## 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 == *$message
assertErrV <- function(...) tools::assertError(..., verbose=TRUE)
`%||%` <- function (L, R) if(is.null(L)) R else L
##' get value of `expr` and keep warning as attribute (if there is one)
getVaW <- function(expr) {
W <- NULL
withCallingHandlers(val <- expr,
warning = function(w) {
W <<- conditionMessage(w)
invokeRestart("muffleWarning") })
structure(val, warning = W)
}
options(nwarnings = 10000, # (rather than just 50)
warn = 2, # only caught or asserted warnings
width = 99) # instead of 80
onWindows <- .Platform$OS.type == "windows"
englishMsgs <- {
## 1. LANGUAGE takes precedence over locale settings:
if(nzchar(lang <- Sys.getenv("LANGUAGE")))
lang == "en"
else { ## 2. Query the locale
if(!onWindows) {
## sub() :
lc.msgs <- sub("\\..*", "", print(Sys.getlocale("LC_MESSAGES")))
lc.msgs == "C" || substr(lc.msgs, 1,2) == "en"
} else { ## Windows
lc.type <- sub("\\..*", "", sub("_.*", "", print(Sys.getlocale("LC_CTYPE"))))
lc.type == "English" || lc.type == "C"
}
}
}
cat(sprintf("English messages: %s\n", englishMsgs))
Sys.setenv("_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_" = "true")# just in case
## very small size hashed environments
n <- 123
l <- 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 4 109 109
stopifnot(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#18324
rd <- 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 Murdoch
txts <- 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 them
msgs <- 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 == 1L
nC == 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#18336
d <- 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/gid
if(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
} else
message("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#18335
chkSortP <- 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=NA
Ls <- 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) partials
mip <- 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 1:12800
x <- runif(rpois(1, 100))
x[sample(length(x), 12)] <- NA
p <- 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#18357
assertErrV( head(letters, "3") )
## returned complete 'letters' w/o a warning
stopifnot(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) -> msg
msg; 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)^2
set.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-7
all.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 names
stopifnot(
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#18389
factor( levels = c("a", "b"), ordered=TRUE) -> o1
ordered(levels = c("a", "b")) -> o2
stopifnot(identical(o1,o2))
## the ordered() call has failed in R <= 4.2.x
## source() with multiple encodings
if (l10n_info()$"UTF-8" || l10n_info()$"Latin-1") {
writeLines('x <- "fa\xE7ile"', tf <- tempfile(), useBytes = TRUE)
tools::assertError(source(tf, encoding = "UTF-8"))
source(tf, encoding = c("UTF-8", "latin1"))
## in R 4.2.{0,1} gave Warning (that would now be an error):
## 'length(x) = 2 > 1' in coercion to 'logical(1)'
if (l10n_info()$"UTF-8") stopifnot(identical(Encoding(x), "UTF-8"))
}
## multi-line Rd macro definition
rd <- tools::parse_Rd(textConnection(r"(
\newcommand{\mylongmacro}{
\LaTeX
}
\mylongmacro
)"), fragment = TRUE)
tools::Rd2txt(rd, out <- textConnection(NULL, "w"), fragment = TRUE)
stopifnot(any(as.character(rd) != "\n"),
identical(textConnectionValue(out)[2L], "LaTeX")); close(out)
## empty output in R <= 4.2.x
## expand.model.frame() for non-data fits (PR#18414)
y <- 1:10
g <- gl(2, 5)
fit <- lm(log(y) ~ g, subset = y > 3)
mf <- expand.model.frame(fit, ~0)
stopifnot(all.equal(fit$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 integer
x <- 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#17863
f1 <- 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#18422
i0 <- 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 dot
stopifnot(!isS3method(".Internal"))
## failed with "invalid first argument" in R <= 4.2.x
## cor.test.formula() scoping issue -- PR#18439
form <- ~ CONT + INTG
local({
USJudgeRatings <- head(USJudgeRatings)
stopifnot(cor.test(form, data = USJudgeRatings)$parameter == 4)
})
## R <= 4.2.x evaluated the constructed call in environment(formula)
## PR # 18421 by Benjamin Feakins (and follow up):
## ---------- "roman", "hexcode" and "octcode" all cannot easily be added to data frames
for(x in list(as.roman(1:14), as.octmode(1:11), as.hexmode(1:19), as.raw(0:65), (0:17) %% 7 == 0,
as.difftime(c(0,30,60:64), units="mins"),
seq(ISOdate(2000,2,10), by = "23 hours", length.out = 50)
)) {
cat("x:"); str(x, vec.len=8)
## the error can be triggered by the following methods:
### 1. as.data.frame()
dat1 <- as.data.frame(x) # now works, previously signalled
## Error in as.data.frame.default(x) :
## cannot coerce class ‘"roman"’ to a data.frame
### 2. data.frame()
dat2 <- data.frame(x) # gave error as above, now works
stopifnot(identical(dat1, dat2),
identical( data.frame(my.x = x),
as.data.frame(x, nm="my.x")))
### 3. cbind()
dat3 <- data.frame(y = seq_along(x))
dat3 <- cbind(dat3, x) # gave error, now works
stopifnot(identical(dat2, dat3[,"x", drop=FALSE]))
## These worked already previously:
dat <- data.frame(x = integer(length(x)))
dat$x <- x
datl <- 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) <- cls
be <- 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], "") == cls
vapply(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 warning
is.character(asDwarn <- vapply(asDF, attr, "<text>", "warning"))
!englishMsgs || all(grepl(dfWarn, asDwarn))
length(unique(vapply(cls, \(cl) sub(cl, "<class>", asDwarn[[cl]], fixed=TRUE), ""))) == 1L
all.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#18447
mkCh <- 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 <= 4.2.2
clsMethErr <- 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#18455
op <- 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("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 macros
ref <- 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#18456
mod <- 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 environment
identical(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 1
y <- rep(0,5)
lm(rep(0,5) ~ x + offset({ print("hello"); x+2*y }),
offset = { print("world"); x-y })
}) # rank-deficient in "subtle" way {warning/NA may not be needed}; just show for now:
nd <- data.frame(x = 1:5)
tools::assertWarning(print(predict(mod2, newdata=nd, rankdeficient = "warnif")))
predict(mod2, newdata=nd, rankdeficient = "NA")
nm5 <- as.character(1:5)
stopifnot(exprs = {
all.equal(setNames(rep(0, 5), nm5), predict(mod2), tol=1e-13) # pred: 1.776e-15
is.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" methods
x <- 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 <= 4.2.2
mChk <- 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 interval
f <- function(x) 4469/x - 572/(1-x)
str(urf <- uniroot(f, c(1e-6, 1))) # interval = (eps, 1]; f(1) = Inf
stopifnot(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 errors
tools::assertWarning(subset(data.frame(y = 1), y = 2), verbose = TRUE)
## R < 4.3.0 was silent about unused ... arguments
## a:b -- both should be of length 1 -- PR#18419
Sys.getenv("_R_CHECK_LENGTH_COLON_") -> oldV
Sys.setenv("_R_CHECK_LENGTH_COLON_" = "true")# ~> the future behavior
a <- 1:2
assertErrV(a:1) # numerical expression has length > 1
assertErrV(2:a) # " " " "
Sys.unsetenv("_R_CHECK_LENGTH_COLON_")
tools::assertWarning(s1 <- a:1, verbose=TRUE)
tools::assertWarning(s2 <- 2:a, verbose=TRUE)
stopifnot(identical(s1, 1L), identical(s2, 2:1))
Sys.setenv("_R_CHECK_LENGTH_COLON_" = oldV)# reset
## always only warned in R <= 4.2.z
## keep rm(list=NULL) working (now documentedly) {PR#18422}
a <- ls() # 'a' is part
rm() ; 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)$rank == 4)
if(no.splines) unloadNamespace("splines")
## ns() gave Error in qr.default(t(const)) : NA/NaN/Inf in foreign function call
## methods() in {base} pkg are visible
mmeths <- methods(merge)
imeth <- attr(mmeths, "info")
stopifnot(exprs = {
sum(iB <- imeth[,"from"] == "base") >= 2 # 'default' and 'data.frame'
imeth[iB, "visible"] # {base} methods *are* visible
})
## was wrong in R 4.3.0 (and R-devel for a while)
## Methods of a non-generic function
foo <- function(x) { bar(x) }
(m <- methods(foo))
stopifnot(inherits(m, "MethodsFunction"), length(m) == 0L)
## .S3methods() failed in R-devel for a few days after r84400.
## getS3method() error
myFUN <- function(x) UseMethod("myFUN")
(msg <- tryCmsg(getS3method("myFUN", "numeric")))
if(englishMsgs)
stopifnot(grepl("S3 method 'myFUN.numeric' not found", msg))
## failed with "wrong" message after r84400
## head(.,n) / tail(.,n) error reporting - PR#18362
try(head(letters, 1:2)) # had "Error in checkHT(..)"); now ".. in head.default(..)"
try(tail(letters, NA))
try(head(letters, "1"))
tryCcall1 <- function(expr) tryCid(expr)$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-ts
x <- 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 -- TODO
n0 <- 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() entry
if(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 4.3.0
library(stats)# almost surely unneeded
##
methi <- function(...) attr(methods(...), "info")
(mdensi <- methi(density)) # only density.default
stopifnot(mdensi["density.default", "visible"]) # FALSE in R 4.3.0
if(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")
## ... and
detach("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 .GlobalEnv
stopifnot(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 change
rm(coef.foo)
m4 <- methi(coef)
stopifnot(!m4["coef.foo", "visible"],
m4["coef.foo", "from"] == "registered S3method for coef")
## coef.foo part always worked
## contrib.url() should "recycle0"
stopifnot(identical(contrib.url(character()), character()))
## R <= 4.3.1 returned "/src/contrib" or similar
## `substr<-` overrun in case of UTF-8 --- private bug report by 'Architect 95'
s0 <- "123456"; nchar(s0) # 6
substr(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" , 6
substr(s1, 6, 7) <- "cc"
# Now s1 should be "字aaaac", but actually did overrunn nchar(s1);
s1; nchar(s1) ## was "字aaaacc", nchar = 7
(s2 <- intToUtf8(c(23383, 98, 98))); nchar(s2) # "字bb" 3
substr(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" 6
substr(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" 5
substr(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 ok
identical(utf8ToInt(s1), c(23383L, rep(97L, 4), 99L)) ; nchar(s1) == 6
identical(utf8ToInt(s2), c(23383L, 98L, 98L)) ; nchar(s2) == 3
identical(utf8ToInt(s3), c(23383L, 97L, 97L, 97L, 97L, 23383L)) ; nchar(s3) == 6
identical(utf8ToInt(s4), c(23383L, 98L, 98L, 98L, 100L)) ; nchar(s4) == 5
Encoding(c(s1,s2,s3,s4)) == rep("UTF-8", 4)
})
## did partly overrun to invalid strings, nchar(.) giving error in R <= 4.3.1
## 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. warning
r <- 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 <= 4.3.1
str(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 ..
## qqplot(x,y, *) confidence bands for unequal sized x,y, PR#18570:
x <- (7:1)/8; y <- (1:63)/64
r <- 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
## isoreg() seg.faulted with Inf - PR#18603 - in R <= 4.3.1
assertErrV(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
## Conversion of LaTeX accents: \~{n} etc vs. \~{}, accented I and i
stopifnot(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 <= 4.3.1
stopifnot(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
## 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]$sec <- 1/4
dL. <- dL2 ; dL.[6]$sec <- 1e-9
stopifnot(exprs = {
inherits(dCT, "POSIXct")
inherits(dLT, "POSIXlt")
!duplicated(dCT)
dd == 1
units(dd) == "hours"
diff(as.integer(dCT)) == 3600L # seconds
identical(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 ok
identical(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 message
writeLines(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
## 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 + b
stopifnot(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 formula
tto <- 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:
t2 <- terms(~ a + b)
str(dt2 <- drop.terms(t2, 1, keep.response = TRUE))
stopifnot( drop.terms(t2, 1) == dt2, dt2 == ~ b)
## gave a+b ~ b in R <= 4.3.2
## cov2cor(<0x0>) PR#18423
m00 <- 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) -> r0
stopifnot(all.equal(r, r0, tol = 0, check.attributes = FALSE),# always ok
length(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
## startDynamicHelp(): port out of range, PR#18645
op <- options(help.ports = 123456L)
assertErrV(tools::startDynamicHelp())
assertErrV(help.start(browser = identity))
options(op)
## silently failed much later in R <= 4.3.2.
## keep at end
rbind(last = proc.time() - .pt,
total = proc.time())