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third-party-mirror / R / refs/heads/R-3-6-3-tag / . / tests / reg-tests-1d.R
blob: 42002063ff6f2c1d27ef56763541299c6bbad9ee [file] [log] [blame]
## Regression tests for R >= 3.4.0
pdf("reg-tests-1d.pdf", encoding = "ISOLatin1.enc")
.pt <- proc.time()
tryCid <- function(expr) tryCatch(expr, error = identity)
## body() / formals() notably the replacement versions
x <- NULL; tools::assertWarning( body(x) <- body(mean)) # to be error
x <- NULL; tools::assertWarning(formals(x) <- formals(mean)) # to be error
x <- NULL; tools::assertWarning(f <- body(x)); stopifnot(is.null(f))
x <- NULL; tools::assertWarning(f <- formals(x)); stopifnot(is.null(f))
## these all silently coerced NULL to a function in R <= 3.2.x
## A good guess if we have _not_ translated error/warning/.. messages:
## (should something like this be part of package tools ?)
englishMsgs <- {
## 1. LANGUAGE takes precedence over locale settings:
if(nzchar(lang <- Sys.getenv("LANGUAGE")))
lang == "en"
else { ## query the locale
if(.Platform$OS.type != "windows") {
## 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))
## match(x, t): fast algorithm for length-1 'x' -- PR#16885
## a) string 'x' when only encoding differs
tmp <- "年付"
tmp2 <- "\u5e74\u4ed8" ; Encoding(tmp2) <- "UTF-8"
for(ex in list(c(tmp, tmp2), c("foo","foo"))) {
cat(sprintf("\n|%s|%s| :\n----------\n", ex[1], ex[2]))
for(enc in c("latin1", "UTF-8", "unknown")) { # , "MAC", "WINDOWS-1251"
cat(sprintf("%9s: ", enc))
tt <- ex[1]; Encoding(tt) <- enc; t2 <- ex[2]
if(identical(i1 <- ( tt %in% t2),
i2 <- (c(tt, "a") %in% t2)[1]))
cat(i1,"\n")
else
stop("differing: ", i1, ", ", i2)
}
}
##
outerID <- function(x,y, ...) outer(x,y, Vectorize(identical,c("x","y")), ...)
## b) complex 'x' with different kinds of NaN
x0 <- c(0,1, NA_real_, NaN)
z <- outer(x0,x0, complex, length.out=1L)
z <- c(z[is.na(z)], # <- of length 4 * 4 - 2*2 = 12
as.complex(NaN), as.complex(0/0), # <- typically these two differ in bits
complex(real = NaN), complex(imaginary = NaN),
NA_complex_, complex(real = NA), complex(imaginary = NA))
## 1..12 all differ, then
symnum(outerID(z,z, FALSE,FALSE,FALSE,FALSE))# [14] differing from all on low level
symnum(outerID(z,z)) # [14] matches 2, 13,15
(mz <- match(z, z)) # (checked with m1z below)
zRI <- rbind(Re=Re(z), Im=Im(z)) # and see the pattern :
print(cbind(format = format(z), t(zRI), mz), quote=FALSE)
stopifnot(apply(zRI, 2, anyNA)) # NA *or* NaN: all TRUE
is.NA <- function(.) is.na(.) & !is.nan(.)
(iNaN <- apply(zRI, 2, function(.) any(is.nan(.))))
(iNA <- apply(zRI, 2, function(.) any(is.NA (.)))) # has non-NaN NA's
## use iNA for consistency check once FIXME happened
m1z <- sapply(z, match, table = z)
stopifnot(exprs = {
identical(m1z, mz)
identical(m1z == 1L, iNA)
identical(match(z, NA, 0) == 1L, iNA)
identical(mz[mz != 1L], c(2L, 4L, 9L, 10L, 12L, 2L, 2L, 2L, 9L))
})
## m1z uses match(x, *) with length(x) == 1 and failed in R 3.3.0
set.seed(17)
for(. in 1:20) {
zz <- sample(z)
stopifnot(identical(match(zz,zz), vapply(zz, match, -1L, table = zz)))
}
##
## PR#16909 - a consequence of the match() bug; check here too:
dvn <- paste0("var\xe9", 1:2); Encoding(dvn) <- "latin1"
dv <- data.frame(1:3, 3); names(dv) <- dvn; dv[,"var\u00e92"] <- 2
stopifnot(ncol(dv) == 2, dv[,2] == 2, identical(names(dv), dvn))
## in R 3.3.0, got a 3rd column
## deparse(<complex>, "digits17")
fz <- format(z <- c(outer(-1:2, 1i*(-1:1), `+`)))
(fz0 <- sub("^ +","",z))
r <- c(-1:1,100, 1e20); z2 <- c(outer(pi*r, 1i*r, `+`)); z2
dz2 <- deparse(z2, control="digits17")
stopifnot(exprs = {
identical(deparse(z, 200, control = "digits17"),
paste0("c(", paste(fz0, collapse=", "), ")"))
print((sum(nchar(dz2)) - 2) / length(z2)) < 22 # much larger in <= 3.3.0
## deparse <-> parse equivalence, 17 digits should be perfect:
all.equal(z2, eval(parse(text = dz2)), tolerance = 3e-16) # seen 2.2e-35 on 32b
})
## deparse() for these was "ugly" in R <= 3.3.x
## deparse of formals of a function
fun <- function(a=1,b){}
frmls <- tryCatch(eval(parse(text=deparse(formals(fun)))), error = identity)
stopifnot(identical(frmls, formals(fun)))
## length(environment(.)) == #{objects}
stopifnot(identical(length( baseenv()),
length(names(baseenv()))))
## was 0 in R <= 3.3.0
## "srcref"s of closures
op <- options(keep.source = TRUE)# as in interactive use
getOption("keep.source")
stopifnot(exprs = {
identical(function(){}, function(){})
identical(function(x){x+1},
function(x){x+1})
}); options(op)
## where all FALSE in 2.14.0 <= R <= 3.3.x because of "srcref"s etc
## PR#16925, radix sorting INT_MAX w/ decreasing=TRUE and na.last=TRUE
## failed ASAN check and segfaulted on some systems.
data <- c(2147483645L, 2147483646L, 2147483647L, 2147483644L)
stopifnot(identical(sort(data, decreasing = TRUE, method = "radix"),
c(2147483647L, 2147483646L, 2147483645L, 2147483644L)))
## as.factor(<named integer>)
ni <- 1:2; Nni <- names(ni) <- c("A","B")
stopifnot(exprs = {
identical(Nni, names(as.factor(ni)))
identical(Nni, names( factor(ni)))
identical(Nni, names( factor(ni+0))) # +0 : "double"
identical(Nni, names(as.factor(ni+0)))
})
## The first one lost names in 3.1.0 <= R <= 3.3.0
## strtrim(<empty>, *) should work as substr(<empty>, *) does
c0 <- character(0)
stopifnot(identical(c0, strtrim(c0, integer(0))))
## failed in R <= 3.3.0
## Factors with duplicated levels {created via low-level code}:
set.seed(11)
f0 <- factor(sample.int(9, 20, replace=TRUE))
(f <- structure(f0, "levels" = as.character(c(2:7, 2:4))))
tools::assertWarning(print(f))
tools::assertError(validObject(f))
## no warning in print() for R <= 3.3.x
## R <= 3.3.0 returned integer(0L) from unlist() in this case:
stopifnot(identical(levels(unlist(list(factor(levels="a")))), "a"))
## diff(<difftime>)
d <- as.POSIXct("2016-06-08 14:21", tz="UTC") + as.difftime(2^(-2:8), units="mins")
dd <- diff(d)
ddd <- diff(dd)
d3d <- diff(ddd)
d7d <- diff(d, differences = 7)
(ldd <- list(dd=dd, ddd=ddd, d3d=d3d, d7d=d7d))
stopifnot(exprs = {
identical(ddd, diff(d, differences = 2))
identical(d3d, diff(d, differences = 3))
vapply(ldd, units, "") == "secs"
vapply(ldd, class, "") == "difftime"
lengths(c(list(d), ldd)) == c(11:8, 11-7)
})
## was losing time units in R <= 3.3.0
## sample(NA_real_) etc
for(xx in list(NA, NA_integer_, NA_real_, NA_character_, NA_complex_, "NA", 1i))
stopifnot(identical(xx, sample(xx)))
## error in R <= 3.3.1
## merge.data.frame with names matching order()'s arguments (PR#17119)
nf <- names(formals(order))
nf <- nf[nf != "..."]
v1 <- c(1,3,2)
v2 <- c(4,2,3)
for(nm in nf) {
cat(nm,":\n")
mdf <- merge(
as.data.frame(setNames(list(v1), nm=nm)),
as.data.frame(setNames(list(v2), nm=nm)), all = TRUE)
stopifnot(identical(mdf,
as.data.frame(setNames(list(0+ 1:4), nm=nm))))
}
## some were wrong, others gave an error in R <= 3.3.1
## PR#16936: table() dropping "NaN" level & 'exclude' sometimes failing
op <- options(warn = 2)# no warnings allowed
(fN1 <- factor(c("NA", NA, "NbN", "NaN")))
(tN1 <- table(fN1)) ##--> was missing 'NaN'
(fN <- factor(c(rep(c("A","B"), 2), NA), exclude = NULL))
(tN <- table(fN, exclude = "B")) ## had extraneous "B"
(tN. <- table(fN, exclude = c("B",NA))) ## had extraneous "B" and NA
stopifnot(exprs = {
identical(c(tN1), c(`NA`=1L, `NaN`=1L, NbN=1L))
identical(c(tN), structure(2:1, .Names = c("A", NA)))
identical(c(tN.), structure(2L, .Names = "A"))
})
## both failed in R <= 3.3.1
stopifnot(identical(names(dimnames(table(data.frame(Titanic[2,2,,])))),
c("Age", "Survived", "Freq"))) # was wrong for ~ 32 hours
##
## Part II:
x <- factor(c(1, 2, NA, NA), exclude = NULL) ; is.na(x)[2] <- TRUE
x # << two "different" NA's (in codes | w/ level) looking the same in print()
stopifnot(identical(x, structure(as.integer(c(1, NA, 3, 3)),
.Label = c("1", "2", NA), class = "factor")))
(txx <- table(x, exclude = NULL))
stopifnot(identical(txx, table(x, useNA = "ifany")),
identical(as.vector(txx), c(1:0, 3L)))
## wrongly gave 1 0 2 for R versions 2.8.0 <= Rver <= 3.3.1
u.opt <- list(no="no", ifa = "ifany", alw = "always")
l0 <- c(list(`_` = table(x)),
lapply(u.opt, function(use) table(x, useNA=use)))
xcl <- list(NULL=NULL, none=""[0], "NA"=NA, NANaN = c(NA,NaN))
options(op) # warnings ok:
lt <- lapply(xcl, function(X)
c(list(`_` = table(x, exclude=X)), #--> 4 warnings from (exclude, useNA):
lapply(u.opt, function(use) table(x, exclude=X, useNA=use))))
(y <- factor(c(4,5,6:5)))
ly <- lapply(xcl, function(X)
c(list(`_` = table(y, exclude=X)), #--> 4 warnings ...
lapply(u.opt, function(use) table(y, exclude=X, useNA=use))))
lxy <- lapply(xcl, function(X)
c(list(`_` = table(x, y, exclude=X)), #--> 4 warnings ...
lapply(u.opt, function(use) table(x, y, exclude=X, useNA=use))))
op <- options(warn = 2)# no warnings allowed
stopifnot(exprs = {
vapply(lt, function(i) all(vapply(i, class, "") == "table"), NA)
vapply(ly, function(i) all(vapply(i, class, "") == "table"), NA)
vapply(lxy,function(i) all(vapply(i, class, "") == "table"), NA)
identical((ltNA <- lt [["NA" ]]), lt [["NANaN"]])
identical((ltNl <- lt [["NULL"]]), lt [["none" ]])
identical((lyNA <- ly [["NA" ]]), ly [["NANaN"]])
identical((lyNl <- ly [["NULL"]]), ly [["none" ]])
identical((lxyNA <- lxy[["NA" ]]), lxy[["NANaN"]])
identical((lxyNl <- lxy[["NULL"]]), lxy[["none" ]])
})
## 'NULL' behaved special (2.8.0 <= R <= 3.3.1) and
## *all* tables in l0 and lt were == (1 0 2) !
ltN1 <- ltNA[[1]]; lyN1 <- lyNA[[1]]; lxyN1 <- lxyNA[[1]]
lNl1 <- ltNl[[1]]; lyl1 <- lyNl[[1]]; lxyl1 <- lxyNl[[1]]
stopifnot(exprs = {
vapply(names(ltNA) [-1], function(n) identical(ltNA [[n]], ltN1 ), NA)
vapply(names(lyNA) [-1], function(n) identical(lyNA [[n]], lyN1 ), NA)
vapply(names(lxyNA)[-1], function(n) identical(lxyNA[[n]], lxyN1), NA)
identical(lyN1, lyl1)
identical(2L, dim(ltN1)); identical(3L, dim(lyN1))
identical(3L, dim(lNl1))
identical(dimnames(ltN1), list(x = c("1","2")))
identical(dimnames(lNl1), list(x = c("1","2", NA)))
identical(dimnames(lyN1), list(y = paste(4:6)))
identical( 1:0 , as.vector(ltN1))
identical(c(1:0,3L), as.vector(lNl1))
identical(c(1:2,1L), as.vector(lyN1))
identical(c(1L, rep(0L, 5)), as.vector(lxyN1))
identical(dimnames(lxyN1), c(dimnames(ltN1), dimnames(lyN1)))
identical(c(1L,1:0), as.vector(table(3:1, exclude=1, useNA = "always")))
identical(c(1L,1L ), as.vector(table(3:1, exclude=1)))
})
x3N <- c(1:3,NA)
(tt <- table(x3N, exclude=NaN))
stopifnot(exprs = {
tt == 1
length(nt <- names(tt)) == 4
is.na(nt[4])
identical(tt, table(x3N, useNA = "ifany"))
identical(tt, table(x3N, exclude = integer(0)))
identical(t3N <- table(x3N), table(x3N, useNA="no"))
identical(c(t3N), setNames(rep(1L, 3), as.character(1:3)))
##
identical(c("2" = 1L), c(table(1:2, exclude=1) -> t12.1))
identical(t12.1, table(1:2, exclude=1, useNA= "no"))
identical(t12.1, table(1:2, exclude=1, useNA= "ifany"))
identical(structure(1:0, .Names = c("2", NA)),
c( table(1:2, exclude=1, useNA= "always")))
})
options(op) # (revert to default)
## contour() did not check args sufficiently
tryCatch(contour(matrix(rnorm(100), 10, 10), levels = 0, labels = numeric()),
error = function(e) e$message)
## caused segfault in R 3.3.1 and earlier
## unique.warnings() needs better duplicated():
.tmp <- lapply(list(0, 1, 0:1, 1:2, c(1,1), -1:1), function(x) wilcox.test(x))
stopifnot(length(print(uw <- unique(warnings()))) == 2)
## unique() gave only one warning in R <= 3.3.1
options(warn = 2)# no warnings allowed
## findInterval(x, vec) when 'vec' is of length zero
n0 <- numeric(); TF <- c(TRUE, FALSE)
stopifnot(0 == unlist(lapply(TF, function(L1)
lapply(TF, function(L2) lapply(TF, function(L3)
findInterval(x=8:9, vec=n0, L1, L2, L3))))))
## did return -1's for all.inside=TRUE in R <= 3.3.1
## droplevels(<factor with NA-level>)
L3 <- c("A","B","C")
f <- d <- factor(rep(L3, 2), levels = c(L3, "XX")); is.na(d) <- 3:4
(dn <- addNA(d)) ## levels: A B C XX <NA>
stopifnot(exprs = {
identical(levels(print(droplevels(dn))), c(L3, NA))
## only XX must be dropped; R <= 3.3.1 also dropped <NA>
identical(levels(droplevels(f)), L3)
identical(levels(droplevels(d)), L3) # do *not* add <NA> here
identical(droplevels(d ), d [, drop=TRUE])
identical(droplevels(f ), f [, drop=TRUE])
identical(droplevels(dn), dn[, drop=TRUE])
})
## summary.default() no longer rounds (just its print() method does):
set.seed(0)
replicate(256, { x <- rnorm(1); stopifnot(summary(x) == x)}) -> .t
replicate(256, { x <- rnorm(2+rpois(1,pi))
stopifnot(min(x) <= (sx <- summary(x)), sx <= max(x))}) -> .t
## was almost always wrong in R <= 3.3.x
## NULL in integer arithmetic
i0 <- integer(0)
stopifnot(exprs = {
identical(1L + NULL, 1L + integer())
identical(2L * NULL, i0)
identical(3L - NULL, i0)
})
## gave double() in R <= 3.3.x
## factor(x, exclude) when 'x' or 'exclude' are character -------
stopifnot(identical(factor(c(1:2, NA), exclude = ""),
factor(c(1:2, NA), exclude = NULL) -> f12N))
fab <- factor(factor(c("a","b","c")), exclude = "c")
stopifnot(identical(levels(fab), c("a","b")))
faN <- factor(c("a", NA), exclude=NULL)
stopifnot(identical(faN, factor(faN, exclude="c")))
## differently with NA coercion warnings in R <= 3.3.x
## factor(x, exclude = X) - coercing 'exclude' or not
## From r-help/2005-April/069053.html :
fNA <- factor(as.integer(c(1,2,3,3,NA)), exclude = NaN)
stopifnot(identical(levels(fNA), c("1", "2", "3", NA)))
## did exclude NA wrongly in R <= 3.3.x
## Now when 'exclude' is a factor,
cc <- c("x", "y", "NA")
ff <- factor(cc)
f2 <- factor(ff, exclude = ff[3]) # it *is* used
stopifnot(identical(levels(f2), cc[1:2]))
## levels(f2) still contained NA in R <= 3.3.x
## arithmetic, logic, and comparison (relop) for 0-extent arrays
(m <- cbind(a=1[0], b=2[0]))
Lm <- m; storage.mode(Lm) <- "logical"
Im <- m; storage.mode(Im) <- "integer"
stopifnot(exprs = {
identical( m, m + 1 ); identical( m, m + 1 [0]); identical( m, m + NULL)
identical(Im, Im+ 1L); identical(Im, Im + 1L[0]); identical(Im, Im + NULL)
identical(m, m + 2:3); identical(Im, Im + 2:3)
identical(Lm, m & 1); identical(Lm, m | 2:3)
identical(Lm, m & TRUE [0])
identical(Lm, Lm | FALSE[0])
identical(Lm, m & NULL) # gave Error (*only* place where NULL was not allowed)
identical(Lm, m > 1)
identical(Lm, m > .1[0]); identical(Lm, m > NULL)
identical(Lm, m <= 2:3)
})
mm <- m[,c(1:2,2:1,2)]
tools::assertError(m + mm) # ... non-conformable arrays
tools::assertError(m | mm) # ... non-conformable arrays
tools::assertError(m == mm)# ... non-conformable arrays
## in R <= 3.3.x, relop returned logical(0) and m + 2:3 returned numeric(0)
## arithmetic, logic, and comparison (relop) -- inconsistency for 1x1 array o <vector >= 2>:
(m1 <- matrix(1,1,1, dimnames=list("Ro","col")))
(m2 <- matrix(1,2,1, dimnames=list(c("A","B"),"col")))
if(FALSE) { # in the future (~ 2018):
tools::assertError(m1 + 1:2) ## was [1] 2 3 even w/o warning in R <= 3.3.x
} else tools::assertWarning(m1v <- m1 + 1:2); stopifnot(identical(m1v, 1+1:2))
tools::assertError(m1 & 1:2) # ERR: dims [product 1] do not match the length of object [2]
tools::assertError(m1 <= 1:2) # ERR: (ditto)
##
## non-0-length arrays combined with {NULL or double() or ...} *fail*
n0 <- numeric(0)
l0 <- logical(0)
stopifnot(exprs = {
identical(m1 + NULL, n0) # as "always"
identical(m1 + n0 , n0) # as "always"
identical(m1 & NULL, l0) # ERROR in R <= 3.3.x
identical(m1 & l0, l0) # ERROR in R <= 3.3.x
identical(m1 > NULL, l0) # as "always"
identical(m1 > n0 , l0) # as "always"
## m2 was slightly different:
identical(m2 + NULL, n0) # ERROR in R <= 3.3.x
identical(m2 + n0 , n0) # ERROR in R <= 3.3.x
identical(m2 & NULL, l0) # ERROR in R <= 3.3.x
identical(m2 & l0 , l0) # ERROR in R <= 3.3.x
identical(m2 == NULL, l0) # as "always"
identical(m2 == n0 , l0) # as "always"
})
## strcapture()
stopifnot(identical(strcapture("(.+) (.+)",
c("One 1", "noSpaceInLine", "Three 3"),
proto=data.frame(Name="", Number=0)),
data.frame(Name=c("One", NA, "Three"),
Number=c(1, NA, 3))))
## PR#17160: min() / max() arg.list starting with empty character
TFT <- 1:3 %% 2 == 1
stopifnot(exprs = {
identical(min(character(), TFT), "0")
identical(max(character(), TFT), "1")
identical(max(character(), 3:2, 5:7, 3:0), "7")
identical(min(character(), 3:2, 5:7), "2")
identical(min(character(), 3.3, -1:2), "-1")
identical(max(character(), 3.3, 4:0), "4")
})
## all gave NA in R <= 3.3.0
## PR#17147: xtabs(~ exclude) fails in R <= 3.3.1
exc <- exclude <- c(TRUE, FALSE)
xt1 <- xtabs(~ exclude) # failed : The name 'exclude' was special
xt2 <- xtabs(~ exc)
xt3 <- xtabs(rep(1, length(exclude)) ~ exclude)
noCall <- function(x) structure(x, call = NULL)
stripXT <- function(x) structure(x, call = NULL, dimnames = unname(dimnames(x)))
stopifnot(exprs = {
identical(dimnames(xt1), list(exclude = c("FALSE", "TRUE")))
identical(names(dimnames(xt2)), "exc")
all.equal(stripXT(xt1), stripXT(xt2))
all.equal(noCall (xt1), noCall (xt3))
})
## [fix was to call table() directly instead of via do.call(.)]
## str(xtabs( ~ <var>)):
stopifnot(grepl("'xtabs' int", capture.output(str(xt2))[1]))
## did not mention "xtabs" in R <= 3.3.1
## findInterval(x_with_ties, vec, left.open=TRUE)
stopifnot(identical(
findInterval(c(6,1,1), c(0,1,3,5,7), left.open=TRUE), c(4L, 1L, 1L)))
set.seed(4)
invisible(replicate(100, {
vec <- cumsum(1 + rpois(6, 2))
x <- rpois(50, 3) + 0.5 * rbinom(50, 1, 1/4)
i <- findInterval(x, vec, left.open = TRUE)
.v. <- c(-Inf, vec, Inf)
isIn <- .v.[i+1] < x & x <= .v.[i+2]
if(! all(isIn)) {
dump(c("x", "vec"), file=stdout())
stop("not ok at ", paste(which(!isIn), collapse=", "))
}
}))
## failed in R <= 3.3.1
## PR#17132 -- grepRaw(*, fixed = TRUE)
stopifnot(
identical(1L, grepRaw("abcd", "abcd", fixed = TRUE)),
identical(integer(), grepRaw("abcdefghi", "a", all = TRUE, fixed = TRUE)))
## length 0 and seg.faulted in R <= 3.3.2
## format()ing invalid hand-constructed POSIXlt objects
if(hasTZ <- nzchar(.TZ <- Sys.getenv("TZ"))) cat(sprintf("env.var. TZ='%s'\n",.TZ))
d <- as.POSIXlt("2016-12-06")
op <- options(warn = 1)# ==> assert*() will match behavior
for(EX in expression({}, Sys.setenv(TZ = "UTC"), Sys.unsetenv("TZ"))) {
cat(format(EX),":\n---------\n")
eval(EX)
dz <- d$zone
d$zone <- 1
tools::assertError(format(d))
d$zone <- NULL # now has 'gmtoff' but no 'zone' --> warning:
tools::assertWarning(stopifnot(identical(format(d),"2016-12-06")))
d$zone <- dz # = previous, but 'zone' now is last
tools::assertError(format(d))
}
if(hasTZ) Sys.setenv(TZ = .TZ); options(op)# revert
dlt <- structure(
list(sec = 52, min = 59L, hour = 18L, mday = 6L, mon = 11L, year = 116L,
wday = 2L, yday = 340L, isdst = 0L, zone = "CET", gmtoff = 3600L),
class = c("POSIXlt", "POSIXt"), tzone = "CET")
dlt$sec <- 10000 + 1:10 # almost three hours & uses re-cycling ..
fd <- format(dlt)
stopifnot(length(fd) == 10, identical(fd, format(dct <- as.POSIXct(dlt))))
dlt2 <- as.POSIXlt(dct)
stopifnot(identical(format(dlt2), fd))
## The two assertError()s gave a seg.fault in R <= 3.3.2
stopifnot(inherits(methods("("), "MethodsFunction"),
inherits(methods("{"), "MethodsFunction"))
## methods("(") and ..("{") failed in R <= 3.3.2
## moved after commit in r71778
f <- eval(parse(text = "function() { x <- 1 ; for(i in 1:10) { i <- i }}",
keep.source = TRUE))
g <- removeSource(f)
stopifnot(is.null(attributes(body(g)[[3L]][[4L]])))
## pmin/pmax of ordered factors -- broken in R 3.3.2 [PR #17195]
of <- ordered(c(1,5,6))
set.seed(6); rof <- sample(of, 12, replace=TRUE)
stopifnot(exprs = {
identical(pmax(rof, of), ordered(pmax(c(rof), c(of)), labels=levels(rof)) -> pmar)
identical(pmax(of, rof), pmar)
identical(pmin(rof, of), ordered(pmin(c(rof), c(of)), labels=levels(rof)) -> pmir)
identical(pmin(of, rof), pmir)
identical(pmin(rof, 5), ordered(pmin(c(rof), 2), levels=1:3, labels=levels(rof)))
identical(pmax(rof, 6), ordered(pmax(c(rof), 3), levels=1:3, labels=levels(rof)))
identical(pmax(rof, 1), rof)
identical(pmin(rof, 6), rof)
identical(pmax(of, 5, rof), ordered(pmax(c(of),2L,c(rof)), levels=1:3,
labels=levels(of)))
})
## these were "always" true .. but may change (FIXME ?)
stopifnot(exprs = {
identical(of, pmin(of, 3)) # what? error? at least warning?
identical(pmar, pmax(of, 3, rof))
})
## pmin/pmax() of 0-length S3 classed [PR #17200]
for(ob0 in list(I(character()), I(0[0]), I(0L[0]),
structure(logical(), class="L"),
structure(character(), class="CH"))) {
stopifnot(exprs = {
identical(ob0, pmax(ob0, ob0))
identical(ob0, pmin(ob0, ob0))
identical(ob0, pmin(ob0, FALSE))
identical(ob0, pmax(ob0, FALSE))
})
}
## pmin()/pmax() of matching numeric data frames
mUSJ <- data.matrix(dUSJ <- USJudgeRatings)
stopifnot(exprs = {
identical( pmin(dUSJ, 10 - dUSJ),
as.data.frame(pmin(mUSJ, 10 - mUSJ)))
identical( pmax(dUSJ, 10 - dUSJ),
as.data.frame(pmax(mUSJ, 10 - mUSJ)))
})
## had failed for a while. Note however :
d1 <- data.frame(y0 = 0:3 +1/2) ; (d1.2 <- d1[1:2, , drop=FALSE])
stopifnot(exprs = { ## FIXME: The 'NA's really are wrong
identical(pmax(d1,2), data.frame(y0 = c(2, NA, 2.5, 3.5)))
identical(pmax(d1, 3-d1), data.frame(y0 = .5+c(2, 1:3)))
identical(pmax(d1.2, 2), data.frame(y0 = c(2, NA)))
identical(pmax(d1.2, 2-d1.2),data.frame(y0=c(1.5,1.5)))
identical(pmin(d1, 2), data.frame(y0 = c(.5+0:1, NA,NA)))
identical(pmin(d1, 3-d1), data.frame(y0 = .5+c(0, 1:-1)))
identical(pmin(d1.2, 2), data.frame(y0 = c(.5, 1.5)))
identical(pmin(d1.2, 2-d1.2),data.frame(y0 = c(.5,.5)))
})
## some CRAN pkgs have been relying that these at least "worked somehow"
## quantile(x, prob) monotonicity in prob[] - PR#16672
sortedQ <- function(x, prob, ...)
vapply(1:9, function(type)
!is.unsorted(quantile(x, prob, type=type, names=FALSE, ...)), NA)
xN <- c(NA, 10.5999999999999996, NA, NA, NA, 10.5999999999999996,
NA, NA, NA, NA, NA, 11.3000000000000007, NA, NA,
NA, NA, NA, NA, NA, 5.2000000000000002)
sQ.xN <- sortedQ(xN, probs = seq(0,1,1/10), na.rm = TRUE)
x2 <- rep(-0.00090419678460984, 602)
stopifnot(sQ.xN, sortedQ(x2, (0:5)/5))
## both not fulfilled in R < 3.4.0
## seq.int() anomalies in border cases, partly from Mick Jordan (on R-devel):
stopifnot(exprs = {
identical(1, seq.int(to=1, by=1 ))
identical(1:2, seq.int(to=2L, by=1L))
identical(c(1L, 3L), seq.int(1L, 3L, length.out=2))
})
## the first was missing(.), the others "double" in R < 3.4.0
tools::assertError(seq(1,7, by = 1:2))# gave warnings in R < 3.4.0
## seq() for <complex> / <integer>
stopifnot(exprs = {
all.equal(seq(1+1i, 9+2i, length.out = 9) -> sCplx,
1:9 + 1i*seq(1,2, by=1/8))
identical(seq(1+1i, 9+2i, along.with = 1:9), sCplx)
identical(seq(1L, 3L, by=1L), 1:3)
})
## had failed in R-devel for a few days
D1 <- as.Date("2017-01-06")
D2 <- as.Date("2017-01-12")
seqD1 <- seq.Date(D1, D2, by = "1 day")
stopifnot(exprs = {
identical(seqD1, seq(D1, D2, by = "1 days"))
## These two work "accidentally" via seq -> seq.default + "Date"-arithmetic
identical(seqD1, seq(by = 1, from = D1, length.out = 7))
identical(seqD1, seq(by = 1, to = D2, length.out = 7))
## swap order of (by, to) ==> *FAILS* because directly calls seq.Date() - FIXME?
TRUE ||
identical(seqD1, seq(to = D2, by = 1, length.out = 7))
## above had failed in R-devel for a couple of days
identical(seq(9L, by = -1L, length.out = 4L), 9:6)
identical(seq(9L, by = -1L, length.out = 4 ), 9:6)
})
## for consistency, new in R >= 3.4.0
## Underflow happened when parsing small hex constants PR#17199
stopifnot(exprs = {
as.double("0x1.00000000d0000p-987") > 0 # should be 7.645296e-298
as.double("0x1.0000000000000p-1022") > 0 # should be 2.225074e-308
as.double("0x1.f89fc1a6f6613p-974") > 0 # should be 1.23456e-293
})
##
## format.POSIX[cl]t() after print.POSIXct()
dt <- "2012-12-12 12:12:12"
x <- as.POSIXct(dt, tz = "GMT")
stopifnot(identical(format(x), dt))
op <- options(warn=1)# allow
(Sys.t <- Sys.timezone()) # may occasionally warn (and work)
options(op)
someCET <- paste("Europe", c("Berlin", "Brussels", "Copenhagen", "Madrid",
"Paris", "Rome", "Vienna", "Zurich"), sep="/")
if(Sys.t %in% someCET)
stopifnot(print(TRUE), identical(format(x, tz = ""), "2012-12-12 13:12:12"))
## had failed for almost a month in R-devel & R-patched
## xtabs() , notably with NA's :
asArr <- function(x) {
attributes(x) <- list(dim=dim(x), dimnames=dimnames(x)); x }
as_A <- function(x, A) array(x, dim=dim(A), dimnames=dimnames(A))
eq_A <- function(a,b) ## equality of arrays, notably sparseMatrix vs dense
identical(dim(a),dim(b)) && identical(dimnames(a),dimnames(b)) &&
identical(as.vector(a), as.vector(b))
esoph2 <- droplevels(subset(esoph, subset = tobgp > "10-19" & alcgp >= "40-79"))
(xt <- xtabs(~ agegp + alcgp + tobgp, esoph2))
stopifnot(identical(dim(xt), c(6L, 3L, 2L)), # of the 6 x 3 x 2 = 36 entries,
identical(which(xt == 0), c(7L, 12L, 18L, 23L, 30L, 32L, 36L)),
## the above 8 are zeros and the rest is 1 :
all(xt[xt != 0] == 1))
xtC <- xtabs(ncontrols ~ agegp + alcgp + tobgp, data = esoph2)
stopifnot(# no NA's in data, hence result should have none, just 0's:
identical(asArr(unname(xtC)),
array(c(4, 14, 15, 17, 9, 3, 0, 2, 5, 6, 3, 0, 1, 4, 3, 3, 1, 0,
7, 8, 7, 6, 0, 1, 2, 1, 4, 4, 1, 0, 2, 0, 4, 6, 1, 0),
dim = dim(xt))))
DF <- as.data.frame(UCBAdmissions)
xt <- xtabs(Freq ~ Gender + Admit, DF)
stopifnot(identical(asArr(xt),
array(c(1198, 557, 1493, 1278), dim = c(2L, 2L),
dimnames = list(Gender = c("Male", "Female"),
Admit = c("Admitted", "Rejected")))))
op <- options(na.action = "na.omit")
DN <- DF; DN[cbind(6:9, c(1:2,4,1))] <- NA; DN
tools::assertError(# 'na.fail' should fail :
xtabs(Freq ~ Gender + Admit, DN, na.action = na.fail))
xt. <- xtabs(Freq ~ Gender + Admit, DN)
xtp <- xtabs(Freq ~ Gender + Admit, DN, na.action = na.pass)
xtN <- xtabs(Freq ~ Gender + Admit, DN, addNA = TRUE)
stopifnot(exprs = {
identical(asArr(xt - xt.), as_A(c(120,17, 207, 8 ), xt))
identical(asArr(xt - xtp), as_A(c(120,17, 207, NA), xt)) # not ok in R <= 3.3.2
identical(asArr(-xtN + rbind(cbind(xt, 0), 0)),
as_A(c(120, 17, -17, 207, NA, 0, -327, 0, 0), xtN))
})
## 'sparse = TRUE requires recommended package Matrix
if(requireNamespace('Matrix', lib.loc=.Library)) {
xtS <- xtabs(Freq ~ Gender + Admit, DN, na.action = na.pass, sparse = TRUE)# error in R <= 3.3.2
xtNS <- xtabs(Freq ~ Gender + Admit, DN, addNA = TRUE, sparse = TRUE)
stopifnot(
eq_A(xt., xtabs(Freq ~ Gender + Admit, DN, sparse = TRUE)),
eq_A(xtp, xtS),
eq_A(xtN, xtNS)
)
}
## NA treatment partly wrong in R < 3.4.0; new option 'addNA'
ee <- esoph[esoph[,"ncases"] > 0, c(1:2,4)]
ee[,"ncases"] <- as.integer(ee[,"ncases"])
(tt <- xtabs(ncases ~ ., ee)); options(op)
stopifnot(identical(as.vector(tt[1:2,]), # *integer* + first value
c(0L, 1L, 0L, 4L, 0L, 0L, 1L, 4L)))
## keeping integer in sum()mation of integers
## tapply() with FUN returning raw | with factor -> returning integer
stopifnot(identical(tapply(1:3, 1:3, as.raw),
array(as.raw(1:3), 3L, dimnames=list(1:3))), ## failed in R < 3.4.0
identical(3:1, as.vector(tapply(1:3, 1:3, factor, levels=3:1))))
x <- 1:2 ; (txx <- tapply(x, list(x, x), function(x) "a"))
## 1 2
## 1 "a" NA
## 2 NA "a"
stopifnot(identical(txx,
matrix(c("a", NA, NA, "a"), 2, dimnames = rep(list(as.character(x)),2L))))
## Failed in R 3.4.[01]
## str(<list of list>, max.level = 1)
LoL <- function(lenC, FUN = identity)
lapply(seq_along(lenC), function(i) lapply(seq_len(lenC[i]), FUN))
xx <- LoL(c(7,3,17,798,3))
str(xx, list.len = 7, max.level = 1)
str2 <- capture.output(
str(xx, list.len = 7, max.level = 2))
stopifnot(exprs = {
grepl("List of ", capture.output(str(xx, list.len = 7, max.level = 1)))
length(str2) == 35
sum(grepl("list output truncated", str2)) == 2
vapply(paste("List of", lengths(xx)), function(pat) any(grepl(pat, str2)), NA)
})
## wrongly showed '[list output truncated]' in R < 3.4.0
## stopifnot(all.equal(.)) message abbreviation
msg <- tryCatch(stopifnot(all.equal(rep(list(pi),4), list(3.1, 3.14, 3.141, 3.1415))),
error = conditionMessage)
writeLines(msg)
stopifnot(length(strsplit(msg,"\n")[[1]]) == 1+3+1)
## was wrong for months in R-devel only
## available.packages() (not) caching in case of errors
tools::assertWarning(ap1 <- available.packages(repos = "http://foo.bar"))
tools::assertWarning(ap2 <- available.packages(repos = "http://foo.bar"))
stopifnot(nrow(ap1) == 0, identical(ap1, ap2))
## had failed for a while in R-devel (left empty *.rds file)
## rep()/rep.int() : when 'times' is a list
stopifnot(exprs = {
identical(rep (4, list(3)), c(4,4,4))
identical(rep.int(4, list(3)), c(4,4,4))
identical(rep.int(4:5, list(2,1)), c(4L,4:5))
identical(rep (4:5, list(2,1)), c(4L,4:5))
})
## partly failed in R 3.3.{2,3}
## quantile(ordered(.)) - error message more directly useful
OL <- ordered(sample(LETTERS, 20, replace=TRUE))
(e <- tryCatch(quantile(OL), error = conditionMessage))
stopifnot(exprs = {
grepl("type.*1.*3", e) # typically works in several locales
is.ordered(quantile(OL, type = 1))
is.ordered(quantile(OL, type = 3))
})
## gave "factors are not allowed" in R <= 3.3.x
## terms() ignored arg names (PR#17235)
a1 <- attr(terms(y ~ f(x, a = z) + f(x, a = z)),
"term.labels")
a2 <- attr(terms(y ~ f(x, a = z) + f(x, b = z)),
"term.labels")
stopifnot(length(a1) == 1, length(a2) == 2)
## both gave length 1
## by.data.frame() called not from toplevel w different arg names
dby <- function(dat, ind, F) by(dat, ind, FUN=F)
dby(warpbreaks, warpbreaks[,"tension"], summary)
stopifnot(is.list(r <- .Last.value), inherits(r, "by"))
## failed after r72531
## status returned by 'R CMD Sweave'
fil <- "Sweave-test-1.Rnw"
file.copy(system.file("Sweave", fil, package="utils"), tempdir())
owd <- setwd(tempdir())
(o <- capture.output(utils:::.Sweave(fil, no.q = TRUE), type = "message"))
stopifnot(grepl("exit status 0", o[2]))
setwd(owd)
## R CMD Sweave gave status 1 and hence an error in R 3.4.0 (only)
## print.noquote(*, right = *)
nq <- noquote(LETTERS[1:9]); stopifnot(identical(nq, print(nq, right = TRUE)))
## print() failed a few days end in R-devel ca. May 1, 2017; non-identical for longer
tt <- table(c(rep(1, 7), 2,2,2))
stopifnot(identical(tt, print.noquote(tt)))
## print.noquote(<table>) failed for 6 weeks after r72638
## accessing ..1 when ... is empty and using ..0, etc.
t0 <- function(...) ..0
t1 <- function(...) ..1
t2 <- function(...) ..2
stopifnot(identical(t1(pi, 2), pi), identical(t1(t1), t1),
identical(t2(pi, 2), 2))
et1 <- tryCatch(t1(), error=identity)
if(englishMsgs)
stopifnot(identical("the ... list contains fewer than 1 element",
conditionMessage(et1)))
## previously gave "'nthcdr' needs a list to CDR down"
et0 <- tryCatch(t0(), error=identity); (mt0 <- conditionMessage(et0))
et2.0 <- tryCatch(t2(), error=identity); (mt2.0 <- conditionMessage(et2.0))
et2.1 <- tryCatch(t2(1), error=identity); (mt2.1 <- conditionMessage(et2.1))
if(englishMsgs)
stopifnot(grepl("indexing '...' with .* index 0", mt0),
identical("the ... list contains fewer than 2 elements", mt2.0),
identical(mt2.0, mt2.1))
tools::assertError(t0(1))
tools::assertError(t0(1, 2))
## the first gave a different error msg, the next gave no error in R < 3.5.0
## stopifnot(e1, e2, ...) .. evaluating expressions sequentially
one <- 1
try(stopifnot(3 < 4:5, 5:6 >= 5, 6:8 <= 7, one <<- 2))
stopifnot(identical(one, 1)) # i.e., 'one <<- 2' was *not* evaluated
## all the expressions were evaluated in R <= 3.4.x
(et <- tryCatch(stopifnot(0 < 1:10, is.numeric(..vaporware..), stop("FOO!")),
error=identity))
stopifnot(exprs = {
inherits(et, "simpleError")
## condition call now *does* contain 'stopifnot':
## !grepl("^stopifnot", deparse(conditionCall(et), width.cutoff=500))
grepl("'..vaporware..'", conditionMessage(et))
})
## call was the full 'stopifnot(..)' in R < 3.5.0 ...
## path.expand shouldn't translate to local encoding PR#17120
## This has been fixed on Windows, but not yet on Unix non-UTF8 systems
if(.Platform$OS.type == "windows") {
filename <- "\U9b3c.R"
stopifnot(identical(path.expand(paste0("~/", filename)),
paste0(path.expand("~/"), filename)))
}
## Chinese character was changed to hex code
## aggregate.data.frame(*, drop=FALSE) {new feature in R 3.3.0}
## PR#16918 : problem with near-eq. factor() levels "not quite matching"
group <- c(2 + 2^-51, 2)
d1 <- data.frame(n = seq(group))
b1 <- list(group = group)
stopifnot(
identical(aggregate(d1, b1, length, drop = TRUE),
aggregate(d1, b1, length, drop = FALSE)))
## drop=FALSE gave two rows + deprec. warning in R 3.3.x, and an error in 3.4.0
## line() [Tukey's resistant line]
cfs <- t(sapply(2:50, function(k) {x <- 1:k; line(x, 2+x)$coefficients }))
set.seed(7)
cf2 <- t(sapply(2:50, function(k) {
x <- sample.int(k)
line(x, 1-2*x)$coefficients }))
stopifnot(all.equal(cfs, matrix(c(2, 1), 49, 2, byrow=TRUE), tol = 1e-14), # typically exact
all.equal(cf2, matrix(c(1, -2), 49, 2, byrow=TRUE), tol = 1e-14))
## had incorrect medians of the left/right third of the data (x_L, x_R), in R < 3.5.0
## 0-length Date and POSIX[cl]t: PR#71290
D <- structure(17337, class = "Date") # Sys.Date() of "now"
D; D[0]; D[c(1,2,1)] # test printing of NA too
stopifnot(identical(capture.output(D[0]), "Date of length 0"))
D <- structure(1497973313.62798, class = c("POSIXct", "POSIXt")) # Sys.time()
D; D[0]; D[c(1,2,1)] # test printing of NA too
stopifnot(identical(capture.output(D[0]), "POSIXct of length 0"))
D <- as.POSIXlt(D)
D; D[0]; D[c(1,2,1)] # test printing of NA too
stopifnot(identical(capture.output(D[0]), "POSIXlt of length 0"))
## They printed as '[1] "Date of length 0"' etc in R < 3.5.0
## aggregate.data.frame() producing spurious names PR#17283
dP <- state.x77[,"Population", drop=FALSE]
by <- list(Region = state.region, Cold = state.x77[,"Frost"] > 130)
a1 <- aggregate(dP, by=by, FUN=mean, simplify=TRUE)
a2 <- aggregate(dP, by=by, FUN=mean, simplify=FALSE)
stopifnot(exprs = {
is.null(names(a1$Population))
is.null(names(a2$Population))
identical(unlist(a2$Population), a1$Population)
all.equal(unlist(a2$Population),
c(8802.8, 4208.12, 7233.83, 4582.57, 1360.5, 2372.17, 970.167),
tol = 1e-6)
})
## in R <= 3.4.x, a2$Population had spurious names
## factor() with duplicated labels allowing to "merge levels"
x <- c("Male", "Man", "male", "Man", "Female")
## The pre-3.5.0 way {two function calls, nicely aligned}:
xf1 <- factor(x, levels = c("Male", "Man", "male", "Female"))
levels(xf1) <- c("Male", "Male", "Male", "Female")
## the new "direct" way:
xf <- factor(x, levels = c("Male", "Man", "male", "Female"),
labels = c("Male", "Male", "Male", "Female"))
stopifnot(identical(xf1, xf),
identical(xf, factor(c(rep(1,4),2), labels = c("Male", "Female"))))
## Before R 3.5.0, the 2nd factor() call gave an error
aN <- c("a",NA)
stopifnot(identical(levels(factor(1:2, labels = aN)), aN))
## the NA-level had been dropped for a few days in R-devel(3.5.0)
##
## Factor behavior -- these have been unchanged, also in R >= 3.5.0 :
ff <- factor(c(NA,2,3), levels = c(2, NA), labels = c("my", NA), exclude = NULL)
stopifnot(exprs = { ## all these have been TRUE "forever" :
identical(as.vector(ff), as.character(ff))
identical(as.vector(ff), c(NA, "my", NA))
identical(capture.output(ff), c("[1] <NA> my <NA>",
"Levels: my <NA>"))
identical(factor(ff),
structure(c(NA, 1L, NA), .Label = "my", class = "factor"))
identical(factor(ff, exclude=NULL),
structure(c(2L, 1L, 2L), .Label = c("my", NA), class = "factor"))
identical(as.integer( ff), c(2:1,NA))
identical(as.integer(factor(ff, exclude=NULL)), c(2:1,2L))
})
## within.list({ .. rm( >=2 entries ) }) :
L <- list(x = 1, y = 2, z = 3)
stopifnot(identical(within(L, rm(x,y)), list(z = 3)))
## has failed since R 2.7.2 patched (Aug. 2008) without any noticeable effect
sortN <- function(x) x[sort(names(x))]
LN <- list(y = 2, N = NULL, z = 5)
stopifnot(exprs = {
identical(within(LN, { z2 <- z^2 ; rm(y,z,N) }),
list(z2 = 5^2)) ## failed since Aug. 2008
identical(within(LN, { z2 <- z^2 ; rm(y,z) }),
list(N = NULL, z2 = 5^2)) ## failed for a few days in R-devel
## within.list() fast version
identical(sortN(within(LN, { z2 <- z^2 ; rm(y,z) }, keepAttrs=FALSE)),
sortN(list(N = NULL, z2 = 5^2)))
})
## write.csv did not signal an error if the disk was full PR#17243
if (file.access("/dev/full", mode = 2) == 0) { # Not on all systems...
# Large writes should fail mid-write
stopifnot(inherits(tryCatch(write.table(data.frame(x=1:1000000),
file = "/dev/full"),
error = identity),
"error"))
# Small writes should fail on closing
stopifnot(inherits(tryCatch(write.table(data.frame(x=1),
file = "/dev/full"),
warning = identity),
"warning"))
}
## Silently failed up to 3.4.1
## model.matrix() with "empty RHS" -- PR#14992 re-opened
row.names(trees) <- 42 + seq_len(nrow(trees))
.RN <- row.names(mf <- model.frame(log(Volume) ~ log(Height) + log(Girth), trees))
stopifnot(identical(.RN, row.names(model.matrix(~ 1, mf))),
identical(.RN, row.names(model.matrix(~ 0, mf))))
## had 1:nrow() up to 3.4.x
## "\n" etc in calls and function definitions
(qq <- quote(-"\n"))
stopifnot(exprs = {
identical('-"\\n"', cq <- capture.output(qq))
identical(5L, nchar(cq))
identical(6L, nchar(capture.output(quote(("\t")))))
})
## backslashes in language objects accidentally duplicated in R 3.4.1
## length(<pairlist>) <- N
pl <- pairlist(a=1, b=2); length(pl) <- 1
al <- formals(ls); length(al) <- 2
stopifnot(identical(pl, pairlist(a = 1)),
identical(al, as.pairlist(alist(name = , pos = -1L))))
## both `length<-` failed in R <= 3.4.1; the 2nd one for the wrong reason
## dist(*, "canberra") :
x <- cbind(c(-1,-5,10), c(-2,7,8)); (dc <- dist(x, method="canberra"))
## 1 2
## 2 1.666667
## 3 2.000000 1.066667
stopifnot(all.equal(as.vector(dc), c(25, 30, 16)/15))
## R's definition wrongly assumed x[] entries all of the same sign
## sigma( <rank-deficient model> ), PR#17313
dd <- data.frame(x1 = LETTERS[c(1,2,3, 1,2,3, 1,2,3)],
x2 = letters[c(1,2,1, 2,1,1, 1,2,1)], y = 1:9)
(sf <- summary(fit <- lm(y ~ x1*x2, data = dd))) ## last coef is NA
stopifnot(all.equal(sigma(fit)^2, 27/2, tol = 1e-14),
all.equal(sigma(fit), sf$sigma, tol = 1e-14))
## was too large because of wrong denom. d.f. in R <= 3.4.1
## nclass.FD() and nclass.scott() for "extreme" data, PR#17274
NC <- function(x) c(Sturges = nclass.Sturges(x),
Scott = nclass.scott(x), FD = nclass.FD(x))
xE <- function(eps, n = 5) {
stopifnot(n >= 2, is.numeric(eps), eps >= 0)
c(rep.int(1, n-2), 1+eps, 2)
}
ncE <- c(Sturges = 4, Scott = 2, FD = 3)
stopifnot(exprs = {
sapply(-5:-16, function(E) identical(NC(xE(10^E)), ncE))
identical(NC(xE(1e-4)), c(Sturges = 4, Scott = 2, FD = 8550))
identical(NC(xE(1e-3)), c(Sturges = 4, Scott = 2, FD = 855))
})
## for these, nclass.FD() had "exploded" in R <= 3.4.1
## Extremely large diff(range(.)) :
XXL <- c(1:9, c(-1,1)*1e300)
stopifnot(nclass.scott(XXL) == 1)
## gave 0 in R <= 3.4.1
tools::assertWarning(hh <- hist(XXL, "FD", plot=FALSE))
stopifnot(sum(hh$counts) == length(XXL))
## gave error from pretty.default + NA coercion warning in R <= 3.4.1
## methods:::rbind / cbind no longer deeply recursive also fixes bug:
library(methods)
myM <- setClass("myMatrix", contains="matrix")
T <- rbind(1:2, c=2, "a+"=10, myM(4:1,2), deparse.level=0)
stopifnot(identical(rownames(T), c("", "c", "a+", "", "")))
## rownames(.) wrongly were NULL in R <= 3.4.1
proc.time() - .pt; .pt <- proc.time()
## qr.coef(qr(X, LAPACK=TRUE)) when X has column names, etc
X <- cbind(int = 1,
c2 = c(2, 8, 3, 10),
c3 = c(2, 5, 2, 2)); rownames(X) <- paste0("r", 1:4)
y <- c(2,3,5,7); yc <- as.complex(y)
q.Li <- qr(X); cfLi <- qr.coef(q.Li, y)
q.LA <- qr(X, LAPACK=TRUE); cfLA <- qr.coef(q.LA, y)
q.Cx <- qr(X + 0i); cfCx <- qr.coef(q.Cx, y)
e1 <- tryCatch(qr.coef(q.Li, y[-4]), error=identity); e1
e2 <- tryCatch(qr.coef(q.LA, y[-4]), error=identity)
stopifnot(exprs = {
all.equal(cfLi, cfLA , tol = 1e-14)# 6.376e-16 (64b Lx)
all.equal(cfLi, Re(cfCx), tol = 1e-14)# (ditto)
identical(conditionMessage(e1), conditionMessage(e2))
})
## 1) cfLA & cfCx had no names in R <= 3.4.1
## 2) error messages were not consistent
## invalid user device function options(device = *) -- PR#15883
graphics.off() # just in case
op <- options(device=function(...){}) # non-sense device
tools::assertError(plot.new(), verbose = TRUE)
if(no.grid <- !("grid" %in% loadedNamespaces())) requireNamespace("grid")
tools::assertError(grid::grid.newpage(), verbose = TRUE)
if(no.grid) unloadNamespace("grid") ; options(op)
## both errors gave segfaults in R <= 3.4.1
## readRDS(textConnection())
abc <- c("a", "b", "c"); tmpC <- ""
zz <- textConnection('tmpC', 'wb')
saveRDS(abc, zz, ascii = TRUE)
sObj <- paste(textConnectionValue(zz), collapse='\n')
close(zz); rm(zz)
stopifnot(exprs = {
identical(abc, readRDS(textConnection(tmpC)))
identical(abc, readRDS(textConnection(sObj)))
})
## failed in R 3.4.1 only
## Ops (including arithmetic) with 0-column data frames:
d0 <- USArrests[, FALSE]
stopifnot(exprs = {
identical(d0, sin(d0))
identical(d0, d0 + 1); identical(d0, 2 / d0) # failed
all.equal(sqrt(USArrests), USArrests ^ (1/2)) # now both data frames
is.matrix(m0 <- 0 < d0)
identical(dim(m0), dim(d0))
identical(dimnames(m0)[1], dimnames(d0)[1])
identical(d0 & d0, m0)
})
## all but the first failed in R < 3.5.0
## pretty(x, n) for n = <large> or large diff(range(x)) gave overflow in C code
(fLrg <- Filter(function(.) . < 9e307, c(outer(1:8, 10^(0:2))*1e306)))
pL <- vapply(fLrg, function(f)length(pretty(c(-f,f), n = 100, min.n = 1)), 1L)
pL
pL3 <- vapply(fLrg, function(f)length(pretty(c(-f,f), n = 10^3, min.n = 1)), 1L)
pL3
stopifnot(71 <= pL, pL <= 141, # 81 <= pL[-7], # not on Win-64: pL[-15] <= 121,
701 <= pL3, pL3 <= 1401) # <= 1201 usually
## in R < 3.5.0, both had values as low as 17
## without long doubles, min(pl[-7]) is 71.
### Several returnValue() fixes (r 73111) --------------------------
## =============
## returnValue() corner case 1: return 'default' on error
hret <- NULL
fret <- NULL
h <- function() {
on.exit(hret <<- returnValue(27))
stop("h fails")
}
f <- function() {
on.exit(fret <<- returnValue(27))
h()
1
}
res <- tryCatch(f(), error=function(e) 21)
stopifnot(exprs = {
identical(fret, 27)
identical(hret, 27)
identical(res, 21)
})
##
## returnValue corner case 2: return 'default' on non-local return
fret <- NULL
gret <- NULL
f <- function(expr) {
on.exit(fret <<- returnValue(28))
expr
1
}
g <- function() {
on.exit(gret <<- returnValue(28))
f(return(2))
3
}
res <- g()
stopifnot(exprs = {
identical(fret, 28)
identical(gret, 2)
identical(res, 2)
})
##
## returnValue corner case 3: return 'default' on restart
mret <- NULL
hret <- NULL
lret <- NULL
uvarg <- NULL
uvret <- NULL
h <- function(x) {
on.exit(hret <<- returnValue(29))
withCallingHandlers(
myerror = function(e) invokeRestart("use_value", 1),
m(x)
)
}
m <- function(x) {
on.exit(mret <<- returnValue(29))
res <- withRestarts(
l(x),
use_value = function(x) {
on.exit(uvret <<- returnValue(29))
uvarg <<- x
3
}
)
res
}
l <- function(x) {
on.exit(lret <<- returnValue(29))
if (x > 1) {
res <- x+1
return(res)
}
cond <- structure(
class = c("myerror", "error", "condition"),
list(message = c("This is not an error", call = sys.call()))
)
stop(cond)
}
res <- h(1)
stopifnot(exprs = {
identical(res, 3)
identical(mret, 3)
identical(hret, 3)
identical(lret, 29)
identical(uvarg, 1)
identical(uvret, 3)
})
##
## returnValue: callCC
fret <- NULL
f <- function(exitfun) {
on.exit(fret <<- returnValue(30))
exitfun(3)
4
}
res <- callCC(f)
stopifnot(identical(res, 3), identical(fret, 30))
##
## returnValue: instrumented callCC
fret <- NULL
mycallCCret <- NULL
funret <- NULL
mycallCC <- function(fun) {
value <- NULL
on.exit(mycallCCret <<- returnValue(31))
delayedAssign("throw", return(value))
fun(function(v) {
on.exit(funret <<- returnValue(31))
value <<- v
throw
})
}
f <- function(exitfun) {
on.exit(fret <<- returnValue(31))
exitfun(3)
4
}
res <- mycallCC(f)
stopifnot(exprs = {
identical(res, 3)
identical(fret, 31)
identical(mycallCCret, 3)
identical(funret, 31)
})
## end{ returnValue() section}
## array(<empty>, *) should create (corresponding) NAs for non-raw atomic:
a <- array(character(), 1:2)
stopifnot(identical(a, matrix(character(), 1,2)), is.na(a))
## had "" instead of NA in R < 3.5.0
## chaining on.exit handlers with return statements
x <- 0
fret1 <- NULL
fret2 <- NULL
f <- function() {
on.exit(return(4))
on.exit({fret1 <<- returnValue(); return(5)}, add = T)
on.exit({fret2 <<- returnValue(); x <<- 2}, add = T)
3
}
res <- f()
stopifnot(exprs = {
identical(res, 5)
identical(x, 2)
identical(fret1, 4)
identical(fret2, 5)
})
## splineDesign(*, derivs = <too large>):
if(no.splines <- !("splines" %in% loadedNamespaces())) requireNamespace("splines")
x <- (0:8)/8
aKnots <- c(rep(0, 4), c(0.3, 0.5, 0.6), rep(1, 4))
tools::assertError(splines::splineDesign(aKnots, x, derivs = 4), verbose = TRUE)
## gave seg.fault in R <= 3.4.1
## allow on.exit handlers to be added in LIFO order
x <- character(0)
f <- function() {
on.exit(x <<- c(x, "first"))
on.exit(x <<- c(x, "last"), add = TRUE, after = FALSE)
}
f()
stopifnot(identical(x, c("last", "first")))
##
x <- character(0)
f <- function() {
on.exit(x <<- c(x, "last"), add = TRUE, after = FALSE)
}
f()
stopifnot(identical(x, "last"))
## deparse(<symbol>)
##_reverted_for_now
##_ brc <- quote(`{`)
##_ stopifnot(identical(brc, eval(parse(text = deparse(brc, control="all")))))
## default was to set backtick=FALSE so parse() failed in R <= 3.4.x
## sys.on.exit() is called in the correct frame
fn <- function() {
on.exit("foo")
identity(sys.on.exit())
}
stopifnot(identical(fn(), "foo"))
## rep.POSIXt(*, by="n DSTdays") - PR#17342
x <- seq(as.POSIXct("1982-04-15 05:00", tz="US/Central"),
as.POSIXct("1994-10-15", tz="US/Central"), by="360 DSTdays")
stopifnot(length(x) == 13, diff((as.numeric(x) - 39600)/86400) == 360)
## length(x) was 1802 and ended in many NA's in R <= 3.4.2
## 0-length logic with raw()
r0 <- raw(0)
stopifnot(exprs = {
identical(r0 & r0, r0)
identical(r0 | r0, r0)
})
## gave logical(0) in R 3.4.[012]
## `[[` and `[[<-` indexing with <symbol>
x <- c(a=2, b=3)
x[[quote(b)]] <- pi
stopifnot(exprs = {
identical(2, x[[quote(a)]])
identical(x, c(a=2, b=pi))
})
## `[[` only worked after fixing PR#17314, i.e., not in R <= 3.4.x
## range(<non-numeric>, finite = TRUE)
stopifnot(identical(0:1, range(c(NA,TRUE,FALSE), finite=TRUE)))
## gave NA's in R <= 3.4.2
## `[<-` : coercion should happen also in 0-length case:
x1 <- x0 <- x <- n0 <- numeric(); x0[] <- character(); x1[1[0]] <- character()
x[] <- numeric()
stopifnot(identical(x0, character()), identical(x1, x0), identical(x, n0))
## x0, x1 had remained 'numeric()' in R <= 3.4.x
x[1] <- numeric(); stopifnot(identical(x, n0))
## had always worked; just checking
NUL <- NULL
NUL[3] <- integer(0); NUL[,2] <- character() ; NUL[3,4,5] <- list()
stopifnot(is.null(NUL))
## above had failed for one day in R-devel; next one always worked
NUL <- NULL; NUL[character()] <- "A"
stopifnot(identical(NUL, character()))
## 0-0-length subassignment should not change atomic to list:
ec <- e0 <- matrix(, 0, 4) # a 0 x 4 matrix
ec[,1:2] <- list()
x <- 1[0]; x[1:2] <- list()
a <- a0 <- array("", 0:2); a[,1,] <- expression()
stopifnot(exprs = {
identical(ec, e0)
identical(x, 1[0])
identical(a, a0)
})## failed for a couple of days in R-devel
## as.character(<list>) should keep names in some nested cases
cl <- 'list(list(a = 1, "B", ch = "CH", L = list(f = 7)))'
E <- expression(list(a = 1, "B", ch = "CH", L = list(f = 7)))
str(ll <- eval(parse(text = cl)))
stopifnot(exprs = {
identical(eval(E), ll[[1]])
identical(as.character(E), as.character(ll) -> cll)
grepl(cll, cl, fixed=TRUE) # currently, cl == paste0("list(", cll, ")")
## the last two have failed in R-devel for a while
identical(as.character(list(list(one = 1))), "list(one = 1)")
identical(as.character(list( c (one = 1))), "c(one = 1)")
})## the last gave "1" in all previous versions of R
## as.matrix( <data.frame in d.fr.> ) -- prompted by Patrick Perry, R-devel 2017-11-30
dm <- dd <- d1 <- data.frame(n = 1:3)
dd[[1]] <- d1 # -> 'dd' has "n" twice
dm[[1]] <- as.matrix(d1) # (ditto)
d. <- structure(list(d1), class = "data.frame", row.names = c(NA, -3L))
d2. <- data.frame(ch = c("A","b"), m = 10:11)
d2 <- data.frame(V = 1:2); d2$V <- d2.; d2
d3 <- structure(list(A = 1:2, HH = cbind(c(.5, 1))),
class = "data.frame", row.names=c(NA,-2L))
d3.2 <- d3; d3.2 $HH <- diag(2)
d3.2.<- d3; d3.2.$HH <- matrix(1:4, 2,2, dimnames=list(NULL,c("x","y")))
d0 <- as.data.frame(m0 <- matrix(,2,0))
d3.0 <- d3; d3.0 $HH <- m0
d3.d0<- d3; d3.d0$HH <- d0
stopifnot(exprs = {
identical(unname(as.matrix(d0)), m0)
identical(capture.output(dd),
capture.output(d.))
identical(as.matrix(d3.0 ), array(1:2, dim = 2:1, dimnames = list(NULL, "A")) -> m21)
identical(as.matrix(d3.d0), m21)
identical(as.matrix(dd), (cbind(n = 1:3) -> m.))
identical(as.matrix(d.), m.)
identical(as.matrix(d2), array(c("A", "b", "10", "11"), c(2L, 2L),
dimnames = list(NULL, c("V.ch", "V.m"))))
identical(as.matrix(dm), m.)
identical(as.matrix(d1), m.)
identical(colnames(m2 <- as.matrix(d2)), c("V.ch", "V.m"))
identical(colnames(as.matrix(d3 )), colnames(d3 )) # failed a few days
identical(colnames(as.matrix(d3.2 )), colnames(format(d3.2 )))
identical(colnames(as.matrix(d3.2 )), c("A", paste("HH",1:2,sep=".")))
identical(colnames(as.matrix(d3.2.)), colnames(format(d3.2.)))
identical(colnames(as.matrix(d3.2.)), c("A", "HH.x", "HH.y"))
})
## the first 5 as.matrix() have failed at least since R-1.9.1, 2004
## Impossible conditions should at least give a warning - PR#17345
tools::assertWarning(
power.prop.test(n=30, p1=0.90, p2=NULL, power=0.8)
) ## may give error in future
## silently gave p2 = 1.03 > 1 in R versions v, 3.1.3 <= v <= 3.4.3
## 1) removeSource() [for a function w/ body containing NULL]:
op <- options(keep.source=TRUE)
bod <- quote( foo(x, NULL) )
testf <- function(x) { }; body(testf)[[2]] <- bod
testf
testfN <- removeSource(testf)
stopifnot(identical(body(testf )[[2]], bod)
, identical(body(testfN)[[2]], bod)
)
## erronously changed '(x, NULL)' to '(x)' in R version <= 3.4.3
##
## 2) source *should* be kept:
f <- function(x=1) { # 'x' not really needed
x+x + 2*x+1 # (note spaces)
}
stopifnot(exprs = {
identical(capture.output(f) -> fsrc,
capture.output(print(f)))
length(fsrc) == 3
grepl("(x=1)", fsrc[1], fixed=TRUE)
grepl("really needed", fsrc[1], fixed=TRUE)
grepl("x + 2*x+1 # (note", fsrc[2], fixed=TRUE)
})
options(op)
## (was fine, but not tested in R <= 3.5.0)
## ar.yw(x) with missing values in x, PR#17366
which(is.na(presidents)) # in 6 places
arp <- ar(presidents, na.action = na.pass)
## check "some" consistency with cheap imputation:
prF <- presidents
prF[is.na(presidents)] <- c(90, 37, 40, 32, 63, 66) # phantasy
arF <- ar(prF)
stopifnot(exprs = {
all.equal(arp[c("order", "ar", "var.pred", "x.mean")],
list(order = 3, ar = c(0.6665119, 0.2800927, -0.1716641),
var.pred = 96.69082, x.mean = 56.30702), tol = 7e-7)
all.equal(arp$ar, arF$ar, tol = 0.14)
all.equal(arp$var.pred, arF$var.pred, tol = 0.005)
all.equal(arp$asy.var.coef, arF$asy.var.coef, tol = 0.09)
})
## Multivariate
set.seed(42)
n <- 1e5
(i <- sample(n, 12))
u <- matrix(rnorm(2*n), n, 2)
y <- filter(u, filter=0.8, "recursive")
y. <- y; y.[i,] <- NA
est <- ar( y , aic = FALSE, order.max = 2) ## Estimate VAR(2)
es. <- ar( y. , aic = FALSE, order.max = 2, na.action=na.pass)
## checking ar.yw.default() multivariate case
estd <- ar(unclass(y) , aic = FALSE, order.max = 2) ## Estimate VAR(2)
es.d <- ar(unclass(y.), aic = FALSE, order.max = 2, na.action=na.pass)
stopifnot(exprs = {
all.equal(est$ar[1,,], diag(0.8, 2), tol = 0.08)# seen 0.0038
all.equal(est[1:6], es.[1:6], tol = 5e-3)
all.equal(estd$x.mean, es.d$x.mean, tol = 0.01) # seen 0.0023
all.equal(estd[c(1:3,5:6)],
es.d[c(1:3,5:6)], tol = 1e-3)## seen {1,3,8}e-4
all.equal(lapply(estd[1:6],unname),
lapply(est [1:6],unname), tol = 2e-12)# almost identical
all.equal(lapply(es.d[1:6],unname),
lapply(es. [1:6],unname), tol = 1e-11)
})
## NA's in x gave an error, in R versions <= 3.4.3
## as.list(<Date>) method:
toD <- Sys.Date(); stopifnot(identical(as.list(toD)[[1]], toD))
## was wrong for 20 hours
options(warn = 2)# no warnings allowed
## PR#17372: sum(<ints whose sum overflows>, <higher type>)
iL <- rep(1073741824L, 2) # 2^30 + 2^30 = 2^31 integer overflows to NA
r1 <- tryCatch(sum("foo", iL), error=function(e) conditionMessage(e))
r2 <- tryCatch(sum(iL, "foo"), error=function(e) conditionMessage(e))
stopifnot(exprs = {
identical(r1, r2)
grepl("invalid 'type' (character) ", r1, fixed=TRUE)
## each _gave_ an overflow warning + NA
identical(sum(3.14, iL), sum(iL, 3.14))
identical(sum(1+2i, iL), sum(iL, 1+2i))
if(identical(.Machine$sizeof.longlong, 8L))
TRUE # no longer overflows early when we have LONG_INT :
else { # no LONG_INT [very rare in 2018-02 !]
identical(sum(3.14, iL), NA_real_) &&
identical(sum(1+2i, iL), NA_complex_)
}
})
## r2 was no error and sum(iL, 1+2i) gave NA_real_ in R <= 3.4.x
## Was PR#1408 Inconsistencies in sum() {in ./reg-tests-2.R}
x <- as.integer(2^31 - 1)## = 2147483647L = .Machine$integer.max ("everywhere")
x24 <- rep.int(x, 2^24) # sum = 2^55 - 2^24
stopifnot(exprs = {
sum(x, x) == 2^32-2 # did not warn in 1.4.1 -- no longer overflows in 3.5.0
sum(c(x,x)) ==(2^32-2 -> sx2) # did warn -- no longer overflows
(z <- sum(x, x, 0.0)) == sx2 # was NA in 1.4.1
typeof(z) == "double"
is.integer(x24)
sum(x24) == 2^55 - 2^24 # was NA (+ warning) in R <= 3.4.x
})
## aggregate.data.frame(*, drop=FALSE) wishlist PR#17280
## [continued from above]
aF <- aggregate(dP, by=by, FUN=mean, drop=FALSE)
lF <- aggregate(dP, by=by, FUN=length, drop=FALSE)
stopifnot(exprs = {
identical(dim(aF), c(8L, 3L))
identical(aF[6,3], NA_real_)
identical(lF[6,3], NA_integer_)
})
DF <- data.frame(a=rep(1:3,4), b=factor(rep(1:2,6), levels=1:3))
aT <- aggregate(DF["a"], DF["b"], length)# drop=TRUE
aF <- aggregate(DF["a"], DF["b"], length, drop=FALSE)
stopifnot(exprs = {
identical(dim(aT), c(2L,2L))
identical(dim(aF), c(3L,2L))
identical(aT, aF[1:2,])
identical(aF[3,"a"], NA_integer_)
})
## In R <= 3.4.x, the function (FUN) was called on empty sets, above,
## giving NaN (and 0) or <nothing>; now the result is NA.
## PR#16107 is.na(NULL) throws warning (contrary to all other such calls)
stopifnot(identical(is.na(NULL), logical(0)))
## gave a warning in R <= 3.4.x
## subtle [[<- , e.g., <nestedList>[[ c(i,j,k) ]] <- val :
xx0 <-
xx <- list(id = 1L,
split = list(varid = 1L, breaks = NULL,
index = 1:3, right = TRUE, info = "s"),
kids = list(id = 2L,
split = list(varid = 3L, breaks = 75,
right = TRUE, info = "KS"),
kids = list(list(id = 3L, info = "yes"),
list(id = 4L, info = "no")),
info = NULL),
list(id = 5L,
split = list(varid = 3L, breaks = 20,
right = TRUE, info = "4s"),
kids = list(list(id = 6L, info = "no"),
list(id = 7L, info = "yes")),
info = NULL),
info = NULL)
## no-ops:
xx[[1]] <- xx0[[1]]
xx[["kids"]] <- xx0[["kids"]]
xx[[2:1]] <- xx0[[2:1]] ; stopifnot(identical(xx, xx0))
xx[[3:1]] <- xx0[[3:1]] ; stopifnot(identical(xx, xx0)) # (err)
## replacements
xx[[c(2,3)]] <- 5:3
xx[[c(4,2,4)]] <- c(4,2,c=4) # (err: wrong xx)
xx[[c(4,2,3)]] <- c(ch="423")# (err)
xx[[c(3,2,2)]] <- 47 # (err)
stopifnot(exprs = {
identical(xx[[c(2,3)]], 5:3)
identical(xx[[c(4,2,4)]], c(4,2,c=4))
identical(xx[[c(4,2,3)]], c(ch="423"))
identical(xx[[c(3,2,2)]], 47)
identical(lengths(xx), lengths(xx0))
identical( names(xx), names(xx0))
identical(lapply(xx, lengths),
lapply(xx0,lengths))
identical(lapply(xx, names),
lapply(xx0,names))
})
## several of these failed for a bit more than a day in R-devel
## PR#17369 and PR#17381 -- duplicated() & unique() data frame methods:
d22 <- data.frame(x = c(.3 + .6, .9), y = 1)
d21 <- d22[,"x", drop=FALSE]
dRT <- data.frame(x = c("\r", "\r\r"), y = c("\r\r", "\r"))
stopifnot(exprs = {
identical(unique(d22), d22) # err
is.data.frame(d21)
identical(dim(d21), 2:1)
identical(unique(d21), d21)
identical(unique(dRT), dRT) # err
})
## with a POSIXct column (with tz during Daylight Saving change):
Sys.setenv("TZ" = "Australia/Melbourne") # <== crucial (for most)!
x <- as.POSIXct(paste0("2013-04-06 ", 13:17, ":00:00"), tz = "UTC")
attr(x, "tzone") <- ""
(xMelb <- as.POSIXct(x, tz = "Australia/Melbourne"))# shows both AEDT & AEST
dMb <- data.frame(x = xMelb, y = 1)
stopifnot(exprs = {
identical(unique(dMb), dMb)
identical(anyDuplicated(dMb), 0L)
}) # both differing in R <= 3.4.x
## when sep is given, an opening quote may be preceded by non-space
stopifnot( ncol(read.table( text="=\"Total\t\"\t1\n",sep="\t")) == 2)
stopifnot(length(scan(what=list("foo",1), text="=\"Total\t\"\t1\n",sep="\t")) == 2)
##
## in 3.4.x, read.table failed on this
stopifnot( ncol(read.table( text="=\"CJ01 \"\t550\n",sep="\t")) == 2)
stopifnot(length(scan(what=list("foo",1), text="=\"CJ01 \"\t550\n",sep="\t")) == 2)
##
## when no sep is given, quotes preceded by non-space have no special
## meaning and are retained (related to PR#15245)
stopifnot(read.table( text="HO5\'\'\tH")[1,1] == "HO5\'\'")
stopifnot(read.table( text="HO5\'\tH")[1,1] == "HO5\'")
stopifnot(scan(what=list("foo","foo"),text="HO5\'\'\tH")[[1]] == "HO5\'\'")
stopifnot(scan(what=list("foo","foo"),text="HO5\'\tH")[[1]] == "HO5\'")
##
## when no sep is given, there does not have to be a separator between
## quoted entries; testing here to ensure read.table and scan agree,
## but without claiming this particular behavior is needed
stopifnot(read.table( text="\"A\"\" B \"")$V2 == " B ")
stopifnot(scan(what=list("foo","foo"),text="\"A\"\" B \"")[[2]] == " B ")
## merge() names when by.y
parents <- data.frame(name = c("Sarah", "Max", "Qin", "Lex"),
sex = c("F", "M", "F", "M"), age = c(41, 43, 36, 51))
children <- data.frame(parent = c("Sarah", "Max", "Qin"),
name = c("Oliver", "Sebastian", "Kai-lee"),
sex = c("M", "M", "F"), age = c(5,8,7))
# merge.data.frame() no longer creating a duplicated col.names
(m <- merge(parents, children, by.x = "name", by.y = "parent"))
m._ <- merge(parents, children, by.x = "name", by.y = "parent", all.x=TRUE)
(m_. <- merge(parents, children, by.x = "name", by.y = "parent", all.y=TRUE))
m__ <- merge(parents, children, by.x = "name", by.y = "parent", all = TRUE)
## all four gave duplicate column 'name' with a warning in R <= 3.4.x
stopifnot(exprs = {
identical(m, m_.)
identical(m._, m__)
## not identical(m, m__[-1,]) : row.names differ
identical(names(m), names(m__))
all(m == m__[-1,])
identical(dim(m), c(3L, 6L))
identical(dim(m__), c(4L, 6L))
})
## scale(*, <non-numeric>)
if(requireNamespace('Matrix', lib.loc=.Library)) {
de <- data.frame(Type = structure(c(1L, 1L, 4L, 1L, 4L, 2L, 2L, 2L, 4L, 1L),
.Label = paste0("T", 1:4), class = "factor"),
Subj = structure(c(9L, 5L, 8L, 3L, 3L, 4L, 3L, 6L, 6L, 1L),
.Label = as.character(1:9), class = "factor"))
show(SM <- xtabs(~ Type + Subj, data = de, sparse=TRUE))
stopifnot(exprs = {
inherits(SM, "sparseMatrix")
all.equal(scale(SM, Matrix::colMeans(SM)),
scale(SM, Matrix::colMeans(SM, sparse=TRUE)),
check.attributes=FALSE)
})
}
## 2nd scale() gave wrong error "length of 'center' must equal [..] columns of 'x'"
## in R <= 3.4.x
## as.data.frame.matrix() method not eliminating duplicated rownames
(m <- rbind(x = 1:3, x = 2:4, z = 0)) # matrix with duplicated rownams
rownames(d <- as.data.frame(m)) # --> fixed up to "x" "x.1" "z"
## new feature -- 'make.names = *' with '*' in non-defaults :
dN <- as.data.frame(m, make.names=NA)
tools::assertError( dF <- as.data.frame(m, make.names=FALSE) )
stopifnot(exprs = {
!anyDuplicated(rownames(d))
identical(colnames(d), paste0("V", 1:3))
## dN has correct automatic row names:
identical(.row_names_info(dN, 0), .set_row_names(3L))
})
## as.data.frame(m) kept the duplicated row names in R 3.4.x
## check that sorting preserves names and no other attributes
v <- sort(c(1,2,3))
names(v) <- letters[1:3]
stopifnot(identical(sort(v), v))
vv <- sort(c(1,2,3))
names(vv) <- names(v)
attr(vv, "foo") <- "bar"
stopifnot(identical(sort(vv), v))
## failed initially in ALTREP
## check that "TRUE", "FALSE" work in order, sort.int
order(1:3, decreasing = "TRUE")
order(1:3, decreasing = "FALSE")
sort.int(1:3, decreasing = "TRUE")
sort.int(1:3, decreasing = "FALSE")
## failed initially in ALTREP
## this failed until 3.5.x
c1 <- c(1,1,2,2)
c2 <- as.Date(c("2010-1-1", "2011-1-1", "2013-1-1", "2012-1-1"))
order(c1, c2, decreasing = c(TRUE, FALSE), method="radix")
## check sort argument combinations
sort(1:3, decreasing = TRUE, na.last = NA)
sort(1:3, decreasing = TRUE, na.last = TRUE)
sort(1:3, decreasing = TRUE, na.last = FALSE)
sort(1:3, decreasing = FALSE, na.last = NA)
sort(1:3, decreasing = FALSE, na.last = TRUE)
sort(1:3, decreasing = FALSE, na.last = FALSE)
## match.arg()s 'choices' evaluation, PR#17401
f <- function(x = y) {
y <- c("a", "b")
match.arg(x)
}
stopifnot(identical(f(), "a"))
## failed in R <= 3.4.x
## getOption(op, def) -- where 'def' is missing (passed down):
getO <- function(op, def) getOption(op, def)
stopifnot(is.null(getO("foobar")))
## failed for a few days in R-devel, when using MD's proposal of PR#17394,
## notably "killing" parallelMap::getParallelOptions()
## Mantel-Haenszel test in "large" case, PR#17383:
set.seed(101); n <- 500000
aTab <- table(
educ = factor(sample(1:3, replace=TRUE, size=n)),
score= factor(sample(1:5, replace=TRUE, size=n)),
sex = sample(c("M","F"), replace=TRUE, size=n))
(MT <- mantelhaen.test(aTab))
stopifnot(all.equal(
lapply(MT[1:3], unname),
list(statistic = 9.285642, parameter = 8, p.value = 0.3187756), tol = 6e-6))
## gave integer overflow and error in R <= 3.4.x
## check for incorect inlining of named logicals
foo <- compiler::cmpfun(function() c("bar" = TRUE),
options = list(optimize = 3))
stopifnot(identical(names(foo()), "bar"))
foo <- compiler::cmpfun(function() c("bar" = FALSE),
options = list(optimize = 3))
stopifnot(identical(names(foo()), "bar"))
## Failed after changes to use isTRUE/isFALSE instead of identical in r74403.
## check that reverse sort is stable
x <- sort(c(1, 1, 3))
stopifnot(identical(sort.list(x, decreasing=TRUE), as.integer(c(3, 1, 2))))
stopifnot(identical(order(x, decreasing=TRUE), as.integer(c(3, 1, 2))))
## was incorrect with wrapper optimization (reported by Suharto Anggono)
## dump() & dput() where influenced by "deparse.max.lines" option
op <- options(deparse.max.lines=NULL) # here
oNam <- "simplify2array" # (base function which is not very small)
fn <- get(oNam)
ffn <- format(fn)
dp.1 <- capture.output(dput(fn))
dump(oNam, textConnection("du.1", "w"))
stopifnot(length(ffn) > 3, identical(dp.1, ffn), identical(du.1[-1], dp.1))
options(deparse.max.lines = 2) ## "truncate heavily"
dp.2 <- capture.output(dput(fn))
dump(oNam, textConnection("du.2", "w"))
stopifnot(identical(dp.2, dp.1),
identical(du.2, du.1))
options(op); rm(du.1, du.2) # connections
writeLines(tail(dp.2))
## dp.2 and du.2 where heavily truncated in R <= 3.4.4, ending " ..."
## optim() with "trivial bounds"
flb <- function(x) { p <- length(x); sum(c(1, rep(4, p-1)) * (x - c(1, x[-p])^2)^2) }
o1 <- optim(rep(3, 5), flb)
o2 <- optim(rep(3, 5), flb, lower = rep(-Inf, 5))
stopifnot(all.equal(o1,o2))
## the 2nd optim() call gave a warning and switched to "L-BFGS-B" in R <= 3.5.0
## Check that call matching doesn't mutate input
cl <- as.call(list(quote(x[0])))
cl[[1]][[3]] <- 1
v <- .Internal(match.call(function(x) NULL, cl, TRUE, .GlobalEnv))
cl[[1]][[3]] <- 2
stopifnot(v[[1]][[3]] == 1)
## initial patch proposal to reduce duplicating failed on this
## simulate.lm(<glm gaussian, non-default-link>), PR#17415
set.seed(7); y <- rnorm(n = 1000, mean = 10, sd = sqrt(10))
fmglm <- glm(y ~ 1, family = gaussian(link = "log"))
dv <- apply(s <- simulate(fmglm, 99, seed=1), 2, var) - var(y)
stopifnot(abs(dv) < 1.14, abs(mean(dv)) < .07)
## failed in R <= 3.5.0 (had simulated variances ~ 0.1)
## unlist() failed for nested lists of empty lists:
isLF <- function(x) .Internal(islistfactor(x, recursive=TRUE))
ex <- list(x0 = list()
, x1 = list(list())
, x12 = list(list(), list())
, x12. = list(list(), expression(list()))
, x2 = list(list(list(), list())) # <-- Steven Nydick's example
, x212 = list(list(list(), list(list())))
, x222 = list(list(list(list()), list(list())))
)
(exis <- vapply(ex, isLF, NA))
ue <- lapply(ex, unlist)# gave errors in R <= 3.3.x but not 3.{4.x,5.0}
stopifnot(exprs = {
!any(exis)
identical(names(ue), names(ex))
vapply(ue[names(ue) != "x12."], is.null, NA)
})
## qr.coef(qr(<all 0, w/ colnames>))
qx <- qr(x <- matrix(0, 10, 2, dimnames = list(NULL, paste0("x", 1:2))))
qc <- qr.coef(qx, x[,1])
stopifnot(identical(qc, c(x1 = NA_real_, x2 = NA_real_)))
## qr.coef() gave Error ...: object 'pivotted' not found | in R <= 3.5.0
## unlist(<factor-leaves>)
x <- list(list(v=factor("a")))
y <- list(data.frame(v=factor("a")))
x. <- list(list(factor("a")), list(factor(LETTERS[2:4])), factor("lol"))
fN <- factor(LETTERS[c(2:4,30)])
xN <- list(list(factor("a")), list(list(fN)), L=factor("lol"))
stopifnot(exprs = {
.valid.factor(ux <- unlist(x))
identical(ux, unlist(y))
identical(ux, as.factor(c(v="a")))
.valid.factor(ux. <- unlist(x.))
.valid.factor(uxN <- unlist(xN))
identical(levels(ux.), c("a", "B", "C", "D", "lol"))
identical(levels (uxN), levels(ux.))
identical(as.character(uxN), levels(ux.)[c(1:4,11L,5L)])
})
## gave invalid factor()s [if at all]
## printCoefMat() w/ unusual arguments
cm <- matrix(c(9.2, 2.5, 3.6, 0.00031), 1, 4,
dimnames = list("beta", c("Estimate", "Std.Err", "Z value", "Pr(>z)")))
cc <- capture.output(printCoefmat(cm))
stopifnot(grepl(" [*]{3}$", cc[2]),
identical(cc, capture.output(
printCoefmat(cm, right=TRUE))))
## gave Error: 'formal argument "right" matched by multiple actual arguments'
## print.noquote() w/ unusual argument -- inspite of user error, be forgiving:
print(structure("foo bar", class="noquote"), quote=FALSE)
## gave Error: 'formal argument "quote" matched by multiple actual arguments'
## agrep(".|.", ch, fixed=FALSE)
chvec <- c(".BCD", "yz", "AB", "wyz")
patt <- "ABC|xyz"
stopifnot(identical(c(list(0L[0]), rep(list(1:4), 2)),
lapply(0:2, function(m) agrep(patt, chvec, max.distance=m, fixed=FALSE))
))
## all three were empty in R <= 3.5.0
## str(<invalid>)
typeof(nn <- c(0xc4, 0x88, 0xa9, 0x02))
cc <- ch <- rawToChar(as.raw(nn))
str(ch)# worked already
nchar(cc, type="bytes")# 4, but nchar(cc) gives "invalid multibyte string"
Encoding(cc) <- "UTF-8" # << makes it invalid for strtrim(.)!
as.octmode(as.integer(nn))
str(cc)
## In R <= 3.5.0, [strtrim() & nchar()] gave invalid multibyte string at '<a9>\002"'
## multivariate <empty model> lm():
y <- matrix(cos(1:(7*5)), 7,5) # <- multivariate y
lms <- list(m0 = lm(y ~ 0), m1 = lm(y ~ 1), m2 = lm(y ~ exp(y[,1]^2)))
dcf <- sapply(lms, function(fm) dim(coef(fm)))
stopifnot(dcf[1,] == 0:2, dcf[2,] == 5)
## coef(lm(y ~ 0)) had 3 instead of 5 columns in R <= 3.5.1
proc.time() - .pt; .pt <- proc.time()
## confint(<mlm>)
n <- 20
set.seed(1234)
datf <- local({
x1 <- rnorm(n)
x2 <- x1^2 + rnorm(n)
y1 <- 100*x1 + 20*x2 + rnorm(n)
data.frame(x1=x1, x2=x2, y1=y1, y2 = y1 + 10*x1 + 50*x2 + rnorm(n))
})
fitm <- lm(cbind(y1,y2) ~ x1 + x2, data=datf)
zapsmall(CI <- confint(fitm))
ciT <- cbind(c(-0.98031, 99.2304, 19.6859, -0.72741, 109.354, 69.4632),
c( 0.00984, 100.179, 20.1709, 0.60374, 110.63, 70.1152))
dimnames(ciT) <- dimnames(CI)
## also checking confint(*, parm=*) :
pL <- list(c(1,3:4), rownames(CI)[c(6,2)], 1)
ciL <- lapply(pL, function(ii) confint(fitm, parm=ii))
ciTL <- lapply(pL, function(ii) ciT[ii, , drop=FALSE])
stopifnot(exprs = {
all.equal(ciT, CI, tolerance = 4e-6)
all.equal(ciL, ciTL,tolerance = 8e-6)
})
## confint(<mlm>) gave an empty matrix in R <= 3.5.1
## For an *empty* mlm :
mlm0 <- lm(cbind(y1,y2) ~ 0, datf)
stopifnot(identical(confint(mlm0),
matrix(numeric(0), 0L, 2L, dimnames = list(NULL, c("2.5 %", "97.5 %")))))
## failed inside vcov.mlm() because summary.lm()$cov.unscaled was NULL
## cooks.distance.(<mlm>), rstandard(<mlm>) :
fm1 <- lm(y1 ~ x1 + x2, data=datf)
fm2 <- lm(y2 ~ x1 + x2, data=datf)
stopifnot(exprs = {
all.equal(cooks.distance(fitm),
cbind(y1 = cooks.distance(fm1),
y2 = cooks.distance(fm2)))
all.equal(rstandard(fitm),
cbind(y1 = rstandard(fm1),
y2 = rstandard(fm2)))
all.equal(rstudent(fitm),
cbind(y1 = rstudent(fm1),
y2 = rstudent(fm2)))
})
## were silently wrong in R <= 3.5.1
## kruskal.test(<non-numeric g>), PR#16719
data(mtcars)
mtcars$type <- rep(letters[1:2], c(16, 16))
kruskal.test(mpg ~ type, mtcars)
## gave 'Error: all group levels must be finite'
## Multivariate lm() with matrix offset, PR#17407
ss <- list(s1 = summary(fm1 <- lm(cbind(mpg,qsec) ~ 1, data=mtcars, offset=cbind(wt,wt*2))),
s2 = summary(fm2 <- lm(cbind(mpg,qsec) ~ offset(cbind(wt,wt*2)), data=mtcars)))
## drop "call" and "terms" parts which differ; rest must match:
ss[] <- lapply(ss, function(s) lapply(s, function(R) R[setdiff(names(R), c("call","terms"))]))
stopifnot(all.equal(ss[["s1"]], ss[["s2"]], tolerance = 1e-15))
## lm() calls gave error 'number of offsets is 64, should equal 32 ...' in R <= 3.5.1
## print.data.frame(<non-small>)
USJ <- USJudgeRatings
USJe6 <- USJudgeRatings[rep_len(seq_len(nrow(USJ)), 1e6),]
op <- options(max.print=500)
system.time(r1 <- print(USJ))
system.time(r2 <- print(USJe6))# was > 12 sec in R <= 3.5.1, now typically 0.01
# because the whole data frame was formatted.
## Now the timing ratio between r1 & r2 print()ing is typically in [1,2]
system.time(r3 <- print(USJe6, row.names=FALSE))
out <- capture.output(print(USJe6, max = 600)) # max > getOption("max.print")
stopifnot(exprs = {
identical(r1, USJ )# print() must return its arg
identical(r2, USJe6)
identical(r3, USJe6)
length(out) == 52
grepl("CALLAHAN", out[51], fixed=TRUE)
identical(2L, grep("omitted", out[51:52], fixed=TRUE))
})
options(op); rm(USJe6)# reset
## hist.default() in rare cases
hh <- hist(seq(1e6, 2e6, by=20), plot=FALSE)
hd <- hh$density*1e6
stopifnot(0.999 <= hd, hd <= 1.001)
## in R <= 3.5.1: warning 'In n * h : NAs produced by integer overflow' and then NA's
## some things broken by sort.int optimization for sorted integer vectors
sort.int(integer(0)) ## would segfault with barrier testing
stopifnot(identical(sort.int(NA_integer_), integer(0)))
## attribute handling in the fastpass was not quite right
x <- sort.int(c(1,2))
dim(x) <- 2
dimnames(x) <- list(c("a", "b"))
stopifnot(! is.null(names(sort.int(x))))
## match() with length one x and POSIXlt table (PR#17459):
d <- as.POSIXlt("2018-01-01")
match(0, d)
## Gave a segfault in R < 3.6.0.
proc.time() - .pt; .pt <- proc.time()
## as(1L, "double") - PR#17457
stopifnot(exprs = {
identical(as(1L, "double"), 1.) # new
identical(new("double"), double())
## 1. "double" is quite the same as "numeric" :
local({
i1 <- 1L; as(i1, "numeric") <- pi
i2 <- 1L; as(i2, "double" ) <- pi
identical(i1, i2)
})
validObject(Dbl <- getClass("double"))
validObject(Num <- getClass("numeric"))
c("double", "numeric") %in% extends(Dbl)
setdiff(names(Num@subclasses),
names(Dbl@subclasses) -> dblSub) == "double"
"integer" %in% dblSub
## 2. These all remain as they were in R <= 3.5.x , the first one important for back-compatibility:
identical(1:2, local({
myN <- setClass("myN", contains="numeric", slots = c(truly = "numeric"))
myN(log(1:2), truly = 1:2) })@truly)
removeClass("myN")
identical(as(1L, "numeric"), 1L) # << disputable, but hard to change w/o changing myN() behavior
identical(as(TRUE, "double"), 1.)
identical(as(TRUE,"numeric"), 1.)
!is(TRUE, "numeric") # "logical" should _not_ be a subclass of "numeric"
## We agree these should not change :
typeof(1.0) == "double" & typeof(1L) == "integer"
class (1.0) == "numeric" & class (1L) == "integer"
mode (1.0) == "numeric" & mode (1L) == "numeric"
})
## as(*, "double") now gives what was promised
## next(n) for largish n
stopifnot(exprs = {
nextn(214e7 ) == 2^31
nextn(2^32+1) == 4299816960
identical(nextn(NULL), integer())
})
## nextn(214e7) hang in infinite loop; nextn(<large>) gave NA in R <= 3.5.1
## More strictness in '&&' and '||' :
Sys.getenv("_R_CHECK_LENGTH_1_LOGIC2_", unset=NA) -> oEV
Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_" = "warn") # only warn
tools::assertWarning(1 && 0:1)
Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_" = TRUE) # => error (when triggered)
tools::assertError(0 || 0:1)
if(is.na(oEV)) { # (by default)
Sys.unsetenv ("_R_CHECK_LENGTH_1_LOGIC2_")
2 && 0:1 # should not even warn
} else Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_" = oEV)
## polym() in "vector" case PR#17474
fm <- lm(Petal.Length ~ poly(cbind(Petal.Width, Sepal.Length), 2),
data = iris)
p1 <- predict(fm, newdata = data.frame(Petal.Width = 1, Sepal.Length = 1))
stopifnot(all.equal(p1, c("1" = 4.70107678)))
## predict() calling polym() failed in R <= 3.5.1
## sample.int(<fractional>, k, replace=TRUE) :
(tt <- table(sample.int(2.9, 1e6, replace=TRUE)))
stopifnot(length(tt) == 2)
## did "fractionally" sample '3' as well in 3.0.0 <= R <= 3.5.1
## lm.influence() for simple regression through 0:
x <- 1:7
y <- c(1.1, 1.9, 2.8, 4, 4.9, 6.1, 7)
f0 <- lm(y ~ 0+x)
mi <- lm.influence(f0)
stopifnot(identical(dim(cf <- mi$coefficients), c(7L, 1L)),
all.equal(range(cf), c(-0.0042857143, 0.0072527473)))
## gave an error for a few days in R-devel
## cut(<constant 0>), PR#16802
c0 <- cut(rep(0L, 7), breaks = 3)
stopifnot(is.factor(c0), length(c0) == 7, length(unique(c0)) == 1)
## cut() gave error _'breaks' are not unique_ in R <= 3.5.1
## need to record OutDec in deferred string conversions (reported by
## Michael Sannella).
op <- options(scipen=-5, OutDec=",")
xx <- as.character(123.456)
options(op)
stopifnot(identical(xx, "1,23456e+02"))
## parseRd() and Rd2HTML() with some \Sexpr{} in *.Rd:
x <- tools::Rd_db("base")
## Now check that \Sexpr{} "installed" correctly:
of <- textConnection("DThtml", "w")
tools::Rd2HTML(x$DateTimeClasses.Rd, out = of, stages = "install"); close(of)
(iLeap <- grep("leap seconds", DThtml)[[1]])
stopifnot(exprs = {
grepl("[0-9]+ days", DThtml[iLeap+ 1])
any(grepl("20[1-9][0-9]-01", DThtml[iLeap+ 2:4]))
})
## if( "length > 1" ) buglet in plot.data.frame()
Sys.getenv("_R_CHECK_LENGTH_1_CONDITION_", unset=NA) -> oEV
Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = "true")
plot(data.frame(.leap.seconds))
if(!is.na(oEV)) Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = oEV)
## gave Error in ... the condition has length > 1, in R <= 3.5.1
## duplicated(<dataframe with 'f' col>) -- PR#17485
d <- data.frame(f=gl(3,5), i=1:3)
stopifnot(exprs = {
identical(which(duplicated(d)), c(4:5, 9:10, 14:15))
identical(anyDuplicated(d), 4L)
identical(anyDuplicated(d[1:3,]), 0L)
})
## gave error from do.call(Map, ..) as Map()'s first arg. is 'f'
## print.POSIX[cl]t() - not correctly obeying "max.print" option
op <- options(max.print = 50, width = 85)
cc <- capture.output(print(dt <- .POSIXct(154e7 + (0:200)*60)))
c2 <- capture.output(print(dt, max = 6))
writeLines(tail(cc, 4))
writeLines(c2)
stopifnot(expr = {
grepl("omitted 151 entries", tail(cc, 1))
!anyDuplicated(tail(cc, 2))
grepl("omitted 195 entries", tail(c2, 1))
}); options(op)
## the omission had been reported twice because of a typo in R <= 3.5.1
## <data.frame>[ <empty>, ] <- v should be a no-op and
## <data.frame>[ <empty>, <existing column>] <- v a no-op, too
df <- d0 <- data.frame(i=1:6, p=pi)
n <- nrow(df)
as1NA <- function(x) `is.na<-`(rep_len(unlist(x), 1L), TRUE)
for(i in list(FALSE, integer(), -seq_len(n)))
for(value in list(numeric(), 7, "foo", list(1))) {
df[i , ] <- value
df[i , 1] <- value # had failed after svn c75474
stopifnot(identical(df, d0))
## "expand": new column created even for empty <i>; some packages rely on this
df[i, "new"] <- value ## -> produces new column of .. NA
stopifnot(identical(df[,"new"], rep(as1NA(value), n)))
df <- d0
}
## gave error in R <= 3.5.1
df[7:12,] <- d0 + 1L
stopifnot(exprs = {
is.data.frame(df)
identical(dim(df), c(12L, 2L))
identical(df[1:6,], d0)
})
## had failed after svn c75474
## Check that active binding uses primitive quote() and doesn't pick
## up `quote` binding on the search path
quote <- function(...) stop("shouldn't be called")
if (exists("foo", inherits = FALSE)) rm(foo)
makeActiveBinding("foo", identity, environment())
x <- (foo <- "foo")
stopifnot(identical(x, "foo"))
rm(quote, foo, x)
## .format.zeros() when zero.print is "wide":
x <- c(outer(c(1,3,6),10^(-5:0)))
(fx <- formatC(x))
stopifnot(identical(nchar(fx), rep(c(5L, 6:3, 1L), each=3)))
x3 <- round(x, 3)
tools::assertWarning(
fz1. <- formatC(x3, zero.print="< 0.001", replace.zero=FALSE))# old default
(fz1 <- formatC(x3, zero.print="< 0.001"))#,replace.zero=TRUE : new default
(fzw7 <- formatC(x3, width=7, zero.print="< 0.001"))
for(fz in list(fz1, fz1., fzw7)) stopifnot(identical(grepl("<", fz), x3 == 0))
## fz1, fzw7 gave error (for 2 bugs) in R <= 3.5.x
## Attempting to modify an object in a locked binding could succeed
## before signaling an error:
foo <- function() {
zero <- 0 ## to fool constant folding
x <- 1 + zero ## value of 'x' has one reference
lockBinding("x", environment())
tryCatch(x[1] <- 2, ## would modify the value, then signal an error
error = identity)
stopifnot(identical(x, 1))
}
foo()
## formalArgs() should conform to names(formals()) also in looking up fun: PR#17499
by <- function(a, b, c) "Bye!" # Overwrites base::by, as an example
foo <- function() {
f1 <- function(a, ...) {}
list(nf = names(formals("f1")),
fA = formalArgs ("f1"))
}
stopifnot(exprs = {
identical(names(formals("by")), letters[1:3])
identical(formalArgs ("by") , letters[1:3])
{ r <- foo(); identical(r$nf, r$fA) }
})
## gave "wrong" result and error in R <= 3.5.x
## Subassigning multiple new data.frame columns (with specified row), PR#15362, 17504
z0 <- z1 <- data.frame(a=1, s=1)
z0[2, c("a","r","e")] <- data.frame(a=1, r=8, e=9)
z1[2, "r"] <- data.frame(r=8)
x <- x0 <- data.frame(a=1:3, s=1:3)
x[2, 3:4] <- data.frame(r=8, e=9)
stopifnot(exprs = {
identical(z0, data.frame(a = c(1, 1), s = c(1, NA), r = c(NA, 8), e = c(NA, 9)))
identical(z1, data.frame(a = c(1,NA), s = c(1, NA), r = c(NA, 8)))
identical(x, cbind(x0,
data.frame(r = c(NA, 8, NA), e = c(NA, 9, NA))))
})
d0 <- d1 <- d2 <- d3 <- d4 <- d5 <- d6 <- d7 <- data.frame(n=1:4)
##
d0[, 2] <- c2 <- 5:8
d0[, 3] <- c3 <- 9:12
d1[, 2:3] <- list(c2, c3)
d2[ 2:3] <- list(c2, c3)
d3[TRUE, 2] <- c2 ; d3[TRUE, 3] <- c3
d4[TRUE, 2:3] <- list(c2, c3)
d5[1:4, 2:3] <- list(c2, c3)
d6[TRUE, 1:2] <- list(c2, c3)
d7[ , 1:2] <- list(c2, c3)
stopifnot(exprs = {
identical(d0, d1)
identical(d0, d2)
identical(d0, d3)
identical(d0, d4)
identical(d0, d5)
##
identical(d6, d7)
identical(d6, structure(list(n = c2, V2 = c3),
row.names = c(NA, -4L), class = "data.frame"))
})
## d4, d5 --> 'Error in `*tmp*`[[j]] : subscript out of bounds'
## d6 --> 'Error in x[[j]] <- `*vtmp*` :
## more elements supplied than there are to replace
## in R <= 3.5.1
## str() now even works with invalid S4 objects:
## this needs Matrix loaded to be an S4 generic
if(requireNamespace('Matrix', lib.loc = .Library)) {
moS <- mo <- findMethods("isSymmetric")
attr(mo, "arguments") <- NULL
print(validObject(mo, TRUE)) # shows what's wrong
tools::assertError(capture.output( mo ))
op <- options(warn = 1)# warning:
str(mo, max.level = 2)
options(op)# revert
## in R <= 3.5.x, str() gave error instead of the warning
}
## seq.default() w/ integer overflow in border cases: -- PR#17497, Suharto Anggono
stopifnot(is.integer(iMax <- .Machine$integer.max), iMax == 2^31-1,
is.integer(iM2 <- iMax-1L), # = 2^31 - 2
(t30 <- 1073741824L) == 2^30 ,
is.integer(i3t30 <- c(-t30, 0L, t30)))
for(seq in c(seq, seq.int)) # seq() -> seq.default() to behave as seq.int() :
stopifnot(exprs = {
seq(iM2, length=2L) == iM2:(iM2+1L) # overflow warning and NA
seq(iM2, length=3L) == iM2:(iM2+2 ) # Error in if (from == to) ....
seq(-t30, t30, length=3) == i3t30 # overflow warning and NA
## Next two ok for the "seq.cumsum-patch" (for "seq.double-patch", give "double"):
identical(seq(-t30, t30, length=3L), i3t30)# Error in if(is.integer(del <- to - from)
identical(seq(-t30, t30, t30) , i3t30)# Error .. invalid '(to-from)/by'+NA warn.
})
## each of these gave integer overflows errors or NA's + warning in R <= 3.5.x
stopifnot(identical(7:10, seq.default(7L, along.with = 4:1) ))
## errored for almost a day after r76062
## seq.int(*, by=<int.>, length = n) for non-integer 'from' or 'to'
stopifnot(exprs = {
identical(seq.int(from = 1.5, by = 2, length = 3),
s <- seq(from = 1.5, by = 2, length = 3))
s == c(1.5, 3.5, 5.5)
identical(seq.int(to = -0.1, by = -2, length = 2),
s <- seq(to = -0.1, by = -2, length = 2))
all.equal(s, c(1.9, -0.1))
identical(seq.int(to = pi, by = 0, length = 1), pi)
})
## returned integer sequences in all R versions <= 3.5.1
## Check for modififation of arguments
## Issue originally reported by Lukas Stadler
x <- 1+0
stopifnot(x + (x[] <- 2) == 3)
f <- compiler::cmpfun(function(x) { x <- x + 0; x + (x[] <- 2) })
stopifnot(f(1) == 3)
x <- 1+0
stopifnot(log(x, x[] <- 2) == 0)
f <- compiler::cmpfun(function(x) { x <- x + 0; log(x, x[] <- 2)})
stopifnot(f(1) == 0)
f <- function() x + (x[] <<- 2)
x <- 1 + 0; stopifnot(f() == 3)
fc <- compiler::cmpfun(f)
x <- 1 + 0; stopifnot(fc() == 3)
f <- function() x[{x[2] <<- 3; 1}] <<- 2
fc <- compiler::cmpfun(f)
x <- c(1,2); f(); stopifnot(x[2] == 2)
x <- c(1,2); fc(); stopifnot(x[2] == 2)
x <- 1+0
stopifnot(c(x, x[] <- 2)[[1]] == 1)
f <- compiler::cmpfun(function(x) { x <- x + 0; c(x, x[] <- 2)})
stopifnot(f(1)[[1]] == 1)
x <- c(1,2)
x[{x[2] <- 3; 1}] <- 2
stopifnot(x[2] == 2)
f <- compiler::cmpfun(function(a,b) { x <- c(a, b); x[{x[2] <- 3; 1}] <- 2; x})
f(1, 2)
stopifnot(f(1, 2) == 2)
m <- matrix(1:4, 2)
i <- (1:2) + 0
stopifnot(m[i, {i[] <- 2; 1}][1] == 1)
f <- compiler::cmpfun(function(i) { i <- i + 0; m[i, {i[] <- 2; 1}]})
stopifnot(f(1:2)[1] == 1)
m <- matrix(1:4, 2)
eval(compiler::compile(quote(m[1,1])))
stopifnot(max(.Internal(named(m)), .Internal(refcnt(m))) == 1)
ma <- .Internal(address(m))
eval(compiler::compile(quote(m[1,1] <- 2L)))
stopifnot(identical(.Internal(address(m)), ma))
a <- array(1:8, rep(2, 3))
eval(compiler::compile(quote(a[1,1,1])))
stopifnot(max(.Internal(named(a)), .Internal(refcnt(a))) == 1)
aa <- .Internal(address(a))
eval(compiler::compile(quote(a[1,1,1] <- 2L)))
stopifnot(identical(.Internal(address(a)), aa))
m <- matrix(1:4, 2)
i <- (1:2) + 0
stopifnot(m[i, {i[] <- 2; 1}][1] == 1)
f <- compiler::cmpfun(function(i) { i <- i + 0; m[i, {i[] <- 2; 1}]})
stopifnot(f(1:2)[1] == 1)
a <- array(1:8, rep(2, 3))
i <- (1:2) + 0
stopifnot(a[i, {i[] <- 2; 1}, 1][1] == 1)
f <- compiler::cmpfun(function(i) { i <- i + 0; a[i, {i[] <- 2; 1}, 1]})
stopifnot(f(1:2)[1] == 1)
i <- (1:2) + 0
stopifnot(a[i, {i[] <- 2; 1}, 1][1] == 1)
f <- compiler::cmpfun(function(i) { i <- i + 0; a[1, i, {i[] <- 2; 1}]})
stopifnot(f(1:2)[1] == 1)
x <- 1 + 0
stopifnot(identical(rep(x, {x[] <- 2; 2}), rep(1, 2)))
x <- 1 + 0
v <- eval(compiler::compile(quote(rep(x, {x[] <- 2; 2}))))
stopifnot(identical(v, rep(1, 2)))
x <- 1 + 0
stopifnot(round(x, {x[] <- 2; 0}) == 1)
x <- 1 + 0
v <- eval(compiler::compile(quote(round(x, {x[] <- 2; 0}))))
stopifnot(v == 1)
f <- function() {
x <- numeric(1)
y <- 0
rm("y")
makeActiveBinding("y", function() { x[] <<- 1; 0}, environment())
x + y
}
stopifnot(f() == 0)
stopifnot(compiler::cmpfun(f)() == 0)
f <- function(y = {x[] <- 1; 0}) { x <- numeric(1); x + y }
stopifnot(f() == 0)
stopifnot(compiler::cmpfun(f)() == 0)
## This failed under REFCNT:
for (i in 1:2) { if (i == 1) { x <- i; rm(i) }}
stopifnot(x == 1)
## gamma & lgamma should not warn for correct limit cases:
stopifnot(exprs = {
lgamma(0:-10) == Inf
gamma(-180.5) == 0
gamma(c(200,Inf)) == Inf
lgamma(c(10^(306:310), Inf)) == Inf
})
## had "Warning message: value out of range in 'lgamma' " for ever
## sub() with non-ASCII replacement failed to set encodings (PR#17509):
x <- c("a", "b")
x <- sub("a", "\u00e4", x)
stopifnot(Encoding(x)[1L] == "UTF-8")
x <- sub("b", "\u00f6", x)
stopifnot(Encoding(x)[2L] == "UTF-8")
## [1] has been "unknown" in R <= 3.5.x
## formula(model.frame()) -- R-devel report by Bill Dunlap
d <- data.frame(A = log(1:6), B = LETTERS[1:6], C = 1/(1:6), D = letters[6:1], Y = 1:6)
m0 <- model.frame(Y ~ A*B, data=d)
stopifnot(exprs = {
DF2formula(m0) == (Y ~ A+B) # the previous formula(.) behavior
formula(m0) == (Y ~ A*B)
})
## formula(.) gave Y ~ A + B in R <= 3.5.x
## These used to fail (PR17514) in a NAMED build but not with REFCNT:
L <- matrix(list( c(0) ), 2, 1)
L[[2]][1] <- 11
stopifnot(L[[1]] == 0)
L <- matrix(list( c(0) ), 2, 1, byrow = TRUE)
L[[2]][1] <- 11
stopifnot(L[[1]] == 0)
## ar.ols() - PR#17517
ar_ols <- ar.ols(lynx)
stopifnot(exprs = {
is.list(pa <- predict(ar_ols, n.ahead = 2))# must *not* warn
all.equal(ar_ols$var.pred, 592392.12774) # not a matrix
})
## .$var.pred had been a 1x1 matrix in R <= 3.5.2
## check that parse lines are properly initialized in the parser
d <- getParseData(parse(text="{;}", keep.source=TRUE))
l <- d[ d[,"token"] == "exprlist", "line1" ]
stopifnot(identical(l, 1L))
## failed in 3.5 and earlier
## check that NA is treated as non-existent file (not file named "NA")
tools::assertError (normalizePath(c(NA_character_,getwd()), mustWork=TRUE))
tools::assertWarning(normalizePath(c(NA_character_,getwd()), mustWork=NA))
stopifnot(identical (normalizePath(c(NA_character_,getwd()), mustWork=FALSE)[1],
NA_character_))
stopifnot(identical(unname(file.access(NA_character_)), -1L))
## NA treated as error
tools::assertError(file.edit(NA_character_))
tools::assertError(file(NA_character_))
## strtoi("") :
stopifnot(is.na(strtoi("")),
is.na(strtoi("", 2L)))
## was platform dependent [libC strtol()] in R <= 3.5.x
## formula.data.frame() thinko at modularization [r75911]:
f <- function(df) {
stopifnot(is.data.frame(df))
d <- 4
f2(formula(df))
}
f2 <- function(form) eval(quote(d), envir = environment(form))
rf <- f(data.frame(x=1, f="b")) ## gave error inside f2() in R-devel
stopifnot(identical(rf, 4))
## as after 75911 a wrong parent.frame() was used.
## format(.) when there's no method gives better message:
ee <- tryCatch(format(.Internal(bodyCode(ls))), error=identity)
stopifnot(exprs = {
conditionCall(ee)[[1]] == quote(format.default)
grepl("no format() method", conditionMessage(ee), fixed=TRUE)
})
## signalled from long .Internal(...) call + "must be atomic" in R <= 3.5.x
## writeLines(readLines(F), F) -- PR#17528
tf <- tempfile("writeL_test")
writeLines("1\n2\n3", tf)
c123 <- paste(1:3)
stopifnot(identical(readLines(tf), c123))
writeLines(readLines(tf), tf)
stopifnot(identical(readLines(tf), c123))
## writeLines had opened the output for writing before readLines() read it
## max.col(<empty>)
stopifnot(identical(NA_integer_, max.col(matrix(,1,0))))
## gave 1 in R <= 3.5.x
## model.matrix() should warn on invalid 'contrasts.arg'
## suggested by Ben Bolker on R-devel list, Feb 20, 2019
data(warpbreaks)
mf1 <- model.matrix(~tension, data=warpbreaks) # default
tools::assertWarning(
mf2 <- model.matrix(~tension, data=warpbreaks, contrasts.arg = "contr.sum") )# wrong
tools::assertWarning(
mf3 <- model.matrix(~tension, data=warpbreaks, contrasts.arg = contr.sum) ) # wrong
mf4 <- model.matrix(~tension, data=warpbreaks, contrasts.arg = list(tension=contr.sum))
stopifnot(exprs = {
identical(mf1, mf2)
identical(mf1, mf3)
## and mf4 has sum contrasts :
is.matrix(C <- attr(mf4, "contrasts")$tension)
identical(dim(C), 3:2)
all.equal(unname(C), rbind(diag(2), -1))
})
## gave no warnings but same results in R <= 3.5.0
## axTicks() should zap "almost zero" to zero, PR#17534
## (caused by non-exact floating point arithmetic -- (platform dependently!)
plot(c(-0.1, 0.2), axes=FALSE, ann=FALSE)
(a2 <- axTicks(2)) # -0.10 -0.05 0.00 0.05 0.10 0.15 0.20
axis(2, at = a2) # was ugly
stopifnot(exprs = {
a2[3] == 0 # exactly
all.equal(a2, (-2:4)/20, tol=1e-14) # closely
})
## a2[3] was 1.38778e-17 on typical platforms in R <= 3.5.x
## isSymmetric(<1x1-matrix>) and <0x0 matrix> with dimnames
stopifnot(exprs = {
! isSymmetric(matrix(0, dimnames = list("A","b"))) # *non*-symmetric dimnames
isSymmetric(matrix(0, dimnames = list("A","b")), check.attributes=FALSE) # dimn. not checked
## isSymmetric() gave TRUE wrongly in R versions 3.4.0 -- 3.5.x
! isSymmetric(matrix(1, dimnames = list("A", NULL)))
! isSymmetric(matrix(1, dimnames = list(NULL, "A")))
isSymmetric(matrix(1, dimnames = list(NULL, "A")), check.attributes=FALSE)
isSymmetric(matrix(1))
isSymmetric(matrix(1, dimnames = list("a", "a")))
isSymmetric(matrix(1, dimnames = list(NULL, NULL)))
isSymmetric(matrix(,0,0, dimnames=list(NULL, NULL)))
isSymmetric(matrix(,0,0))
})
## bxp() did not signal anything about duplicate actual arguments:
set.seed(3); bx.p <- boxplot(split(rt(100, 4), gl(5, 20)), plot=FALSE)
tools::assertWarning(bxp(bx.p, ylab = "Y LAB", ylab = "two"))
w <- tryCatch(bxp(bx.p, ylab = "Y LAB", ylab = "two", xlab = "i", xlab = "INDEX"),
warning = conditionMessage)
stopifnot(is.character(w), grepl('ylab = "two"', w), grepl('xlab = "INDEX"', w))
## reformulate() bug PR#17359
(form <- reformulate(c("u", "log(x)"), response = "log(y)"))
stopifnot(identical(form, log(y) ~ u + log(x)))
## had *symbol* `log(y)` instead of call in R <= 3.5.1
newf <- function(terms, resp)
list(e = environment(),
form= reformulate(terms, resp))
ef <- newf("x", "log(y)")
stopifnot( identical(ef$e, environment(ef$form)),
!identical(ef$e, .GlobalEnv),
identical(format(ef$form), "log(y) ~ x"))
## Back compatibility + deprecation warning:
notC <- "Model[no 4]"
form <- `Model[no 4]` ~ .
stopifnot(exprs = {
identical(form, suppressWarnings(reformulate(".", notC))) # << will STOP working!
identical(form, reformulate(".", as.name(notC)))
identical(form, reformulate(".", paste0("`", notC, "`")))
inherits(tt <- tryCatch(reformulate(".", notC), warning=identity),
"deprecatedWarning")
inherits(tt, "warning")
conditionCall(tt)[[1]] == quote(reformulate)
})
writeLines(conditionMessage(tt))
## stopifnot() now works *nicely* with expression object (with 'exprs' name):
ee <- expression(exprs=all.equal(pi, 3.1415927), 2 < 2, stop("foo!"))
te <- tryCatch(stopifnot(exprs = ee), error=identity)
stopifnot(conditionMessage(te) == "2 < 2 is not TRUE")
## conditionMessage(te) was "ee are not all TRUE" in R 3.5.x
##
## Empty 'exprs' should work in almost all cases:
stopifnot()
stopifnot(exprs = {})
e0 <- expression()
stopifnot(exprs = e0)
do.call(stopifnot, list(exprs = expression()))
do.call(stopifnot, list(exprs = e0))
## the last three failed in R 3.5.x
## as.matrix.data.frame() w/ character result and logical column, PR#17548
cx <- as.character(x <- c(TRUE, NA, FALSE))
stopifnot(exprs = {
identical(cx, as.matrix(data.frame(x, y="chr"))[,"x"])
identical(x, as.logical(cx))
})
## str2expression(<empty>) :
stopifnot(identical(str2expression(character()), expression()))
## quasi(*, variance = list()) - should not deparse(); PR#17560
## like quasipoisson() :
devRes <- function(y, mu, wt) { 2 * wt * (y * log(ifelse(y == 0, 1, y/mu)) - (y-mu)) }
init <- expression({
if(any(y < 0)) stop("y < 0")
n <- rep.int(1, nobs)
mustart <- y + 0.1
})
myquasi <- quasi(link = "log",
variance = list(name = "my quasi Poisson",
varfun = function(mu) mu,
validmu = function(mu) all(is.finite(mu)) && all(mu > 0),
dev.resids = devRes,
initialize = init))
x <- runif(100, min=0, max=1)
y <- rpois(100, lambda=1)
fq1 <- glm(y ~ x, family = myquasi)
fqP <- glm(y ~ x, family = quasipoisson)
str(keep <- setdiff(names(fq1), c("family", "call")))
identNoE <- function(x,y, ...) identical(x,y, ignore.environment=TRUE, ...)
stopifnot(exprs = {
all.equal(fq1[keep], fqP[keep])
## quasi() failed badly "switch(vtemp, ... EXPR must be a length 1 vector" in R <= 3.6.0
identNoE(quasi(var = mu), quasi(variance = "mu"))
identNoE(quasi(var = mu(1-mu)), quasi(variance = "mu(1- mu)"))# both failed in R <= 3.6.0
identNoE(quasi(var = mu^3), quasi(variance = "mu ^ 3")) # 2nd failed in R <= 3.6.0
is.character(msg <- tryCatch(quasi(variance = "log(mu)"), error=conditionMessage)) &&
grepl("variance.*log\\(mu\\).* invalid", msg) ## R <= 3.6.0: 'variance' "NA" is invalid
})
## rbind.data.frame() should *not* drop NA level of factors -- PR#17562
fcts <- function(N=8, k=3) addNA(factor(sample.int(k, N, replace=TRUE), levels=1:k))
set.seed(7) # <- leads to some "0 counts" [more interesting: they are kept]
dfa <- data.frame(x=fcts())
dfb <- data.frame(x=fcts()) ; rbind(table(dfa), table(dfb))
dfy <- data.frame(y=fcts())
yN <- c(1:3, NA_character_, 5:8)
dfay <- cbind(dfa, dfy)
dfby <- cbind(dfa, data.frame(y = yN))
dfcy <- dfa; dfcy$y <- yN # y: a <char> column
## dNay := drop unused levels from dfay incl NA
dNay <- dfay; dNay[] <- lapply(dfay, factor)
str(dfay) # both (x, y) have NA level
str(dfby) # (x: yes / y: no) NA level
str(dNay) # both: no NA level
stopifnot(exprs = { ## "trivial" (non rbind-related) assertions :
identical(levels(dfa$x), c(1:3, NA_character_) -> full_lev)
identical(levels(dfb$x), full_lev)
identical(levels(dfay$x), full_lev) # cbind() does work
identical(levels(dfay$y), full_lev)
identical(levels(dfby$x), full_lev)
is.character(dfcy$y)
anyNA(dfcy$y)
identical(levels(dfby$y), as.character((1:8)[-4]) -> levN) # no NA levels
identical(lapply(dNay, levels),
list(x = c("2","3"), y = levN[1:3])) # no NA levels
})
## R in 3.6.z, z >= 1 needs 'factor.exclude=NULL'
dfaby <- rbind(dfay, dfby, factor.exclude=NULL)
dNaby <- rbind(dNay, dfby, factor.exclude=NULL)
dfacy <- rbind(dfay, dfcy, factor.exclude=NULL)
dfcay <- rbind(dfcy, dfay, factor.exclude=NULL) # 1st arg col. is char => rbind() keeps char
stopifnot(exprs = {
identical(levels(rbind(dfa, dfb, factor.exclude=NULL)$x), full_lev)
identical(levels(dfaby$x), full_lev)
identical(levels(dfaby$y), yN) # failed a while
identical(levels(dNaby$y), levN) # (ditto)
identical(dfacy, dfaby)
is.character(dfcay$y)
anyNA(dfcay$y)
identical(dfacy$x, dfcay$x)
identical(lapply(rbind(dfby, dfay, factor.exclude=NULL), levels),
list(x = full_lev, y = c(levN, NA)))
identical(lapply(rbind(dfay, dfby, factor.exclude = NA), levels),
list(x = as.character(1:3), y = levN))
identical(lapply(rbind(dfay, dfby, factor.exclude=NULL), levels),
list(x = full_lev, y = yN))
})
## rbind.data.frame() should work in all cases with "matrix-columns":
m <- matrix(1:12, 3) ## m.N := [m]atrix with (row)[N]ames :
m.N <- m ; rownames(m.N) <- letters [1:3]
## data frames with these matrices as *column*s:
dfm <- data.frame(c = 1:3, m = I(m))
dfm.N <- data.frame(c = 1:3, m = I(m.N))
(mNm <- rbind(m.N, m))
dfmmN <- rbind(dfm, dfm.N)
dfmNm <- rbind(dfm.N, dfm)
stopifnot(exprs = {
identical( dim(dfmNm), c(6L, 2L))
identical(dimnames(dfmNm), list(c(letters[1:3],1:3), c("c","m")))
is.matrix(m. <- dfmNm[,"m"])
identical(dim(m.), c(6L, 4L))
identical(dfmNm, dfmmN[c(4:6, 1:3), ])
identical(unname(mNm), unname(m.))
})
## The last rbind() had failed since at least R 2.0.0
## as.data.frame.array(<1D array>) -- PR#17570
str(x2 <- as.data.frame(array(1:2)))
stopifnot(identical(x2[[1]], 1:2))
## still was "array" in R <= 3.6.0
## vcov(<quasi>, dispersion = *) -- PR#17571
counts <- c(18,17,15,20,10,20,25,13,12)
treatment <- gl(3,3)
outcome <- gl(3,1,9)
## Poisson and Quasipoisson
poisfit <- glm(counts ~ outcome + treatment, family = poisson())
qpoisfit <- glm(counts ~ outcome + treatment, family = quasipoisson())
spois <- summary( poisfit)
sqpois <- summary(qpoisfit)
sqpois.d1 <- summary(qpoisfit, dispersion=1)
SE1 <- sqrt(diag(V <- vcov(poisfit)))
(noLdbl <- (.Machine$sizeof.longdouble <= 8)) ## TRUE when --disable-long-double
stopifnot(exprs = { ## Same variances and same as V
all.equal(vcov(spois), V)
all.equal(vcov(qpoisfit, dispersion=1), V) ## << was wrong
all.equal(vcov(sqpois.d1), V)
all.equal(spois $coefficients[,"Std. Error"], SE1)
all.equal(sqpois.d1$coefficients[,"Std. Error"], SE1)
all.equal(sqpois $coefficients[,"Std. Error"],
sqrt(sqpois$dispersion) * SE1)
})
## vcov(. , dispersion=*) was wrong on R versions 3.5.0 -- 3.6.0
## runmed(<x_with_NA>, "Turlach") still seg.faults in 3.6.0 {reported by Hilmar Berger}
dd1 <- c(rep(NaN,82), rep(-1, 144), rep(1, 74))
xT1 <- runmed(dd1, 21, algorithm="T", print.level=1)# gave seg.fault
xS1 <- runmed(dd1, 21, algorithm="S", print.level=1)
if(FALSE)
cbind(dd1, xT1, xS1)
nN <- !is.na(xT1)
stopifnot(xT1[nN] == c(rep(-1, 154), rep(1, 74)))
dd2 <- c(rep(-1, 144), rep(1, 74), rep(NaN,82))
xS2 <- runmed(dd2, 21, algorithm = "Stuetzle", print.level=1)
xT2 <- runmed(dd2, 21, algorithm = "Turlach" , print.level=1)
if(FALSE)
cbind(dd2, xS2, xT2) # here, "St" and "Tu" are "the same"
nN <- !is.na(xT2)
stopifnot(exprs = { ## both NA|NaN and non-NA are the same:
identical(xT2[nN], xS2[nN])
identical(is.na(xS2) , !nN)
{ i <- 1:(144+74); xT2[i] == dd2[i] }
})
## close to *minimal* repr.example:
x5 <- c(NA,NA, 1:3/4)
rS <- runmed(x5, k= 3, algorithm = "St", print.level=3)
rT <- runmed(x5, k= 3, algorithm = "Tu", print.level=3)
stopifnot(exprs = {
identical(rS, rT)
rT == c(1,1,1:3)/4
})
## a bit larger:
x14 <- c(NA,NA,NA,NA, 1:10/4)
rS14 <- runmed(x14, k = 7, algorithm="S", print.level=2)
rT14 <- runmed(x14, k = 7, algorithm="T", print.level=2)
## cbind(x14, rT14, rS14)
(naActs <- eval(formals(runmed)$na.action)); names(naActs) <- naActs
allT14 <- lapply(naActs, function(naA)
tryCatch(runmed(x14, k = 7, algorithm="T", na.action=naA, print.level=2),
error=identity, warning=identity))
rTo14 <- runmed(na.omit(x14), k=7, algorithm="T")
stopifnot(exprs = {
identical( rT14, rS14)
identical(c(rT14), c(NaN,NaN, .5, .5, .5, .75, x14[-(1:6)]))
identical( rT14, allT14$"+Big_alternate")
(allT14$"-Big_alternate" >= rT14)[-(1:2)] # slightly surprisingly
identical(allT14$na.omit[-(1:4)], c(rTo14))
inherits(Tfail <- allT14$fail, "error")
grepl("^runmed\\(.*: .*NA.*x\\[1\\]", Tfail$message)
})
## misleading error message when coercing language object to atomic, etc:
e <- tryCid(as.double(quote(foo(1))))
stopifnot(inherits(e, "error"), grepl("'language'", e$message, fixed=TRUE))
## had 'pairlist' in R <= 3.6.1
## print(ls.str(<environment with error object with "missing" in message text>))
msg <- "arguments in the signature are missing"
e1 <- new.env(hash=FALSE)
e1$Err <- structure(list(message = msg, call = quote(foo(bar))),
class = c("simpleError", "error", "condition"))
writeLines(prE <- capture.output(ls.str(e1)))
## was "Err: <missing>" in R <= 3.6.1
stopifnot(exprs = { length(prE) >= 3
grepl("List of 2", prE[[1]], fixed=TRUE)
grepl(msg, prE[[2]], fixed=TRUE)
grepl("call.* foo\\(bar\\)", prE[[3]])
})
.M <- .Machine
str(.M[grep("^sizeof", names(.M))]) ## also differentiate long-double..
b64 <- .M$sizeof.pointer == 8
arch <- Sys.info()[["machine"]]
onWindows <- .Platform$OS.type == "windows"
if(!(onWindows && arch == "x86")) {
## PR#17577 - dgamma(x, shape) for shape < 1 (=> +Inf at x=0) and very small x
stopifnot(exprs = {
all.equal(dgamma(2^-1027, shape = .99 , log=TRUE), 7.1127667376, tol=1e-10)
all.equal(dgamma(2^-1031, shape = 1e-2, log=TRUE), 702.8889158, tol=1e-10)
all.equal(dgamma(2^-1048, shape = 1e-7, log=TRUE), 710.30007699, tol=1e-10)
all.equal(dgamma(2^-1048, shape = 1e-7, scale = 1e-315, log=TRUE),
709.96858768, tol=1e-10)
})
## all gave Inf in R <= 3.6.1
} else cat("PR#17577 bug fix not checked, as it may not work on this platform\n")
## x %% +- Inf -- PR#17611 // also %/% for "large" args
for(x in list(0:3, c(0, 0.5+0:2))) {
xp <- x[x != 0] # x "positive"
for(L in c(2^(2:9), 1000^(1:7), Inf))
stopifnot(exprs = {
## ----------------- %% -------------
## same signs :
x %% L == x
(-x) %% -L == -x
## opposite signs, x > 0 :
(-xp) %% L == L-xp
xp %% -L == xp-L
## ----------------- %/% ------------
x %/% L == pmin(0, sign(x))
(-x) %/% -L == x %/% L
(-x) %/% L == pmin(0, sign(-x))
x %/% -L == (-x) %/% L
## L . x :
L %/% xp == (-L) %/% -xp
L %/% -xp == (-L) %/% xp
})
stopifnot(exprs = {
Inf %/% x == sign( x+(x==0))*Inf
Inf %/% -xp == -Inf
})
}
## these all returned NaN when L == Inf in R <= 3.6.1
##
## Further - very basics and some large (working "since ever"):
stopifnot(exprs = {
-6:17 %% 3L == 0:2
-5:15 %% -3L == -2:0
is.finite(x <- 2^(1:1022))
x %% (x.2 <- x/2) == 0
x %/% 2 == x.2
x[1:52] %% 3 == 2:1
-x[1:52] %% 3 == 1:2
}) # larger x suffer from cancellation (well, warning too early now):
tools::assertWarning(x[60:68] %% 3)
## grepl(<NA>, ...)
N <- grepl(NA_character_, "something")
stopifnot(is.na(N), is.logical(N))
## gave integer instead of logical in R <= 3.6.1
## options(warn=1e11) leading to infinite loop -> "C Stack ..." error
tools::assertError(options(warn = 1+.Machine$integer.max))
## "worked" and gave problems later in R <= 3.6.1
## PR#17628
df <- data.frame(x = 1, y = 2); class(df$y) <- "object_size"
df ## --> print.data.frame(*, digits=NULL)' -- error in R <= 3.6.1
format(object.size(pi), digits=NULL)
## error in R <= 3.6.1
## PR#15522
pos <- barplot(1:2, space=c(9, 1),
ylim=c(0, 21), xlim=c(0, 11), horiz=TRUE,
plot=FALSE)
stopifnot(all.equal(pos, cbind(c(9.5, 11.5))))
## bar spacing was wrong in R <= 3.6.1
## PR#13624 : get_all_vars(*, <matrix>):
ok_get_all_vars <- function(form,d) { ## get_all_vars() :<=> model_frame() apart from "terms"
mf <- if(missing(d)) model.frame(form) else model.frame(form,d)
attr(mf, "terms") <- NULL
identical(mf,
if(missing(d)) get_all_vars(form) else get_all_vars(form,d))
}
M <- matrix(1:15, 5,3)
n <- 26:30
T <- TRUE
m <- 2:7
stopifnot(exprs = {
ok_get_all_vars(~ M)
ok_get_all_vars(~M+n)
ok_get_all_vars(~ X , list(X= M))
ok_get_all_vars(~z+X, list(X= M, z=n))
ok_get_all_vars(~z+X, list(X=I(M), z=n))
ok_get_all_vars(~z+X, data.frame( X=I(M), z=n))
ok_get_all_vars(~z+X, data.frame(list(X=I(M), z=n)))
ok_get_all_vars(~z+X, as.data.frame(list(X=I(M), z=n)))
lengths(d <- get_all_vars(~ n + T, "2n" = 2*n)) == 5L
identical(d[,"T"], rep.int(TRUE, 5))
## recycling works when commensurate:
lengths(d6 <- get_all_vars(~ m + T, one=1, "2 s"=1:2, "3's"=3:1, `f 3` = gl(3,2))) == 6
identical(colnames(d6), c("m", "T", "one", "2 s", "3's", "f 3"))
})
## all but the first 4 cases worked already in R <= 3.6.1
## power.t.test() failure for very small (unreasonable) n; R-devel m.list Oct.4, 2019
(ptt0 <- power.t.test(delta=10, sd=1, power=0.9 , sig.level=0.05, tol = 1e-8))
(ptt1 <- power.t.test(delta=0.6, sd=0.00001, power=0.9 , sig.level=0.05))
(ptt2 <- power.t.test(delta=2, sd = 1e-8, power=0.99, sig.level=0.01))
stopifnot(exprs = {
all.equal(0.9, power.t.test(delta=10, sd=1, n = ptt0 $ n)$power)
all.equal(ptt1$n, 1.00428, tol = 1e-5)
all.equal(ptt2$n, 1.1215733, tol = 1e-5)
})
## when uniroot() was trying n < 1, the code failed previously (in 2nd and 3rd case)
## get_all_vars() when some variables are data frames - PR#14905
x <- (1:10)/10
Y <- data.frame(A = 2^x, B = pi*x)
gav <- get_all_vars(Y[,1] ~ x)
stopifnot(exprs = {
is.data.frame(gav)
ncol(gav) == 3
identical(gav, cbind(Y, x))
identical(get_all_vars(x ~ Y), cbind(x, Y))
})
## the last were wrong in R <= 3.6.1
## keep at end
rbind(last = proc.time() - .pt,
total = proc.time())