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## Regression tests for R >= 4.3.0.pt <- proc.time()tryCid <- function(expr) tryCatch(expr, error = identity)tryCmsg<- function(expr) tryCatch(expr, error = conditionMessage) # typically == *$messageassertErrV <- function(...) tools::assertError(..., verbose=TRUE)`%||%` <- function (L, R) if(is.null(L)) R else L##' get value of `expr` and keep warning as attribute (if there is one)getVaW <- function(expr) {W <- NULLwithCallingHandlers(val <- expr,warning = function(w) {W <<- conditionMessage(w)invokeRestart("muffleWarning") })structure(val, warning = W)}options(nwarnings = 10000, # (rather than just 50)warn = 2, # only caught or asserted warningswidth = 99) # instead of 80onWindows <- .Platform$OS.type == "windows"englishMsgs <- {## 1. LANGUAGE takes precedence over locale settings:if(nzchar(lang <- Sys.getenv("LANGUAGE")))lang == "en"else { ## 2. Query the localeif(!onWindows) {## sub() :lc.msgs <- sub("\\..*", "", print(Sys.getlocale("LC_MESSAGES")))lc.msgs == "C" || substr(lc.msgs, 1,2) == "en"} else { ## Windowslc.type <- sub("\\..*", "", sub("_.*", "", print(Sys.getlocale("LC_CTYPE"))))lc.type == "English" || lc.type == "C"}}}cat(sprintf("English messages: %s\n", englishMsgs))Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = "true")# just in case## very small size hashed environmentsn <- 123l <- setNames(vector("list", n), seq_len(n))ehLs <- lapply(1:6, function(sz) list2env(l, hash=TRUE, size = sz))(nch <- vapply(ehLs, \(.) env.profile(.)$nchains, 0))# gave 1 2 3 4 109 109stopifnot(nch >= 24) # seeing 106 .. 106 111## hashed environments did not grow for size <= 4 in R <= 4.1.x## as.character.Rd(deparse = TRUE) with curly braces in TEXT -- PR#18324rd <- tools::parse_Rd(textConnection(txt0 <- r"(\link[=Paren]{\{})"),fragment = TRUE)cat(txt1 <- paste0(as.character(rd, deparse = TRUE), collapse = ""))stopifnot(identical(paste0(txt0, "\n"), txt1))## failed to re-escape curly brace in R <= 4.2.x## curly braces used for grouping tokens are not escaped:rdgroup <- tools::parse_Rd(textConnection(r"(a {b} c)"), fragment = TRUE)stopifnot(identical(as.character(rdgroup, deparse = TRUE),as.character(rdgroup, deparse = FALSE)))#### Errors from parsing (notably with |> ) now return *classed* errors with line numbers## From PR#18328 - by Duncan Murdochtxts <- setNames(, c("f <- function(x, x) {}", "123 |> str", "123 |> return()", "123 |> `+`(_, 4)", "123 |> (_ + 4)", "123 |> f(a = _, b = _)", "123 |> (\\(x) foo(bar = _))()", "123 |> x => log(x)", "'\\uh'", "'\\Uh'", "'\\xh'", "'\\c'", "'\\0'", "'\\U{badf00d}", "'\\Ubadf00d"))errs <- lapply(txts, function(ch) tryCatch(parse(text = ch), error=identity))## nicely print themmsgs <- lapply(errs, `[[`, "message") ; str(msgs)(cls <- t(sapply(errs, class)))uerrs <- unname(errs) # (speed)nL <- vapply(uerrs, `[[`, 0L, "lineno")nC <- vapply(uerrs, `[[`, 0L, "colno")stopifnot(exprs = {vapply(uerrs, inherits, NA, what = "error")vapply(uerrs, inherits, NA, what = "parseError")nL == 1LnC == c(18L, rep(8L, 6), 10L, rep(3L, 5), 12L, 10L)## see all "<l>:<n>" strings as part of the message:mapply(grepl, paste(nL, nC, sep = ":"), msgs)})## gave just simpleError s; no line:column numbers in R <= 4.2.0## fisher.test() with "too full" table: PR#18336d <- matrix(c(1,0,5,2,1,90,2,1,0,2,3,89,0,0,0,1,0,14,0,0,0,0,0, 5,0,0,0,0,0, 2,0,0,0,0,0, 2), nrow=6, byrow = TRUE)(r <- tryCid(fisher.test(d)))stopifnot(inherits(r, "error"))if(englishMsgs)stopifnot(grepl("hash key .* > INT_MAX", conditionMessage(r)))## gave a seg.fault in R <= 4.2.0## Testing fix for PR#18344 [ tar() warning about illegal uid/gid ]:sys <- Sys.info() # Only 'root' can create files with illegal uid/gidif(sys[["sysname"]] == "Linux" & sys[["effective_user"]] == "root"## not a "weakened root". Or just && !nzchar(Sys.getenv("container")) :&& !(Sys.getenv("container") %in% c("oci", "docker", "podman"))) {dir.create(mdir <- file.path(tempdir(),"stuff"))for(f in letters[1:3])writeLines("first line", file.path(mdir, f))owd <- setwd(tempdir())system(paste("chown 654321 stuff/a")) ## system(paste("chgrp 123456 stuff/b"))r <- tryCatch( tar('stuff.tar', "stuff"), warning = identity)stopifnot(inherits(r, "warning"))if(englishMsgs)stopifnot(grepl("^invalid uid ", conditionMessage(r)))## cat("Inside directory ", getwd(),":\n"); system("ls -l stuff.tar")setwd(owd)# go back} elsemessage("You are not root, hence cannot change uid / gid to invalid values")## gave 2 warnings per wrong file; the first being In sprintf(gettext(....):## "one argument not used by format 'invalid uid value replaced .... 'nobody''"## sort(x, partial, *) notably for na.last=FALSE and TRUE -- PR#18335chkSortP <- function(x, partial) {stopifnot(partial == as.integer(partial),1 <= partial, partial <= length(x))nok <- sum(!is.na(x))if(anyNA(x) && any(partial > nok)) ## cannot use na.last=NALs <- c( FALSE,TRUE)else Ls <- c(NA,FALSE,TRUE)S <- lapply(Ls, function(v) sort(x, na.last=v))P <- lapply(Ls, function(v) sort(x, na.last=v, partial=partial))ok1 <- identical(lapply(S, `[`, partial),lapply(P, `[`, partial))## test "ones below" and "ones above" the (min and max) partialsmip <- min(partial)map <- max(partial)noNA <- function(u) u[!is.na(u)]chkPord <- function(y) {n <- length(y)all(noNA(y[if(mip > 1) 1L:(mip-1L)]) <= noNA(y[mip])) &&all(noNA(y[if(map < n) (map+1L):n]) >= noNA(y[map]))}ok1 && all(vapply(P, chkPord, logical(1)))}x <- c(7, 2, 4, 5, 3, 6, NA)x1 <- c( 2,3,1, NA)x2 <- c(NA,3,1, NA)x14 <- c(7, 2, 0, 8, -1, -2, 9, 4, 5, 3, 6, 1, NA,NA)stopifnot(exprs = {chkSortP(x, partial = 3)chkSortP(x, partial = c(3,5))chkSortP(x1, partial = 3)chkSortP(x1, partial = 4)chkSortP(x1, partial = 3:4)chkSortP(x2, partial = 4)chkSortP(x2, partial = 3)chkSortP(x2, partial = 2:4)sapply(seq_along(x14), function(p) chkSortP(x14, partial = p))chkSortP(x14, partial = c(10, 13))chkSortP(x14, partial = c(2, 14))})set.seed(17)for(i in 1:128) { # tested for 1:12800x <- runif(rpois(1, 100))x[sample(length(x), 12)] <- NAp <- sample(seq_along(x), size = max(1L, rpois(1, 3)))stopifnot(chkSortP(x, partial = p))}## several of these failed for na.last=FALSE and TRUE## head(letters, "7") should not silently do nonsense; PR#18357assertErrV( head(letters, "3") )## returned complete 'letters' w/o a warningstopifnot(identical("a", head(letters, TRUE)))## keep treating <logical> n as integer## x[[]] should give error in all cases, even for NULL; PR#18367(E <- tryCid(c(a = 1, 2)[[]]))xx <- c(a = 1, 2:3)E2 <- tryCid(xx[[]])EN <- tryCid(NULL[[]]) # <=> c()[[]]stopifnot(exprs = {inherits(E, "error")inherits(E, "MissingSubscriptError")identical(quote(c(a = 1, 2)[[]]), E$call)identical(class(E), class(E2))identical(class(E), class(EN))identical(msg <- "missing subscript", conditionMessage(E2))identical(msg, conditionMessage(EN))(nm <- c("call","object")) %in% names(EN)identical(EN[nm], list(call = quote(NULL[[]]), object = NULL))})## [[]] matched '2' as which has name ""E <- tryCid(xx[[]] <- pi)stopifnot(inherits(E, "MissingSubscriptError"))## using new error class## PR#18375, use PRIMNAME not *VAL in message:(M <- tryCmsg(date > 1))stopifnot(grepl("(>)", M, fixed=TRUE))## showed '(6)' previously## isGeneric() with wrong name -- correct warning msg (PR#18370)setGeneric("size", function(x) standardGeneric("size"))tryCatch(stopifnot(!isGeneric("haha", fdef = size)),warning = conditionMessage) -> msgmsg; if(englishMsgs)stopifnot(grepl("name .size. instead of .haha.", msg))## msg was confusing### poly(<Date>,*) etc: lm(... ~ poly(<Date>, .)) should work :d. <- data.frame(x = (1:20)/20, f = gl(4,5), D = .Date(17000 + c(1:7, 1:13 + 100)))cf0 <- c(Int=100, x=10, f = 5*(1:3))nD <- as.numeric(d.[,"D"])y0 <- model.matrix(~x+f, d.) %*% cf0 + 10*(nD - 17000) - 20*((nD - 17000)/10)^2set.seed(123)head(d. <- cbind(d., y = y0 + rnorm(20)))fm1 <- lm(y ~ x + f + poly(D,3), data = d.)fm1r <- lm(y ~ x + f + poly(D,2, raw=TRUE), data = d.)newd <- data.frame(x = seq(1/3, 1/2, length=5), f = gl(4,5)[5:9], D = .Date(17000 + 51:55))yhat <- unname(predict(fm1, newdata = newd))yh.r <- unname(predict(fm1r, newdata = newd))cbind(yhat, yh.r)stopifnot(all.equal(yhat, c(96.8869, 92.3821, 81.9967, 71.2076, 60.0147), tol=1e-6), # 3e-7all.equal(yh.r, c(97.7595, 93.0218, 82.3533, 71.2806, 59.8036), tol=1e-6))## poly(D, 3) failed since R 4.1.x, poly(.., raw=TRUE) in all earlier R versions## as.difftime() tweaks: coerce to "double", keep namesstopifnot(identical(as.difftime(c(x = 1L), units="secs"),.difftime(c(x = 1.), units="secs")))## integers where kept (and difftime arithmetic could overflow) in R <= 4.2.x## ordered() with missing 'x' -- PR#18389factor( levels = c("a", "b"), ordered=TRUE) -> o1ordered(levels = c("a", "b")) -> o2stopifnot(identical(o1,o2))## the ordered() call has failed in R <= 4.2.x## source() with multiple encodingsif (l10n_info()$"UTF-8" || l10n_info()$"Latin-1") {writeLines('x <- "fa\xE7ile"', tf <- tempfile(), useBytes = TRUE)tools::assertError(source(tf, encoding = "UTF-8"))source(tf, encoding = c("UTF-8", "latin1"))## in R 4.2.{0,1} gave Warning (that would now be an error):## 'length(x) = 2 > 1' in coercion to 'logical(1)'if (l10n_info()$"UTF-8") stopifnot(identical(Encoding(x), "UTF-8"))}## multi-line Rd macro definitionrd <- tools::parse_Rd(textConnection(r"(\newcommand{\mylongmacro}{\LaTeX}\mylongmacro)"), fragment = TRUE)tools::Rd2txt(rd, out <- textConnection(NULL, "w"), fragment = TRUE)stopifnot(any(as.character(rd) != "\n"),identical(textConnectionValue(out)[2L], "LaTeX")); close(out)## empty output in R <= 4.2.x## expand.model.frame() for non-data fits (PR#18414)y <- 1:10g <- gl(2, 5)fit <- lm(log(y) ~ g, subset = y > 3)mf <- expand.model.frame(fit, ~0)stopifnot(all.equal(fit$model, mf, check.attributes = FALSE))myexpand <- function(model) expand.model.frame(model, "y")stopifnot(identical(myexpand(fit)$y, 4:10)) # failed in R <= 1.4.1 (PR#1423)env <- list2env(list(y = y, g = g))rm(y, g)fit2 <- with(env, lm(log(y) ~ g, subset = y > 3))stopifnot(identical(myexpand(fit2)$y, 4:10)) # failed in R <= 4.2.1 with## Error in eval(predvars, data, env) : object 'y' not found## time() returning numbers very slightly on the wrong side of an integerx <- ts(2:252, start = c(2002, 2), freq = 12)true.year <- rep(2002:2022, each = 12)[-1]stopifnot(floor(as.numeric(time(x))) == true.year)## seen 10 differences in R <= 4.2.x## Sorted printing of factor analysis loadings with 1 factor, PR#17863f1 <- factanal(d <- mtcars[,1:4], factors = 1) ; print(f1, sort=TRUE)prl <- capture.output(print(loadings(f1), sort=TRUE))stopifnot(identical(1:4, charmatch(colnames(d),prl[charmatch("Loadings", prl)+ 1:4+1L])))## printed these as vector instead of 1-column matrix in R <= 4.2.x## print() of zero - length, PR#18422i0 <- integer(0)stopifnot(exprs = {identical("<0-length octmode>", capture.output(as.octmode(i0)))identical("<0-length hexmode>", capture.output(as.hexmode(i0)))identical("<0-length roman>", capture.output(as.roman (i0)))identical("person()", capture.output( person()))identical("bibentry()", capture.output( bibentry()))identical("<0-length citation>",capture.output( citation()[0L]))})## printed nothing at all or invalid R-code in R <= 4.2.x## isS3method() for names starting with a dotstopifnot(!isS3method(".Internal"))## failed with "invalid first argument" in R <= 4.2.x## cor.test.formula() scoping issue -- PR#18439form <- ~ CONT + INTGlocal({USJudgeRatings <- head(USJudgeRatings)stopifnot(cor.test(form, data = USJudgeRatings)$parameter == 4)})## R <= 4.2.x evaluated the constructed call in environment(formula)## PR # 18421 by Benjamin Feakins (and follow up):## ---------- "roman", "hexcode" and "octcode" all cannot easily be added to data framesfor(x in list(as.roman(1:14), as.octmode(1:11), as.hexmode(1:19), as.raw(0:65), (0:17) %% 7 == 0,as.difftime(c(0,30,60:64), units="mins"),seq(ISOdate(2000,2,10), by = "23 hours", length.out = 50))) {cat("x:"); str(x, vec.len=8)## the error can be triggered by the following methods:### 1. as.data.frame()dat1 <- as.data.frame(x) # now works, previously signalled## Error in as.data.frame.default(x) :## cannot coerce class ‘"roman"’ to a data.frame### 2. data.frame()dat2 <- data.frame(x) # gave error as above, now worksstopifnot(identical(dat1, dat2),identical( data.frame(my.x = x),as.data.frame(x, nm="my.x")))### 3. cbind()dat3 <- data.frame(y = seq_along(x))dat3 <- cbind(dat3, x) # gave error, now worksstopifnot(identical(dat2, dat3[,"x", drop=FALSE]))## These worked already previously:dat <- data.frame(x = integer(length(x)))dat$x <- xdatl <- list2DF(list(x=x))stopifnot(identical(dat, dat2),identical(dat, datl))}## --- such data.frame() coercions gave errors in R <= 4.2.x## Deprecation of {direct calls to} as.data.frame.<cls>()cls <- c("raw", "logical", "integer", "numeric", "complex","factor", "ordered", "Date", "difftime", "POSIXct","noquote", "numeric_version")names(cls) <- clsbe <- baseenv()asF <- lapply(cls, \(cl) be[[paste0("as.",cl)]] %||% be[[cl]])obs <- lapply(cls, \(cl) asF[[cl]](switch(cl, "difftime" = "2:1:0", "noquote" = letters, 1:2)))asDF <- lapply(cls, \(cl) getVaW(be[[paste0("as.data.frame.", cl)]](obs[[cl]])))r <- local({ g <- as.data.frame.logical; f <- function(L=TRUE) g(L)getVaW(f()) })dfWarn <- "deprecated.*as\\.data\\.frame\\.vector"stopifnot(exprs = {vapply(obs, \(.) class(.)[1], "") == clsvapply(asDF, is.data.frame, NA)## the first column of each data frame is of the original class:vapply(lapply(asDF, `[[`, 1), \(.) class(.)[1], "") == cls## all should have a deprecation warningis.character(asDwarn <- vapply(asDF, attr, "<text>", "warning"))!englishMsgs || all(grepl(dfWarn, asDwarn))length(unique(vapply(cls, \(cl) sub(cl, "<class>", asDwarn[[cl]], fixed=TRUE), ""))) == 1Lall.equal(r, data.frame(L=TRUE), check.attributes=FALSE)!englishMsgs || grepl(dfWarn, attr(r, "warning"))})## as.data.frame.<cls>(.) worked w/o deprecation warning in R <= 4.2.x## useMethod() dispatch error in case of long class strings - PR#18447mkCh <- function(n, st=1L) substr(strrep("123456789 ", ceiling(n/10)), st, n)useMethErr <- function(n=500, nrep=25)(function(.) UseMethod("foo")(.))(structure(1, class = paste(sep=":", format(1:nrep),mkCh(n, 2L + (nrep > 9)))))tools::assertError( useMethErr(500,25) )## gave a segfault in R <= 4.2.2clsMethErr <- function(...) {sub( '"[^"]*$', "",sub('^[^"]*"', "", tryCmsg(useMethErr(...))))}showC <- function(..., n1=20, n2=16) {r <- clsMethErr(...)cat(sprintf('%d: "%s<....>%s"\n', (nr <- nchar(r)),substr(r, 1,n1), substr(r, nr-n2, nr)))invisible(r)}invisible(lapply(11:120, function(n) showC(n, 1030 %/% n)))## (mostly the truncation works "nicely", but sometimes even misses the closing quote)## download.file() with invalid option -- PR#18455op <- options(download.file.method = "no way")Edl <- tryCid(download.file("http://httpbin.org/get", "ping.txt"))stopifnot(inherits(Edl, "error"),!englishMsgs || grepl("should be one of .auto.,", conditionMessage(Edl)))options(op)## error was "object 'status' not found" in R <= 4.2.2## handling of invalid Encoding / unsupported conversion in packageDescription()dir.create(pkgpath <- tempfile())writeLines(c("Version: 1.0", "Encoding: FTU-8"), # (sic!)file.path(pkgpath, "DESCRIPTION"))stopifnot(suppressWarnings(packageVersion(basename(pkgpath),dirname(pkgpath))) == "1.0")## outputs try()-catched iconv() errors but does not fail## gave a "packageNotFoundError" in 3.5.0 <= R <= 4.2.2## format.bibentry() with preloaded Rd macrosref <- bibentry("misc", author = "\\authors", year = 2023)macros <- tools::loadRdMacros(textConnection("\\newcommand{\\authors}{\\R}"))stopifnot(identical(print(format(ref, macros = macros)), "R (2023)."))## macro definitions were not used in R <= 4.2.2## predict.lm() environment used for evaluating offset -- PR#18456mod <- local({y <- rep(0,10)x <- rep(c(0,1), each=5)list(lm(y ~ x),lm(y ~ offset(x)))})stopifnot(exprs = {## works fine, using the x variable of the local environmentidentical(predict(mod[[1]], newdata=data.frame(z=1:10)),setNames(rep(0,10), as.character(1:10)))## gave error in offset(x) : object 'x' not found :identical(predict(mod[[2]], newdata=data.frame(z=1:10)),setNames(rep(c(-.5,.5), each=5), as.character(1:10)))})x <- rep(1,5)mod2 <- local({x <- rep(2,5) # 2, not 1y <- rep(0,5)lm(rep(0,5) ~ x + offset({ print("hello"); x+2*y }),offset = { print("world"); x-y })}) # rank-deficient in "subtle" way {warning/NA may not be needed}; just show for now:nd <- data.frame(x = 1:5)tools::assertWarning(print(predict(mod2, newdata=nd, rankdeficient = "warnif")))predict(mod2, newdata=nd, rankdeficient = "NA")nm5 <- as.character(1:5)stopifnot(exprs = {all.equal(setNames(rep(0, 5), nm5), predict(mod2), tol=1e-13) # pred: 1.776e-15is.numeric(p2 <- predict(mod2, newdata = data.frame(y=rep(1,5)))) # no warning, no NA:identical(p2, predict(mod2, newdata = data.frame(y=rep(1,5)), rankdeficient="NA"))all.equal(p2, setNames(rep(1, 5), nm5), tol=1e-13)# off.= x+2y + x-y = 2x+y =4+1=5; 5+<intercept> = 1})## fine, using model.offset() now## "numeric_version" methodsx <- numeric_version(c("1", "2.0"))stopifnot(identical(format(x[,2]), c(NA_character_, "0")))is.na(x)[1] <- TRUE; stopifnot(identical(is.na(x), c(TRUE, FALSE)))## gave two spurious warnings in R <= 4.2.2mChk <- function(m) stopifnot(exprs = {identical(attributes(m), list(dim=2:3))identical(class(m), c("matrix", "array"))})(m <- m0 <- diag(1:3, 2,3))mChk(m)##class(m) <- "matrix" # instead of c("matrix", "array") ...mChk(m); stopifnot(identical(m, m0))# .. m is *unchanged* - back compatibly## since R 4.0.0,class(m) # is "matrix" "array"class(m) <- class(m) # should *not* change 'm'mChk(m); stopifnot(identical(m, m0))# m is unchanged as it should, but## failed in R version v 4.0.0 <= v <= 4.2.x : 'm' got a class *attribute* there.## uniroot() close to Inf function values could wrongly converge outside intervalf <- function(x) 4469/x - 572/(1-x)str(urf <- uniroot(f, c(1e-6, 1))) # interval = (eps, 1]; f(1) = Infstopifnot(all.equal(urf$root, 0.88653, tolerance = 1e-4))## Instead of 0.886.., gave a small *negative* root in R < 4.3.0## chkDots() in subset.data.frame() to prevent usage errorstools::assertWarning(subset(data.frame(y = 1), y = 2), verbose = TRUE)## R < 4.3.0 was silent about unused ... arguments## a:b -- both should be of length 1 -- PR#18419Sys.getenv("_R_CHECK_LENGTH_COLON_") -> oldVSys.setenv("_R_CHECK_LENGTH_COLON_" = "true")# ~> the future behaviora <- 1:2assertErrV(a:1) # numerical expression has length > 1assertErrV(2:a) # " " " "Sys.unsetenv("_R_CHECK_LENGTH_COLON_")tools::assertWarning(s1 <- a:1, verbose=TRUE)tools::assertWarning(s2 <- 2:a, verbose=TRUE)stopifnot(identical(s1, 1L), identical(s2, 2:1))Sys.setenv("_R_CHECK_LENGTH_COLON_" = oldV)# reset## always only warned in R <= 4.2.z## keep rm(list=NULL) working (now documentedly) {PR#18422}a <- ls() # 'a' is partrm() ; rm(list=NULL)stopifnot(identical(a, ls()))## (for a short time, list=NULL failed)## ns() fails when quantiles end on the boundary {PR#18442}if(no.splines <- !("splines" %in% loadedNamespaces())) require("splines")tt <- c(55, 251, 380, 289, 210, 385, 361, 669)nn <- rep(0:7, tt) # => knots at (0.25,0.5,0.75); quantiles = (2,5,7)tools::assertWarning(verbose=TRUE, ns.n4 <- ns(nn,4))stopifnot(is.matrix(ns.n4), ncol(ns.n4) == 4, qr(ns.n4)$rank == 4)if(no.splines) unloadNamespace("splines")## ns() gave Error in qr.default(t(const)) : NA/NaN/Inf in foreign function call## keep at endrbind(last = proc.time() - .pt,total = proc.time())