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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 == *$messageassertErrV <- function(...) tools::assertError (..., verbose=TRUE)assertWarnV <- function(...) tools::assertWarning(..., verbose=TRUE)`%||%` <- function (L, R) if(is.null(L)) R else L##' get value of `expr` and keep warning as attribute (if there is one)getVaW <- function(expr, obj=FALSE) {W <- NULLwithCallingHandlers(val <- expr,warning = function(w) {W <<- if(obj) w else conditionMessage(w)invokeRestart("muffleWarning") })structure(val %||% quote(._NULL_()), warning = W) # NULL cannot have attr.}options(nwarnings = 10000, # (rather than just 50)warn = 2, # only caught or asserted warningswidth = 99) # instead of 80onWindows <- .Platform$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))## 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## 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]])## objects of the respective class:obs <- lapply(cls, \(cl) asF[[cl]](switch(cl, "difftime" = "2:1:0", "noquote" = letters,"numeric_version" = as.character(1:2), 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")# website does not matter as will not be contacted.Edl <- tryCid(download.file("http://cran.r-project.org/", "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(sprintf("Package: %s", basename(pkgpath)),"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)assertWarnV(print(predict(mod2, newdata=nd, rankdeficient = "warnif")))predict(mod2, newdata=nd, rankdeficient = "NA") # NA's but no warningnm5 <- 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 errorsassertWarnV(subset(data.frame(y = 1), y = 2))## 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_")assertWarnV(s1 <- a:1)assertWarnV(s2 <- 2:a)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## Krylov's issue with sum(), min(), etc on R-devel: Now errors instead of silently computing:mT <- tryCid( sum(3,4,na.rm=5, 6, NA, 8, na.rm=TRUE) )mF <- tryCid( min(3,4,na.rm=5, 6, NA, 8, na.rm=FALSE) )stopifnot(inherits(mT, "error"),inherits(mF, "error"), all.equal(mT, mF))if(englishMsgs)stopifnot(grepl("formal argument \"na.rm\" matched by multiple", conditionMessage(mT)))## these gave numeric (or NA) results without any warning in R <= 4.3.z## as.complex(NA_real_) |-> ... Im(.) == 0 as for NA (logical) and NA_integer_if(FALSE) # in R-devel Apr--Sep 2023 only:stopifnot(identical(as.complex(NA_real_), NA_complex_))Cmplx <- function(re = numeric(), im = numeric()) complex(real = re, imaginary = im)showC <- function(z) noquote(sprintf("(R = %g, I = %g)", Re(z), Im(z)))showC(print(asCnum <- Cmplx(NA_real_, 0)))showC(print(NA_rP0i <- NA_real_ + 0i)) # arithmetic here via as.complex(.)stopifnot(exprs = {identical(as.complex(NA_real_), asCnum)identical(as.complex(NA_integer_), asCnum)identical(as.complex(NA), asCnum)identical(NA_rP0i, asCnum)identical(as.complex( NaN), Cmplx(NaN, 0))identical(as.complex( Inf), Cmplx(Inf, 0))identical(as.complex(-Inf),Cmplx(-Inf, 0))})## as.complex( <real-number-like> ) keeps imaginary part 0 even for NA## methods() in {base} pkg are visiblemmeths <- methods(merge)imeth <- attr(mmeths, "info")stopifnot(exprs = {sum(iB <- imeth[,"from"] == "base") >= 2 # 'default' and 'data.frame'imeth[iB, "visible"] # {base} methods *are* visible})## was wrong in R 4.3.0 (and R-devel for a while)## Methods of a non-generic functionfoo <- function(x) { bar(x) }(m <- methods(foo))stopifnot(inherits(m, "MethodsFunction"), length(m) == 0L)## .S3methods() failed in R-devel for a few days after r84400.## getS3method() errormyFUN <- function(x) UseMethod("myFUN")(msg <- tryCmsg(getS3method("myFUN", "numeric")))if(englishMsgs)stopifnot(grepl("S3 method 'myFUN.numeric' not found", msg))## failed with "wrong" message after r84400## head(.,n) / tail(.,n) error reporting - PR#18362try(head(letters, 1:2)) # had "Error in checkHT(..)"); now ".. in head.default(..)"try(tail(letters, NA))try(head(letters, "1"))tryCcall1 <- function(expr) tryCid(expr)$call[[1L]]stopifnot(exprs = {tryCcall1(head(letters, 1:2)) == quote(head.default)tryCcall1(tail(letters, NA )) == quote(tail.default)tryCcall1(head(letters, "1")) == quote(head.default)})## more helpful error msg## na.contiguous() w/ result at beginning -- Georgi Boshnakov, R-dev, 2023-06-01## and does not set "tsp" for non-tsx <- c(1:3, NA, NA, 6:8, NA, 10:12)(naco <- na.contiguous( x ))(nact <- na.contiguous(as.ts(x)))dput( setdiff(attributes(nact), attributes(naco)) ) # and check -- TODOn0 <- numeric(0)stopifnot(identical(`attributes<-`(naco, NULL), 1:3), identical(na.contiguous(n0), n0), is.null(attr(naco, "tsp")), nact == naco, identical(c(na.contiguous(presidents)), presidents[32:110]))## 'naco' gave *2nd*, not *first* run till R 4.3.0## accidental duplicated options() entryif(i <- anyDuplicated(no <- names(ops <- options())))stop("duplicated options(): ", no[i])## had one in R 4.3.0 (and R-devel)## .S3methods() and methods() in R 4.3.0library(stats)# almost surely unneeded##methi <- function(...) attr(methods(...), "info")(mdensi <- methi(density)) # only density.defaultstopifnot(mdensi["density.default", "visible"]) # FALSE in R 4.3.0if(requireNamespace('cluster', lib.loc=.Library, quietly = TRUE)) withAutoprint({try(detach("package:cluster"), silent=TRUE)# just in case(mCf1 <- methi(coef))require(cluster)(mCf2 <- methi(coef))stopifnot(mCf2["coef.hclust", "visible"],mCf2["coef.hclust", "from"] == "cluster")## ... anddetach("package:cluster")(mcf <- methods(coef)) # again gets marked as invisible: coef.hclust*stopifnot(!attr(mcf, "info")["coef.hclust", "visible"])}) # when {cluster}## in any case {and "always" worked}:coef.foo <- function(object, ...) "the coef.foo() method"(m3 <- methi(coef))# -> coef.foo is visible in .GlobalEnvstopifnot(m3["coef.foo", "visible"],m3["coef.foo", "from"] == ".GlobalEnv")## *and* this is still true, after registering it:.S3method("coef", "foo", coef.foo)stopifnot(identical(methi(coef), m3)) # did not changerm(coef.foo)m4 <- methi(coef)stopifnot(!m4["coef.foo", "visible"],m4["coef.foo", "from"] == "registered S3method for coef")## coef.foo part always worked## R <= 4.3.z would split into two invalid characters (PR#18546)splitmbcs <- length(strsplit("\u00e4", "^", perl=TRUE)[[1]])stopifnot(identical(splitmbcs, 1L))## contrib.url() should "recycle0"stopifnot(identical(contrib.url(character()), character()))## R <= 4.3.1 returned "/src/contrib" or similar## .local() S4 method when generic has '...' *not* at end, PR#18538foo <- function(x, ..., z = 22) zsetMethod("foo", "character", function(x, y = -5, z = 22) y)stopifnot(identical(foo("a"), -5))removeGeneric("foo")## foo("a") gave 22 in R <= 4.3.z## `substr<-` overrun in case of UTF-8 --- private bug report by 'Architect 95's0 <- "123456"; nchar(s0) # 6substr(s0, 6, 7) <- "cc"s0 ; nchar(s0) # {"12345c", 6}: all fine: no overrun, silent truncation(s1 <- intToUtf8(c(23383, 97, 97, 97, 97, 97))); nchar(s1) # "字aaaaa" , 6substr(s1, 6, 7) <- "cc"# Now s1 should be "字aaaac", but actually did overrun nchar(s1);s1; nchar(s1) ## was "字aaaacc", nchar = 7(s2 <- intToUtf8(c(23383, 98, 98))); nchar(s2) # "字bb" 3substr(s2, 4, 5) <- "dd" # should silently truncate as with s0:## --> s2 should be "字bb", but was "字bbdddd\x97" (4.1.3) or "字bbdd字" (4.3.1)s2; nchar(s2) ## was either 6 or "Error ... : invalid multibyte string, element 1"#-------------## Example where a partial UTF-8 character is included in the second string## 3) all fine(s3 <- intToUtf8(c(23383, 97, 97, 97, 97, 97))); nchar(s3) # "字aaaaa" 6substr(s3, 6, 6) <- print(intToUtf8(23383)) # "字"s3 ; nchar(s3) # everything as expected: ("字aaaa字", 6)## 4) not good(s4 <- intToUtf8(c(23383, 98, 98, 98, 98))); nchar(s4) # "字bbbb" 5substr(s4, 5, 7) <- "ddd"# Now s4 should be "字bbbd", but was "字bbbddd\x97", (\x97 = last byte of "字" in UTF-8)s4; nchar(s4)## gave "字bbbddd\x97" and "Error ...: invalid multibyte string, element 1"stopifnot(exprs = {identical(s0, "12345c") # always okidentical(utf8ToInt(s1), c(23383L, rep(97L, 4), 99L)) ; nchar(s1) == 6identical(utf8ToInt(s2), c(23383L, 98L, 98L)) ; nchar(s2) == 3identical(utf8ToInt(s3), c(23383L, 97L, 97L, 97L, 97L, 23383L)) ; nchar(s3) == 6identical(utf8ToInt(s4), c(23383L, 98L, 98L, 98L, 100L)) ; nchar(s4) == 5Encoding(c(s1,s2,s3,s4)) == rep("UTF-8", 4)})## did partly overrun to invalid strings, nchar(.) giving error in R <= 4.3.1## PR#18555 : see ---> ./misc-devel.R## PR#18557 readChar() with large 'nchars'ch <- "hello\n"; tf <- tempfile(); writeChar(ch, tf)tools::assertWarning((c2 <- readChar(tf, 4e8)))stopifnot(identical(c2, "hello\n"))## had failed w/ cannot allocate memory block of size 16777216 Tb## Deprecation of *direct* calls to as.data.frame.<someVector>dpi <- as.data.frame(pi)d1 <- data.frame(dtime = as.POSIXlt("2023-07-06 11:11")) # gave F.P. warningr <- lapply(list(1L, T=T, pi=pi), as.data.frame)stopifnot(is.list(r), is.data.frame(d1), inherits(d1[,1], "POSIXt"), is.data.frame(r$pi), r$pi == pi)stopifnot(local({adf <- as.data.frame; identical(adf(1L),(as.data.frame)(1L))}))## Gave 1 + 3 + 2 F.P. deprecation warnings in 4.3.0 <= R <= 4.3.1str(d2 <- mapply(as.data.frame, x=1:3, row.names=letters[1:3]))stopifnot(is.list(d2), identical(unlist(unname(d2)), 1:3))## gave Error .. sys.call(-1L)[[1L]] .. comparison (!=) is possible only ..#### Should not warn for a call from a derivedDefaultMethod to the## raw S3 method -- implementation detail of S4 dispatchsetGeneric('as.data.frame')as.data.frame(factor(1))removeGeneric('as.data.frame')## wrongly gave " Direct call of 'as.data.frame.factor()' is deprecated. "## qqplot(x,y, *) confidence bands for unequal sized x,y, PR#18570:x <- (7:1)/8; y <- (1:63)/64r <- qqplot(x,y, plot.it=FALSE, conf.level = 0.90)r2<- qqplot(y,x, plot.it=FALSE, conf.level = 0.90)(d <- 64 * as.data.frame(r)[,3:4])stopifnot(identical(d, data.frame(lwr = c(NA, NA, NA, 6, 15, 24, 33),upr = c(31, 40, 49, 58, NA, NA, NA))),identical(8 * as.data.frame(r2[3:4]),data.frame(lwr = c(NA,NA,NA, 1:4 +0), upr = c(4:7 +0, NA,NA,NA))))## lower and upper confidence bands were nonsensical in R <= 4.3.1## New <object> type {{partly experimental}}mkObj <- function(...) {ob <- asS3(getClass("S4")@prototype, complete=FALSE) # "hack"if(...length()) attributes(ob) <- list(...)ob}(oo <- mkObj())str(oo) # the same: '<object>'(x4 <- asS4(oo))dput(x4) # same as print(.)dput(oo) # <object> again {possibly to be changed}(o2 <- mkObj(name = "Obi", age = 67))str(o2) # good!dput(o2) # <object> .. to be changed -- once something like mkObj() becomes APIstopifnot(exprs = {identical(x4, getClass("S4")@prototype)identical(oo, get("oo", mode="object"))identical(x4, get("x4", mode="S4"))identical(attr(o2, "name"), "Obi")})assertErrV(o2[ 1 ])assertErrV(o2[[1]])stopifnot(isFALSE(inherits(oo, "S4")))stopifnot(isTRUE(inherits(oo, "object")))stopifnot(isTRUE(inherits(x4, "S4")))stopifnot(isFALSE(inherits(x4, "object")))assertErrV(get("oo", .GlobalEnv, mode = "S4"))stopifnot(identical(get("oo", .GlobalEnv, mode = "object"), oo))stopifnot(identical(get("x4", .GlobalEnv, mode = "S4"), x4))assertErrV(get("x4", .GlobalEnv, mode = "object"))assertErrV(get("oo", mode = "integer"))assertErrV(get("x4", .GlobalEnv, mode = "integer"))## kappa(), rcond() [& norm()] -- new features and several bug fixes, PR#18543:(m <- rbind(c(2, 8, 1),c(6, 4, 3),c(5, 7, 9)))## 1) kappa(z=<n-by-n>, norm="1", method="direct")` ignores lower triangle of zkm1d <- kappa(m, norm = "1", method = "direct")all.equal(km1d, 7.6, tol=0) # 1.17e-16 {was wrongly 11.907 in R <= 4.3.1}## 2) kappa(z, norm="2", LINPACK=TRUE) silently returns estimate of the *1*-norm cond.nr.(km1 <- kappa(m, norm = "1")) # 4.651847 {unchanged}assertWarnV( km2L <- kappa(m, norm="2", LINPACK=TRUE)) # now *warns*## 3) kappa(z, norm="2", LINPACK=FALSE) throws an errorassertWarnV(km2La <- kappa(m, norm="2", LINPACK=FALSE))# same warning (1-norm instead of 2-)km2La## 4) kappa.qr(z) implicitly assumes nrow(z$qr) >= ncol(z$qr), not true in general(kqrm2 <- kappa(qr(cbind(m, m + 1))))## Error in .kappa_tri(R, ...) : triangular matrix should be square## 5) rcond(x=<n-by-n>, triangular=TRUE) silently ignores the lower (rather than upper)## triangle of `x`, contradicting `help("rcond")`.## ==> Fixing help page; but *also* adding uplo = "U" argumentall.equal(4/65, (rcTm <- rcond(m, triangular=TRUE)), tol = 0) # {always}all.equal(9/182,(rcTL <- rcond(m, triangular=TRUE, uplo="L")), tol=0) # 1.4e-16#### New features, can use norm "M" or "F" for exact=TRUE via norm(*, type=<norm>)(kM <- kappa(m, norm="M", exact = TRUE)) # 2.25 "M" is allowed type for norm()(kF <- kappa(m, norm="F", exact = TRUE)) # 6.261675 "F" is allowed type for norm()all.equal(6.261675485, kF, tol=0) # 2.81e-11stopifnot(exprs = {all.equal(4.6518474224, km1)km1 == kappa(m) # same computationkm1 == kappa(qr.R(qr(m))) # "all.equal(km1d, 7.6, tol = 1e-15)km1d == kappa(m, method = "direct") # identical computation {always ok}identical(km2L, km1)all.equal(km2La, 5.228678219)all.equal(kqrm2, km1) # even identicalrcTm == rcond(m, triangular=TRUE, uplo = "U") # uplo="U" was default alwaysall.equal(4/65, rcTm, tol = 1e-14)all.equal(9/182, rcTL, tol = 1e-13)1/rcond(m) == km1d # same underlying Lapack code## 6) kappa(z=<m-by-0>) throws bad errors due to 1:0 in kappa.qr():kappa(m00 <- matrix(0, 0L, 0L)) == 0kappa(m20 <- matrix(0, 2L, 0L)) == 0## 7) kappa(z=<0-by-0>, norm="1", method="direct", LINPACK=)## is an error for LINPACK=FALSE & returns Inf for L..=TRUE)kappa(m00, norm = "1", method = "direct", LINPACK= TRUE) == 0kappa(m00, norm = "1", method = "direct", LINPACK=FALSE) == 0## Fixed more problems (by MM):rcond( m00 ) == Inf # gave errorrcond( m20 ) == Inf # gave error from infinite recursionrcond(t(m20)) == Inf # (ditto)## norm "M" or "F" for exact=TRUE:2.25 == kM # exactlyall.equal(6.261675485, kF, tol=1e-9)})## -- Complex matrices --------------------------------------------------(zm <- m + 1i*c(1,-(1:2))*(m/4))(kz1d <- kappa(zm, norm = "1", method = "direct"))(kz1 <- kappa(zm, norm = "1"))# meth = "qr"assertWarnV(kz2L <- kappa(zm, norm="2", LINPACK=TRUE))# now *warns* {gave *error* previously}assertWarnV(kz2La <- kappa(zm, norm="2", LINPACK=FALSE))# same warning (1-norm instead of 2-)kz2La## 4) kappa.qr(z) implicitly assumes nrow(z$qr) >= ncol(z$qr) ..(kzqr2 <- kappa(qr(cbind(zm, zm + 1)))) # gave Error .. matrix should be squareall.equal(0.058131632, print(rcTm <- rcond(zm, triangular=TRUE )), tol=0) # 3.178e-9all.equal(0.047891278, print(rcTL <- rcond(zm, triangular=TRUE, uplo="L")), tol=0) # 4.191e-9## New: can use norm "M" or "F" for exact=TRUE:(kz <- kappa(zm, norm="M", exact = TRUE)) # 2.440468(kF <- kappa(zm, norm="F", exact = TRUE)) # 6.448678stopifnot(exprs = {all.equal(7.8370264, kz1d) # was wrong {wrongly using .kappa_tri()}all.equal(6.6194289, kz1) # {always ok}all.equal(0.058131632, rcTm) # "all.equal(0.047891278, rcTL)all.equal(6.82135883, kzqr2)all.equal(2.44046765, kz, tol = 1e-9) # 1.8844e-10all.equal(6.44867822, kF, tol = 4e-9) # 4.4193e-10})## norm() and kappa(., exact=TRUE, ..) now work ok in many more cases## argument matching for round/signif (not handled properly in R <= 4.3.x)round("days", x = Sys.time())round(, x = 1)signif(, x = 1)(function(...) round(..., 1, ))()(function(...) signif(..., 1, ))()tools::assertError(round(digits = 1, x =))tools::assertError(signif(digits = 1, x =))## transform() should not check.names -- PR#17890df <- data.frame(`A-1` = 11:12, B = 21:22, check.names = FALSE)stopifnot(identical(transform(df), df)) # no-opstopifnot(exprs = {identical(names(transform(df, `A-1` = `A-1` + 1)), names(df))identical(names(transform(df, C = 3)), c(names(df), "C"))identical(transform(as.matrix(df), B = B), df)})## in all three cases, "A-1" inadvertently became "A.1" in R < 4.4.0## byte compiled sqrt() was not warning about creating NaNs for## negative integer scalarstools::assertWarning(compiler::cmpfun(function(x) sqrt(x))(-1L))## is.atomic(NULL) is no longer trueif(is.atomic(NULL)) stop("Should no longer happen: 'NULL' is not atomic")## untested previouslystopifnot(is.null(sort(NULL)), is.null(sort.int(NULL)))## failed in first version of `R-is` branch## isoreg() seg.faulted with Inf - PR#18603 - in R <= 4.3.1assertErrV(isoreg(Inf))assertErrV(isoreg(c(0,Inf)))assertErrV(isoreg(rep(1e307, 20))) # no Inf in 'y'## ==> Asserted error: non-finite sum(y) == inf is not allowed## format() and print() of complex numbers, PR#16752100+ 0:4 + 10000i # no 'e'100+ 0:4 + 100000i # using 'e' as it is shorterz <- 100+ 0:4 + 1e9i## for a long time printed identical 5 time 0e+00+1e+09i(asCz <- as.character(z))oZ <- capture.output(z)stopifnot(exprs = {substr(asCz, 1,6) == paste0(100+ 0:4, "+1e")as.complex(asCz) == z # has been fulfilled for a long timeidentical(oZ, paste("[1]", paste(asCz, collapse=" ")))})## had exponential/scientific format for Re() as well, from R 3.3.0 to R 4.3.z## PR#18579 (thanks to Mikael Jagan) -- cbind/rbind deparse.level for *methods*.S3method("cbind", "zzz",function(..., deparse.level = 1)if(!missing(deparse.level)) deparse.level)x <- structure(0, class = "zzz")stopifnot(exprs = {is.null(cbind(x)) # deparse.level *missing* {always ok}identical(0, cbind(x, deparse.level = 0))identical(1, cbind(x, deparse.level = 1))identical(2, cbind(x, deparse.level = 2))identical(2L, cbind(x, deparse.level = 2L))})## passing to S3/S4 method did not work in R <= 4.3.x## Conversion of LaTeX accents: \~{n} etc vs. \~{}, accented I and istopifnot(identical(print(tools::parseLatex("El\\~{}Ni\\~{n}o") |>tools::latexToUtf8() |>tools::deparseLatex(dropBraces = TRUE)),"El~Ni\u00F1o")) # "El~Niño"## gave "El~Ni~no" in R 4.3.{0,1} (\~ treated as 0-arg macro)stopifnot(tools:::cleanupLatex(r"(\`{I}\'{I}\^{I}\"{I})")== "\u00cc\u00cd\u00ce\u00cf")## was wrongly converted as "ËÌÍÏ" in R <= 4.3.1stopifnot(tools:::cleanupLatex(r"(\`{i}\'{i}\^{i}\"{i})")== "\u00ec\u00ed\u00ee\u00ef")## codes with i instead of \i were unknown thus not converted in R <= 4.3.1## tools::deparseLatex() can drop successive LaTeX groupsbib1 <- bibentry("misc", key = "test", year = "2023",author = r"(averig{\"u}{\'e})")bib2 <- bib1; bib2$author$family <- r"(averig\"{u}\'{e})"roundtrip <- function (tex, drop = FALSE)tex == tools::deparseLatex(tools::parseLatex(tex), dropBraces = drop)stopifnot(exprs = {citeNatbib("test", bib1) == "(averig\u00fc\u00e9 2023)"citeNatbib("test", bib2) == citeNatbib("test", bib1)roundtrip(r"(\{R\})", TRUE) # escaped braces are not droppedroundtrip(r"(\href{https://bugs.R-project.org/}{Bugs})", TRUE)})## the first produced "(averigü{é} 2023)" in R < 4.4.0stopifnot(roundtrip(r"(\item text)"))## space was lost in R < 4.4.0## PR#18618: match() incorrect with POSIXct || POSIXlt || fractional sec(dCT <- seq(as.POSIXct("2010-10-31", tz = "Europe/Berlin"), by = "hour", length = 5))(dd <- diff(dCT))chd <- as.character(dCT)vdt <- as.vector (dCT)dLT <- as.POSIXlt (dCT)dat <- as.Date (dCT)dL2 <- dLT[c(1:5,5)]; dL2[6]$sec <- 1/4dL. <- dL2 ; dL.[6]$sec <- 1e-9stopifnot(exprs = {inherits(dCT, "POSIXct")inherits(dLT, "POSIXlt")!duplicated(dCT)dd == 1units(dd) == "hours"diff(as.integer(dCT)) == 3600L # secondsidentical(match(chd, chd), c(1:3, 3L, 5L))identical(match(vdt, vdt), seq_along(vdt))identical(match(dat, dat), c(1L,1L, 3L,3L,3L)) # always okidentical(match(dCT, dCT), seq_along(dCT)) # wrong in 4.3.{0,1,2}identical(match(dLT, dLT), seq_along(dLT)) # " " "identical(match(dL2, dL2), seq_along(dL2)) # " " "identical(match(dL., dL.), seq_along(dL.)) # " " now ok, as indeed,! identical(dL.[5], dL.[6]) # NB: `==`, diff(), ... all lose precision, from as.POSIXct():inherits(dC. <- as.POSIXct(dL.), "POSIXct")identical(match(dC., dC.), c(1:5, 5L))identical(dC.[5], dC.[6])dC.[5] == dC.[6]} )## failed (partly) in R versions 4.3.0 -- 4.3.2## PR#18598: *wrong* error messagewriteLines(eMsg <- tryCmsg(diff(1:6, differences = integer(0L))))if(englishMsgs) stopifnot(grepl("must be integers >= 1", eMsg))## errored with "missing value where TRUE/FALSE needed" in R <= 4.3.2## PR#18563: drop.terms(*, dropx = <0-length vector>)tt <- terms(y ~ a+b)stopifnot(identical(tt, drop.terms(tt, dropx = 0[0], keep.response=TRUE)))## errored in R <= 4.3.2## as.complex("<num>i") -- should work (and fail/warn) as the parser does:assertWarnV( cc <- as.complex("12iL"))tools::assertWarning(cF <- as.complex("12irene"))tools::assertWarning(cI <- as.complex("12I"))stopifnot(is.na(cc), is.na(cF), is.na(cI),identical(cc, cF), identical(cF, cI), identical(cI, NA_complex_))stopifnot(exprs = {identical(1i, as.complex("1i"))identical(4i, as.complex("+4.i"))identical(-0.1i, as.complex("-.1i"))identical(-4.321i, as.complex("-4.321i"))identical(-4.3e-17i, as.complex("-4.3e-17i"))identical(+.123e6i, as.complex("+.123e6i"))identical(-4.3e6i, as.complex("-4.3e6i"))identical( 30000i, as.complex("+.3e+5i"))})## returned NA_complex_ *with* a warning, in R <= 4.4.0## c(NA, <cplx>); cumsum(<cplx_w_NA>) -- related to as.complex(NA_real_); R-devel MLcx <- function(r,i) complex(real=r, imaginary=i)pz <- function(z) noquote(paste0("(", Re(z), ",", Im(z), ")"))pz(z <- c(1i, NA))NA.1 <- cx(NA, 1)stopifnot(exprs = {Im(z) == 1:0 # was (TRUE NA)identical(z, cx(c(0,NA), c(1,0))) # newidentical(sum(z), NA.1) # "## these were all TRUE already :identical(prod(z), NA_complex_)identical(Im(cumsum(z)), cumsum(Im(z)))identical(Re(cumsum(z)), cumsum(Re(z)))identical( sum(z), tail( cumsum(z), 1L))identical(prod(z), tail(cumprod(z), 1L))})## gave NA_complex_ in more cases in R <= 4.4.0## PR#18627 - getS3method() should match method dispatch {and isS3method()}stopifnot(exprs = {! isS3method("t", "test")is.null( getS3method("t", "test", optional=TRUE) )identical(dim(t(structure(matrix(, 3, 2), class = "test"))), # t.test() is *not* called:2:3)})## getS3method(..) did return the t.test function, in R <= 4.3.2## PR#18564,5,6: drop.terms(*)tt <- terms(y ~ a+b)stopifnot(formula(drop.terms(tt)) == { ~ a+b }) # was y ~ a + bstopifnot(formula(drop.terms(tt, keep.response=TRUE)) == { y ~ a+b }) # (unchanged)## did not drop y (with default keep.response=FALSE) in R <= 4.3.2#### PR#18565: offset() in formulatto <- terms(y ~ a + b + offset(h))(ttF <- drop.terms(tto, 1L, keep.response = FALSE))(ttT <- drop.terms(tto, 1L, keep.response = TRUE ))(tt.2 <- tto[2L])stopifnot(exprs = {formula(ttF) == ~ b + offset(h)formula(ttT) == { y ~ b + offset(h) }formula(tt.2)== { y ~ b + offset(h) }identical(attr(ttF, "offset"), 2L)identical(attr(ttT, "offset"), 3L)identical(attr(tt.2,"offset"), 3L)}) ## all dropped 'offset' in R <= 4.3.2#### PR#18566:remattr <- function(x) { attributes(x) <- NULL; x } ## do we already have this?t2 <- terms(~ a + b)str(dt2 <- drop.terms(t2, 1, keep.response = TRUE))stopifnot( drop.terms(t2, 1) == dt2, remattr(dt2) == quote(~ b))## gave a+b ~ b in R <= 4.3.2## cov2cor(<0x0>) PR#18423m00 <- matrix(0,0,0)stopifnot(identical(cov2cor(m00), m00))## gave error in R <= 4.3.2## cov2cor(.) warning(s) with negative/NA diag(.) - PR#18424(D_1 <- diag(-1, 3L))op <- options(warn=1)m <- capture.output(r <- cov2cor(D_1), type = "message")matrix(rep_len(c(1, rep(NaN,3)),3*3), 3) -> r0stopifnot(all.equal(r, r0, tol = 0, check.attributes = FALSE),# always oklength(m) == 2, grepl("^ *diag.V. ", m[2]))options(op) # revert## cov2cor() gave 2 warnings on 3 lines, the 2nd one inaccurate in R <= 4.3.2## `formals<-` failing for _explicit_ constant body and empty formalsfbList <- c(Sys.info, body, lm## constant body:, function() "foo", function()r"(')", function() 1L, function() TRUE, function() 1i, function() 3.14, function() Inf)for(f in fbList) {g <- f ; formals(g) <- formals(g)h <- f ; body(h) <- body(h)stopifnot(identical(g, f),identical(h, f))}## those w/ constant body failed in `formals<-` in R <= 4.3.x## with Error in as.function.default(....): list argument expected## fix error message of as.function(..1, *)(msg <- tryCmsg(as.function(list({}, 1), .GlobalEnv)))stopifnot(!englishMsgs || grepl("invalid formal argument list", msg),grepl('"as.function"', msg, fixed=TRUE))## had "function" wrongly in R <= 4.3.x## removeSource() checking *formals* incl in sub-functions -- PR#18638f <- function(x = {}) {function(y = {}) { NULL }}str(lapply(formals(f), attributes)) # list(x = list(srcref = .., srcfile = .. wholeSrcref = ..))f0 <- removeSource(f) # was unchanged in R <= 4.3.2## in sub function {not atttrib}:(toplev <- !sys.nframe())op <- options(keep.source = TRUE)qf <- quote(function() NULL)str(qf4 <- qf[[4]]) # srcref, now removed:qf0 <- removeSource(qf)stopifnot(exprs = {## no "srcref" anymore for the formals of f0 or its result:identical(lapply(formals(f0), attributes), list(x = NULL))identical(lapply(formals(f0()), attributes), list(y = NULL))##length(qf) == 4Llength(qf0)== 4Lis.integer(qf4)length(qf4) >= 8if(toplev) # e.g., when source()dqf4 == c(1L, 13L, 1L, 27L, 13L, 27L, 1L, 1L) # in qf[] but not in qf0[]elseqf4 >= 1Lis.null(qf0[[4L]])})options(op)## f0 and qf0 were unchanged, keeping srcref in R <= 4.3.*## startDynamicHelp(): port out of range, PR#18645op <- options(help.ports = 123456L)assertErrV(tools::startDynamicHelp())assertErrV(help.start(browser = identity))options(op)## silently failed much later in R <= 4.3.2.## checks for x == y when operands are call objects, PR18676## disabled if == for calls would signal an errorif (is.na(Sys.getenv("_R_COMPARE_LANG_OBJECTS", unset = NA_character_))) {stopifnot(quote({a}) != quote({b}))stopifnot(quote(c(1)) != quote(c(1L)))stopifnot(quote(c(1.234567890123456)) != quote(c(1.2345678901234567)))}## <POSIXlt>[] -- PR#18681(x <- as.POSIXlt(.POSIXct(0, tz = "UTC"))) # "1970-01-01 UTC"x$mon <- 12Lstopifnot(exprs = {identical(12L, x[,"mon"]) # had "balanced" attr.!identical(x, (x1 <- (x[1L])))identical(12L, x1$mon) # (never bug)identical("1971-01-01 UTC", format(x, usetz=TRUE)) # "identical(71L, balancePOSIXlt(x)$year) # "is.na(attr(x1, "balanced")) # was 'TRUE'})## subsetting set "balanced" incorrectly sometimes in R 4.3.*## str(<classed-language>)x_u <- structure(quote(a > 2 * b), class = 'new_class')writeLines(sto <- capture.output(str(x_u)))stopifnot(grepl("a > 2 * b", sto[[1]], fixed=TRUE), # had ' > a 2 * b'grepl('attr\\(\\*,.*"new_class"', sto[[2]]))## previously used as.character() as "last resort" in R <= 4.3.*## Rd2ex() with code directly following a \dont...{} tagrd <- tools::parse_Rd(textConnection(c("\\name{test}\\title{test}\\examples{","\\dontshow{if(TRUE)} stop('catch me')","print(0)}")))tools::Rd2ex(rd, tf <- tempfile())tools::assertError(source(tf), verbose = TRUE)## skipped the stop() and printed 0 in R < 4.4.0## as.data.frame(<empty matrix) ; Davis Vaughan R-devel, 2024-03-21for(nr in 0:2) {dput(d0 <- as.data.frame(matrix(nrow = nr, ncol = 0)))stopifnot("names" %in% names(attributes(d0)),identical(character(), names(d0)))}## had no .$names at all in R < 4.4.0## C level R_nonInt() less tolerant, used more often(gd <- getVaW(dbinom(1234560:1234570, 9876543.2, .5)))gp <- getVaW(pbinom(1234560:1234570, 9876543.2, 1/8))(gdp <- getVaW(dpois(9876543 + (2:8)/10, 1e7)))stopifnot(exprs = {!englishMsgs ||identical(gd, structure(rep(NaN, 11), warning = "NaNs produced"))identical(gd, gp)identical(gdp, structure(rep(0,7), # only *last* warning:warning = "non-integer x = 9876543.800000"))})## did not warn; just treat 98... as an integer in R < 4.4.0## Finally deprecate terms.formula()'s 'abb' and 'neg.out' args:tt <- terms(y ~ a+b)t0 <- getVaW(terms(y ~ a+b, abb = 1))t1 <- getVaW(terms(y ~ a+b, neg.out = 0))t2 <- getVaW(terms(y ~ a+b, abb=NA, neg.out=NA))stopifnot(exprs = {!englishMsgs ||identical(t0, structure(tt, warning = "setting 'abb' in terms.formula() is deprecated"))!englishMsgs ||identical(t1, structure(tt, warning = "setting 'neg.out' in terms.formula() is deprecated"))identical(t2, t1)})## deprecation was only on help page for R 4.3.*## error jump happened after mutation through R 4.3.3x <- expression(a)tryCatch(x[[2]] <- list(), error = invisible)stopifnot(identical(x, expression(a)))## table |> as.data.frame() |> xtabs() round-trip with missing countstab <- replace(UCBAdmissions[,,1], 1, NA)stopifnot(identical(c(xtabs(Freq ~ ., as.data.frame(tab))), c(tab)))## NA turned into 0 in R < 4.4.0## PR#16358 overflowing exponents.x <- 1e999999999999stopifnot(identical(x, Inf))## PR#17199: these were zero on systems where long double == double.x <- as.numeric(c("0x1.00000000d0000p-987","0x1.0000000000000p-1022","0x1.f89fc1a6f6613p-974"))xy <- c(7.645296e-298, 2.225074e-308, 1.23456e-293)stopifnot(all.equal(x, y))## require a non-empty exponent digit sequence in R_strtod.## R 4.4.0 (and many accounts) accepted empty one.{## someone set options(warn = 2) aboveop <- options(warn = 1L)stopifnot(is.na(as.numeric("1234E" )), is.na(as.numeric("0x1234p")),is.na(as.numeric("1234E+")), is.na(as.numeric("0x1234p-")))stopifnot(as.numeric("1234E0") == 1234, as.numeric("0x1234p0") == 4660)options(op)}## as.<atomic>(<list of raw(1)>) , PR#18696i <- 1:11 ; il <- as.list(i)ch <- as.character(i); cl <- as.list(ch)r <- as.raw (i); rl <- as.list(r)stopifnot(exprs = {is.list(cl) ; is.list(il) ; is.list(rl)## as.<atomType>(<list of <atomType>(1)):identical(ch, as.character(cl))identical(i, as.integer (il))identical(r, as.raw (rl))## as.integer() works for the "character list" `cl` :identical(as.integer(cl), i)identical(as.integer(cl),as.integer(ch))## as.double() works for "integer list" `il`identical(as.double(il),as.double(i))## new as.integer() for raw:identical(i, as.integer(rl))})## as.raw(rl) and as.integer(rl) failed in R <= 4.4.x## as.data.frame.matrix(<NA in rownames>, make.names = NA)(m12 <- matrix(1:6, 2,3, dimnames=list(rn <- c('r1', 'r2'),cn <- c(NA, "NA", 'c3'))))m2 <- m12; rownames(m2)[1] <- NA; m2m <- m2 ; rownames(m )[2] <- "NA"; md <- as.data.frame(m)d2 <- as.data.frame(m2)d12 <- as.data.frame(m12)d0 <- d; row.names(d0) <- NULL; d0## NA NA c3## 1 1 3 5## 2 2 4 6stopifnot(exprs = {identical(2:3, dim(m))identical(2:3, dim(m2))identical(cn, colnames(m))identical(cn, colnames(m2))identical(cn, colnames(m12))## data frames tooidentical(2:3, dim(d))identical(2:3, dim(d2))identical(cn, colnames(d))identical(cn, colnames(d2))identical(cn, colnames(d12))})## (*not* wrongly):rownames(d) # [1] "NA..1" "NA."rownames(d2) # [1] "NA." "r2"rownames(d12)# [1] "r1" "r2"## want the rownames to be treated differently ---> bug for make.names=NAas.data.frame(m, make.names=FALSE) |> assertErrV()as.data.frame(m2, make.names=FALSE) |> assertErrV()as.data.frame(m2, make.names=TRUE) # (the PR#18702 -- print.data.frame "bug")(m0 <- m[FALSE, ])i0 <- integer(0); (d00 <- `names<-`(data.frame(i0, i0, i0), cn))stopifnot(exprs = {identical(d00, as.data.frame(m0, make.names=TRUE))identical(d00, as.data.frame(m0, make.names=NA))identical(d00, as.data.frame(m0, make.names=FALSE))identical(d12, as.data.frame(m12, make.names=TRUE)) ## as above; rownames "r1" "r2"identical(d12, as.data.frame(m12, make.names=NA))identical(d12, as.data.frame(m12, make.names=FALSE))identical(d0, as.data.frame(m, make.names=NA)) # internal default row namesidentical(-2L, .row_names_info(d0))})## the last lost row.names => dim(.) was 0 x 3 instead of d0's 2 x 3, in R <= 4.4.0## Scan should not treat "NA" as double/complex when na.strings doesn't## include it (PR#17289)(r <- tryCid(scan(text="NA", what=double(), na.strings=character())))stopifnot(inherits(r, "error"))(r <- tryCid(scan(text="NA", what=complex(), na.strings=character())))stopifnot(inherits(r, "error"))## PR#18143: debugcall(<S3Generic>()) when an S4-generic version is cachedstopifnot(exprs = {isGeneric("summary", getNamespace("stats4"))isNamespaceLoaded("stats4")isS3stdGeneric(summary) # cached S4 generic is not visible})debugcall(summary(factor(1)))## failed in R <= 4.4.0 with Error in fdef@signature :## no applicable method for `@` applied to an object of class "function"stopifnot(isdebugged(summary.factor))undebug(summary.factor)stopifnot(!isdebugged(summary.factor))unloadNamespace("stats4")## PR#18674 - toTitleCase() incorrectly capitalizes conjunctions## (e.g. 'and') when using suspensive hyphenationstopifnot(exprs = {identical(tools::toTitleCase("pre and post estimation"), "Pre and Post Estimation")identical(tools::toTitleCase("pre- and post estimation"), "Pre- and Post Estimation")identical(tools::toTitleCase("pre- and post-estimation"), "Pre- and Post-Estimation")})## PR#18724 - toTitleCase(character(0))ch0 <- character(0L)stopifnot(identical(ch0, tools::toTitleCase(ch0)))## was list() in R <= 4.4.0## PR#18745 (+ PR#18702) format.data.frame() -> as.data.frame.list()x <- setNames(data.frame(TRUE), NA_character_)(fx <- format(x))dN <- data.frame(a = c(1,NA), b = c("a",NA),c3 = c("NA", NA), c4 = c(NA, FALSE))names(dN) <- nms <- c("num", "ch", NA, NA)(fdN <- format(dN))L <- list(A = FALSE); names(L) <- NAnames(dL <- as.data.frame.list(L)) # "NA."names(dL1 <- as.data.frame.list(L, col.names = names(L))) # "NA."names(dL2 <- as.data.frame.list(L, col.names = names(L), check.names=FALSE)) # NA (was "NA")names(dL1.<- as.data.frame.list(L, check.names=FALSE)) # "NA"names(dLn <- as.data.frame.list(L, new.names = TRUE, check.names=FALSE)) # NA (was "NA")prblN <- c("", "var 2"); L2 <- `names<-`(list(1, 23), prblN)## check.names = TRUE, fix.empty.names = TRUE are default :dp11 <- as.data.frame(L2)dp01 <- as.data.frame(L2, check.names=FALSE)dp00 <- as.data.frame(L2, check.names=FALSE, fix.empty.names=FALSE)dp10 <- as.data.frame(L2, check.names=TRUE , fix.empty.names=FALSE)L3 <- c(L, list(row.names = 2))names(dL3 <- as.data.frame.list(L3)) # "NA." "row.names"names(dL3n <- as.data.frame.list(L3, check.names=FALSE)) # NA "row.names", was "NA" "rown..."names(dL3nn<- as.data.frame.list(L3, check.names=FALSE, new.names=FALSE)) # # "NA" "rown..."stopifnot(exprs = {is.na(names(x))is.data.frame(fx)identical(NA_character_, names(x))identical(NA_character_, names(fx)) # was "NA" wronglyidentical(NA_character_, names(dLn))# " "identical(NA_character_, names(dL2))# " "identical(nms, names( dN))identical(nms, names(fdN)) # was .. .. "NA" "NA"identical(dLn, dL2) # was always TRUE; ditto these {wrong for a couple of hours}:names(dp11) == c("X1", "var.2")names(dp01) == c( "1", "var 2")names(dp00) == c( "" , "var 2") # == prblNnames(dp10) == c( "" , "var.2")identical(names(L3), names(dL3n)) # now. The next 3 are not new:identical("NA.", names(dL))identical("NA.", names(dL3) [[1]])identical("NA" , names(dL3nn)[[1]])})## format() and as.data.frame(<list>, col.names=*, check.names=FALSE) *did*## change NA names() into "NA" for R <= 4.4.1## warning for even *potential* underflowB <- 2e306stopifnot(beta(B, 4*B) == 0,all.equal(-5.00402423538187888e306, lbeta(B, 4*B), tolerance = 5e-16))## no longer warns - as we require IEEE_745## as reg-tests-1<ch>.R run with LC_ALL=C -- test Sys.setLanguage() heretry( 1 + "2")oL <- tryCatch(warning = identity,Sys.setLanguage("fr")) # e.g. on Windows: .. C locale, could not change language"if(inherits(oL, "warning")) {print(oL)oL <- structure(conditionMessage(oL), ok = FALSE)}(out <- tryCmsg(1 + "2"))if(attr(oL, "ok") && capabilities("NLS") && !is.na(.popath)&& !grepl("macOS", osVersion) # macOS fails currently) {## .+ to work with multi-byte characters in C encodingstopifnot(is.character(print("checking 'out' : ")),grepl("^argument non num.+rique pour un ", out))## was *not* switched to French (when this was run via 'make ..')## reset {just in case}:Sys.setLanguage("en")}## print( ls.str() ) using '<missing>' also in non-English setup:## {test may give false negative, unproblematically}M <- alist(.=)$.stopifnot(missing(M))try( M ) # --> Error: argument "M" is missing, with no default (typically English)(e0 <- tryCatch(M, error=identity)) # <evalError: argument "M" is missing, with no default>stopifnot(c("evalError", "missingArgError", "error") %in% class(e0))ls.str(pattern = "^M$") # (typically:) M : <missing>(oL <- tryCatch(Sys.setLanguage("de"), warning = identity, error = identity))try( M ) # in good case --> Error : Argument "M" fehlt (ohne Standardwert)(out <- capture.output(ls.str(pattern = "^M$")))rm(M); if(isTRUE(attr(oL,"ok"))) Sys.setLanguage(oL) # reset LANGUAGE etcstopifnot(endsWith(out, "<missing>"))## failed in R <= 4.4.1; out was "M : Argument \"M\" fehlt <...>"## "missingArgError" w/ subclasses:getER <- function(expr) tryCatch(force(expr), error=\(.).)(ee <- getER((function(x)x)()))class(ee) # "evalError" "missingArgError" "error" "condition"f <- function() identity()e2 <- attr(try(f()), "condition") # Error in identity() : argument "x" is missing, with no defaultf <- compiler::cmpfun(f)e3 <- getER(f())f <- function(arg) is.factor(arg)g <- function(x) f(x)e4 <- getER(f())e5 <- getER(g())f <- compiler::cmpfun(f)g <- compiler::cmpfun(g)e4c <- getER(f())e5c <- getER(g())eev <- getER((function() eval(quote(expr = )))())is.evalErr <- function(E) c("evalError", "missingArgError", "error") %in% class(E)is.getvarErr <- function(E) c("getvarError", "missingArgError", "error") %in% class(E)f <- function(x) exp(x); eM <- getER(f()) # *not* the same as e2eM2 <- getER((function(x) exp(x))()) # same as eMstopifnot(exprs = {is.evalErr(ee)is.evalErr(e4)is.evalErr(e5)is.evalErr(eev)is.evalErr(eM)is.evalErr(eM2)identical(e2, e3)is.getvarErr(e2)is.getvarErr(e4c)is.getvarErr(e5c)})## all these classed errors are new in R >= 4.5.0## colSums / rowSums(*, dims = <not scalar>) - PR#18811A <- array(1:120, dim=2:5)ch1 <- tryCmsg(colSums (A, dims=1:2))ch2 <- tryCmsg(rowMeans(A, dims=1:2))stopifnot(identical(ch1, ch2),identical(ch1, "invalid 'dims'"))## error msg was "'length = 2' in coercion to 'logical(1)'"## kappa(*, exact=TRUE) for exactly singular cases - PR#18817for(x in list(x3 = {n <- 3L; x <- diag(n); x[n,n] <- 0; x},z2 = rbind(1:2, 0),D0 = diag(0, nrow = 3))) { print(x)stopifnot(exprs = {identical(Inf, kappa(x, exact = TRUE))identical(Inf, kappa(x, exact = TRUE, norm = "2"))identical(Inf, .kappa_tri(x, exact = TRUE, norm = "2"))})}## kappa(..) returned 1 or {0 with a warning} in R <= 4.4.2## hexadecimal constants with and without exponent.0x1.234p00x1.234p70x1.234p-70x1.234## last was a (deliberate) parse error in R <= 4.4.2, but not as documented.## PR#18822 -- debug("<S4-generic>")m0 <- selectMethod("Ops", signature = (SIG <- c("array", "array")))stopifnot(is.function(m0), inherits(m0, "PossibleMethod"))debug ("Ops", signature = SIG) # gave Error(m1 <- selectMethod("Ops", SIG))untrace("Ops", signature=SIG) ; m2 <- selectMethod("Ops", SIG)debugonce("Ops", signature = SIG) # Error ..m3 <- selectMethod("Ops", SIG)untrace("Ops", signature=SIG) ; m4 <- selectMethod("Ops", SIG)stopifnot(exprs = {is(m0, "MethodDefinition")identical(m0, m2)identical(m0, m4)is(m1, "MethodDefinitionWithTrace")is(m3, "MethodDefinitionWithTrace") # but not the same})## both debug(..) and debugonce(..) failed## debugonce(<simple>) error when called twice -- PR#18824setGeneric("zzz", function(x) standardGeneric("zzz"))setMethod("zzz", c(x = "NULL"), function(x) NULL)m0 <- selectMethod(zzz, signature = "NULL")debugonce(zzz, signature = "NULL")m1 <- selectMethod(zzz, signature = "NULL")debugonce(zzz, signature = "NULL") # gave error "cannot use 'at' argument unless ..."m2 <- selectMethod(zzz, signature = "NULL")untrace(zzz, signature = "NULL")m3 <- selectMethod(zzz, signature = "NULL")stopifnot(exprs = {is(m0, "MethodDefinition")is(m1, "MethodDefinitionWithTrace")identical(m0, m3)identical(m1, m2)})## 2nd debugonce() call failed in R <= 4.4.2## options(scipen = <invalid>)scipenO <- getOption("scipen")assertErrV(options(scipen = NULL))# would work (but ..) in R <= 4.4.2assertErrV(options(scipen = 1:2)) # would just workassertErrV(options(scipen = 1e99))# would "work" w/ 2 warnings and invalid settingstopifnot(identical(getOption("scipen"), scipenO))# unchangedassertWarnV(options(scipen = -100))# warns and sets to min = -9stopifnot(identical(getOption("scipen"), -9L))assertWarnV(options(scipen = 100000))# warns and sets to max = 9999stopifnot(identical(getOption("scipen"), 9999L))options(scipen=scipenO) # revert## setting to NULL would invalidate as.character(Sys.time())## PR#18369 (patch by Mikael Jagan)stopifnot(!isGeneric(fdef = print), !isGeneric(fdef = c), isGeneric(fdef = show))## gave Error argument "f" is missing ... in R <= 4.4.2## [cr]bind invoilving raw vectors -- follow up to r57065x <- as.raw(1:6)stopifnot(identical(cbind(x, c(TRUE,FALSE)), cbind(x=rep(TRUE,6), c(TRUE,FALSE))),identical(cbind(x, 1:6), cbind(x=1:6, 1:6)),identical(cbind(x, pi), cbind(x=1:6, pi)),identical(cbind(x, pi+1i), cbind(x=1:6, pi+1i)),# first three were wrong before R 4.4.3identical(rbind(x, c(TRUE,FALSE)), rbind(x=rep(TRUE,6), c(TRUE,FALSE))),identical(rbind(x, 1:6), rbind(x=1:6, 1:6)),identical(rbind(x, pi), rbind(x=1:6, pi)),identical(rbind(x, pi+1i), rbind(x=1:6, pi+1i)))## [cr]bind had segfaults when R was built for LTO and C99 inlining semantics## The semantics (inherited from S) are that zero-length inputs## (including NULL) are ignored unless all inputs are zero-length.## next four segafaultedcbind(NULL, logical(0))cbind(NULL, integer(0))rbind(NULL, integer(0))rbind(NULL, logical(0))## and these could havecbind(NULL, double(0))cbind(NULL, complex(0))rbind(NULL, double(0))rbind(NULL, complex(0))## and check some other edge cases(X <- matrix(integer(0),2,0))stopifnot(is.null(cbind(NULL)),is.null(rbind(NULL)),is.null(cbind(NULL, NULL)),is.null(rbind(NULL, NULL)),dim(cbind(NULL, pi)) == c(1L, 1L),dim(rbind(NULL, pi)) == c(1L, 1L),# zero-length inputs are ignored except for zero-length resultidentical(cbind(X, X), X),identical(cbind(X, 1:2), matrix(1:2)))## isGeneric(., getName = TRUE, ..) w/ or w/o fdef -- PR#18829setClass("zzz")setMethod("+", c(e1 = "zzz", e2 = "missing"), function(e1, e2) e1)(gen <- isGeneric("+", fdef = `+`, getName = TRUE)) # wrongly returned just TRUEstopifnot(identical(gen, isGeneric("+", getName = TRUE)), # the latter always workedidentical(gen, structure("+", package = "base")),isGeneric("+"), isGeneric("+", fdef = `+`))## These gave array-access errors and perhaps segfaults in R <= 4.4.2ix <- integer(0)sort.int(ix, method = "quick")sort.int(ix, method = "quick", index.return = TRUE)x <- double(0)sort.int(x, method = "quick")sort.int(x, method = "quick", index.return = TRUE)## More warning for _illegal_ OutDec -- even auto print() ing now warns when OutDec is illegal:assertWarnV(op <- options(OutDec = "_._", scipen = 6, warn = 1))assertWarnV( print(pi) ) # _new_ warning ... "will become an error"writeLines(m <- capture.output(format(pi), type = "message"))## Warning in prettyNum(.Internal(format(x, trim, digits, nsmall, width, 3L, :## the decimal mark is more than one character wide; this will become an errorassertWarnV(options(OutDec = ""))m2 <- tryCatch(print(pi), warning = conditionMessage)assertWarnV( print(pi * 10^(-4:4)) ) # _new_ warningif(englishMsgs) stopifnot(exprs = {grepl("^Warning in prettyNum\\(\\.Internal\\(format\\(", m[1])grepl("the decimal mark is more than one character wide", m[length(m)])grepl("the decimal mark is less than one character wide", m2)})## now warn from format() and (only once) from print()options(op) # return to sanity + warn=2## sessionInfo() *prints* La_version() when not emptyop <- options(warn = 1) # possible warning from Sys.timezone() --> timezone.Rsi <- sessionInfo()str( osi <- capture.output(si)); si$LAPACK <- ""osi.noLA <- capture.output(si)if(any(gBL <- grepl("^BLAS/LAPACK:", osi))) {## *.noLA will have _2_ lines instead, as LAPACK != BLAS nowprint(osi[[iLA <- which(gBL)]])v.iLA <- sub(".*; ", " ", osi[iLA])v.noLA <- osi.noLA[iLA+1L]} else {stopifnot(length(osi) == length(osi.noLA))iLA <- which(osi != osi.noLA)print(cbind(osi, osi.noLA)[iLA,]) # was empty ..v.iLA <- osi[iLA]v.noLA <- osi.noLA[iLA]}if(length(iLA) && nzchar(La_version())) { cat("sessionInfo - La_* checking: ")stopifnot(nzchar(v.noLA),grepl(paste0(v.noLA,"$"), v.iLA))cat("ok\n")}## the "LAPACK: .." was entirely empty when si$LAPACK was ""options(op)## arima(*, seasonal = <numeric>)(m <- tryCmsg( arima(presidents, order=c(2,0,1), seasonal=c(1, 0)) ))mlnx <- arima(lynx, order = c(0,1,0))stopifnot(exprs = {all.equal(1922.636, mlnx$aic, tolerance = 1e-6) # failed for daysgrepl("'seasonal'", m, fixed=TRUE)!englishMsgs ||grepl("must be a non-negative numeric vector", m, fixed=TRUE)})## gave solve.default() error (as wrong model failed fitting)## binomial()$ linkinv(<int>) and binomial()$ mu.eta(<int>)lnks <- c("logit", "probit", "cloglog", "cauchit", "log")binIlink <- function(eta) sapply(lnks, function(lnk) binomial(lnk)$linkinv(eta))binImuEt <- function(eta) sapply(lnks, function(lnk) binomial(lnk)$mu.eta (eta))stopifnot(identical(binIlink( 0:3),binIlink(as.double(0:3))))stopifnot(identical(binImuEt( 0:3),binImuEt(as.double(0:3))))## integer type was not allowed for logit (only) in R <= 4.4.2## {any}duplicated(), unique() for expressionsexpr9 <- expression(1,0+1, x+1, x+2, x+1, (x)+1, 1, (1), (x+1))l9 <- as.list(expr9)ch9 <- vapply(l9, deparse, "")stopifnot(exprs = {identical(anyDuplicated(l9), 5L)identical(anyDuplicated(l9), anyDuplicated(expr9))identical(duplicated(expr9), duplicated(ch9))identical(unique(expr9), expr9[-c(5,7)])})## did not work for expressions in R < 4.5.0## print(summary.default()) should lose less accuracy; print(.) <=> format(.) :## Ex. from ISwR (PD), sort(hellung$conc) - "compacted"helconc <- as.integer(.5 + 1000 *c(11, 11, 11.6, 13, 13.5, 14, 14.5, 16, 20, 21, 22, 24, 27, 28+(0:3)*2,35, 38, 41, 46, 52, 55, 62, 66, 69, 70, 78, 90, 111, 129, 130, 137, 165,175,195,199, 201, 285,302, 321,332,385, 416,461,475, 501, 563, 592, 630, 631))shN <- 100 * c(110, 275, 690, 1643.25, 2430, 6310)dput(shel <- summary(helconc))stopifnot(identical("164325", format(shel)[["Mean"]]),identical(shN, scan(quiet=TRUE, text = capture.output(shel)[[2]])))## for all but *one* `zdigits = <d>` the double-rounding works fine:names(shN) <- names(shel)shfmt <- sapply(setNames(, 3:6), simplify = "array", function(dig)sapply(setNames(, -3:9), function(zd) format(shel, digits = dig, zdigits = zd)))str(ushfmt <- lapply(apply(aperm(shfmt, 3:1), 3L, unique), \(.) unique(as.numeric(.))))shN2 <- as.list(shN); shN2[["Mean"]] <- shN[["Mean"]] + 0:1stopifnot(identical(shN2, ushfmt))## Mean was wrongly double-rounded to "164326" for years in R < 4.5.0## summary.data.frame(*, digits=NULL)(sdf <- summary(data.frame(x = seq_along(helconc), helconc), digits = NULL))stopifnot(is.table(sdf), is.matrix(sdf), identical(dim(sdf), c(6L, 2L)))## failed for a few days only## summary(<difftime>) and its print()ingxt <- .POSIXct(1737745992 + 2/7 + 10000 * (0:7))(dt <- diff(xt)) # |--> diff.POSIXt() -- perfect(sdt <- summary(dt))stopifnot(exprs = {inherits(dt, "difftime")inherits(sdt, "difftime")inherits(diff(sdt), "difftime")diff(sdt) == 0inherits(sdt, "summaryDefault")identical(capture.output(sdt), c("Time differences in hours"," Min. 1st Qu. Median Mean 3rd Qu. Max. ",strrep(' 2.778 ', 6)))})## summary(<difftime>) was not useful in R < 4.5.0## unique(<difftime>)(unidt <- unique(dt))stopifnot(inherits(unidt, "difftime"), length(unidt) <= 2) # '2': allow "inaccuracy"## unique() lost the class in R < 4.5.0## optimize(f(x), *) message when f(x) is not finiteff <- function(x) ifelse(x < -10, (x+10)*exp(x^2),ifelse(x > 100, NaN,ifelse(x > 30, exp((x-20)^2),(4 - x)^2)))cf <- as.data.frame(curve(ff, -20, 120, ylim = c(-2,200)))str(ok <- optimize(ff, c(-10, 10)))stopifnot(all.equal(list(minimum = 4, objective = 0), ok))op <- options(warn=0)str(of2 <- optimize(ff, c(-140, 250))); summary(warnings()); uw2 <- unique(warnings())## NA/NaN and -Inf (no +Inf)str(of3 <- optimize(ff, c(-20, 120))); summary(warnings()); uw3 <- unique(warnings())## only 1 Infstr(of4 <- optimize(ff, c(-10, 180))); summary(warnings()); uw4 <- unique(warnings())## +Inf and many NA/NaNc(uw2, uw3, uw4)stopifnot(all.equal(of3, ok),identical(c(2:1,2L), lengths(list(uw2, uw3, uw4))))if(englishMsgs)stopifnot(identical(c("-Inf replaced by maximally negative value","Inf replaced by maximum positive value","NA/NaN replaced by maximum positive value"),sort(unique(c(names(uw2), names(uw3), names(uw4))))))options(op)# reverting## in R < 4.4.z only *one* message .. "NA/Inf replaced by ...."## as.environment(x = .) should workee <- as.environment(x = list(a = 1, bb = 2))stopifnot(is.environment(ee), length(ee) == 2L)## instead, for R <= 4.4.z, no name or as.environment(object = .) was needed## tools::parseLatex issues -- PR#18855assertErrV(tools::parseLatex("{"))tools::parseLatex("\\begin{foo}\\end{foo}")tools::parseLatex("\\Sexpr{ 1 + {1} }")assertErrV(tools::parseLatex("\\begin{foo} abc \\end{bar}"))tools::parseLatex("\\newcommand{\\test}{\\begin{foo}}")## quantile.default() needing fuzz PR#15811x <- 1:1390stopifnot(identical(print(quantile(x, 0.7, type=2)),c(`70%` = 973.5)))## was 973 in R <= 4.4.x## drop.terms(<"one" term>, 1) should work, PR#18861stopifnot(exprs = {identical( ~ 1, reformulate(character()))identical( ~ -1, reformulate(character(), intercept = FALSE))identical(terms( ~ 1 ), drop.terms(terms(y ~ 1 + w), 1))identical(terms( ~ 1 ), drop.terms(terms(y ~ w), 1))identical(terms( ~ -1), drop.terms(terms(y ~ w - 1), 1))identical(terms( ~ -1), drop.terms(terms(y ~ w + 0), 1))identical(terms(y ~ 1), drop.terms(terms(y ~ w), 1, keep.response = TRUE))})## all these used to error in reformulate() in R < 4.5.0## duplicated(<numeric_version>), especially for empty inputoptions(warn = 2) # should already be set from the topx <- numeric_version("1")stopifnot(exprs = {identical(duplicated(x[NULL]), logical(0L)) # should not warnidentical(duplicated(x), FALSE)identical(duplicated(c(x,x)), c(FALSE, TRUE))})## only in R-devel with PR#18699, the first produced a warning## In max(lens) : no non-missing arguments to max; returning -Inf## better error messages when not finding variables in model.frame() -- PR#18860dd <- mtcars ; m <- model.matrix(mpg ~ wt, data = dd) # finedd2 <- dd[-match("mpg", names(dd))]if(exists("mpg")) rm(mpg)getErrMsg <- function(expr) conditionMessage(assertErrV( expr )[[1L]])eee <- c(getErrMsg(m <- model.matrix(mpg ~ wt, data = dd2)),getErrMsg(local({mpg <- USJudgeRatingsmodel.matrix(mpg ~ wt, data = dd2) # still useful})),getErrMsg(local({model.matrix(count ~ wt, data = dd)})) ## OK (i.e. useful error message, "object 'count' not found"),getErrMsg(local({count <- function(x, ..., wt = NULL) { UseMethod("count") }model.matrix(count ~ wt, data = dd)})))if(englishMsgs)stopifnot(identical(eee,c("object 'mpg' not found","invalid type (list) for variable 'mpg'","object 'count' not found","invalid type (closure) for variable 'count'")))## the last one differed## Setting attributes on primitive functions .. [Henrik Bengtsson, R-devel]stopifnot(is.primitive(sum))msum <- sumassertErrV(void <- structure(sum, foo = TRUE))assertErrV(attributes(msum) <- list(foo = NA))## a few days later: Disable working via attr(*, "<name>") <- value as well:assertErrV( attr(msum, "foo") <- NA )stopifnot(identical(sum, msum), is.null(attributes(msum)))## all 3 examples, the first a special case of the 2nd, did not error, but *modified* the base::sum primitive## terms.formula(*, specials="<non-syntactic>") -- PR#18568f1 <- y ~ x1 + `|`(x2, f)t1 <- terms(f1, specials = "|")(cs <- colSums(attr(t1, "factors")[attr(t1, "specials")[["|"]], , drop=FALSE]))(drp <- which(as.logical(cs))) # 2(dt1 <- drop.terms(t1, drp, keep.response = TRUE))stopifnot(identical(attr(t1, "specials"), pairlist(`|` = 3L)),inherits(dt1, "terms"), dt1 == (y ~ x1))f3 <- y ~ x1 + (x2 | f) + (x3 | g)t3 <- terms(f3, specials = "|")str(t3)dropx <- which(as.logical(colSums(attr(t3, "factors")[attr(t3, "specials")[["|"]], ])))dt3 <- drop.terms(t3, dropx, keep.response = as.logical(attr(t3, "response")))stopifnot(identical(attr(t3, "specials"),pairlist(`|` = 3:4)),dt3 == (y ~ x1))## was unchanged y ~ x1 + (x2 | f) + (x3 | g)## setting environment(<primitive>) -- was mutilating the base object (in R <= 4.4.x)s <- sum ; assertWarnV(environment(s) <- baseenv())environment(s) <- NULL # no warning (and no effect)r <- return; assertWarnV(environment(r) <- baseenv())## then an error for about one day; now is deprecated (and no longer mutating).## signif(<LRG>, dig) -- PR#18889stopifnot(all.equal(1.1e308, signif(1.06e308, 2)),all.equal(1.01e308, signif(1.0055e308, 3)))## prettyNum(.., zero.print = <2-or-more-char>, replace.zero=TRUE) --zp <- "--"; num <- -1:2assertWarnV(p1 <- prettyNum(num, zero.print = zp) )p2 <- prettyNum(num, zero.print = zp, replace.zero=TRUE) # was Error (converted from warning)stopifnot(identical(p1[2], substr(zp,1,1)),identical(p2[2], zp),identical(p1[num != 0], p2[num != 0]),identical(p2, local({ p <- as.character(num); p[p == 0] <- zp; p })))## p2 gave warning too, and was the same as p1, erronously in R <= 4.5.0## `[.table` consistency, PR#18845T <- table(c(0:3,3:1,1:0), c(0:4,3:0)) ; class(T) <- c("myT", class(T))T1 <- T[,3 , drop=FALSE]; dim(T1) <- length(T1); str(T1) # 1d tablestopifnot(exprs = {identical(T, T[TRUE,]) # [..] had lost "myT" classidentical(T, T[,TRUE])identical(T1, T1[TRUE]) # (worked before)identical(class(T1), class(T)) # failedidentical(T1, T1[TRUE])})## subsetting only kept "table" class in R <= 4.5.x## t.test(<Inf>...) -- PR#18901x <- c(1:6,Inf); y <- c(1:20, Inf); yN <- c(-Inf, 1:20)(tt1 <- t.test(x))tt2. <- t.test(x, y)(tt2N <- t.test(x, yN))stopifnot(exprs = {inherits(tt1, "htest"); is.na(c(tt1 $p.value, tt1 $conf.int))inherits(tt2., "htest"); is.na(c(tt2.$p.value, tt2.$conf.int))inherits(tt2N, "htest"); is.na(c(tt2N$p.value, tt2N$conf.int))tt1$estimate == Inftt2N$estimate == c(Inf, -Inf)})## The t.test() calls errored all in R <= 4.5.1## long standing "FIXME" fixed:stopifnot(is.ts(ts(1:711, frequency=2*pi, start = 1, end = 114)))assertErrV( ts(1:711, frequency=2*pi, start = 1, end = 114, ts.eps = 1e-6) )## did *not* error in R <= 4.5.1, as 'ts.eps' was *not* passed to C code## match(<Date>, <character>) and vice versaop <- options(warn = 1)# PR#18931 - does warn for 32-bit time_tdate_seq <- seq(as.Date("1705-01-01"), as.Date("2024-12-31"), by="days")options(op)dt1 <- as.Date("2024-05-01")dt3 <- c(dt1, as.Date(c("1800-01-01", "2025-02-02")))system.time({tmp <- dt1 %in% date_seqtm3 <- dt3 %in% date_seq})# 0.260 in R 4.3.0 ff## 0.003 or so after fixingstopifnot(tmp, identical(tm3, c(TRUE, TRUE, FALSE)))## The 1-1 case (fast branch in C's match5()):ch <- "2025-05-05" ; D <- as.Date(ch)c2 <- "1925-05-05"c(cDT = ch %in% D, DcT = D %in% ch,cDF = c2 %in% D, DcF = D %in% c2)stopifnot(ch %in% D, D %in% ch, !(c2 %in% D), !(D %in% c2))## had failed in R-devel around 2025-06-26 (and before R 4.3.0)## length(<expression>) <- valuex <- expression(.)length(x) <- 0Lstopifnot(identical(x, expression()),identical(`length<-`(x, 2L), expression(NULL, NULL)))## (fix|assign)InNamespace(<S3method>) when the generic is not in search()try(detach("package:tools"), silent = TRUE) # just in caseassertValueIs <- function (value) stopifnot(exprs = {identical(tools:::toRd.default(1), value)identical(tools::toRd(1), value)})assertValueIs("1")## modify the default method to return an empty string:omethod <- tools:::toRd.defaultassignInNamespace("toRd.default", `body<-`(omethod, value = ""), "tools")## R <= 4.5.1 gave Error: object 'toRd' of mode 'function' was not foundassertValueIs("") # failed for tools::toRd(1): S3 table was not updated## now restore the original definition, testing fixInNamespace():fixInNamespace("toRd.default", "tools", editor = function (...) omethod)## failed in R <= 4.5.1assertValueIs("1")## No warnings for hist(.., log="x") -- PR#18921hist(1:100, breaks = 2^(0:8), log = "x")## used to signal 3 warnings## subassigning from real to complex keeping zero imaginary partll <- as.list(c(NA, 0L, NA_integer_, 0, NA_real_, NaN, -Inf, Inf,complex(real = 2:-1, imaginary = c(-Inf, 0:1, Inf)), NA_complex_))rr <- vapply(ll, Re, 0)ii <- vapply(ll, Im, 0) # all 0, but the very lastchk <- function (x, y = as.vector(x)) stopifnot(identical(Re(y), rr),identical(Im(y), ii))chk(unlist(ll))a1 <- a2 <- complex(m <- length(ll))for (i in seq_len(m)) a1[i] <- a2[[i]] <- ll[[i]]chk(a1); chk(a2)a1 <- a2 <- array(0i, c(m))for (i in seq_len(m)) a1[i] <- a2[[i]] <- ll[[i]]chk(a1); chk(a2)a1 <- a2 <- array(0i, c(m, 1L))for (i in seq_len(m)) a1[i, 1L] <- a2[[i, 1L]] <- ll[[i]]chk(a1); chk(a2)a1 <- a2 <- array(0i, c(m, 1L, 1L))for (i in seq_len(m)) a1[i, 1L, 1L] <- a2[[i, 1L, 1L]] <- ll[[i]]chk(a1); chk(a2)## Im(.)s had more NA's than just at the end, in R <= 4.5.z## format(<list of objects>) -- now dispatches correctlydts <- seq(.Date(11100), .Date(11111))(fD <- format(Ldt <- as.list(dts)))stopifnot(is.list(Ldt), vapply(Ldt, inherits, NA, "Date"),identical(fD, format.Date(dts)))# fD was "11100" "11101" .... "11111" in R <= 4.5.z## hist(*, plot=FALSE) warning about "nonsensical" argumentshiW <- getVaW(hist(1:22, log = "x", plot = FALSE))hi. <- hist(1:22, log = "x", plot = FALSE, warn.unused = FALSE) # no warningnoA <- \(x) `attributes<-`(x, NULL)stopifnot(exprs = {nzchar(print(wmsg <- attr(hiW,"warning")))grepl(sQuote("log"), wmsg)identical(noA(hiW), noA(hi.))})## warning msg confusingly had '...' instead of 'log'## requireNamespace(versionCheck) for loaded namespace #PR18255versionCheck <- list(op = ">", version = getRversion())requireNamespace("stats", versionCheck = versionCheck) # did not show errorstopifnot(!requireNamespace("stats", versionCheck = versionCheck, quietly = TRUE))## *not* successful, when versionCheck fails## reading an empty file via gzcon() returned non-deterministic non-empty## content (PR#18887)fempty <- tempfile(tmpdir = getwd())cat("", file=fempty)gcon <- gzcon(file(fempty, "rb"))lines2 <- readLines(gcon)close(gcon)stopifnot(identical(lines2, character(0)))gcon <- gzfile(fempty, "rb") ## also test gzfilelines <- readLines(gcon)close(gcon)stopifnot(identical(lines, character(0)))unlink(fempty)## concatenated gzipped streams were not supported by gzconfconcat <- tempfile(tmpdir = getwd())gcon <- gzfile(fconcat, "w")cat("Hello ", file=gcon)close(gcon)gcon <- gzfile(fconcat, "a")cat("World\n", file=gcon)close(gcon)gcon <- gzcon(file(fconcat, "rb"))lines2 <- readLines(gcon)close(gcon)stopifnot(identical(lines2, "Hello World"))gcon <- gzfile(fconcat, "rb") ## also test gzfilelines <- readLines(gcon)close(gcon)stopifnot(identical(lines, "Hello World"))## Fading out "slave" terminology in {tcltk} -- PR#17835if(require("tcltk")) withAutoprint({ # some setups may lack tcltk (right ?)tclServiceMode(FALSE) # no displaytop <- tktoplevel()(ww <- tryCatch(tkpack.slaves(top), warning=identity))if(package_version(tcltk::tclVersion()) >= "8.6")stopifnot(exprs = {inherits(ww, "deprecatedWarning")identical(ww$new, "tkpack.child")})detach("package:tcltk", unload=TRUE)})## three tk*.slaves() should be substituted by tk*.child()## invalid `versionCheck` should error even when `quietly`assertErrV( requireNamespace("tcltk", quietly = TRUE, versionCheck = "999.0") )## silently returned FALSE previously, leading to further confusion## rep() error messages -- PR#18926repXerr <- quote({rep(1, times = 4503599627370496, each = 2)rep(1:2, times = 4503599627370496)rep(1:2^30, each = 2^31+2)rep(1:(2^31+1), each = 2^31+2)rep(1:(2^31+1), times = 1:(2^31+3), each = 2^31+2)rep(1:3, times = 1:3, each = 0)rep(1:3, times = 1:3, each = 2)rep(1, times = -1)rep(1, times = NA)rep(1:3, times = 1:4)rep(1:(2^31+1), times = 1:(2^31+3))})writeLines(repE <- vapply(repXerr[-1L], \(xpr) tryCatch(eval(xpr), error=conditionMessage), "<err>"))if (.Machine$sizeof.pointer == 8)stopifnot(identical(repE, repE[c(rep(1,4), rep(5,3), rep(8,4))]))if(englishMsgs)stopifnot(exprs = {identical(repE[[1]],if (.Machine$sizeof.pointer == 4) "invalid 'times' argument"else "length(x) * 'times' * 'each' is too large")identical(repE[[7]], "invalid 'times' argument, given the value of 'each'")identical(repE[[8]], "invalid 'times' argument")})## in all cases, msg was "invalid 'times' argument"; in some cases, misleadingly## implement chkDots's `allowed` argument -- PR#18936f <- function(...) chkDots(..., allowed = "foo")stopifnot(is.null(f()),is.null(f(foo = 1))) # NB warn = 2assertWarnV(f(bar = "foo"))assertWarnV(f(bar = "foo", foo = 2))assertWarnV(f(1, 2))r <- getVaW(f(1, foo=2), TRUE)stopifnot(r == quote(._NULL_()),inherits(print(attr(r, "warning")), "chkDotsWarning"))## _classed_ warning## implement messageCondition and use it in packageStartupMessageclasses <- c("testMessage", "message", "condition")tools::assertCondition(message(messageCondition("a test", class = "testMessage")),classes) |> suppressMessages()classes <- c("packageStartupMessage", "simpleMessage", "message", "condition")tools::assertCondition(packageStartupMessage("a startup message"),classes) |> suppressMessages()suppressPackageStartupMessages(packageStartupMessage("shouldn't see me"))## "dumping" nothing to an existing connection was an error in R <= 4.5## PR#18729tmpfile <- tempfile()con <- file(tmpfile, "w")dump(character(), con)close(con)unlink(tmpfile)## colSums() .. rowMeans() with complex z, where Re() and Im() contain NAs in different places.## "Obviously correct" versions (w/o 'dims' arg):colSumsC <- function(x, na.rm = FALSE) apply(x, 2L, sum, na.rm=na.rm)rowSumsC <- function(x, na.rm = FALSE) apply(x, 1L, sum, na.rm=na.rm)colMeansC <- function(x, na.rm = FALSE) apply(x, 2L, mean, na.rm=na.rm)rowMeansC <- function(x, na.rm = FALSE) apply(x, 1L, mean, na.rm=na.rm)y <- 1:12; y[c(2,3,5,7,11)] <- NA(z <- matrix(complex(re = 12:1, im = y), 3))## [,1] [,2] [,3] [,4]## [1,] 12+1i 9+4i NA 3+10i## [2,] NA NA 5+8i NA## [3,] NA 7+6i 4+9i 1+12istopifnot(!any(is.na(Re(z)))) # no NA's in real partfor(na in c(TRUE, FALSE))stopifnot(exprs = {identical(colSumsC (z, na.rm=na),colSums (z, na.rm=na))identical(colMeansC(z, na.rm=na),colMeans (z, na.rm=na))identical(rowSumsC (z, na.rm=na),rowSums (z, na.rm=na))identical(rowMeansC(z, na.rm=na),rowMeans (z, na.rm=na))identical(sum(colSums(z, na.rm=na)), sum(z, na.rm=na) -> sz)identical(sum(rowSums(z, na.rm=na)), sz)})## almost all differed in R <= 4.5.1## Ben Bolker + Kasper Kri...'s PR#18946 -- lbeta(<complex>, *)(Lb <- list(b1 = tryCid( beta(1i, 1) ), b2 = tryCid( beta(1, 1i) ), l1 = tryCid( lbeta(1i, 1) ), l2 = tryCid( lbeta(1, 1i) )))stopifnot(vapply(Lb, inherits, what="error", NA))## l1 was not an error, but non-sense complex, in R <= 4.5.1stopifnot(identical(log10(1i), log(1i, 10)), log2(c(1,2,4) + 0i) == 0:2)## (< 24h) lapsus "unimplemented complex fn."## jitter(): more "robust"ii5 <- rep(1000, 5)i12 <- rep(1:4, each=3)iI <- c(-Inf, 3,3,3)assertWarnV(iN <- sqrt(-1:1)) # NaNs producedset.seed(12)(j1 <- jitter(ii5, factor = -1/4)) # ok - no longer NaN(j2 <- jitter(i12, amount = -1/4)) # (ditto)(jI <- jitter(iI))(jN <- jitter(iN))stopifnot(990 < j1, j1 < 1010, 0.9 < j2, j2 < 4.4,jI[1] == -Inf, 2.9 < jI[-1], jI[-1] < 3.1,is.na(jN[1]), -1/4 < jN[-1], jN[-1] < 1.1)## x in {Inf,NA,..} failed for 'd' computation; negative amount / factor gave NaN## substr() / substring() -- allowing stop|last = NULL to mean "suffix" -- PR#18851(nL <- nchar(Lstr <- strrep(paste(letters,collapse=""), 4e4))) # nchar(.) > 1e6ss <- substring(Lstr, 1e6)stopifnot(exprs = {nchar(ss) == nL - 1e6 + 1startsWith(ss, "nopqrst")endsWith (ss, "xyz")identical(substring(ss, nchar(ss)-7), "stuvwxyz")}) ## were all FALSE in R <= 4.5.1: `last = 1000000L' was not large enough## pretty(<very small>, eps.correct=2) would produce huge vectorsassertWarnV(pp <- .pretty(c(0, 1e-322), eps.correct = 2))str(pp)E <- 2e-314stopifnot(all.equal(list(l = -E, u = E, n = 2L), pp, tolerance = 1e-12))## n = 1112538 (Lnx 64b) in R <= 4.5.1 ^^^^^^## poly(<factor>, .)hf <- c(-1, 1.2, -1.5, -0.75, -2)x <- c("c", "b", "a", "b", "a")xf <- as.factor(x)xo <- as.ordered(x)tools::assertError(verbose=TRUE, lm(hf ~ poly(x, 2)))tools::assertError(verbose=TRUE, lm(hf ~ poly(xf, 2)))coef(om <- lm(hf ~ poly(xo, 2)))stopifnot(all.equal(coef(om), tolerance = 5e-5,c("(Intercept)" = -0.81, "poly(xo, 2)1" = 1.01, "poly(xo, 2)2" = -1.7105)))## poly(xf, .) gave no error in R 4.1.1--4.5.x## PR#15275## terms.formula(x, ...) when RHS of 'x' has logical/numeric NA;## "equal" variables were not matchedchkv <- function(formula, variables, do.eval = FALSE)identical(attr(terms(formula), "variables") |> print(), ## MM: print() just for testing with prev Rif(do.eval) variables else substitute(variables))stopifnot(exprs = { ## logical/numeric mixtures:## equal non-NA were matched, equal NA were notchkv(~x + f(FALSE) + f(FALSE) + g(NA) + g(NA),list(x, f(FALSE), g(NA)))chkv(~x + f(FALSE) + f(FALSE) + g(NaN) + g(NaN),list(x, f(FALSE), g(NaN)))chkv(~x + f(FALSE) + f(0L) + g(NA) + g(NA_integer_),list(x, f(FALSE), g(NA)))chkv(~x + f(FALSE) + f(0) + g(NA) + g(NA_real_),list(x, f(FALSE), g(NA)))## complex: matching never supported; chkv() |-> TRUEchkv(~x + f(0) + f(0i) + g(NA_real_) + g(NA_complex_),list(x, f(0), f(0i), g(NA_real_), g(NA_complex_)))chkv(~x + f(0i) + f(0i) + g(NA_complex_) + g(NA_complex_),list(x, f(0i), f(0i), g(NA_complex_), g(NA_complex_)))## character: matching always supported (only w/o mixture)chkv(~x + f(0) + f("0") + g(NA_real_) + g(NA_character_),list(x, f(0), f("0"), g(NA_real_), g(NA_character_)))chkv(~x + f("0") + f("0") + g(NA_character_) + g(NA_character_),list(x, f("0"), g(NA_character_)))## "extra": it was possible to trigger STRING_ELT(<empty>, 0){e <- list(. = character(0L))chkv(as.formula(substitute(~x + f(.) + f(.), e)),substitute(list(x, f(.)), e), do.eval = TRUE)}})## now does match f(NA) etc correctly## check that dim and dimnames are dropped when extending with GROWABLEx <- 1:49x[50] <- 50Ldim(x) <- c(25, 2)dimnames(x) <- list(NULL, c("a", "b"))a <- .Internal(address(x))x[51] <- 51Lstopifnot(identical(a, .Internal(address(x)))) ## reused xstopifnot(is.null(attributes(x))) ## dim and dimnames have been dropped## dim and dimnames were kept in R <= 4.5.z## all.equal(*, check.class=FALSE)two <- structure(2, foo = 1, class = "bar")c2 <- `storage.mode<-`(two, "character")r2 <- `storage.mode<-`(two, "raw")stopifnot(exprs = {is.character(ae <- all.equal(two^20, 2^20, check.attributes = FALSE))grepl(" bar.* numeric", ae)## above were TRUE already, these did *still* check class:all.equal(two^20, 2^20, check.attributes = FALSE, check.class = FALSE)all.equal(c2, "2", check.attributes = FALSE, check.class = FALSE)all.equal(r2, as.raw(2), check.attributes = FALSE, check.class = FALSE)})## 'check.class' was not passed downstream in R <= 4.5.2## diff(x=<m-by-n>, l, d) dropped dimensions when l*d >= mm <- provideDimnames(matrix(0, 10L, 1L))names(dimnames(m)) <- c("row", "col").difftime1 <- .difftime # diff() shouldn't hard code units="days"formals(.difftime1)$units <- "secs"##' list_(a, b, cc) creates a *named* list using the actual arguments' nameslist_ <- function(...) `names<-`(list(...), vapply(sys.call()[-1L], as.character, ""))L <- lapply(list_(identity, ts, .Date, .POSIXct, .difftime1),\(fn) { fnm0 <- (fnm <- fn(m))[0L, , drop = FALSE]list(f0 = fnm0, f = diff(fnm, lag = 2L, differences = 5L)) })str(L, give.attr=FALSE) # now 0 x 1 matricesvapply(L, \(.) identical(.$f0, .$f), NA) # where all FALSE; now not all TRUEstopifnot( print(vapply(L, \(.) identical(.$f0 - .$f0, .$f), NA) ) )## were all FALSE : diff(fnm, 2,5) was not a matrixm <- ts(matrix(1)) # ts-matrix boundary caseassertWarnV(d1 <- m - lag(m, -1)) # "non-intersecting series"d2 <- diff(m)stopifnot(identical(d1,d2), identical(dim(d1), 0:1))## both d1 & d2 were *not* matrix in R <= 4.5.2## str.{Date,POSIXt}(<length 0>, give.attr=FALSE) - now workschk0 <- function(x) identical(capture.output(str(x, give.attr = FALSE)),capture.output(str(`attr<-`(x, "foobar", NULL))))stopifnot(chk0(structure(.Date (numeric()), foobar = list(Dt = "A"))),chk0(structure(.POSIXct(numeric()), foobar = list(ct = "C"))))## in R <= 4.5.2, give.attr=FALSE was not obeyed for 0-length "Date" / "POSIXt"## guard against mutation through active bindingsy <- 1 + 0if (exists("x")) rm(x)makeActiveBinding("x", function(v) y, .GlobalEnv)x[1] <- 2stopifnot(y == 1)rm(x)## PR#18304 -- recycling `nvec` argument of sequence.default()chkS <- function(n, nvec, recyc=FALSE) {lxn <- rep.int(1L, n)stopifnot(exprs = {identical(sequence.default(from = lxn, by = 1L, nvec = nvec, recycle=recyc),sequence.default(from = 1L, by = lxn, nvec = nvec, recycle=recyc) -> s1)is.integer(s2 <- unlist(mapply(seq, from = lxn, by = 1L,length.out = rep_len(nvec, n),# <- to avoid warning: longer argument# not a multiple of length of shorterSIMPLIFY=FALSE, USE.NAMES=FALSE)))identical(s1, if(recyc || n <= length(nvec)) s2 else s2[seq_along(s1)])})s1}for(recycl in c(FALSE, TRUE)) withAutoprint({cat("\n>>>> recycl: ", recycl, "-----\n",strrep("-", 25),"\n", sep="")## These all worked identically previously:chkS(1, 1, recyc = recycl) # 1chkS(2, 1:2, recyc = recycl) # 1, 1 2chkS(3, 1:3, recyc = recycl) # 1, 1 2, 1 2 3chkS(3, 3:1, recyc = recycl) # 1 2 3, 1 2, 1chkS(4, 1:4, recyc = recycl) # 1, 1 2, 1 2 3, 1 2 3 4chkS(4, 4:1, recyc = recycl) # 1 2 3 4, 1 2 3, 1 2, 1chkS(5, 1:5, recyc = recycl) # 1, 1 2, 1 2 3, 1 2 3 4, 1 2 3 4 5## These did not: length(nvec) < n :if(recycl) chkS(3, 2:3, recyc = TRUE)else { rF <- getVaW( chkS(3, 2:3, recyc = FALSE) )## the very first produces a __once per R session__ warning:if(!is.null(wrn <- attr(rF, "warning"))) {cat("Caught warning: ")writeLines(wrn) } # recycl: FALSE || TRUEas.vector(rF) } # 1 2, 1 2 3 || 1 2, 1 2 3, 1 2chkS(5, 2:3, recyc = recycl) # 1 2, 1 2 3 || 1 2, 1 2 3, 1 2, 1 2 3, 1 2chkS(6, 2:3, recyc = recycl) # 1 2, 1 2 3 || 1 2, 1 2 3, 1 2, 1 2 3, 1 2, 1 2 3chkS(4, 2:1, recyc = recycl) # 1 2, 1 || 1 2, 1, 1 2, 1chkS(4, 5:6, recyc = recycl) # 1 2 3 4 5, 1 2 3 4 5 6 || 1 2 3 4 5, 1 2 3 4 5 6, 1 2 3 4 5, 1 2 3 4 5 6chkS(5, 1:4, recyc = recycl) # 1, 1 2, 1 2 3, 1 2 3 4 || 1, 1 2, 1 2 3, 1 2 3 4, 1## the last 6 cases all failed chkS() for recycle = TRUE})## <1d-arrary>[<name>] <- <val> -- dropped dim & dimnames in transforming to atomic vector -- PR#18973mk1d <- function(N) {stopifnot(length(N) == 1, N >= 1, is.integer(n <- 1:N))array(n, dimnames = list(letters[n]))}chk1d <- function(a)stopifnot(is.array(a), length(d <- dim(a)) == 1L, is.list(dn <- dimnames(a)), length(dn) == 1L)str(x <- mk1d(3)); chk1d(x)x[1] <- 99 ; chk1d(x)x["a"] <- 100; chk1d(x)## x["a"] <- .. did drop dim() & dimnames() {getting names() instead}.## error message when length(dim) == 0:(m1 <- tryCmsg(array(NULL )))(m2 <- tryCmsg(array(,NULL)))if(englishMsgs)stopifnot(grepl(" was 'NULL'", m1, fixed=TRUE),grepl("'dim' cannot ", m2, fixed=TRUE))## had 'dims'## this legal, though strange, code fails used to fail with## Error: object '*tmp*' not foundf <-function(x, y) x`f<-` <- function(x, y, value) { y; x}x <- 1y <- 2f(x, y[] <- 1) <- 3## Conversion of LaTeX accents in more bibentry fieldsbib <- bibentry("book", author = person("Anonymous"), title = "Title", year = 1,publisher = "Universidad de Ja{\\'e}n",series = "Os {Economistas}")(rd <- tools::toRd(bib)) # formatBook() from the default "JSS" stylestopifnot(endsWith(rd, "Ja\u00e9n."), grepl("Os Economistas", rd))## Publisher and Series were not subject to cleanupLatex() in R <= 4.5.2## After adding bounds checking in STRING_ELT this use to signal an## error in a barrier build.order(NA_character_, 'c', method = 'radix', na.last = NA)## provideDimnames(use.names=) for names(dimnames(.))pDF <- provideDimnamesformals(pDF)$base <- quote(list("uu" = "a", "vv" = "b"))pDT <- pDFformals(pDT)$use.names <- TRUEdn <- function(x, dn = dimnames(x))if(!is.null(dn)) list(names(dn), `names<-`(dn, NULL))dnF <- function(...) dn(pDF(...))dnT <- function(...) dn(pDT(...))(N4 <- N4. <- array(0, rep(1L, 4L)))dimnames(N4.) <- `names<-`(vector("list", 4L), c("ww", "", "", ""))N4.L4 <- L4. <- list(NULL, list("a", "b", "a", "b"))L4.[[1L]] <- names(dimnames(N4.))stopifnot(identical(dnF(N4 ), L4 ),identical(dnF(N4.), L4.),identical(dnT(N4 , sep = "~"),`[[<-`(L4 , 1L, c("uu", "vv", "uu~1", "vv~1"))),identical(dnT(N4., unique = FALSE),`[[<-`(L4., 1L, c("ww", "vv", "uu" , "vv" ))),## now composition ('T' always wins):vapply(list(N4, N4.),function(.) identical(pDF(pDF(.)), pDF(.)) &&identical(pDF(pDT(.)), pDT(.)) &&identical(pDT(pDF(.)), pDT(.)) &&identical(pDT(pDT(.)), pDT(.)), NA))## besselJ(pi/22, 1e-15) anomaly, R-help, 28 Dec 2025, Leo Madax <- 0:41; bJ <- besselJ(0:41, 1e-15)bJ16xct <-c(0, 0.76519769, 0.22389078, -0.26005195, -0.39714981, -0.17759677,0.15064526, 0.30007927, 0.17165081, -0.090333611, -0.24593576,-0.1711903, 0.047689311, 0.2069261, 0.17107348, -0.014224473)all.equal(bJ16xct, bJ[1:16], tolerance=0) # 8.3888e-9 [was +1e15 since r32446, 2005-01-03]stopifnot(all.equal(bJ16xct, bJ[1:16]),max(abs(bJ[17:42])) < 0.175)## besselJ(x, nu)'s C code now works for very small nu## pretty(<char>) bug introduced > 15 yrs agostopifnot(identical(20 * 0:5, pretty(c("1", "9", "100"))))## wrongly gave 0 2 4 6 8 10## summary() of an empty character vector (after PR#16750)stopifnot(all.equal(summary(nchar(character()))[c("Min.", "Max.")] |> print(),summary(character())[c("Min.nchar", "Max.nchar")],check.names = FALSE))## gave +-Inf (with warnings) rather than NA, for a few days in the trunk## asymmetric toeplitz(x, r), when length(r) < 2 and {x, r} differ by type -- PR#18996chkToep <- function(tx, lx, tr, lr) {x <- vector(tx, lx)r <- vector(tr, lr)identical(toeplitz(x, r), matrix(c(FALSE, x[0L], r[0L]), lx, lr))}t3 <- c("integer", "double", "complex")i02 <- 0L:2Ltail(L <- expand.grid(tx=t3, lx=i02, tr=t3, lr=i02,KEEP.OUT.ATTRS = FALSE, stringsAsFactors=FALSE))stopifnot(unlist(.mapply(chkToep, L, NULL)))## had 18 (out of 81) FALSE in R <= 4.5.z## format(<named raw>):rr <- as.raw(seq(0, 255, by = 7))names(rr) <- nn <- outer(c(LETTERS, letters), c("","_"), paste0)[seq_along(rr)]head(fr <- format(rr))stopifnot(identical(names(fr), nn))## lost names() in R <= 4.5.z## rep.int() and rep_len() on factor had names, not as documented -- PR#18999## From example in ?repx <- factor(LETTERS[1:4]); names(x) <- letters[1:4]stopifnot(is.null(names(rep.int(x, 2))),is.null(names(rep_len(x, 10))))## had names in 4.0.0 <= R <= 4.5.z because of dispatch to rep() method## str(<obj_w_method using NextMethod>) -- PR#19001aa <- grid::arrow(type = "closed")writeLines(stro <- capture.output(str(aa, give.attr=FALSE)))noListof <- function(st) !grepl("list of ", st, ignore.case=TRUE)stopifnot(noListof(stro), length(stro) == 1 + 4)## had extra 2nd line "Class 'arrow' hidden list of 4"strSome <- str.someclass <- function(object, ...) {cat(if(is.null(pr <- attr(.Class, "previous")))sprintf("<%s> .Method for .Class '%s' (length %d)\n",as.character(.Method), deparse1(.Class), length(object))else sprintf("<%s> .Method for .Class '%s' -- after previous '%s'\n",as.character(.Method), deparse1(as.vector(.Class)), paste0(pr, collapse=",")))NextMethod()}x <- structure(list(a = 1, b = 2, c = 3), class = "someclass")writeLines(str1 <- capture.output(str(x)))rm(str.someclass) # and _register_ it ==> should str() identically:.S3method("str", "someclass", strSome)str2 <- capture.output(str(x))getA3 <- list(name = "str.someclass", where = "registered S3 method for str", visible = FALSE)stopifnot(exprs = {noListof(str2)identical(str1, str2)identical(getA3, unclass(getAnywhere("str.someclass"))[names(getA3)])})## str2 had extra line 'List of ..' -- now one more level:str.s2class <- strSomex2 <- structure(list(a = 1, S = 2), class = c("s2class", "someclass"))xs2 <- structure(list(a = 1, S = 2), class = c("someclass", "s2class"))writeLines(strX2 <- capture.output(str(x2)))writeLines(strXs2 <- capture.output(str(xs2)))rm(str.s2class) # and _register_ it ....S3method("str", "s2class", strSome)strX2. <- capture.output(str(x2))strXs2. <- capture.output(str(xs2))stopifnot(identical(strX2 , strX2. ), noListof(strX2. ),identical(strXs2, strXs2.), noListof(strXs2.))## strXs?2. did have 'List of' in R <= 4.5.z## simple test for R_GetBindingTypelocal({getBindingType <- function(sym, env = parent.frame()) {if (is.character(sym))sym <- as.name(sym).Internal(getBindingType(sym, env))}f0 <- function() getBindingType("x")stopifnot(f0() == "unbound")f1 <- function() { x <- 1; getBindingType("x")}stopifnot(f1() == "value")f2 <- function(x) getBindingType("x")stopifnot(f2() == "missing")f3 <- function(x) getBindingType("x")stopifnot(f3(1) == "delayed")f4 <- function(x) { x; getBindingType("x")}stopifnot(f4(1) == "forced")f5 <- function() {makeActiveBinding("x", \(x) 1, environment())getBindingType("x")}stopifnot(f5() == "active")})## R_GetBindingType with promise chains from `...` expansion (PR#18928)## Expanding `...` into named parameters creates promise chains where## PRCODE of the wrapper is the original PROMSXPlocal({getBindingType <- function(sym, env = parent.frame()) {if (is.character(sym))sym <- as.name(sym).Internal(getBindingType(sym, env))}g <- function(x) getBindingType("x")# `...` expansion into a named parameter wraps the dot promisex <- 1f <- function(...) g(...)stopifnot(f(x) == "delayed")# Forcing the dot then expanding: unwrapping must detect the forced innerf <- function(...) { force(..1); g(...) }stopifnot(f(x) == "forced")# Deeper chain: `...` -> `...` -> named parametermid <- function(...) g(...)f <- function(...) mid(...)stopifnot(f(x) == "delayed")# Force at the top of a deeper chainf <- function(...) { force(..1); mid(...) }stopifnot(f(x) == "forced")})## R_GetBindingType with symbol bindings (base namespace)local({getBindingType <- function(sym, env) {if (is.character(sym))sym <- as.name(sym).Internal(getBindingType(sym, env))}stopifnot(getBindingType("T", baseenv()) == "value")stopifnot(getBindingType("c", baseenv()) == "value")stopifnot(getBindingType(".TAOCP1997init", baseenv()) == "delayed")stopifnot(getBindingType(".Library.site", baseenv()) == "active")stopifnot(getBindingType("..nonexistent..", baseenv()) == "unbound")})## Binding accessors with symbol bindings (base namespace)local({delayedExpr <- function(sym, env) {if (is.character(sym)) sym <- as.name(sym).Internal(delayedBindingExpression(sym, env))}delayedEnv <- function(sym, env) {if (is.character(sym)) sym <- as.name(sym).Internal(delayedBindingEnvironment(sym, env))}forcedExpr <- function(sym, env) {if (is.character(sym)) sym <- as.name(sym).Internal(forcedBindingExpression(sym, env))}# `.TAOCP1997init` is lazily loaded in base. We're checking this one# because it's unlikely to have been forced by another test.expr <- delayedExpr(".TAOCP1997init", baseenv())stopifnot(is.language(expr))env <- delayedEnv(".TAOCP1997init", baseenv())stopifnot(is.environment(env))force(.TAOCP1997init)expr <- forcedExpr(".TAOCP1997init", baseenv())stopifnot(is.language(expr))# `.Library.site` is an active binding in basefn <- activeBindingFunction(as.name(".Library.site"), baseenv())stopifnot(is.function(fn))})## R_DelayedBindingExpression and R_DelayedBindingEnvironmentlocal({delayedExpr <- function(sym, env = parent.frame()) {if (is.character(sym)) sym <- as.name(sym).Internal(delayedBindingExpression(sym, env = parent.frame()))}delayedEnv <- function(sym, env = parent.frame()) {if (is.character(sym)) sym <- as.name(sym).Internal(delayedBindingEnvironment(sym, env))}e <- environment()x <- 1g <- function(x) delayedExpr("x")stopifnot(identical(g(x), quote(x)))g <- function(x) delayedEnv("x", environment())stopifnot(identical(g(x), e))# Through forwarded ...get_expr <- function(x) delayedExpr("x")get_env <- function(x) delayedEnv("x")f <- function(...) get_expr(...)stopifnot(identical(f(x), quote(x)))f <- function(...) get_env(...)stopifnot(identical(f(x), e))# Deeper chainmid_expr <- function(...) get_expr(...)f <- function(...) mid_expr(...)stopifnot(identical(f(x), quote(x)))mid_env <- function(...) get_env(...)f <- function(...) mid_env(...)stopifnot(identical(f(x), e))})## R_ForcedBindingExpressionlocal({forcedExpr <- function(sym, env = parent.frame()) {if (is.character(sym)) sym <- as.name(sym).Internal(forcedBindingExpression(sym, env))}x <- 1g <- function(x) { force(x); forcedExpr("x") }stopifnot(identical(g(x), quote(x)))# Through forwarded ...get_expr <- function(x) { force(x); forcedExpr("x") }f <- function(...) get_expr(...)stopifnot(identical(f(x), quote(x)))# Forced at outer level, then forwarded into named paraminner <- function(x) forcedExpr("x")f <- function(...) { force(..1); inner(...) }stopifnot(identical(f(x), quote(x)))# Deeper chainmid <- function(...) inner(...)f <- function(...) { force(..1); mid(...) }stopifnot(identical(f(x), quote(x)))})## R_DotsElt errors on missing dot argumentlocal({f <- function(...) ...elt(1)x <- 1stopifnot(identical(f(x), 1))stopifnot(inherits(tryCatch(f(, 1), error = identity), "missingArgError"))# This is another error pathstopifnot(grepl("the ... list contains fewer than",tryCatch(f(), error = conditionMessage)))})## simple test for R_GetDotTypelocal({getDotType <- function(i, env = parent.frame(), inherits = TRUE).Internal(getDotType(i, env, inherits))g <- function(...) getDotType(1L, environment())x <- 1stopifnot(g(x) == "delayed")stopifnot(g(, 1) == "missing")h <- function(...) { force(..1); getDotType(1L, environment()) }stopifnot(h(x) == "forced")})## R_GetDotType with promise chains from `...` expansionlocal({getDotType <- function(i, env = parent.frame(), inherits = TRUE).Internal(getDotType(i, env, inherits))inner <- function(...) getDotType(1L)x <- 1f <- function(...) inner(...)stopifnot(f(x) == "delayed")# Forced inner, then forwardedf <- function(...) { force(..1); inner(...) }stopifnot(f(x) == "forced")# Deeper chainmid <- function(...) inner(...)f <- function(...) mid(...)stopifnot(f(x) == "delayed")f <- function(...) { force(..1); mid(...) }stopifnot(f(x) == "forced")})## R_DotDelayedExpression and R_DotDelayedEnvironmentlocal({dotDelayedExpr <- function(i, env = parent.frame(), inherits = TRUE).Internal(dotDelayedExpression(i, env, inherits))dotDelayedEnv <- function(i, env = parent.frame(), inherits = TRUE).Internal(dotDelayedEnvironment(i, env, inherits))get_expr <- function(...) dotDelayedExpr(1L)get_env <- function(...) dotDelayedEnv(1L)e <- environment()x <- 1stopifnot(identical(get_expr(x), quote(x)))stopifnot(identical(get_env(x), e))# Through forwarded ...outer_expr <- function(...) get_expr(...)outer_env <- function(...) get_env(...)stopifnot(identical(outer_expr(x), quote(x)))stopifnot(identical(outer_env(x), e))# Deeper chainmid_expr <- function(...) get_expr(...)deep_expr <- function(...) mid_expr(...)mid_env <- function(...) get_env(...)deep_env <- function(...) mid_env(...)stopifnot(identical(deep_expr(x), quote(x)))stopifnot(identical(deep_env(x), e))})## R_DotForcedExpressionlocal({dotForcedExpr <- function(i, env = parent.frame(), inherits = TRUE).Internal(dotForcedExpression(i, env, inherits))get_expr <- function(...) dotForcedExpr(1L)x <- 1g <- function(...) { force(..1); dotForcedExpr(1L) }stopifnot(identical(g(x), quote(x)))# Forced inner, then forwardedh <- function(...) { force(..1); get_expr(...) }stopifnot(identical(h(x), quote(x)))# Deeper chainmid <- function(...) get_expr(...)h <- function(...) { force(..1); mid(...) }stopifnot(identical(h(x), quote(x)))# Forwarded dot forced in place (outermost wrapper is directly forced)inner_forced <- function(...) { force(..1); dotForcedExpr(1L) }f <- function(...) inner_forced(...)stopifnot(identical(f(x), quote(x)))})## R_DotsExist() returns TRUE for empty dots (R_MissingArg)local({dotsExist <- function(env = parent.frame(), inherits = TRUE).Internal(dotsExist(env, inherits))fn <- function(...) dotsExist()fn_no_dots <- function() dotsExist()stopifnot(isTRUE(fn()),isTRUE(fn(1)),isTRUE(fn(1, 2, 3)),isFALSE(fn_no_dots()))## Non-DOTSXP values bound to `...`e <- new.env(parent = emptyenv())e$... <- NULLstopifnot(isFALSE(dotsExist(e)))e$... <- 1stopifnot(isFALSE(dotsExist(e)))})## C API: R_DotsExist() does not reach into parent environments (PR#18928)## (positive tests above in "R_DotsExist() returns TRUE for empty dots")local({dotsExist <- function(env = parent.frame(), inherits = TRUE).Internal(dotsExist(env, inherits))fn <- function(...) local(dotsExist(inherits = FALSE))stopifnot(isFALSE(fn()))stopifnot(isFALSE(fn(1)))stopifnot(isFALSE(fn(1, 2, 3)))})## C API: R_DotsLength() does not reach into parent environments (PR#18928)local({dotsLength <- function(env = parent.frame(), inherits = TRUE).Internal(dotsLength(env, inherits))fn <- function(...) local(dotsLength(inherits = FALSE))stopifnot(grepl("incorrect context",tryCatch(fn(1, 2), error = conditionMessage)))## Works when `...` is directly in the framefn2 <- function(...) dotsLength(inherits = FALSE)stopifnot(fn2() == 0L,fn2(1) == 1L,fn2(1, 2, 3) == 3L)## Works with forwarded dotsinner <- function(...) dotsLength(inherits = FALSE)outer <- function(...) inner(...)stopifnot(outer(1, 2, 3) == 3L)})## C API: R_DotsNames() does not reach into parent environments (PR#18928)local({dotsNames <- function(env = parent.frame(), inherits = TRUE).Internal(dotsNames(env, inherits))fn <- function(...) local(dotsNames(inherits = FALSE))stopifnot(grepl("incorrect context",tryCatch(fn(a = 1), error = conditionMessage)))## Works when `...` is directly in the framefn2 <- function(...) dotsNames(inherits = FALSE)stopifnot(identical(fn2(a = 1, b = 2), c("a", "b")),is.null(fn2(1, 2)),is.null(fn2()))## Works with forwarded dotsinner <- function(...) dotsNames(inherits = FALSE)outer <- function(...) inner(...)stopifnot(identical(outer(x = 10, y = 20), c("x", "y")))})## C API: R_DotsElt() does not reach into parent environments (PR#18928)local({dotsElt <- function(i, env = parent.frame(), inherits = TRUE).Internal(dotsElt(i, env, inherits))fn <- function(...) local(dotsElt(1L, inherits = FALSE))stopifnot(grepl("no ... to look in",tryCatch(fn(42), error = conditionMessage)))## Works when `...` is directly in the framefn2 <- function(...) dotsElt(1L, inherits = FALSE)stopifnot(fn2(42) == 42,identical(fn2("hello"), "hello"))fn3 <- function(...)c(dotsElt(1L, inherits = FALSE), dotsElt(2L, inherits = FALSE))stopifnot(identical(fn3(10, 20), c(10, 20)))## Works with forwarded dotsinner <- function(...) dotsElt(1L, inherits = FALSE)outer <- function(...) inner(...)stopifnot(outer(99) == 99)})## C API: R_GetDotType() does not reach into parent environments (PR#18928)local({getDotType <- function(i, env = parent.frame(), inherits = TRUE).Internal(getDotType(i, env, inherits))fn <- function(...) local(getDotType(1L, inherits = FALSE))stopifnot(grepl("no ... to look in",tryCatch(fn(1), error = conditionMessage)))## (positive tests above in "simple test for R_GetDotType")})## C API: R_DotDelayedExpression()/Environment() do not reach parents## (PR#18928) (positive tests above in "R_DotDelayedExpression and## R_DotDelayedEnvironment")local({dotDelayedExpr <- function(i, env = parent.frame(), inherits = TRUE).Internal(dotDelayedExpression(i, env, inherits))dotDelayedEnv <- function(i, env = parent.frame(), inherits = TRUE).Internal(dotDelayedEnvironment(i, env, inherits))x <- 1fn <- function(...) local(dotDelayedExpr(1L, inherits = FALSE))stopifnot(grepl("no ... to look in",tryCatch(fn(x), error = conditionMessage)))fn2 <- function(...) local(dotDelayedEnv(1L, inherits = FALSE))stopifnot(grepl("no ... to look in",tryCatch(fn2(x), error = conditionMessage)))})## C API: R_DotForcedExpression() does not reach parents (PR#18928)## (positive tests above in "R_DotForcedExpression")local({dotForcedExpr <- function(i, env = parent.frame(), inherits = TRUE).Internal(dotForcedExpression(i, env, inherits))x <- 1fn <- function(...) {force(..1)local(dotForcedExpr(1L, inherits = FALSE))}stopifnot(grepl("no ... to look in",tryCatch(fn(x), error = conditionMessage)))})## R API: ...length() retains inherited scoping (PR#18928)local({## Through local()f <- function(...) local(...length())stopifnot(f(1, 2, 3) == 3L,f() == 0L,f(1) == 1L)## Through nested function without `...`f2 <- function(...) {g <- function() ...length()g()}stopifnot(f2(1, 2) == 2L)## Deeper nestingf3 <- function(...) {g <- function() {h <- function() ...length()h()}g()}stopifnot(f3(1, 2, 3, 4) == 4L)## Direct call still worksf0 <- function(...) ...length()stopifnot(f0(1, 2) == 2L)})## R API: ...names() retains inherited scoping (PR#18928)local({## Through local()f <- function(...) local(...names())stopifnot(identical(f(a = 1, b = 2), c("a", "b")),is.null(f(1, 2)),is.null(f()))## Through nested function without `...`f2 <- function(...) {g <- function() ...names()g()}stopifnot(identical(f2(x = 10, y = 20), c("x", "y")))## Direct call still worksf0 <- function(...) ...names()stopifnot(identical(f0(a = 1), "a"))})## R API: ...elt() retains inherited scoping (PR#18928)local({## Through local()f <- function(...) local(...elt(1))stopifnot(f(42) == 42)## Through nested function without `...`f2 <- function(...) {g <- function() ...elt(2)g()}stopifnot(f2("a", "b") == "b")## Deeper nestingf3 <- function(...) {g <- function() {h <- function() ...elt(1)h()}g()}stopifnot(f3(99) == 99)## Direct call still worksf0 <- function(...) ...elt(1)stopifnot(f0(7) == 7)## Multiple elements through nested scopef4 <- function(...) {g <- function() c(...elt(1), ...elt(2))g()}stopifnot(identical(f4(10, 20), c(10, 20)))## Named dotsf5 <- function(...) local(...elt(2))stopifnot(f5(a = 1, b = 2) == 2)})## R API errors when no `...` in scope at all (PR#18928)local({f <- function() ...length()stopifnot(grepl("incorrect context",tryCatch(f(), error = conditionMessage)))g <- function() ...elt(1)stopifnot(grepl("no ... to look in",tryCatch(g(), error = conditionMessage)))h <- function() ...names()stopifnot(grepl("incorrect context",tryCatch(h(), error = conditionMessage)))## Also through local()f <- function() local(...length())stopifnot(grepl("incorrect context",tryCatch(f(), error = conditionMessage)))g <- function() local(...elt(1))stopifnot(grepl("no ... to look in",tryCatch(g(), error = conditionMessage)))h <- function() local(...names())stopifnot(grepl("incorrect context",tryCatch(h(), error = conditionMessage)))})## R API: `...` overwritten with non-DOTSXP skips frame (PR#18928)local({## Overwritten in current frame: R_findDotsEnv skips it, errorsf <- function(...) { "..." <- 1; ...elt(1) }stopifnot(grepl("no ... to look in",tryCatch(f(1), error = conditionMessage)))f <- function(...) { "..." <- 1:2; ...length() }stopifnot(grepl("incorrect context",tryCatch(f(1), error = conditionMessage)))f <- function(...) { "..." <- NULL; ...names() }stopifnot(grepl("incorrect context",tryCatch(f(a = 1), error = conditionMessage)))## Overwritten in local(): R_findDotsEnv skips local, finds parentf <- function(...) local({ "..." <- 1; ...elt(1) })stopifnot(f(42) == 42)f <- function(...) local({ "..." <- NULL; ...length() })stopifnot(f(1) == 1L)stopifnot(f(1, 2, 3) == 3L)f <- function(...) local({ "..." <- 1; ...names() })stopifnot(identical(f(a = 1, b = 2), c("a", "b")))})## checking isa() consistency, notably S3 vs S4setClass("z4", contains = "numeric")setClass("zz4", contains = "z4")z3 <- `class<-`(0, "z3")zz3 <- `class<-`(1, c("zz3", "z3"))z4 <- new("z4", 0)zz4 <- new("zz4",1)stopifnot(isa(z4, "z4"), isa(zz4, "z4"), !isa(z4, "zz4"),isa(z3, "z3"), isa(zz3, "z3"), !isa(z3, "zz3"),removeClass("zz4"), removeClass("z4"))## union() needed adaptation (fumbled in r89677 before correction):x <- factor(c("a", "b", "a"))y <- factor(c("b", "c"))(uxy <- union(x, y))stopifnot(identical(uxy, factor(c("a", "b", "c"))))## levels were b c a for a few days## Context stack overflow checks (PR#18458)nTXT <- 50 # gram.y has #define CONTEXTSTACK_SIZE 50txtL <- list(brace = strrep("{", nTXT),paren = strrep("(", nTXT),brack = strrep("x[", nTXT),brac2 = strrep("x[[", nTXT %/% 2),cmpIf = paste0("{", strrep("if(1)", nTXT), "}"))E <- lapply(txtL, \(txt) tryCid(parse(text = txt)))E[[1]](isErr <- vapply(E, isa, NA, what = c("contextstackOverflow", "parseError", "error")))stopifnot(isErr)## Used to segfault with ASAN due to off-by-one in context stack checks## out of bounds errors for arrays should include the subscript numberstopifnot(identical(tryCatch(matrix(1:6, nrow = 2)[3, 1],error = identity)$subscript,1L))## Check that headers, WRE, and non-API variables are in synctools:::checkAPI()## New functionality, takes a few secs## cut(*, <empty breaks>) -- PR#19057assertErrV( cut(1:3, {}) )## gave an <NA> vector w/ bizarre levels in R <= 4.6.0## Tailcall in non-tail position: jump, like return()stopifnot((function() 1 + Tailcall(log, 1))() == 0)## Tailcall does not stop at context in .Internal(eval()), unlike return()local({f <- function(x) {e <- environment()g <- function(x) evalq(Tailcall(identity, x), e)g(x)"B"}stopifnot(identical(f("A"), "A"))})## Tailcall handles substitute() missing args in caller like S3 dispatchlocal({f <- function(x) Tailcall(function(y) substitute(y), x)stopifnot(identical(f(1 + 2), quote(1 + 2)))g <- function(x) Tailcall(function(y = 1) y, x)stopifnot(g() == 1)})## Tailcall handles parent.frame() like callerf <- function() Tailcall(function() parent.frame())e <- f()stopifnot(identical(e, .GlobalEnv))## In a --disable-nls configuration, "0 things" should remain plural; PR#19065mE <- tryCid( sin() )stopifnot(inherits(mE, "error"))if(englishMsgs)stopifnot(grepl("0 arguments passed to 'sin'", conditionMessage(mE)))## gave "0 argument passed .." in R <= 4.6.0 (--disable-nls)## as.data.frame.vector() with NA rownames -- PR#19059e1 <- tryCid( as.data.frame(setNames(11:12, c("a", NA))) ) ## and the same, explicitly:e2 <- tryCid( as.data.frame( 11:12, c("a", NA)) )writeLines(as.character(e1))stopifnot(identical(e1$message, e2$message), identical(class(e1), class(e2)))## gave a data frame with `NA` in row names, in R <= 4.6.0dftN <- as.data.frame(tab <- table(ff <- penguins$sex, useNA = "ifany"))stopifnot(identical(3:2, dim(dftN)),identical(structure(c(1:2, NA), levels = levels(ff), class = "factor"),dftN[,"Var1"]))## as.DF(<tab_w_NA>) failed after first fix ..## <symbol> -> <logical> etc via C level coerceSymbol() -- PR#19054assertErrV( all(quote(symbool)) )assertErrV( any(quote(symbool)) )## gave warnings but then TRUE or FALSE in R <= 4.6.0## Platform dependently, stl(.) could severely misbehave when compiled by flang 22, -O2sw <- 0:16r1 <- lapply(sw, function(sWin) stl(ts(rep(1:3, 3), frequency = 3), s.window = sWin))R1 <- lapply(sw, function(sWin) stl(ts(rep(1:3, 3), frequency = 3), s.window = sWin, robust=TRUE))chk1 <- function(stl) {cat("<stl>$win: ", substring(deparse(stl$win), 2),"; jump: ", substring(deparse(stl$jump), 2),"\n", sep="")if(any(abs(stl$weights - 1) > 1e-7))cat(" varying weights: ", sprintf("%.3g", stl$weights), "\n")stopifnot(is.list(stl), inherits(stl, "stl"),identical(stl$deg, c(s=0L, t=1L, l=1L)),is.matrix(mts <- stl$time.series), inherits(mts, "mts"),identical(c(9L, 3L), dim(mts)),identical(c("seasonal", "trend", "remainder"), colnames(mts)))}(swU <- pmax(3L, ifelse(sw %% 2 == 1, sw, sw+1L))) # effectively used s.windowinvisible(lapply(r1, chk1))cat("\n robust=TRUE :\n ===========\n")invisible(lapply(R1, chk1))Seasr <- vapply(r1, function(stl) stl$time.series[,"seasonal"], numeric(3*3))SeasR <- vapply(R1, function(stl) stl$time.series[,"seasonal"], numeric(3*3))Trndr <- vapply(r1, function(stl) stl$time.series[,"trend"], numeric(3*3))TrndR <- vapply(R1, function(stl) stl$time.series[,"trend"], numeric(3*3))aremr <- abs(vapply(r1, function(stl) stl$time.series[,"remainder"], numeric(3*3)))aremR <- abs(vapply(R1, function(stl) stl$time.series[,"remainder"], numeric(3*3)))stopifnot(exprs = {## s.window = 0 is now *equivalent* to s.window = 1:identical(r1[[1]], r1[[2]])identical(R1[[1]], R1[[2]])## Seasonalprint(max(abs(Seasr - rep(-1:1, 3)))) < 1e-13print(max(abs(SeasR - rep(-1:1, 3)))) < 1e-13print(max(Trndr - 2)) < 1e-13print(max(TrndR - 2)) < 1e-13print(max(aremr)) < 1e-13 # 2.22e-15 was 1.24e-14print(max(aremR)) < 1e-13 # 2.88e-15})## partly "exploded" (dumped core), partly did not return constant trend =~= 2## PR#19072stopifnot(identical(attributes(.leap.seconds), list(class = c("POSIXct", "POSIXt"))))## .leap.seconds have no "tzone" attribute (as in R < 4.1.0)## zapsmall(x, digits = Inf) should return x even when that contains +/-InfzapEx <- function(x) rbind(x = x,z = zapsmall(x, 50), zd_4 = zapsmall(x, 50, min.d = -444),zdI = zapsmall(x, 50, min.d = -Inf), zI = zapsmall(x, Inf),zIdI = zapsmall(x, Inf,min.d = -Inf))x2 <- pi * 100^(-2:2)/10; xI <- c(x2, Inf); Ix <- c(-Inf, x2); xII <- c(Ix, Inf)stopifnot(exprs = {zapEx(x2) == rep(x2, each = 6)is.finite(t(print(zapEx(xI)))) == is.finite(xI)is.finite(t( zapEx(Ix ))) == is.finite(Ix)is.finite(t(z <- zapEx(xII))) == is.finite(xII)!anyNA(z)identical(z["zI" , ], xII)identical(z["zIdI",], xII)identical(z["zd_4",], z["zdI",])})## the last two rows of z[,] were all NaN in R <= 4.6.0### wilcox.test(x, exact=FALSE, correct = k), k >= 1 had been missing '* dnorm(z)'#### all possible 'correct = *' settings { correct = 0 <===> correct = TRUE } :corrs <- list(FALSE, TRUE, 1L, 2L, 3L)names(corrs) <- vapply(corrs, as.character, "")####' Compute exact and asymptotic (_incl_ Edgeworth corrections) Wilcoxon test p-values##' (also to be used in further changes, incl 2-sample test)wilcoxAsymp <- function(x, y = NULL, xO = 100* max(abs(x)), yO = Inf,debug = getOption("verbose"), ...) {P <- if(debug) print else identityxo <- c(x, xO)if(is.null(y) || !length(y)) { ##---------- 1-sample : *_one_pval_asymp() ----------------------## 'X' := eXactpv1X <- P(wilcox.test(x , exact=TRUE, ...))$p.valuepv1Xo <- P(wilcox.test(xo, exact=TRUE, ...))$p.valueL1. <- lapply(corrs, function(cr) wilcox.test(x , exact=FALSE, correct = cr, ...))L1o <- lapply(corrs, function(cr) wilcox.test(xo, exact=FALSE, correct = cr, ...))list(pval = c(vapply(L1., `[[`, 0.1, "p.value"), Xact = pv1X),pvalOut = c(vapply(L1o, `[[`, 0.1, "p.value"), Xact = pv1Xo))}else { ##-------------- 2-sample (x, y) : *_two_pval_asymp() ------------------------yo <- c(y, yO)pv2X <- P(wilcox.test(x , y , exact=TRUE, ...))$p.valuepv2Xo <- P(wilcox.test(xo, yo, exact=TRUE, ...))$p.valueL2. <- lapply(corrs, function(cr) wilcox.test(x , y , exact=FALSE, correct = cr, ...))L2o <- lapply(corrs, function(cr) wilcox.test(xo, yo, exact=FALSE, correct = cr, ...))list(pval = c(vapply(L2., `[[`, 0.1, "p.value"), Xact = pv2X ),pvalOut = c(vapply(L2o, `[[`, 0.1, "p.value"), Xact = pv2Xo))}} ## {wilcoxAsymp}## Simulated, rounded and shifted from t_3 and t_4 :x20 <- c(-231, -150, -143, -101, -82, -76, -56, -40, -29, -20,15, 41, 45, 61, 69, 86, 98, 144, 163, 219)y20 <- c(-216, -146, -137, -125, -116, -108, -35, -32, -31, 6,65, 92, 95, 98, 102, 128, 130, 134, 178, 190) + 0.5## chosen to have no ties (correct=* is not used with ties):stopifnot(anyDuplicated(rank(abs( x20 ))) == 0,anyDuplicated(rank(abs(c(x20,y20)))) == 0)roundM <- function(x, dig = 4)round(x, digits = max(1, dig + round( - log10(min(abs(x))))))mkM <- function(c1, c2, m) `dimnames<-`(cbind(c1,c2, deparse.level=0L), dimnames(m))Ax1 <- wilcoxAsymp(x20)(mA1 <- sapply(Ax1, roundM))trA1 <- mkM(c(0.9405, 0.9553, 0.9563, 0.9565, 0.9563, 0.9563),c(0.6639, 0.6766, 0.6826, 0.6834, 0.6827, 0.6827), mA1)(dA1 <- t(t(A <- simplify2array(Ax1))[, -6] - A["Xact",]) |> signif(digits=3))trd1 <- mkM(c(-0.0158, -0.000987, -9.29e-06, 0.000127, 1.79e-06),c(-0.0188, -0.0061, -9.17e-05, 0.000658, 1.08e-05), dA1)Ay1 <- wilcoxAsymp(y20)sapply(Ay1, roundM)(dAy1 <- t(t(A <- simplify2array(Ay1))[, -6] - A["Xact",]) |> signif(digits=3))trdy1 <- mkM(c(-0.0196, -0.00566, -7.8e-05, 0.000666, 1.16e-5),c(-0.0187, -0.00784, -2.0e-04, 0.000638, 1.32e-5), dAy1)Ay1P <- wilcoxAsymp(y20 + 66)sapply(Ay1P, roundM)(dAy1P <- t(t(A <- simplify2array(Ay1P))[, -6] - A["Xact",]) |> signif(digits=3))trd1P <- mkM(c(.00149, .00245, 2.64e-4, 2.04e-5, 3.86e-5),c(.00161, .00215, 2.14e-4, 9.52e-5, 3.11e-5), dAy1P)####--------------------- 2 samples -------------------------------------Axy <- wilcoxAsymp(x20, y20)sapply(Axy, roundM)(dAxy <- t(t(A <- simplify2array(Axy))[, -6] - A["Xact",]) |> signif(digits=3))trd2 <- mkM(c(-0.0132, -0.00357, -2.58e-5, 2.08e-4, 9.28e-6),c(-0.0123, -0.00330, -2.20e-5, 1.86e-4, 7.79e-6), dAxy)Axy40 <- wilcoxAsymp(x20, y20 + 40)sapply(Axy40, roundM)(dAxy40 <- t(t(A <- simplify2array(Axy40))[, -6] - A["Xact",]) |> signif(digits=3))trd2.40 <- mkM(c(-0.00705, -0.00236, -6.97e-5, -4.01e-5, 10.0e-6),c(-0.00745, -0.00265, -6.86e-5, -1.05e-5, 9.18e-6), dAxy40)Axy2c <- wilcoxAsymp(x20, y20 + 200)sapply(Axy2c, roundM)(dAxy2c <- t(t(A <- simplify2array(Axy2c))[, -6] - A["Xact",]) |> signif(digits=3))trd2.2c <- mkM(c(1.36e-5, 1.46e-5, -3.45e-6, -2.47e-6, -1.22e-7),c(3.83e-5, 4.16e-5, -8.54e-6, -2.70e-6, -6.56e-7), dAxy2c)Axy2m <- wilcoxAsymp(x20, y20 + 2000)sapply(Axy2m, roundM)(dAxy2m <- t(t(A <- simplify2array(Axy2m))[, -6] - A["Xact",]) |> signif(digits=3))trd2.2m <- mkM(c(6.3e-8, 6.79e-8, -1.45e-11, -1.45e-11, 7.31e-8),c(4.46e-7, 4.77e-7, -1.01e-08, -1.01e-08, 1.43e-7), dAxy2m)##stopifnot(exprs = { # on x86_64 F42 Linux, all `tolerance = *` could be 0all.equal(trA1, mA1, tolerance = 1e-14)all.equal(trd1, dA1, tolerance = 1e-14)all.equal(trdy1,dAy1, tolerance = 1e-14)all.equal(trd1P,dAy1P,tolerance = 1e-14)## --- 2 ---all.equal(trd2, dAxy, tolerance = 1e-14)all.equal(trd2.40, dAxy40, tolerance = 1e-14)all.equal(trd2.2c, dAxy2c, tolerance = 1e-14)all.equal(trd2.2m, dAxy2m, tolerance = 1e-14)})## The 'correct = 1 | 2 | 3' did *not* improve the p values in R 4.6.0## wilcox.test(*, digits.rank) -- changed default *AND* new digits.zap = digits.rankx3 <- c(1.1, 2, 1.15)wtL <- list({}, wt.00 = wilcox.test(c(x3, 0)), wt.e100dII = wilcox.test(c(x3, 1e-100), digits.rank=Inf), wte_100dII = wilcox.test(c(x3, -1e-100), digits.rank=Inf), wt.e100dI = wilcox.test(c(x3, 1e-100), digits.rank=Inf, digits.zap = 12), wte_100dI = wilcox.test(c(x3, -1e-100), digits.rank=Inf, digits.zap = 12), wt.e100d7 = wilcox.test(c(x3, 1e-100), digits.rank= 7L), wte_100d7 = wilcox.test(c(x3, -1e-100), digits.rank= 7L))P <- if(interactive()) print else identity(pval <- vapply(P(wtL[!sapply(wtL, is.null)]), \(wt) wt$p.value, numeric(1)))noData <- \(x) x[names(x) != "data.name"]stopifnot(exprs = {all.equal(unname(pval), c(.25, 0.125, rep(.25, 5)))with(wtL, all.equal(noData(wt.00),noData(wt.e100dI)))})## the p-values were rep((1:2)/8, 3) in previous R, the first two indeed back compatible.## Bug 19029 - Overly-long dlerror() may corrupt dyn.load() state{ try(dyn.load(strrep("A", 1000))); try(library(cluster)) -> ans }## seg.faulted typically (when 'cluster' was found)if(!inherits(ans, "try-error")) detach("package:cluster", unload = TRUE)## Bug 19086 -- Compiler optimization related -- nlminb() convergence when bounds are activef <- function(x) sum( log(diff(x)^2+.01) + (x[1]-1)^2 )p.s <- c(5:10,2*(6:11)); names(p.s) <- paste0("p=", p.s)optL <- lapply(p.s, function(p) nlminb(rep(0, p), f, lower=-1, upper=3))unique(cbind(msgs <- sapply(optL, `[[`, "message")))## indeed still in Fedora 42; R-4.6.0 self-compiled## in good case:stopifnot(grepl("^relative convergence ", msgs))sapply(optL, `[[`, "iterations") # platform dep.## p=5 p=6 p=7 p=8 p=9 p=10 p=11 p=12 p=22## 28 47 47 55 51 65 77 80 .... 148sapply(optL, `[[`, "evaluations") # probably platform dep.## Test estimated par and objective function:head(obj <- sapply(optL, `[[`, "objective"))str(parL <- lapply(optL, `[[`, "par"))truepL <- lapply(p.s, function(p) rep.int(1, p)) # true par. = (1 1 .. 1)writeLines(all.equal(parL, truepL, tolerance = 0))stopifnot(exprs = {abs((obj / (p.s - 1)) - log(0.01)) < 1e-9all.equal(parL, truepL, tolerance = 4e-5) # p=20, 1.5656e-5 (Windows - arm)})## for p >= 9 did not converge previously (in R <= 4.6.0)## Bug 18930 -- Merge with zero rows df and single column dfa <- data.frame(x=numeric())b <- data.frame(y=1:2)ab <- merge(a, b, all.x = TRUE, all.y = TRUE)stopifnot(identical(names(ab), c(names(a), names(b))))## previously merge dropped column names (in R <= 4.6.0)k <- data.frame(x=numeric(), y=numeric())m <- data.frame(z=1:2)km <- merge(k, m, all.x = TRUE, all.y = TRUE)stopifnot(identical(names(km), c(names(k), names(m))))## previously `y[FALSE, ]` instead of `z` (in R <= 4.6.0)## read.dcf() and write.dcf() always use UTF-8 (r-dev-day issue 156)local({eacute <- intToUtf8(0xe9) # small e with acute, UTF-8ccedil <- intToUtf8(0xe7) # small c with cedilla, UTF-8## The shared base:::.enc2utf8_sub() helper used by read/write.dcf():## convert to UTF-8 honouring the declared encoding, escape invalid## bytes, and pass non-character input through unchanged.lat <- "Fran\xe7ois"; Encoding(lat) <- "latin1"## A string declared UTF-8 but containing a stray invalid byte: must be## escaped regardless of the native encoding (an undeclared literal would## be reinterpreted via the locale codepage on non-UTF-8 platforms).inv <- "a\xffb"; Encoding(inv) <- "UTF-8"stopifnot(identical(.enc2utf8_sub("abc"), "abc"),.enc2utf8_sub(lat) == paste0("Fran", ccedil, "ois"),Encoding(.enc2utf8_sub(lat)) == "UTF-8",.enc2utf8_sub(inv) == "a<ff>b",identical(.enc2utf8_sub(c("a", NA)), c("a", NA)),identical(.enc2utf8_sub(1:3), 1:3))## A DCF file with a valid UTF-8 field and a field with an invalid byte.tf <- tempfile()con <- file(tf, "wb")writeBin(charToRaw("Package: testpkg\nTitle: caf\xc3\xa9\nAuthor: Fran\xffois\n"),con)close(con)## Both the C path (all = FALSE) and the R path (all = TRUE) must agree:## valid UTF-8 is marked as such, invalid bytes are escaped as <xx>.dC <- read.dcf(tf)dR <- read.dcf(tf, all = TRUE)stopifnot(dC[1, "Title"] == paste0("caf", eacute),Encoding(dC[1, "Title"]) == "UTF-8",dC[1, "Author"] == "Fran<ff>ois",identical(unname(dC[1, "Title"]), dR$Title),identical(unname(dC[1, "Author"]), dR$Author))## write.dcf() converts a declared encoding to UTF-8 and escapes any## invalid bytes; the output must be valid UTF-8.x <- data.frame(Package = "testpkg",Author = "Fran\xe7ois",Note = "bad\xffbyte",stringsAsFactors = FALSE)Encoding(x$Author) <- "latin1"Encoding(x$Note) <- "UTF-8" # stray invalid byte, must be escapedtf2 <- tempfile()write.dcf(x, tf2) # always UTF-8, regardless of localestopifnot(validUTF8(rawToChar(readBin(tf2, "raw", file.size(tf2)))))y <- read.dcf(tf2)stopifnot(y[1, "Author"] == paste0("Fran", ccedil, "ois"),Encoding(y[1, "Author"]) == "UTF-8",y[1, "Note"] == "bad<ff>byte")## An invalid byte on a continuation line is escaped, while a valid## UTF-8 character on the same field is preserved.tf3 <- tempfile()con <- file(tf3, "wb")writeBin(charToRaw("Package: p\nDescription: one \xff bad\n caf\xc3\xa9 line\n"),con)close(con)d3C <- read.dcf(tf3)d3R <- read.dcf(tf3, all = TRUE)stopifnot(grepl("<ff>", d3C[1, "Description"], fixed = TRUE),grepl(eacute, d3C[1, "Description"], fixed = TRUE),Encoding(d3C[1, "Description"]) == "UTF-8",identical(unname(d3C[1, "Description"]), d3R$Description))## Valid 3- and 4-byte characters are preserved; the various kinds of## invalid sequence (truncated, overlong, surrogate) are each escaped## per byte, and a literal "<ff>" is not re-escaped. C and R agree.euro <- intToUtf8(0x20AC) # 3-byte UTF-8emoji <- intToUtf8(0x1F600) # 4-byte UTF-8rdb <- function(bytes) {f <- tempfile(); cc <- file(f, "wb"); writeBin(as.raw(bytes), cc); close(cc)on.exit(unlink(f))list(C = read.dcf(f)[1, "X"], R = read.dcf(f, all = TRUE)$X)}cases <- list(list(b = c(charToRaw("Package: p\nX: "), charToRaw(euro),charToRaw(emoji), charToRaw("\n")), want = paste0(euro, emoji)),list(b = c(charToRaw("Package: p\nX: a"), as.raw(0xc3),charToRaw("\n")), want = "a<c3>"),list(b = c(charToRaw("Package: p\nX: "), as.raw(c(0xc0, 0x80)),charToRaw("\n")), want = "<c0><80>"),list(b = c(charToRaw("Package: p\nX: "), as.raw(c(0xed, 0xa0, 0x80)),charToRaw("\n")), want = "<ed><a0><80>"),list(b = charToRaw("Package: p\nX: a<ff>b\n"), want = "a<ff>b"))for (cs in cases) {got <- rdb(cs$b)stopifnot(got$C == cs$want, identical(unname(got$C), got$R))}## An invalid byte in a field name (tag) is escaped; C and R agree.tf4 <- tempfile()con <- file(tf4, "wb")writeBin(c(charToRaw("Package: p\nX"), as.raw(0xff), charToRaw("Y: v\n")), con)close(con)stopifnot("X<ff>Y" %in% colnames(read.dcf(tf4)),identical(colnames(read.dcf(tf4)), names(read.dcf(tf4, all = TRUE))))## A repeated field with an invalid byte: all = TRUE gives a list column.con <- file(tf4, "wb")writeBin(c(charToRaw("Package: p\nX: a\nX: "), as.raw(0xff), charToRaw("\n")), con)close(con)stopifnot(identical(unlist(read.dcf(tf4, all = TRUE)$X), c("a", "<ff>")))## A keep.white field uses the non-folding branch of write.dcf();## a latin1 value is still written as valid UTF-8.v <- "Fran\xe7ois"; Encoding(v) <- "latin1"write.dcf(data.frame(Package = "p", Maintainer = v, stringsAsFactors = FALSE),tf4, keep.white = "Maintainer")stopifnot(validUTF8(rawToChar(readBin(tf4, "raw", file.size(tf4)))),read.dcf(tf4)[1, "Maintainer"] == paste0("Fran", ccedil, "ois"))unlink(c(tf, tf2, tf3, tf4))})## read.dcf() previously returned values with encoding "unknown", and## write.dcf() relied on the Encoding field (in R <= 4.6.0)## seq.int(along.with = *) for non-vector objects (PR#19100)stopifnot(identical(seq.int(along.with = NULL), integer(0)),identical(seq.int(along.with = mean), 1L))## .OBJSXP() and deparse(<bare OBJSXP>), e.g. of S7 objects, RConsortium/S7#524 :exexpr <- quote(structure(.OBJSXP(), class = "S7_object", foo = 1:2))obj <- eval(exexpr)stopifnot(exprs = {typeof(obj) == "object"!isS4(obj)identical(.OBJSXP(), asS3(getClass("S4")@prototype, complete = FALSE))identical(attributes(obj), list(class = "S7_object", foo = 1:2))identical(eval(parse(text = deparse(obj))[[1]]), obj)identical(deparse(obj), format(exexpr))})## .OBJSXP() is new; in R <= 4.x, these deparse()d to the non-parseable "<object>".# Almost perfect fit in summary.aov() -- same warning as in summary.lm() - PR#18341chkFM <- function(mA, mL) {print(smA <- getVaW(summary(mA)))print(smL <- getVaW(summary(mL)))stopifnot(exprs = {identical(coef(mA), coef(mL))!is.null(wA <- attr(smA, "warning"))!is.null(wL <- attr(smL, "warning"))!englishMsgs || grepl("essentially perfect fit", wA)!englishMsgs || grepl("essentially perfect fit", wL)})}## simple case:d30 <- data.frame(x = gl(2, 15), y = 1)fmL <- lm (y~x, data=d30)fmA <- aov(y~x, data=d30)chkFM(fmA, fmL)## ex. with 2 y's :d30 <- data.frame(group = gl(2, 15), weight = 1, height = 1)fmL <- lm (cbind(weight, height) ~ group, data = d30)fmA <- aov(cbind(weight, height) ~ group, data = d30)chkFM(fmA, fmL)## the *A models from aov() / summary.aov() did not raise the warning in R <= 4.6.z#### A case where length(fitted) == 1 gave var(fitted) |-> NAladyB <- data.frame(ID = factor(1:16), Run = gl(2, 8),DPlant = factor(rep((1:8)*10, 2)),Host = factor(rep(rep(2:1, each=4), 2), labels = c("bean", "trefoil")),Ladybird = factor(rep(rep(2:1, each=2), 4), labels = c("-", "+")),Cadaver = rep(c(5, 10), 8),Live = c(15, 12, 20, 20, 18, 17, 20, 20, 18, 17, 20, 20, 15, 19, 20, 20),Infected = c(1, 2, 1, 2, 5, 10, 1, 3, 2, 2, 0, 0, 5, 8, 1, 7))fm <- aov(log(P/(100 - P)) ~ Host * Cadaver * Ladybird + Error(Run/DPlant),data = transform(ladyB, P = 100 * (Infected + 1)/(Live + 2), Cadaver = factor(Cadaver)))summary(fm)## a few days ==> Error in if (is.finite(resvar) && resvar < (mean(fitted)^2 + var(c(fitted))) * :## missing value where TRUE/FALSE needed## keep at endrbind(last = proc.time() - .pt,total = proc.time())