class : chr "\"class\" is a reserved slot name and cannot be redefined" |
| $ comment : logi TRUE |
| $ dim : logi TRUE |
| $ tsp : logi TRUE |
| > 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"}) |
| Creating a generic function for 'sample' from package 'base' in the global environment |
| > 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")) |
| Creating a new generic function for 'qqplot' in the global environment |
| [1] "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)) |
| Creating a generic function for 'is.unsorted' from package 'base' in the global environment |
| > |
| > 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")) |
| function(x, y, ...) { |
| # comment |
| NULL |
| } |
| > getSrcref(getMethod("initialize", "MyClass")) |
| function(.Object, value) { |
| # comment |
| .Object@val <- value |
| return(.Object) |
| } |
| > |
| > |
| > ## PR#15691 |
| > setGeneric("fun", function(x, ...) standardGeneric("fun")) |
| [1] "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")) |
| [1] "f" |
| > setMethod("f", c("numeric", "missing"), function(x, y) x) |
| > try(?f(1)) |
| Error in .helpForCall(topicExpr, parent.frame()) : |
| no documentation for function 'f' and signature 'x = "numeric", y = "missing"' |
| > |
| > ## "..." is not handled |
| > setGeneric("f", function(...) standardGeneric("f")) |
| [1] "f" |
| > setMethod("f", "numeric", function(...) c(...)) |
| > try(?f(1,2)) |
| Error in .helpForCall(topicExpr, parent.frame()) : |
| no documentation for function 'f' and signature '... = "numeric"' |
| > |
| > ## defaults in the generic formal arguments are not considered |
| > setGeneric("f", function(x, y=0) standardGeneric("f")) |
| [1] "f" |
| > setMethod("f", c("numeric", "numeric"), function(x, y) x+y) |
| > try(?f(1)) |
| Error in .helpForCall(topicExpr, parent.frame()) : |
| no documentation for function 'f' and signature 'x = "numeric", y = "numeric"' |
| > |
| > ## Objects with S3 classes fail earlier |
| > setGeneric("f", function(x) standardGeneric("f")) |
| [1] "f" |
| > setMethod("f", "numeric", function(x) x) |
| > setOldClass(c("foo", "numeric")) |
| > n <- structure(1, class=c("foo", "numeric")) |
| > try(?f(n)) |
| Error in .helpForCall(topicExpr, parent.frame()) : |
| no documentation for function 'f' and signature 'x = "numeric"' |
| > ## 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) |
| + } |
| 'a' is not S4 yet |
| > 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!} |
| rbind2(<A>, <matrix>) : x@a done |
| > stopifnot(identical(om1, rbind2(obj1, mat1))) |
| rbind2(<A>, <matrix>) : x@a done |
| > rm(obj1,om1); removeClass("A") |
| [1] TRUE |
| > ## |
| > ## |
| > ###__ 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") |
| [1] TRUE |
| > ## |
| > ## |
| > ###__ 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) |
| m1 three m2 |
| [1,] 1 3 7 |
| [2,] 2 3 8 |
| [3,] 3 3 7 |
| [4,] 4 3 8 |
| > cbind(m1, three, m2, deparse.level = 0) # none |
| [,1] [,2] [,3] |
| [1,] 1 3 7 |
| [2,] 2 3 8 |
| [3,] 3 3 7 |
| [4,] 4 3 8 |
| > cbind(m1, three, m2+3, deparse.level = 1) # "m1" "three" |
| m1 three |
| [1,] 1 3 10 |
| [2,] 2 3 11 |
| [3,] 3 3 10 |
| [4,] 4 3 11 |
| > cbind(m1, three, m2+3, deparse.level = 2) -> m3 |
| > m3 # .... and "m2 + 3" |
| m1 three m2 + 3 |
| [1,] 1 3 10 |
| [2,] 2 3 11 |
| [3,] 3 3 10 |
| [4,] 4 3 11 |
| > 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)) |
| [1] TRUE |
| > validObject(D. <- new("D2", a, design = data.frame(x = 1))) |
| [1] TRUE |
| > ## 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 |
| [1] TRUE |
| > 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")) |
| [1] TRUE |
| > stopifnot(c("package", "names") %in% slotNames(sig)) |
| > str(sig) # failed, too |
| Formal class 'signature' [package "methods"] with 3 slots |
| ..@ .Data : chr "mle" |
| ..@ names : chr "obj" |
| ..@ package: chr "" |
| > |
| > 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")) |
| Loading required package: 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") |
| [1] "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) |
| An object of class "mySubInteger" |
| [1] 1 |
| attr(,"class") |
| [1] "myInteger" |
| > ## caused infinite recursion in R 3.3.0 |
| > |
| > 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"))) |
| [1] "Hi" |
| > stopifnot(require("methods")) |
| Loading required package: 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") |
| Found more than one class "htest1" in cache; using the first, from namespace 'package1' |
| Also defined by 'package2' |
| > 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") |
| [1] "genericExtraArg" |
| > |
| > 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") |
| [1] "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 = "...") |
| [1] "f" |
| > 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")) 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)) |
| + (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"), m) |
| + , identical(as(c2, "matrix"), m) |
| + , identical(as(c3, "matrix"), m) |
| + ) |
| + invisible(lapply(c("Z","C","C2","C3"), removeClass)) |
| + }) |
| > 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)) |
| > (mC <- as(m, "dgCMatrix")) |
| 3 x 5 sparse Matrix of class "dgCMatrix" |
| |
| [1,] . 1 . . 2 |
| [2,] . . 2 . 1 |
| [3,] 2 . 1 . . |
| > (cc <- as(mC, "C")) |
| 3 x 5 sparse Matrix of class "C" |
| |
| [1,] . 1 . . 2 |
| [2,] . . 2 . 1 |
| [3,] 2 . 1 . . |
| > c2 <- as(mC, "C2") |
| > c3 <- as(mC, "C3") |
| > stopifnot(identical(capture.output(c2), sub("C3", "C2", capture.output(c3))), |
| + identical(as(cc, "matrix"), m), identical(as(c2, "matrix"), m), identical(as(c3, |
| + "matrix"), m)) |
| > invisible(lapply(c("Z", "C", "C2", "C3"), removeClass)) |
| > |
| > |
| > ## 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") |
| value <- new("A") |
| > ## was ... <- new(structure("A", package = ".GlobalEnv")) |
| > ## for a few days in R-devel (Nov.2017) |
| > |
| > |
| > ## 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 |
| > |
