## Regression tests for R 3.4.0 to 4.2.x .pt <- proc.time() tryCid <- function(expr) tryCatch(expr, error = identity) tryCmsg<- function(expr) tryCatch(expr, error = conditionMessage) # typically == *$message identCO <- function(x,y, ...) identical(capture.output(x), capture.output(y), ...) assertErrV <- function(...) tools::assertError(..., verbose=TRUE) ##' get value of `expr` and keep warning as attribute (if there is one) getVaW <- function(expr) { W <- NULL withCallingHandlers(val <- expr, warning = function(w) { W <<- conditionMessage(w) invokeRestart("muffleWarning") }) structure(val, warning = W) } onWindows <- .Platform$OS.type == "windows" .M <- .Machine str(.M[grep("^sizeof", names(.M))]) ## also differentiate long-double.. b64 <- .M$sizeof.pointer == 8 options(nwarnings = 10000, # (rather than just 50) width = 99) # instead of 80 ## 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 { ## 2. Query the locale if(!onWindows) { ## sub() : lc.msgs <- sub("\\..*", "", print(Sys.getlocale("LC_MESSAGES"))) lc.msgs == "C" || substr(lc.msgs, 1,2) == "en" } else { ## Windows lc.type <- sub("\\..*", "", sub("_.*", "", print(Sys.getlocale("LC_CTYPE")))) lc.type == "English" || lc.type == "C" } } } cat(sprintf("English messages: %s\n", englishMsgs)) ## 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(, "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 <- tryCid(eval(parse(text=deparse(formals(fun))))) 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() 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(, *) should work as substr(, *) 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() 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)), levels = 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 tryCmsg(contour(matrix(rnorm(100), 10, 10), levels = 0, labels = numeric())) ## caused segfault in R 3.3.1 and earlier ## unique.warnings() needs better duplicated(): invisible(warnings()) .tmp <- lapply(list(0, 1, 0:1, 1:2, c(1,1), -1:1), function(x) wilcox.test(x)) if(!interactive()) 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() 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 stopifnot(exprs = { identical(levels(print(droplevels(dn))), c(L3, NA)) ## only XX must be dropped; R <= 3.3.1 also dropped identical(levels(droplevels(f)), L3) identical(levels(droplevels(d)), L3) # do *not* add 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 = 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( ~ )): 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(FALSE) { ## These become an error in 4.3.0. if(hasTZ <- nzchar(.TZ <- Sys.getenv("TZ"))) cat(sprintf("env.var. TZ='%s'\n",.TZ)) d <- as.POSIXlt("2016-12-06", tz = "Europe/Vienna") hasGMTOFF <- !is.null(d$gmtoff) op <- options(warn = 1)# ==> assert*() will match behavior if(is.null(d$zone)) cat("Skipping timezone-dependent POSIXlt formatting\n") else for(EX in expression({}, Sys.setenv(TZ = "UTC"), Sys.unsetenv("TZ"))) { cat(format(EX),":\n---------\n") eval(EX) dz <- d$zone d$zone <- 1 tools::assertError(format(d)) if (hasGMTOFF) { d$zone <- NULL # now has 'gmtoff' but no 'zone' --> warning: tools::assertWarning(stopifnot(identical(format(d),"2016-12-06"))) d$zone <- dz # = previous, but 'zone' now is last tools::assertError(format(d)) } else cat("Skipping timezone amd gmtoff dependent POSIXlt formatting\n") } if(hasTZ) Sys.setenv(TZ = .TZ); options(op)# revert } dlt <- structure( list(sec = 52, min = 59L, hour = 18L, mday = 6L, mon = 11L, year = 116L, wday = 2L, yday = 340L, isdst = 0L, zone = "CET", gmtoff = 3600L), class = c("POSIXlt", "POSIXt"), tzone = "CET") dlt$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)) asI <- as.integer # < shorter code set.seed(6); rof <- sample(of, 12, replace=TRUE) stopifnot(exprs = { identical(pmax(rof, of), ordered(pmax(asI(rof), asI(of)), labels=levels(rof)) -> pmar) identical(pmax(of, rof), pmar) identical(pmin(rof, of), ordered(pmin(asI(rof), asI(of)), labels=levels(rof)) -> pmir) identical(pmin(of, rof), pmir) identical(pmin(rof, 5), ordered(pmin(asI(rof), 2), levels=1:3, labels=levels(rof))) identical(pmax(rof, 6), ordered(pmax(asI(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(asI(of),2L,asI(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 assertErrV(seq(1,7, by = 1:2))# gave warnings in R < 3.4.0 ## seq() for / 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 = "days" now implicit default identical(seqD1, seq(D1, D2, by = "1 days")) ## These work "accidentally" via seq -> seq.default + "Date"-arithmetic (but *not* seq.Date): ## are equal, but 2nd is "double" seqD1 == seq(by = 1, from = D1, length.out = 7) seqD1 == seq(by = 1, to = D2, length.out = 7) seqD1 == seq(by = 1L, to = D2, length.out = 7) ## not (yet) identical(seqD1, seq(by = 1L, from = D1, 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 }) ## ## 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, 13, 10, 13, 4, 3, 0, 2, 4, 3, 1, 0, 1, 2, 1, 1, 0, 0, 7, 8, 2, 3, 0, 0, 2, 1, 2, 0, 0, 0, 2, 0, 0, 1, 0, 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, na.action = na.omit) xtp <- xtabs(Freq ~ Gender + Admit, DN, na.action = na.pass) xtN <- xtabs(Freq ~ Gender + Admit, DN, addNA = TRUE) res1 <- xt - xtp res1[is.na(res1)] <- NA ## xtabs (tapply/sum) may turn NAs into NaNs res2 <- -xtN + rbind(cbind(xt, 0), 0) res2[is.na(res2)] <- NA ## xtabs (tapply/sum) may turn NAs into NaNs stopifnot(exprs = { identical(asArr(xt - xt.), as_A(c(120,17, 207, 8 ), xt)) identical(asArr(res1), as_A(c(120,17, 207, NA), xt)) # not ok in R <= 3.3.2 identical(asArr(res2), 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, quietly = TRUE)) { 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, na.action = na.omit, 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(, 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 <- tryCmsg(stopifnot(all.equal(rep(list(pi),4), list(3.1, 3.14, 3.141, 3.1415)))) writeLines(msg) stopifnot(length(strsplit(msg,"\n")[[1]]) == 1+3+1) ## was wrong for months in R-devel only ## 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 <- tryCmsg(quantile(OL))) 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) if(!interactive()) 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", tail(o, 1))) 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() 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 <- tryCid(t1()) if(englishMsgs) stopifnot(identical("the ... list contains fewer than 1 element", conditionMessage(et1))) ## previously gave "'nthcdr' needs a list to CDR down" et0 <- tryCid(t0()) ; (mt0 <- conditionMessage(et0)) et2.0 <- tryCid(t2()) ; (mt2.0 <- conditionMessage(et2.0)) et2.1 <- tryCid(t2(1)); (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)) assertErrV(t0(1)) assertErrV(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 <- tryCid(stopifnot(0 < 1:10, is.numeric(..vaporware..), stop("FOO!")))) 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 .. and again in R > 3.6.x ## (don't afford tryCatch()ing everything) ## 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(onWindows) { 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), tolerance = 1e-14), # typically exact all.equal(cf2, matrix(c(1, -2), 49, 2, byrow=TRUE), tolerance = 1e-14)) ## had incorrect medians of the left/right third of the data (x_L, x_R), 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$Population), c(8802.8, 4208.12, 7233.83, 4582.57, 1360.5, 2372.17, 970.167), tolerance = 1e-6) }) ## in R <= 3.4.x, a2$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] my ", "Levels: my ")) identical(factor(ff), structure(c(NA, 1L, NA), levels = "my", class = "factor")) identical(factor(ff, exclude=NULL), structure(c(2L, 1L, 2L), levels = 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... cat("Using /dev/full checking write errors... ") # Large writes should fail mid-write tools::assertError(write.table(data.frame(x=1:1000000), file = "/dev/full")) # Small writes should fail on closing tools::assertWarning(write.table(data.frame(x=1), file = "/dev/full")) cat("[Ok]\n") } ## 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() <- 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( ), 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$sigma, tol = 1e-14)) ## was too large because of wrong denom. d.f. in R <= 3.4.1 ## nclass.FD() and nclass.scott() for "extreme" data, PR#17274 NC <- function(x) c(Sturges = nclass.Sturges(x), Scott = nclass.scott(x), FD = nclass.FD(x)) xE <- function(eps, n = 5) { stopifnot(n >= 2, is.numeric(eps), eps >= 0) c(rep.int(1, n-2), 1+eps, 2) } ncE <- c(Sturges = 4, Scott = 2, FD = 3) stopifnot(exprs = { sapply(-5:-16, function(E) identical(NC(xE(10^E)), ncE)) identical(NC(xE(1e-4)), c(Sturges = 4, Scott = 2, FD = 8550)) identical(NC(xE(1e-3)), c(Sturges = 4, Scott = 2, FD = 855)) }) ## for these, nclass.FD() had "exploded" in R <= 3.4.1 ## Extremely large diff(range(.)) : NB: this gives a UBSAN warning XXL <- c(1:9, c(-1,1)*1e300) stopifnot(nclass.scott(XXL) == 1) ## gave 0 in R <= 3.4.1 tools::assertWarning(hh <- hist(XXL, "FD", plot=FALSE)) stopifnot(sum(hh$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 <- tryCid(qr.coef(q.Li, y[-4])); e1 e2 <- tryCid(qr.coef(q.LA, y[-4])) 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(...){}, warn = 1) # non-sense device assertErrV(plot.new()) if(no.grid <- !("grid" %in% loadedNamespaces())) requireNamespace("grid") assertErrV(grid::grid.newpage()) if(no.grid) unloadNamespace("grid") # Warning: shutting down all devices ... options(op) if(!dev.interactive(orNone = TRUE)) pdf("reg-tests-1d.pdf", encoding = "ISOLatin1.enc")# revert to reasonable device ## 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 = 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(, *) 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 = ): 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)) assertErrV(splines::splineDesign(aKnots, x, derivs = 4)) ## 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() ##_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")) ## 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 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(, 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() 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( ) -- 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) identCO (dd, 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$x.mean, tol = 0.01) # seen 0.0023 all.equal(estd[c(1:3,5:6)], es.d[c(1:3,5:6)], tol = 1e-3)## seen {1,3,8}e-4 all.equal(lapply(estd[1:6],unname), lapply(est [1:6],unname), tol = 2e-12)# almost identical all.equal(lapply(es.d[1:6],unname), lapply(es. [1:6],unname), tol = 1e-11) }) ## NA's in x gave an error, in R versions <= 3.4.3 ## as.list() method: toD <- Sys.Date(); stopifnot(identical(as.list(toD)[[1]], toD)) ## was wrong for 20 hours options(warn = 2)# no warnings allowed ## PR#17372: sum(, ) iL <- rep(1073741824L, 2) # 2^30 + 2^30 = 2^31 integer overflows to NA r1 <- tryCmsg(sum("foo", iL)) r2 <- tryCmsg(sum(iL, "foo")) stopifnot(exprs = { identical(r1, r2) grepl("invalid 'type' (character) ", r1, fixed=TRUE) ## each _gave_ an overflow warning + NA identical(sum(3.14, iL), sum(iL, 3.14)) identical(sum(1+2i, iL), sum(iL, 1+2i)) if(identical(.Machine$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 ; 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., [[ 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(*, ) if(requireNamespace('Matrix', lib.loc=.Library, quietly = TRUE)) { de <- data.frame(Type = structure(c(1L, 1L, 4L, 1L, 4L, 2L, 2L, 2L, 4L, 1L), levels = paste0("T", 1:4), class = "factor"), Subj = structure(c(9L, 5L, 8L, 3L, 3L, 4L, 3L, 6L, 6L, 1L), levels = 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, sparseResult=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(), 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()) 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() 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() 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 '\002"' ## multivariate 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() 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() 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.(), rstandard() : 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(), PR#16719 data(mtcars) mtcars$type <- rep(letters[1:2], c(16, 16)) kruskal.test(mpg ~ type, mtcars) ## gave 'Error: all group levels must be finite' ## Multivariate lm() with matrix offset, PR#17407 ss <- list(s1 = summary(fm1 <- lm(cbind(mpg,qsec) ~ 1, data=mtcars, offset=cbind(wt,wt*2))), s2 = summary(fm2 <- lm(cbind(mpg,qsec) ~ offset(cbind(wt,wt*2)), data=mtcars))) ## drop "call" and "terms" parts which differ; rest must match: ss[] <- lapply(ss, function(s) lapply(s, function(R) R[setdiff(names(R), c("call","terms"))])) stopifnot(all.equal(ss[["s1"]], ss[["s2"]], tolerance = 1e-15)) ## lm() calls gave error 'number of offsets is 64, should equal 32 ...' in R <= 3.5.1 ## print.data.frame() USJ <- USJudgeRatings USJe6 <- USJudgeRatings[rep_len(seq_len(nrow(USJ)), 1e6),] op <- options(max.print=500) system.time(r1 <- print(USJ)) system.time(r2 <- print(USJe6))# was > 12 sec in R <= 3.5.1, now typically 0.01 # because the whole data frame was formatted. ## Now the timing ratio between r1 & r2 print()ing is typically in [1,2] system.time(r3 <- print(USJe6, row.names=FALSE)) out <- capture.output(print(USJe6, max = 600)) # max > getOption("max.print") stopifnot(exprs = { identical(r1, USJ )# print() must return its arg identical(r2, USJe6) identical(r3, USJe6) length(out) == 52 grepl("CALLAHAN", out[51], fixed=TRUE) identical(2L, grep("omitted", out[51:52], fixed=TRUE)) }) options(op); rm(USJe6)# reset ## hist.default() in rare cases hh <- hist(seq(1e6, 2e6, by=20), plot=FALSE) hd <- hh$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)))) ## is.unsorted fastpass incorrectly returned TRUE when constant-valued x was sorted descending x <- c(1, 1, 1) xs <- sort(x, decreasing = TRUE) stopifnot(!is.unsorted(xs, strictly = FALSE)) ## is.unsorted should be FALSE y <- as.integer(x) ys <- sort(x, decreasing = TRUE) stopifnot(!is.unsorted(ys, strictly = FALSE)) ## 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() gave NA in R <= 3.5.1 ## 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(, 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$coefficients), c(7L, 1L)), all.equal(range(cf), c(-0.0042857143, 0.0072527473))) ## gave an error for a few days in R-devel ## cut(), PR#16802 c0 <- cut(rep(0L, 7), breaks = 3) stopifnot(is.factor(c0), length(c0) == 7, length(unique(c0)) == 1) ## cut() gave error _'breaks' are not unique_ in R <= 3.5.1 ## need to record OutDec in deferred string conversions (reported by ## Michael Sannella). op <- options(scipen=-5, OutDec=",") xx <- as.character(123.456) options(op) stopifnot(identical(xx, "1,23456e+02")) ## parseRd() and Rd2HTML() with some \Sexpr{} in *.Rd: x <- tools::Rd_db("base") ## Now check that \Sexpr{} "installed" correctly: of <- textConnection("DThtml", "w") tools::Rd2HTML(x$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() -- 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' ## [ , ] <- v should be a no-op and ## [ , ] <- 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 ; 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 = function(e) NULL) 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, quietly = TRUE)) { 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=, 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 <- tryCid(format(.Internal(bodyCode(ls)))) 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() 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"), verbose=TRUE) 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]` ~ . f1 <- function(p) reformulate(".", notC) f2 <- function(e) f1(e) 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) inherits(t1 <- tryCatch(f1(pi), warning=identity), "deprecatedWarning") inherits(t2 <- tryCatch(f2(27), warning=identity), "deprecatedWarning") all.equal(t1, tt) # including call 'reformulate(..)' all.equal(t2, tt) }) writeLines(conditionMessage(tt)) ## stopifnot() now works *nicely* with expression object (with 'exprs' name): ee <- expression(xpr=all.equal(pi, 3.1415927), 2 < 2, stop("foo!")) te <- tryCid(stopifnot(exprObject = ee)) stopifnot(conditionMessage(te) == "2 < 2 is not TRUE") ## conditionMessage(te) was "ee are not all TRUE" in R 3.5.x t2 <- tryCid(stopifnot(exprs = { T }, exprObject = ee)) t3 <- tryCid(stopifnot(TRUE, 2 < 3, exprObject = ee)) f <- function(ex) stopifnot(exprObject = ex) t4 <- tryCid(f(ee)) stopifnot(grepl("one of 'exprs', 'exprObject' ", conditionMessage(t2)), conditionMessage(t2) == conditionMessage(t3), conditionMessage(t4) == conditionMessage(te) ) (function(e) stopifnot(exprObject = e))(expression(1 < 2, 2 <= 2:4)) ## the latter (with 'exprs = e') gave Error in eval(exprs) : object 'e' not found ## ## Empty 'exprs' should work in almost all cases: stopifnot() stopifnot(exprs = {}) e0 <- expression() stopifnot(exprObject = e0) do.call(stopifnot, list(exprObject = expression())) do.call(stopifnot, list(exprObject = e0)) ## the last three (w 'exprs = ') 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)) }) ## Failed to work after r76382--8: assertErrV(formula("3")) stopifnot(exprs = { ## New formula() specs: ## These give deprecation warnings: is.list(op <- options(warn = 1)) identical(formula("ran = ~ 1|G"), ~ 1 | G) identical(formula(c("~", "foo")), ~ foo ) identical(formula("({y ~ x})"), y ~ x) identical(formula("{ ~ x }"), ~ x) TRUE || { ## all these "bugs" not yet in R <= 3.6.0 identical(formula(c("y", "~", "x + (1 | G)")), y ~ x + (1 | G)) identical(formula(c("y", "~", "x +", "(1 | G)")), y ~ x + (1 | G)) }## not yet identical(formula(c("~", "x","+ (1 | G)")), ~x) ## NOT YET: ~ x + (1 | G)) is.list(options(op)) }) tools::assertWarning(formula("ran= ~ 1|G"),"deprecatedWarning", verbose=TRUE) tools::assertWarning(formula(c("~", "x")), "deprecatedWarning", verbose=TRUE) tools::assertWarning(formula("({y ~ x})"), "deprecatedWarning", verbose=TRUE) tools::assertWarning(formula("{ ~ x }"), "deprecatedWarning", verbose=TRUE) ## str2expression() : 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 <- tryCmsg(quasi(variance = "log(mu)"))) && 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, stringsAsFactors = TRUE)) dfcy <- dfa; dfcy$y <- yN # y: a column ## dNay := drop unused levels from dfay incl NA dNay <- dfay; dNay[] <- lapply(dfay, factor) str(dfay) # both (x, y) have NA level str(dfby) # (x: yes / y: no) NA level str(dNay) # both: no NA level stopifnot(exprs = { ## "trivial" (non rbind-related) assertions : identical(levels(dfa$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$y), as.character((1:8)[-4]) -> levN) # no NA levels identical(lapply(dNay, levels), list(x = c("2","3"), y = levN[1:3])) # no NA levels }) dfaby <- rbind(dfay, dfby) dNaby <- rbind(dNay, dfby) dfacy <- rbind(dfay, dfcy) dfcay <- rbind(dfcy, dfay) # 1st arg col. is char => rbind() keeps char stopifnot(exprs = { identical(levels(rbind(dfa, dfb)$x), full_lev) # <== not in R <= 3.6.0 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$x) identical(lapply(rbind(dfby, dfay), levels), list(x = full_lev, y = c(levN, NA))) identical(lapply(rbind(dfay, dfby, factor.exclude = NA), levels), list(x = as.character(1:3), y = levN)) identical(lapply(rbind(dfay, dfby, factor.exclude=NULL), levels), list(x = full_lev, y = yN)) }) ## rbind.data.frame() should work in all cases with "matrix-columns": m <- matrix(1:12, 3) ## m.N := [m]atrix with (row)[N]ames : m.N <- m ; rownames(m.N) <- letters [1:3] ## data frames with these matrices as *column*s: dfm <- data.frame(c = 1:3, m = I(m)) dfm.N <- data.frame(c = 1:3, m = I(m.N)) (mNm <- rbind(m.N, m)) dfmmN <- rbind(dfm, dfm.N) dfmNm <- rbind(dfm.N, dfm) stopifnot(exprs = { identical( dim(dfmNm), c(6L, 2L)) identical(dimnames(dfmNm), list(c(letters[1:3],1:3), c("c","m"))) is.matrix(m. <- dfmNm[,"m"]) identical(dim(m.), c(6L, 4L)) identical(dfmNm, dfmmN[c(4:6, 1:3), ]) identical(unname(mNm), unname(m.)) }) ## The last rbind() had failed since at least R 2.0.0 ## as.data.frame.array(<1D array>) -- PR#17570 str(x2 <- as.data.frame(array(1:2))) stopifnot(identical(x2[[1]], 1:2)) ## still was "array" in R <= 3.6.0 ## vcov(, dispersion = *) -- PR#17571 counts <- c(18,17,15,20,10,20,25,13,12) treatment <- gl(3,3) outcome <- gl(3,1,9) ## Poisson and Quasipoisson poisfit <- glm(counts ~ outcome + treatment, family = poisson()) qpoisfit <- glm(counts ~ outcome + treatment, family = quasipoisson()) spois <- summary( poisfit) sqpois <- summary(qpoisfit) sqpois.d1 <- summary(qpoisfit, dispersion=1) SE1 <- sqrt(diag(V <- vcov(poisfit))) (noLdbl <- (.Machine$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 proc.time() - .pt; .pt <- proc.time() ## runmed(, "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$fail, "error") !englishMsgs || grepl("^runmed\\(.*: .*NA.*x\\[1\\]", Tfail$message) }) ## conformMethod() "&& logic" bug, by Henrik Bengtsson on R-devel list, 2019-06-22 setClass("tilingFSet", slots = c(x = "numeric")) if(!is.null(getGeneric("oligoFn"))) removeGeneric("oligoFn") setGeneric("oligoFn", function(object, subset, target, value) { standardGeneric("oligoFn") }) Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_" = "true") if(getRversion() <= "3.6")## to run this with R 3.6.0, 3.5.3, .. Sys.unsetenv("_R_CHECK_LENGTH_1_LOGIC2_") setMethod("oligoFn", signature(object = "tilingFSet", value="array"), ## Method _1_ function(object, value) { list(object=object, value=value) }) setMethod("oligoFn", signature(object = "matrix", target="array"), ## Method _2_ function(object, target) list(object=object, target=target)) setMethod("oligoFn", signature(object = "matrix", subset="integer"), ## Method _3_ function(object, subset) list(object=object, subset=subset)) # *no* Note setMethod("oligoFn", signature(object = "matrix"), ## Method _4_ function(object) list(object=object)) # *no* Note setMethod("oligoFn", signature(subset = "integer"), ## Method _5_ function(subset) list(subset=subset)) setMethod("oligoFn", signature(target = "matrix"), ## Method _6_ function(target) list(target=target)) setMethod("oligoFn", signature(value = "array"), ## Method _7_ function(value) list(value=value)) setMethod("oligoFn", signature(subset = "integer", target = "matrix"), ## Method _8_ function(subset, target) list(subset=subset, target=target)) setMethod("oligoFn", signature(subset = "integer", value = "array"), ## Method _9_ function(subset, value) list(subset=subset, value=value)) setMethod("oligoFn", signature(target = "matrix", value = "array"), ## Method _10_ function(target, value) list(target=target, value=value)) ## showMethods("oligoFn", include=TRUE) # F.Y.I.: in R 3.6.0 and earlier: contains "ANY" everywhere ##========= ------------ stopifnot(exprs = { is.function(mm <- getMethod("oligoFn", signature(object="tilingFSet", subset="missing", target="missing", value="array"))) inherits(mm, "MethodDefinition") identical( sort(names(getMethodsForDispatch(oligoFn))) # sort(.) the same for "all" locales ## Now, "ANY" only appear "at the end" .. otherwise have "missing" , c("matrix#ANY#ANY#ANY", "matrix#integer#ANY#ANY", "matrix#missing#array#ANY", "missing#integer#ANY#ANY", "missing#integer#matrix#ANY", "missing#integer#missing#array", "missing#missing#matrix#ANY", "missing#missing#matrix#array", "missing#missing#missing#array", "tilingFSet#missing#missing#array")) }) ## Testing all 10 methods: r1 <- oligoFn(object=new("tilingFSet"), value=array(2)) r2 <- oligoFn(object=diag(2), target=array(42)) ## These 2 work fine in all versions of R: Here the "ANY" remain at the end: r3 <- oligoFn(object=diag(2), subset=1:3) r4 <- oligoFn(object=diag(2)) ## All these do *not* specify 'object' --> Error in R <= 3.6.x {argument ... is missing} r5 <- oligoFn(subset = 1:5) r6 <- oligoFn(target = cbind(7)) r7 <- oligoFn(value = array(47)) r8 <- oligoFn(subset = -1:1, target = diag(3)) r9 <- oligoFn(subset = 2:6, value = array(7)) r10<- oligoFn(target = cbind(1,2), value = array(1,1:3)) ## in R <= 3.6.0, e.g., the first setMethod(..) gave ## Error in omittedSig && (signature[omittedSig] != "missing") : ## 'length(x) = 4 > 1' in coercion to 'logical(1)' ## apply(., MARGIN) when MARGIN is outside length(dim(.)): a <- tryCid(apply(diag(3), 2:3, mean)) stopifnot(exprs = { inherits(a, "error") conditionCall(a)[[1]] == quote(`apply`) !englishMsgs || !grepl("missing", (Msg <- conditionMessage(a)), fixed=TRUE) !englishMsgs || grepl("MARGIN", Msg, fixed=TRUE) }) ## cbind() of data frames with no columns lost names -- PR#17584 stopifnot(identical(names(cbind(data.frame())), character())) stopifnot(identical(names(cbind(data.frame(), data.frame())), character())) ## names() came out as NULL instead of character(). ## NUL inserted incorrectly in adist trafos attribute -- PR#17579 s <- c("kitten", "sitting", "hi") ad <- adist(s, counts = TRUE) adc <- attr(ad, "counts") adt <- attr(ad, "trafos") ## Follow analysis in the bug report: in the diagonal, we should have ## only matches for each character in the given string. stopifnot(exprs = { nchar(diag(adt)) == nchar(s) ## The del/ins/sub counts should agree with the numbers of D/I/S ## occurrences in the trafos. nchar(gsub("[^D]", "", adt)) == adc[, , "del"] nchar(gsub("[^I]", "", adt)) == adc[, , "ins"] nchar(gsub("[^S]", "", adt)) == adc[, , "sub"] }) ## list2env preserves values semantics v <- list(x=c(1)) # << subtlety! e <- list2env(v) with(e, x[[1]] <- 42) v stopifnot(identical(v$x,1)) ## misleading error message when coercing language object to atomic, etc: e <- tryCid(as.double(quote(foo(1)))) stopifnot(inherits(e, "error"), grepl("'language'", e$message, fixed=TRUE)) ## had 'pairlist' in R <= 3.6.1 ## print(ls.str()) msg <- "arguments in the signature are missing" e1 <- new.env(hash=FALSE) e1$Err <- structure(list(message = msg, call = quote(foo(bar))), class = c("simpleError", "error", "condition")) writeLines(prE <- capture.output(ls.str(e1))) ## was "Err: " in R <= 3.6.1 stopifnot(exprs = { length(prE) >= 3 grepl("List of 2", prE[[1]], fixed=TRUE) grepl(msg, prE[[2]], fixed=TRUE) grepl("call.* foo\\(bar\\)", prE[[3]]) }) ## format(x, scientific = FALSE) for large x xMAX <- .Machine$double.xmax ch <- format(xMAX, scientific = 400) # << scientific as 'scipen' op <- options(digits=1, scipen = 303) co <- capture.output(cat(xMAX)) options(op)# back to normal stopifnot(exprs = { nchar(ch) == 309 identical(ch, co) ch == format(xMAX, scientific=FALSE) })## format(*, scientific=FALSE) was "not obeyed" in R < 4.0.0 ## format() aka format() : for(ch in c("foo", "bar", "1", "a:b", "B space A", "`ABC", "'CBA")) stopifnot(identical(ch, format(as.symbol(ch)))) ## gave 'Found no format() method for class "name"' in R <= 3.6.x ## 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"): L <- 1e111 * c(-1,1) stopifnot(exprs = { L %% L == 0 # failed for a few days in R-devel L %% -L == 0 -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): (iCrit <- ## depends on the presence and version of "long double": if(noLdbl) 50:55 else if(is.integer(digLd <- .Machine$longdouble.digits) && digLd == 64) 60:68 else if(is.integer(digLd) && digLd == 113) ## aarch64 {PR#17718} 110:118 else 250:258 # "wild guess" should always work ) tools::assertWarning(x[iCrit] %% 3, verbose=TRUE) ## Hilmar Berger's on R-devel list: 'data.frame() == NULL' etc d0. <- data.frame(a = numeric(0)) # zero length data.frame [ 0 x 1 ] d0 <- unname(d0.) # zero length data.frame __without names__ d3 <- data.frame(a=1:3) # non-empty data.frame d30. <- d3[,FALSE] # <3 x 0> d30 <- unname(d30.) for(DF in list(d0., d0, d30., d30)) for(R in list(1, NULL, logical(0))) stopifnot(exprs = { is.logical(r <- DF == R) is.matrix(r) ## ~~~~~~~ length(r) == 0 dim(r) <= dim(DF) # sometimes r is <0 x 0> when DF is not }) ## many of these '==' calls failed in R <= 3.6.x ## Can selectively suppress warnings w <- function(class) { w <- simpleWarning("warned") w <- structure(w, class = c(class, class(w))) warning(w) } catch <- function(expr) tryCatch({ expr; FALSE }, warning = function(...) TRUE) stopifnot(! catch(suppressWarnings(w("foo")))) stopifnot(! catch(suppressWarnings(w("foo"), classes = c("bar", "foo")))) stopifnot( catch(suppressWarnings(w("foo"), classes = c("bar", "baz")))) rm(w, catch) ## Can selectively suppress messages m <- function(class) { m <- simpleMessage("notified") m <- structure(m, class = c(class, class(m))) message(m) } catch <- function(expr) tryCatch({ expr; FALSE }, message = function(...) TRUE) stopifnot(! catch(suppressMessages(m("foo")))) stopifnot(! catch(suppressMessages(m("foo"), classes = c("bar", "foo")))) stopifnot( catch(suppressMessages(m("foo"), classes = c("bar", "baz")))) rm(m, catch) ## grepl(, ...) N <- grepl(NA_character_, "something") stopifnot(is.na(N), is.logical(N)) ## gave integer instead of logical in R <= 3.6.1 ## options(warn=1e11) leading to infinite loop -> "C Stack ..." error tools::assertError(options(warn = 1+.Machine$integer.max)) ## "worked" and gave problems later in R <= 3.6.1 ## PR#17628 df <- data.frame(x = 1, y = 2); class(df$y) <- "object_size" df ## --> print.data.frame(*, digits=NULL)' -- error in R <= 3.6.1 format(object.size(pi), digits=NULL) ## error in R <= 3.6.1 ## PR#15522 pos <- barplot(1:2, space=c(9, 1), ylim=c(0, 21), xlim=c(0, 11), horiz=TRUE, plot=FALSE) stopifnot(all.equal(pos, cbind(c(9.5, 11.5)))) ## bar spacing was wrong in R <= 3.6.1 ## methods(class = <{length > 1}>) giving many non-helpful warnings tools::assertWarning(mc <- methods(class = class(ordered(4:1))), verbose=TRUE) # class = ".S3methods", stopifnot(is.character(mc), inherits(mc, "MethodsFunction"), is.data.frame(attr(mc,"info"))) ## warns once only, in R >= 3.6.2 ## PR#17580 -- using max.lines, "truncated" op <- options(catch.script.errors = TRUE) # {careful! : errors do *NOT* stop} is.t.back <- function(x) is.pairlist(x) && all(vapply(x, is.character, NA)) f <- function(...) stop(deparse(substitute(...))) g <- function(...) f(...) do.call(g, mtcars) tb. <- .traceback() traceback(tb1 <- .traceback(max.lines=1))# prints with '...' as it's truncated stopifnot(exprs = { is.t.back(tb.) is.t.back(tb1) length(tb.) == length(tb1) vapply(tb1, length, 0L) == 1 length(tb.[[3]]) > 20 }) f <- function() options(warn = 1+.Machine$integer.max) do.call(g, mtcars) tb0 <- .traceback() traceback(tb3 <- .traceback(max.lines = 3)) traceback(tb00 <- .traceback(max.lines = 0)) options(op)# revert to normal stopifnot(exprs = { is.t.back(tb0) is.t.back(tb3) is.t.back(tb00) vapply(tb0, function(.) is.null(attributes(.)), NA) length(tb0) == length(tb3) vapply(tb3 , length, 0L) <= 3 vapply(tb00, length, 0L) == 0L identical(lapply(tb3, attributes), list(list(truncated = TRUE), NULL)) identical(lapply(tb00, attributes), rep(list(list(truncated = TRUE)), 2)) }) f <- function(...) .traceback(2, max.lines=1) g( 'hello hello hello hello hello hello hello hello hello hello hello', 'world world world world world world world world world world world' ) -> tb2n1 stopifnot(is.character(t1 <- tb2n1[[1]]), length(t1) == 1L, attr(t1, "truncated")) ## partly not possible in R < 4.0.0; always deparsed in full ## PR#13624 : get_all_vars(*, ): 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 <- .Date(matrix(1:15, 5,3)) # has class to be kept n <- 26:30 T <- TRUE m <- 2:7 stopifnot(exprs = { is.matrix(M) ; dim(M) == c(5,3) 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 ## multi-arg Rd macros (PR#17627 and PR#18324#c4) parse_Rd_txt <- function(ch) tools::parse_Rd(textConnection(ch), fragment = TRUE) rd1 <- parse_Rd_txt(t1 <- "\\if{html}{\\out{
}}") rd2 <- parse_Rd_txt(t2 <- "\\href{https://www.r-project.org}{some text}") rd3 <- parse_Rd_txt(t3 <- "\\ifelse{a}{b}{c}") (tx1 <- paste(as.character(rd1), collapse = "")) (tx2 <- paste(as.character(rd2), collapse = "")) (tx3 <- paste(as.character(rd3), collapse = "")) stopifnot(exprs = { identical(paste0(t1,"\n"), tx1) identical(paste0(t2,"\n"), tx2) identical(paste0(t3,"\n"), tx3) }) ## had duplicated braces in R < 4.0.0 (if, href) / R < 4.3.0 (ifelse) ## 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$n, 1.1215733, tol = 1e-5) }) ## when uniroot() was trying n < 1, the code failed previously (in 2nd and 3rd case) ## improved error message from contour(): tt <- tryCid(contour(volcano, levels = c(20*c(4:6, -Inf, 8:10)))) print(tt) ## The rest of this message is OS-dependent: gcc 5.x on Solaris has '= -Inf' ## others have " = -inf" stopifnot(inherits(tt, "error"), grepl("non-finite level.*\\[4\\]", tt$message)) ## had "invalid NA contour values" ## 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 ## get all arguments from matched argument list; failed in R <= 4.0.0 y <- list() stopifnot(identical(attr(`attr<-`(y, value = 1, "A"), "A"), 1)) y <- structure(list(), AA = 1) stopifnot(is.null(attr(y, exact = TRUE, "A"))) ## 1) A matrix is an array, too: stopifnot( vapply(1:9, function(N) inherits(array(pi, dim = 1:N), "array"), NA) ) ## was false for N=2 in R < 4.0.0 ## ## 2) Matrix must dispatch for array methods, too : foo <- function(x) UseMethod("foo") foo.array <- function(x) "made in foo.array()" stopifnot( vapply(1:9, function(N) foo(array(pi, dim = 1:N)), "chr") == foo.array()) ## foo(array(*)) gave error for N=2 in R < 4.0.0 ## PR#17659: Some *.colors() producers have appended (alpha=1) info even by default fnms <- c(apropos("[.]colors$"), "rainbow") # 8 x ".colors" + rainbow for(fn in fnms) { Fn <- get(fn, mode="function") cat(sprintf("%14s(n), n = 1,2,3 : ", fn)) for(n in 1:3) stopifnot(length(cc <- Fn(n)) == n, nchar(cc) == 1L+6L, # just RGB, no alpha identical(cc, Fn(n, alpha=NULL))) cat("[Ok]\n") } ## in R <= 3.6.x, four of these functions gave extra alpha=1 info (appended "FF") ## Generalized head(x, n) and tail() methods - for length(n) > 1 and arbitrary array x ## PR#17652 ## -------- pkg glmmTMB uses head(.) on calls quite a bit cForm <- quote(some ~ really + quite + longish + but:still:not:very:long * (formula | reality / extreme:cases:you:never:think:of)) fL <- eval(cForm) length(fRHS <- fL[[3]]) cLong <- quote(fun_with_many_args(1,2,3, 4,5,6, 7,8,9)) a1 <- structure(array(1:7, 7 ), class = "foo") a3 <- structure(array(1:24, 2:4), class = "foo") stopifnot(exprs = { ## these all work as previously head(cForm,1) == quote(`~`()) head(cForm,2) == quote(~some) head(cForm) == cForm is.call(cl <- quote((Days|Subject))) is.call(fL) inherits(fL, "formula") head(fL) == fL ## == tail === identical(tail(cForm,1), cForm[3]) tail(cForm,2) == cForm[2:3] tail(cForm) == cForm tail(fL) == fL ## ## -------------failed from here ----------------------- identical(head(cl), cl) ## for a few days, gave Error in do.call(..): object 'Days' not found identical( head(fRHS), fRHS) identical(head(cLong), cLong[1:6]) identical(head(cLong, 2), cLong[1:2]) identical(head(cLong, 1), quote(fun_with_many_args())) ## == tail === identical(tail(cl), cl) ## for a few days, gave Error ...: object 'Days' not found identical( tail(fRHS), fRHS) identical(tail(cLong), cLong[tail(seq_along(cLong))]) identical(tail(cLong, 2), cLong[9:10]) identical(tail(cLong, 1), cLong[10]) ## funny arrays identical(head(a1,1), a1[1, drop=FALSE]) identical(head(a3,1), a3[1, ,, drop=FALSE]) identical(tail(a3,1), a3[2, ,, drop=FALSE]) }) ## ## Ensure that the code does not access dimensions it does not need (pkg TraMineR): `[.noCol` <- function(x, i, j, drop = FALSE) { if(!missing(j)) stop(" [!] Column subscripts not allowed", call. = FALSE) NextMethod("[") } noC <- structure(datasets::trees, class = c("noCol", "data.frame")) assertErrV( noC[1,2]) # fails indeed stopifnot(exprs = { identical(head(noC), noC[1:6,]) identical(head(noC, 1), noC[1, ]) identical(tail(noC, 1), noC[31,]) }) ## ## For all arrays 'a', head(a, 1) should correspond to a[1, {,}* , drop = FALSE] ## length(n) > length(dim(x)) (or 1L if dim(x) is NULL) is an error str(Alis <- lapply(1:4, function(n) {d <- 1+(1:n); array(seq_len(prod(d)), d) })) h2 <- lapply(Alis, head, 2) t2 <- lapply(Alis, head, 2) assertErrV( head(Alis[[1]], c(1, NA))) assertErrV( tail(1:5, c(1, NA))) h1 <- lapply(Alis, head, 1) t1 <- lapply(Alis, tail, 1) dh1 <- lapply(h1, dim) ## n =1L and n=c(1, NA) equivalent (only ones with 2+ dimensions) Alis2p <- Alis[-1] h1N <- lapply(Alis2p, head, c(1, NA)) t1N <- lapply(Alis2p, tail, c(1, NA)) Foolis <- lapply(Alis, `class<-`, "foo") assertErrV( head(Foolis[[1]], c(1, NA))) h1F <- lapply(Foolis, head, 1) h2F <- lapply(Foolis, head, 2) t1F <- lapply(Foolis, tail, 1) t2F <- lapply(Foolis, tail, 2) Foolis2p <- Foolis[-1] h1FN <- lapply(Foolis2p, head, c(1, NA)) t1FN <- lapply(Foolis2p, tail, c(1, NA)) stopifnot(exprs = { identical(h2, Alis) identical(t2, Alis) vapply(h1, is.array, NA) vapply(t1, is.array, NA) identical(dh1, lapply(1:4, function(n) seq_len(n+1L)[-2L])) identical(dh1, lapply(t1, dim)) identical(h1, c(list(Alis [[1]][1, drop=FALSE]), h1N)) identical(t1, c(list(Alis [[1]][2, drop=FALSE]), t1N)) identical(h1F, c(list(Foolis[[1]][1, drop=FALSE]), h1FN)) identical(t1F, c(list(Foolis[[1]][2, drop=FALSE]), t1FN)) }) ## This was *not the case for 1d arrays in R <= 3.6.x ## tools::assertWarning(t3 <- tail(iris3[,1,], addrownums = FALSE), verbose=TRUE) stopifnot( identical(t3, tail(iris3[,1,], keepnums = FALSE)) ) ## ## 4-dim array ## 4th dimension failed transiently when I using switch() in keepnums logic adims <- c(11, 12, 4, 3) arr <- array(seq_len(prod(adims)), adims) headI4 <- function(M, n) { d <- dim(M) M[head(seq_len(d[1]), n[1]), head(seq_len(d[2]), n[2]), head(seq_len(d[3]), n[3]), head(seq_len(d[4]), n[4]), drop = FALSE] } tailI4 <- function(M, n) { d <- dim(M) M[tail(seq_len(d[1]), n[1]), tail(seq_len(d[2]), n[2]), tail(seq_len(d[3]), n[3]), tail(seq_len(d[4]), n[4]), drop = FALSE] } n.set2 <- lapply(-2:2, rep, times = 4) stopifnot( vapply(n.set2, function(n) identCO (head(arr, n), headI4(arr, n)), NA), vapply(n.set2, function(n) identCO (tail (arr, n, keepnums=FALSE), tailI4(arr, n)), NA), vapply(n.set2, function(n) all.equal(tail(arr, n), tailI4(arr, n), check.attributes=FALSE), NA)) ## full output aco <- capture.output(arr) ## extract all dimnames from full output ## assumes no spaces in names ## assumes NO WRAPPING when printing rows! getnames <- function(txt, ndim = 4) { el <- which(!nzchar(txt)) ## first handled elsewhere, last is just trailing line el <- el[-c(1L, length(el))] hdln <- c(1L, el[seq(2, length(el), by = 2)] - 1L) hdraw <- lapply(txt[hdln], function(tx) strsplit(tx, ", ")[[1L]]) ## line 1 is higher indices, 2 is blank, 3 is columns cnms <- strsplit(trimws(txt[3], which = "left"), split = "[[:space:]]+")[[1]] cnms <- cnms[nzchar(cnms)] matln <- 4:(el[1] - 1L) rnms <- gsub("^([[:space:]]*[^[:space:]]+)[[:space:]].*", "\\1", txt[matln]) hdnms <- lapply(3:ndim, ## blank ones are left in so this is ok function(i) unique(sapply(hdraw, `[`, i ))) c(list(rnms, cnms), hdnms) } fpnms <- getnames(aco, length(adims)) ## ensure all dimnames correct for keepnums = TRUE stopifnot( vapply(n.set2, function(n) identical(dimnames(tail(arr, n)), mapply(function(x, ni) if(ni != 0) tail(x, ni), x = fpnms, ni = n, SIMPLIFY = FALSE)), NA) ) ## mix named and non-named dimensions to catch bug in initial keepnums patch arr2 <- arr adnms <- lapply(seq_along(adims), function(i) paste0("dim_", i, "_", seq(1L, adims[i]))) adnms[3L] <- list(NULL) dimnames(arr2) <- adnms ii <- seq_along(adnms) stopifnot( vapply(n.set2, function(n) identical(dimnames(tail(arr2, n)), mapply(function(i, ni) { x <- adnms[[i]] if(is.null(x)) x <- as.character(seq_len(adims[i])) if(ni != 0L) tail(x, ni) }, i = ii, ni = n, SIMPLIFY = FALSE)), NA) ) ## ## matrix of "language" -- with expression() is.arr.expr <- function(x) is.array(x) && is.expression(x) e <- matrix(expression(foo(2), bar(x), r(foobar), foo(rbar)), 2) str(h1 <- head(e, 1)) str(t1 <- tail(e, 1)) stopifnot(exprs = { is.arr.expr(e) && identical(dim(e), c(2L, 2L)) is.arr.expr(h1) && identical(dim(h1), c(1L, 2L)) is.arr.expr(t1) && identical(dim(t1), c(1L, 2L)) is.arr.expr(ee <- e[rep(1:2, 3), rep(1:2, 2)]) && identical(dim(ee), c(6L, 4L)) is.arr.expr(hee <- head(ee, n=c(2,-1))) && identical(dim(hee), 2:3) is.arr.expr(tee <- tail(ee, n=c(-3,1))) && identical(dim(tee), c(3L, 1L)) }) ## (for length(n) == 1, has worked the same "always") ## Forgotten 'drop=FALSE' in plot.formula() df <- data.frame(x=1:3, grp=c("A","A","B"), stringsAsFactors = TRUE) plot( ~grp, data=df, subset = x > 1) ## failed in R <= 3.6.1 ## dnorm() etc border cases, notably sigma = -Inf tools::assertWarning(v0Neg <- dnorm(0:1, sd = -Inf)) tools::assertWarning(dlInf0 <- dlnorm(Inf,Inf, sd = 0)) stopifnot(is.nan(v0Neg), is.nan(dlInf0)) ## in R <= 3.6.2, v0Neg was 0 w/o any warning; dlnorm(...) was +Inf ## Unusual frequency and start not supported by ts() and window() x <- ts(x, start = 2.5, end = 107.5, frequency = 0.2) (wx <- window(x, start = 20, end = 30, extend = TRUE)) stopifnot(exprs = { all.equal(attributes(x), list(tsp = c(2.5, 107.5, 0.2), class = "ts")) all.equal(wx, structure(c(0.5, 0.6), tsp = c(22.5, 27.5, 0.2), class = "ts")) }) assertErrV(cbind(ts(1:2, start = 0.5, end = 1.5), ts(1:2, start = 0 , end = 1))) ## Wrong results in R < 4.0.0 ## New checks needed tweaks : ## -- 1 -- frYr <- 365.25 tt <- (0:3652)/frYr timeO <- structure(tt, tsp = c(1981, 1990.998631, frYr), class = "ts") ttt <- time(timeO) # Error "'end' must be a whole number of cycles after 'start'" ## -- 2 -- set.seed(7); tt <- ts(rnorm(60), frequency=12) dt2 <- diff(tt, differences = 2) # Error in .cbind.ts(..): not all series have the same phase tsD <- ts(1:49, start=as.Date("2019-12-12"), frequency=12) stopifnot(exprs = { all.equal(timeO, ttt - 1981, tol = 1e-8) inherits(ttt, "ts") inherits(dt2, "ts") length(dt2) == length(tt) - 2L all.equal(6*tsp(dt2), c(7, 35.5, 72)) all.equal(dt2[1:2], c(3.986498, -0.22047961)) all.equal(tsD, structure(1:49, tsp = c(18242, 18246, 12), class = "ts")) }) ## failed for a while in R-devel 2019-12-* ## Using deparse1() fixing potential naming problems in many places, PR#17671 (acl <- do.call(acf, list(lynx, plot=FALSE))) set.seed(7); t44 <- table(sample(LETTERS[1:4], size = 50, replace=TRUE), sample(letters[1:4], size = 50, replace=TRUE)) ft44 <- do.call(fisher.test, list(t44)) stopifnot(length(acl$series) == 1, length(do.call(pacf, list(lynx, plot=FALSE))$series) == 1, identical(t44, eval(str2lang(ft44$data.name)))) ## funny data names in R < 4.0.0 ## wilcox.test(x,{y,} ..): when 'x' and/or 'y' contain +/- Inf dfn <- c(shifted = function(L) 1/8 + c(9:4, L), # <- without, and ties = function(L) c(9:4, L)) # <- with ties oWarn <- getOption("warn") for(nm in names(dfn)) { y7 <- dfn[[nm]] options(warn = if(nm == "ties") 1 else 2) ## "ties" : ==> 2 x 3 (different) warnings w2 <- lapply(c(1000, Inf), function(L) wilcox.test(1:7, y7(L))) w1 <- lapply(c(1000, Inf), function(L) wilcox.test( y7(L) )) w2p <- lapply(c(1000, Inf), function(L) wilcox.test(1:7, y7(L), paired= TRUE)) w2n <- lapply(c(1000, Inf), function(L) wilcox.test(1:7, y7(L), exact = FALSE)) w2pn<- lapply(c(1000, Inf), function(L) wilcox.test(1:7, y7(L), exact = FALSE, paired=TRUE)) stopifnot(exprs = { identical(w2 [[1]], w2 [[2]]) # was FALSE in R <= 3.6.x identical(w1 [[1]], w1 [[2]]) # was FALSE .. identical(w2p [[1]], w2p [[2]]) identical(w2n [[1]], w2n [[2]]) # was FALSE .. identical(w2pn[[1]], w2pn[[2]]) }) }; options(warn = oWarn) ## non-paired cases treated 'Inf' non-robustly in R <= 3.6.x wII <- wilcox.test(c(-Inf, 1:5, Inf), c(-Inf, 4*(0:4), Inf), paired=TRUE) # error in R <= 3.6.x w1 <- wilcox.test(c( 1:5, Inf), c( 4*(0:4), Inf), paired=TRUE) # ditto (w0 <- wilcox.test( 1:5, 4*(0:4), paired=TRUE)) sel <- names(w0) != "data.name" stopifnot(identical(w0[sel], w1[sel]), identical(w0[sel], wII[sel])) ## Inf-Inf etc broken in paired case in R <= 3.6.x if(FALSE){ ## pro tem ## round(x, n) "to even" failed in some cases -- PR#17668 dd <- 0:12 x55 <- 55 + as.numeric(vapply(dd+1, function(k) paste0(".", strrep("5",k)), "")) rnd.x <- vapply(dd+1L, function(k) round(x55[k], dd[k]), 1.1) noquote(formatC(cbind(x55, dd, rnd.x), w=1, digits=15)) signif (rnd.x - x55, 3) # look at .. but don't test (yet) stopifnot(exprs = { all.equal(abs(rnd.x - x55), 5 * 10^-(dd+1), tol = 1e-11) # see diff. of 6e-13 }) ## more than half of the above were rounded *down* in R <= 3.6.x ## Some "wrong" test cases from CRAN packages (partly relying on wrong R <= 3.6.x behavior) stopifnot(exprs = { all.equal(round(10.7775, digits=3), 10.778, tolerance = 1e-12) # even tol=0, was 10.777 all.equal(round(12345 / 1000, 2), 12.35 , tolerance = 1e-12) # even tol=0, was 12.34 in Rd all.equal(round(9.18665, 4), 9.1866, tolerance = 1e-12) # even tol=0, was 9.1867 }) ## This must work, too, the range of 'e' depending on 'd' EE <- c(-307, -300, -250, -200,-100,-50, -20, -10, -2:2, 10, 20, 50, 100, 200, 250, 290:307) for(d in 0:16) { cat("digits 'd' = ", d, ": ") for(e in EE[EE+d <= 308]) { f <- 10^e cat(".") stopifnot(all.equal(tolerance = if(d < 14) 1e-15 else if(d == 14) 1e-14 else 1e-13, round(pi/f, e + d) * f, round(pi, d))) };cat("\n") } ## (2nd part: continued working) i <- c(-2^(33:10), -10:10, 2^(10:33)) for(digi in c(0:10, 500L, 1000L, 100000L, .Machine$integer.max)) stopifnot(identical(i, round(i, digi)), identical(i+round(1/4, digi), round(i+1/4, digi))) x <- 7e-304; rx <- round(x, digits=307:322); xx <- rep(x, length(rx)) print(cbind(rx), digits=16) # not really what ideally round() should do; but "ok" all.equal(rx, xx, tol = 0)# show "average relative difference" ("5.6856 e -16") stopifnot(all.equal(rx, xx, tol = 1e-4)) # tol may change in future ## the round(i, *) failed, for ~ 2 days, in R-devel e <- 5.555555555555555555555e-308 (e10 <- e * 1e298) # 5.555556e-10 -- much less extreme, for comparison ds <- 20:1 ; s.e <- signif(e, ds) ; names(s.e) <- paste0("d", ds) ## currently, for round, digits := pmin(308, digits) -- not going further than 310 d <- 310:305; r.e <- round (e, d) ; names(r.e) <- paste0("d", d) d <- d - 298; r.e10 <- round (e10, d) ; names(r.e10) <- paste0("d", d) op <- options(digits=18) cbind(signif = c(e, s.e)) ##-- this always rounds up (= to even) cbind( round = c(e, r.e), round.10 = c(e10, r.e10)) iSub <- 6 : (18 + capabilities("long.double")) stopifnot(exprs = { ## the regularity of signif()'s result is amazing: is.integer(d <- ds[iSub] - 1L) all.equal(log10(abs(1 - diff(unname(s.e))[iSub] * 1e308*10^d / 4)), d - 16, tol = 0.08) # tol: seen 0.0294 / 0.02988 (Win 32b) all.equal(r.e * 1e298, r.e10, check.attributes = FALSE, countEQ=TRUE, tol=1e-14) }) ## was not true for digits = 309, 310 in R <= 3.6.x ## ## round(*, digits < 0) M <- .Machine$double.xmax rM <- round(M, -(1:400)) stopifnot(exprs = { rM[(1:400) > 308] == 0 ### platform (compiler configuration) dependent: ## identical(which(rM == Inf), ## c(if(!b64) 294L, 298L, 299L, 304:308) -> II) ## is.finite(rM[-II]) }) ## had many Inf and NaN; now looks optimal: 'Inf' are "correct" rounding up ## (mm <- 2^-(1022+52)) # denormalized smallest number mm == 1.49*mm # yes, that's "denormal" dr <- diff(rmm <- round(mm, 301:500)) (inz <- which(dr != 0)) stopifnot(length(inz) == 1, dr[inz] == mm, dr[-inz] == 0, rmm[-(1:23)] == mm) options(op) ## in R <= 3.6.x, all(rmm == 0) } ## update.formula() triggering terms.formula() bug -- PR#16326 mkF <- function(nw) as.formula(paste("y ~ x + x1", paste0("- w", seq_len(nw), collapse="")), env = .GlobalEnv) fterms <- function(n, simplify=TRUE) formula(terms.formula(mkF(n), simplify=simplify)) if(interactive()) for(n in 1:20) print(fterms(66)) # always correct now: y ~ x + x1 ## used to have a '-1' (and much more, see below) in R <= 3.6.2 ## NB: had memory / random behavior -- and sometimes ended in ## malloc(): corrupted top size ## Process R... aborted (core dumped) set.seed(17) N <- 1024 Ns <- sort(1 + rpois(N, 3)+ 16*rpois(N, 3)) FN <- lapply(Ns, fterms) (UFN <- unique(FN)) stopifnot(identical(y ~ x + x1, UFN[[1]])) ## Ended in this error [which really comes from C code trying to set dimnames !] : ## Error in terms.formula(mkF(n), simplify = simplify) : ## 'dimnames' applied to non-array ## ##--TODO: less severe now (no seg.fault / corrupt memory crashes), but still really bad ! --- ## Corner cases in choose(), ## misbehaved when n was _nearly_ int, and n - k < k ; thread ending at .../r-devel/2020-January/078948.html eps <- c(outer(10^-(6:9), -20:20)) # choose( ~4, 4) ~ 1 : stopifnot(abs(choose(4+eps, 4) - 1) < 1e-4) ## choose(4 -/+ 1e-7, 4) gave 0 and 4 in R <= 3.6.x ## correct error message: tt <- tryCid(strptime(100, pi)) stopifnot(inherits(tt, "error"), grepl("'format'", tt$message)) ## had 'x' instead of 'format' ## r() now return double if integer would overflow: set.seed(47) Npi <- rpois(100, 0.9999 *2^31) Npd <- rpois(100, 0.99999*2^31)# had 33 NA's Nbi <- rbinom(100, 2^31, 1/2) Nbd <- rbinom(100, 2^32, 1/2)# 51 NA's Ngi <- rgeom(999, 1e-8) Ngd <- rgeom(999, 1e-9) # 106 NA's stopifnot(is.integer(Npi), is.double(Npd), !anyNA(Npi), !anyNA(Npd), is.integer(Nbi), is.double(Nbd), !anyNA(Nbi), !anyNA(Nbd), is.integer(Ngi), is.double(Ngd), !anyNA(Ngi), !anyNA(Ngd), TRUE) ## had many NA's in 3.0.0 <= R <= 3.6.x ## rhyper() for some large arguments, PR#17694 n <- 2e9 # => .Machine$integer.max ~= 1.07 * N set.seed(6860); N <- rhyper(1, n,n,n) x <- 1.99e9; Nhi <- rhyper(256, x,x,x) stopifnot(#identical(N, 999994112L), # (wrong) implementation detail is.integer(Nhi), all.equal(mean(Nhi), x/2, tol = 6e-6)) # ==> also: no NAs ## NA's and warnings, incl "SHOULD NOT HAPPEN!" in R <= 3.6.2 ## assertCondition(*, "error") etc triggered errors *twice* (accidentally) stopifnot(identical(tools::assertError(sqrt("a")), list( tryCid(sqrt("a"))))) ## The former contained the error object twice in R <= 3.6.2 ## smoothEnds(, .) - PR#17693 y1 <- as.integer(c(8,5,4,1,1,1,1)) y2 <- y1; y2[3] <- 6L s1 <- smoothEnds(y1); s1.5 <- smoothEnds(y1, 5) s2 <- smoothEnds(y2); s2.5 <- smoothEnds(y2, 5) stopifnot(is.integer(y1), is.integer(y2), y1[-3] == y2[-3], is.integer(s1), is.integer(s2), is.integer(s1.5), is.integer(s2.5), s1[1] == 7L, s1[-1] == y1[-1], identical(s1.5, s1), s2[1] == 5L, s2[-1] == y2[-1], identical(s2.5, rep(c(6L, 1L), 3:4))) ## s1, s1.5 were double in R <= 3.6.x ## stopifnot() custom message now via args: e <- assertErrV(stopifnot("ehmm, you must be kidding!" = 1 == 0)) stopifnot(grepl("must be kidding!", e[[1]]$message)) e2 <- assertErrV(stopifnot("2 is not approximately 2.1" = all.equal(2, 2.1))) stopifnot(grepl("not approximately", e2[[1]]$message)) ## did not work in original stopifnot() patch CHK <- function(...) stopifnot(...) e <- tryCid(CHK(1 == 1, 1 == 0)) e2 <- tryCid(CHK(1 == 1, "not possible" = 1 == 0)) stopifnot(inherits(e , "error"), grepl("is not TRUE", e$message), inherits(e2, "error"), identical("not possible", e2$message)) ## wrapping stopifnot() in this way did not work in some unreleased R-devel ## norm(, "2") stopifnot(is.na( norm(diag(c(1, NA)), "2") )) ## gave error from svd() in R <= 3.6.x ## norm(, "F") (m <- cbind(0, c(NA, 0), 0:-1)) nTypes <- eval(formals(base::norm)$type) # "O" "I" "F" "M" "2" print( # stopifnot( -- for now, as Lapack is still broken in some OpenBLAS -- FIXME is.na( print(vapply(nTypes, norm, 0., x = m)) )) # print(): show NA *or* NaN ## "F" gave non-NA with LAPACK 3.9.0, before our patch in R-devel and R-patched ## dimnames()[[.]] <- v -- inconsistency when length(v) == 1 : PR#17719 aa <- matrix(1:2); dimnames(aa)[[1]] <- c("a", "b") # OK (always) a <- matrix(1) ; dimnames(a )[[1]] <- "a" # gave error: 'dimnames' must be a list stopifnot(exprs = { identical(dimnames(a ), list( "a", NULL)) identical(dimnames(aa), list(c("a","b"), NULL)) }) ## The above works, because now, `[[<-` is consistently returning a list: N <- NULL; N[["a"]] <- 1:2; stopifnot(identical(N, list(a = 1:2))) N <- NULL; N[["a"]] <- 1 ; stopifnot(identical(N, list(a = 1))) ## the latter gave c(a = 1) in earlier versions of R ## deparse(), dput(), etc : "all" now includes "digits17"; new "exact" x <- 1 - 2^-51 ; dput(x, , "all") stopifnot(exprs = { identical(deparse(x), as.character(x)) identical(deparse(x), "1") # default only uses 15 (= DBL_DIG) digits if(!capabilities("long.double")) TRUE else identical(x, as.numeric(deparse(x, control="all"))) identical(x, as.numeric(deparse(x, control="exact") -> dx.x)) identical(print(dx.x), deparse(x, control="hexNumeric")) TRUE || ## maybe not on all platforms ? identical(dx.x, "0x1.ffffffffffffcp-1") # on 32-bit, too }) ## "all" gave "1" in R <= 3.6.z ## Can suppress warnings with missing restarts cnd <- simpleWarning("foo") out <- tryCatch(suppressWarnings(stop(cnd)), warning = identity) stopifnot(identical(out, cnd)) ## Can suppress messages with missing restarts cnd <- simpleMessage("foo") out <- tryCatch(suppressMessages(stop(cnd)), message = identity) stopifnot(identical(out, cnd)) ## PR#17730 -- data() should no longer "lie" and warn {already have getOption("warn") == 2 for(p in c("base", "stats")) { dd <- data(package=p) stopifnot(inherits(dd, "packageIQR"), is.list(dd), nrow(dd$results) == 0) } ## gave all data from pkg 'datasets' *and* warned in R <= 3.6.3 ## PR#17756: x[[Inf]] and also x[[ -i ]] , for i in (Inf, 1,2,...): obj <- list( a = 1:3 , L3 = as.list(1:3) , L = list(a = 1:2) , L2 = list(a = 1:2, b = 3:5) , LL2 = list(a = list(a1=1:3, a2=letters[1:4]), b = list(b1=10, b2=-(1:3))) ) obj$ LL3 <- c(obj$ LL2, list(c = list(c1= 7, c2= -11))) stopifnot( print(vapply(obj[-1], function(x) is.null(x[[Inf]]), NA)) ) t_mInf <- lapply(obj, function(x) tryCid(x[[-Inf]])) getMsg <- function(tryClist) vapply(tryClist, conditionMessage, "..") stopifnot(length(print(table(msg_Inf <- getMsg(t_mInf)))) == 1) ## in R <= 3.6.3: ## attempt to select less than one element in get1index : 1 x ## attempt to select more than one element in get1index : 5 x umInf <- unique(msg_Inf) str(t_m1 <- lapply(obj, function(x) tryCid(x[[-1]]))) # L2, LL2 "work" - why? t_m2 <- lapply(obj, function(x) tryCid(x[[-2]])) # L2, LL2 "work" - why? t_m3 <- lapply(obj, function(x) tryCid(x[[-3]])) nonL2 <- grep("L2$", names(t_m1), value=TRUE, invert=TRUE) stopifnot(exprs = { identical(getMsg(t_m3), msg_Inf) identical(t_m2$L2, 1:2) identical(t_m2$LL2, obj$LL2[[1]]) identical(getMsg(t_m1[nonL2]), msg_Inf[nonL2]) identical(getMsg(t_m2[nonL2]), msg_Inf[nonL2]) }) if(englishMsgs) { cat("checking (default = ) English error messages\n") stopifnot(grepl("negative subscript", umInf)) } ## ## paste(..., recycle0=TRUE) uses the "normal" 0-length recycling rule: ## "if one argument has length zero, the result has too." ch0 <- character(0) stopifnot(exprs = { ## a) when paste() has 0 '...' arguments : identical(paste (), ch0) ## collapse = NULL ----------- identical(paste0(), ch0) identical(paste (collapse= "A" ), "") identical(paste0(collapse="foof"), "") identical(paste (collapse= "A" , recycle0 = TRUE), "") # new! identical(paste0(collapse="foof", recycle0 = TRUE), "") # new! ## ## b) when all '...' arguments have length 0 : ## ---- collapse = NULL ------------- identical(paste({}), ch0) identical(paste({}, recycle0 = TRUE), ch0) identical(paste({}, NULL, ch0), ch0) identical(paste({}, NULL, ch0, recycle0 = TRUE), ch0) ## ---- collapse not NULL --------- identical(paste({}, collapse=""), "") identical(paste({}, collapse="", recycle0 = TRUE), "") # new! identical(paste({}, NULL, ch0, collapse=""), "") identical(paste({}, NULL, ch0, collapse="", recycle0 = TRUE), "") # new! ## ## c) when *one* of the ...-args has length 0 : identical(paste ("foo", character(0), "bar", recycle0 = FALSE), "foo bar") identical(paste0("foo", character(0), "bar", recycle0 = FALSE), "foobar") identical(paste ("foo", character(0), "bar", recycle0 = TRUE), ch0) identical(paste0("foo", character(0), "bar", recycle0 = TRUE), ch0) identical(paste ("foo", character(0), "bar", recycle0 = TRUE, collapse="A"), "") identical(paste0("foo", character(0), "bar", recycle0 = TRUE, collapse="A"), "") }) ## 0-length recycling with default recycle0 = FALSE has always been "unusual" ## ----------------- with recycle0 = TRUE returns 0-length i.e. character(0) ## aov() formula deparsing {Jan Hauffa, Apr 11, 2020, on R-devel} mkAov <- function(nms, n = 50) { dflong <- as.data.frame(matrix(pi, n, length(nms), dimnames = list(NULL, nms))) forml <- as.formula(paste0("cbind(", paste(nms, collapse = ","), ") ~ 1 + Error(1)")) aov(forml, data=dflong) } nLng <- paste0("someReallyLongVariableName", 1:20) cf1 <- coef(fm1 <- mkAov(vnms <- paste0("v", 1:20))) cfL <- coef(fmL <- mkAov(nLng)); colnames(cfL[[1]]) <- vnms stopifnot(all.equal(cf1, cfL)) ## mkAov(nLng) failed in R <= 4.0.0 ## UTF8 validity checking internal in R (from PCRE, PR#17755) ## This is the byte representation of U+D800 (a part of a surrogate ## pair) in UTF-8, but do not rely on parser (which on some platforms ## has mis-parsed that) stopifnot(identical(validUTF8("\xed\xa0\x80"), FALSE)) ## summary.warnings() -- reported by Allison Meisner, jhmi.edu testf <- function(x) { if(x > 30) warning("A big problem (should be 20 of these)") else warning("Bigger problem (should be 30 of these)") } op <- options(warn=0) for(i in 1:50) testf(i) # -> 50 warnings .. options(op)# reset (sw <- summary(warnings())) stopifnot(identical(unlist(lapply(names(sw), substr, 1, 6)), c("Bigger", "A big ")), identical(attr(sw, "counts"), c(30L, 20L))) ## was wrong (mis-sorted counts) in R <= 4.0.0 ## plot.formula(.., ylab = ) dd <- list(x = -4:4, w = 1/(1+(-4:4)^2)) plot(w ~ x, data=dd, type = "h", xlab = quote(x[j])) # worked before plot(w ~ x, data=dd, type = "h", xlab = quote(x[j]), ylab = quote(y[j]))# *now* works ## main, sub, xlab worked (PR#10525) but ylab did not in R <= 4.0.0 ## ...names() F <- function(x, ...) ...names() F(a, b="bla"/0, c=c, D=d, ..) # << does *not* evaluate arguments # |-> c("b", "c", "D", "") stopifnot(exprs = { is.null(F(pi)) F(foo = "bar") == "foo" identical(F(., .., .not.ok. = "a"-b, 2, 3, last = LAST), c( "", ".not.ok.", "", "","last")) }) # .. was wrong for a few days ## check raw string parse data p <- parse(text = 'r"-(hello)-"', keep.source = TRUE) stopifnot(identical(getParseData(p)$text, c("r\"-(hello)-\"", ""))) rm(p) # (wrong in R 4.0.0; reported by Gabor Csardi) ## check 0x...L parse data p <- parse(text = '0x2L', keep.source = TRUE) stopifnot(identical(getParseData(p)$text, c("0x2L", ""))) rm(p) # (wrong in R 4.0.0; reported by Gabor Csardi) ## make sure there is no aliasing in assignments with partial matching v <- list(misc = c(1)) v$mi[[1]] <- 2 stopifnot(v$misc == 1) ## check compiled code also (PR18349) v <- list(misc = c(1)) eval(compiler::compile(quote(v$mi[[1]] <- 2))) stopifnot(v$misc == 1) rm(v) ## defensive reference counts needed; missing in R 4.0.0 ## round() & signif() with one / wrong (named) argument(s): cat("Case 1 : round(1.12345): ", round( 1.12345),"\n") cat("Case 2 : round(x=1.12345,2): ", round(x=1.12345, 2),"\n") cat("Case 3 : round(x=1.12345,digits=2): ", round(x=1.12345, digits=2),"\n") cat("Case 4 : round(digits=2,x=1.12345): ", round(digits=2, x=1.12345),"\n") cat("Case 4b: round(digits=2,1.12345): ", round(digits=2,1.12345),"\n") ## R <= 4.0.0 does not produce error in cases 5,6 but should : cat("Case 5: round(digits=x): \n") assertErrV(cat("round(digits=99.23456): ", round(digits=99.23456))) cat("Case 6: round(banana=x): \n") assertErrV(cat("round(banana=99.23456): ", round(banana=99.23456))) ## Cases 7,8 have been given an error already: cat("Case 7: round(x=1.12345, digits=2, banana=3):\n") assertErrV( round(x=1.12345, digits=2, banana=3)) cat("Case 8 : round(x=1.12345, banana=3):\n") assertErrV( round(x=1.12345, banana=3)) ## (by Shane Mueller, to the R-devel m.list) ## source(*, echo=TRUE) with srcref's and empty lines; PR#17769 exP <- parse(text=c("1;2+", "", "3"), keep.source=TRUE) r <- source(exprs=exP, echo=TRUE) stopifnot(identical(r, list(value = 5, visible = TRUE))) ## failed in R <= 4.0.1 ## boxplot() with call (instead of expression) in labels; Marius Hofert on R-devel rm(x,y,X,f) boxplot(cbind(x = 1:10, y = c(16,9:1)), xlab = quote(x^{y[2]}), ylab = quote(X[t]), sub = quote(f^2 == f %*% f), main = quote(e^{-x^2/2})) ## failed in R <= 4.0.1 ## on.exit() argument matching -- PR#17815 f <- function() { on.exit(add=FALSE, expr=cat('bar\n')) ; 'foo' } stopifnot(identical(f(), 'foo')) # and write 'bar' line g <- function() { on.exit(add=stop('boom'), expr={cat('bar\n'); FALSE}) ; "foo" } assertErrV(g()) ## f() :> "Error in on.exit(....): invalid 'add' argument" and no error for g() in R <= 4.0.1 ## multi-encodings in vector-case for duplicated/match -- PR#17809 c_latin1 <- "\xe4" Encoding(c_latin1) <- "latin1" c_utf8 <- enc2utf8(c_latin1) x <- list(c_latin1, c_utf8, letters) stopifnot(identical(duplicated(x)[2], TRUE)) ## failed in R <= 4.0.1 ## str() mixW <- setClass("mixW", contains = "numeric") Summ <- setClass("Summ", representation(call = "language", wts = "mixW")) S <- Summ(call = quote(foo(x)), wts = structure(mixW(pi), CA="sunny")) stopifnot(length(c.str <- capture.output(str(S))) >= 5, grepl(r"(\$ CA: chr "sunny")", c.str[5])) deparse(S)# FIXME: is still wrong (no trace of "CA") ## "CA" was not shown in R <= 4.0.2 ## sort(), order(), rank() for "raw - object": int8 <- function(x) structure(x, class = c("int8", oldClass(x))) `[.int8` <- function(x, ...) structure(NextMethod("["), class=class(x)) set.seed(2); si <- sample.int(37) rI <- int8(as.raw(si)) stopifnot(exprs = { identical(rank (rI), rank (si)) identical(order(rI), order(si)) identical(sort (rI), int8(as.raw(1:37))) }) ## failed in R <= 4.0.2 ## PR#16814: r2dtable() and chisq.test(*, simulate.p.value=TRUE) for large numbers rc <- c(63194L, 4787074L) cc <- c(34677L, 4815591L) set.seed(28); system.time(R2 <- simplify2array(r2dtable(1000, rc, cc))) (c.t <- chisq.test(R2[,,1], simulate.p.value = TRUE)) set.seed(2*3); R2x3 <- r2dtable(5000, c(3,13), c(4,4,8)) stopifnot(exprs = { sum(!(dupR2 <- duplicated.array(R2, MARGIN=3))) == 109 all.equal(c.t$p.value, 1929/2001) ## From here, true also in previous R versions: is.matrix(cR2 <- colSums(R2)) cR2[1,] == cc[1] cR2[2,] == cc[2] identical(c(table(vapply(R2x3, function(m) 10*m[2,1]+m[2,3], 1))), c(`18` = 42L, `27` = 405L, `28` = 217L, `36` = 1021L, `37` = 1159L, `38` = 192L, `45` = 491L, `46` = 967L, `47` = 464L, `48` = 42L)) }) ## The large tables and p-values were completely wrong in R <= 4.0.2 ## PR#16877: glm()-internal refitting for the null deviance y <- c(1, 1, 0, 0) x <- c(5, 3, 2, 4) fit <- glm(y ~ 1 + x + offset(log(x)), family = gaussian("log"), start = c(0,0)) ## failed in R < 4.1.0 due to missing starting values for glm-internal 'fit2' fit0 <- glm.fit(x = rep(1, length(y)), y = y, offset = log(x), family = gaussian("log"), start = 0) stopifnot(all.equal(fit$null.deviance, fit0$deviance)) proc.time() - .pt; .pt <- proc.time() ## c() generic removes all NULL elements --- *but* the first --- before dispatch c.foobar <- function(...) list("ok", ...) foobar <- structure(list(), class = "foobar") stopifnot(exprs = { identical(c(foobar, NULL, one=1,NULL), list("ok", foobar, one=1)) identical(c(a = foobar, pi, NULL, b="B",NULL), list("ok", a = foobar, pi, b="B")) identical(c(a = foobar, b = NULL), list("ok", a = foobar)) identical(c(foobar, b = foobar), list("ok", foobar, b=foobar)) ## Back compatibly, w/ initial NULL, using c()'s default method: ## ==> result has list() for foobar identical(c(NULL, foobar, NULL, NULL, 1), c( list(), 1)) identical(c(NULL, b = foobar, NULL, NULL, 1), c(b=list(), 1)) identical(c(a = NULL, b = foobar), list()) identical(c(a = NULL, b = foobar, c = NULL), list()) identical(c(NULL, a = NULL, b = foobar, c = NULL), list()) }) ## the first three cases failed in R <= 4.0.x ## quantile(*, pr) allows pr values very slightly outside [0,1] -- PR#17891 stopifnot( identical(quantile(0:1, 1+1e-14), c("100%" = 1)) ) ## failed in R <= 4.0.2 ## quantile(*, pr, names=FALSE) with NA's in 'pr' -- PR#17892 x <- (0:99)/64 prN <- c(0.1, 0.5, 1, 2, 5, 10, 50, NA)/100 qxN <- quantile(x, probs = prN) qxNN <- quantile(x, probs = prN, names = FALSE) stopifnot(exprs = { is.null(names(qxNN)) identical(qxNN, unname(qxN)) identical(NA_real_, quantile(x, probs = NA, names = FALSE)) }) ## qxNN gave "Error in names(o.pr)[p.ok] <- names(qs) : ..." in R <= 4.0.2 ## Vectorize() no longer keeps "garbage": vrep <- Vectorize(rep.int, "times") stopifnot(identical(sort(names(environment(vrep))), c("FUN", "SIMPLIFY", "USE.NAMES", "vectorize.args"))) ## names(..) was of length 7 in R <= 4.0.2 ## as.Date( "" ) -- PR#17909 dd <- c("", "2001-09-11") (D1 <- as.Date( dd)) # failed in R <= 4.0.2 (D2 <- as.Date(rev(dd))) stopifnot(is.na(D1[1]), identical(D1, rev(D2))) ## "" was not treated correctly when at [1] in R <= 4.0.2 ## ..elt() propagates visibility consistently with ..n and other args, PR#17905 local({ fn <- function(...) list(withVisible(...elt(1)), withVisible(..2)) stopifnot(identical( fn(invisible(NULL), invisible(NULL)), rep(list(withVisible(invisible(NULL))), 2) )) }) ## PR#17913 -- numToBits() accidentally was destructive n0 <- c(-7.7, 2.34e55) b0 <- numToBits(n0) stopifnot(sum(l0 <- as.logical(b0)) == 62L, identical(which(head(l0, 10)), c(1L, 3:4, 7:8)), identical(n0, c(-7.7, 2.34e55))) ## was '0 0' for almost a month in R-devel ## No longer assuming integer length() if(.Machine$sizeof.pointer >= 8) { .Internal(inspect(-199900000:2e9)) } ## gave an error in R <= 4.0.2 ## PR#17907 -- capture.output() now using standard evaluation (SE) : ## parent.frame() returns the correct environment in capture.output() local({ fn <- function(env = parent.frame()) { capture.output(env) list( env, parent.frame() ) } env <- environment() out <- fn() stopifnot( identical(out[[1]], out[[2]]), identical(out[[1]], env) ) }) ## capture.output() works with forwarded dots local({ wrapper <- function(...) { capture.output(..., type = "output") } out <- local({ foo <- 1 wrapper(foo) }) stopifnot(identical(out, capture.output(1))) }) ## Failed when capture.output() was using NSE ## Inverse of numToBits() via stopifnot(identical(packBits(b0, "double"), n0)) r <- c(pi, 1+ (0:8)/4); head(b <- numToBits(r), 25) stopifnot(identical(packBits(b, "double"), r)) ## thanks to PR#17914 by Bill Dunlap ## quantile(x, probs) when probs has NA's, PR#17899 stopifnot(identical(quantile(NULL), quantile(numeric())), # back-compatibility identical(quantile(structure(numeric(), names = character()), names = FALSE), rep(NA_real_, 5))) L <- list(ordered(letters[1:11]), # class "ordered" "factor" seq(as.Date("2000-01-07"), as.Date("1997-12-17"), by="-1 month")) ct <- seq(as.POSIXct("2020-01-01 12:13:14", tz="UTC"), by="1 hour", length.out = 47) LL <- c(L, list(o0 = L[[1]][FALSE], D0 = L[[2]][FALSE], ct = ct, lt = as.POSIXlt(ct), num= as.numeric(ct))) prb <- seq(0, 1, by=2^-8) # includes 0.25, 0.5, etc for(x in LL) { cat("x : "); str(x, vec.len=3) clx <- class(if(inherits(x, "POSIXlt")) as.POSIXct(x) else x) ## for "ordered" *and* "Date", type must be 1 or 3 for(typ in if(any(clx %in% c("ordered", "Date"))) c(1,3) else 1:7) { cat(typ, ": ") stopifnot(exprs = { identical(clx, class(q1 <- quantile(x, probs= prb, type=typ))) identical(clx, class(qN <- quantile(x, probs=c(prb,NA), type=typ))) # failed ## for "POSIXct", here q1 is integer, qN "double": { if(inherits(q1, "POSIXct")) storage.mode(qN) <- storage.mode(q1); TRUE } identical(qN[seq_along(q1)], q1) is.na( qN[length(qN)]) }) }; cat("\n") } ## qN often lost class() e.g. for "ordered" and "Date" in R <= 4.0.2 ## isS3stdGeneric() traced function: trace(print) stopifnot( isS3stdGeneric(print) ) untrace(print) ## was FALSE in R <= 4.0.2 ## PR#17897: all.equal.factor() did not distinguish the two different NA in factors labs <- c("a", "b", NA) x <- factor( 3:1, labels = labs) y <- factor(c(NA, 2:1), levels = 1:3, labels = labs) x dput(x) ; dput(y) ## --> they are clearly different, but print the same: stopifnot(exprs = { identCO(x,y) is.character(print(ae <- all.equal(x,y))) !englishMsgs || grepl("NA mismatch", ae, fixed=TRUE) }) ## all.equal() gave TRUE wrongly, from 2012 till R <= 4.0.2 ## PR#17935: `[.formula` for formulas with NULL: forms <- list(f0 = (~ NULL) , f1 = (z ~ NULL) , f2 = (NULL ~ x) , f3 = (NULL ~ NULL) ) rr <- lapply(forms, function(f) lapply(seq_along(f), function(ii) f[ii])) cN <- quote(NULL()) stopifnot(exprs = { identical( unique(lapply(rr , `[[`, 1)), list(`~`())) identical( lapply(unname(rr), `[[`, 2), list(cN, quote(z()), cN,cN) ) }) ## subsetting failed for all 4 formulas in R <= 4.0.3 (tm1 <- (~ "~")[-1]) (tq1 <- (~ `~`)[-1]) stopifnot(exprs = { identical((~ NA)[-1], quote(NA())) ## subsetting (~ NA) failed in R <= 4.0.3 identical(tm1, `[[<-`(call("T"), 1L, "~")) ; is.call(tm1) identical(tq1, structure(call("~"), class="formula", ".Environment" = globalenv())) }) ## zero-length formulas from subsetting are now equal to formula(NULL) exps <- expression( (~ x)[FALSE] , (~ x)[rep(FALSE, 2)] , (y ~ x)[FALSE]) formL <- lapply(exps, eval) stopifnot( length(unique(formL)) == 1, all.equal(formL[[1]], formula(NULL)) ) ## Gave error "attempt to set an attribute on NULL" in R <= 4,0.3 ## Regression in .traceback() PR#17930 op <- options(keep.source=TRUE) f <- function() .traceback(1) g <- function() f() x <- g() stopifnot(inherits(attr(x[[1]], 'srcref'), "srcref")) options(op) ## had worked up to R 3.6.3, but not from 4.0.0 to 4.0.3 ## Summary() and Math() data.frame methods with *logical* columns a <- na.omit(airquality) aF <- a[FALSE,] # 0-row version of it dL0 <- data.frame(x=numeric(), L=logical()) # logical column stopifnot(exprs = { ## "Summary" : sum(aF) == 0 # gave Error "only defined on a data frame with all numeric variables" sum(subset(a, Ozone > 200)) == 0 # (ditto) suppressWarnings(range(dL0) == c(Inf, -Inf)) # (2 warnings) ## "Math" , gave Error..: non-numeric variable(s) in data frame : identical(exp(data.frame(L=TRUE)), data.frame(L=exp(TRUE))) identical(sinL0 <- sin(dL0), data.frame(x=numeric(), L=numeric())) identical(sinL0, log1p(dL0)) identical(cumsum(dL0), data.frame(x=numeric(), L=integer())) }) ## probably never worked in any R <= 4.0.3 ## unlist(, recursive=FALSE), PR#17950 l.ex <- list(a = list(1:5, LETTERS[1:5]), b = "Z", c = NA) stopifnot(identical( unlist(as.pairlist(l.ex), recursive = FALSE), unlist( l.ex , recursive = FALSE))) ## l2 <- list(a = "a", b = quote(b), c = pi+2i)# no list-entries stopifnot( identical( unlist(as.pairlist(l2), recursive = FALSE) -> ul2, unlist(as.pairlist(l2))), identical(ul2, unlist(l2, recursive = FALSE))) ## lost content in R <= 4.0.3 ('FIXME' in source went lost in 2006) ## `class<-` was mutating outside of an assignment context x <- c(1) xx <- `class<-`(x, "foo") stopifnot(identical(class(x), "numeric")) ## Can splice expression vectors with attributes -- PR#17869 local({ exprs <- structure(expression(1, 2, 3), attr = TRUE) exprsSrcrefs <- parse(text = "1;2;3", keep.source = TRUE) stopifnot( identical( bquote({ ..(exprs) }, splice = TRUE), call("{", 1, 2, 3) ), identical( bquote({ ..(exprsSrcrefs) }, splice = TRUE), call("{", 1, 2, 3) ) ) }) ## some issues with task callbacks: ## avoid adding a reference to the value: x <- c(1) old_xr <- .Internal(refcnt(x)) TCB <- addTaskCallback(function(...) TRUE) x stopifnot(.Internal(refcnt(x)) == old_xr) removeTaskCallback(TCB) ## these used to fail with "object 'foo' not found": TCB <- addTaskCallback(function(e, v, ...) { v; TRUE}) quote(foo) removeTaskCallback(TCB) TCB <- addTaskCallback(function(...) { length(list(...)); TRUE}, data = quote(foo)) removeTaskCallback(TCB) ## all.equal() should check.environment (Kevin Van Horn, R-devel) f <- function(x) function(y) x+y dif <- all.equal(f(5), f(0)) stopifnot(is.function(f(5)), is.character(dif), grepl("difference", dif)) ## all.equal() gave TRUE in R <= 4.0.x ## p.adjust(, n=0) - PR#18002 ## (1st fix-proposal computed wrongly w/ NAs: pp <- 2^-(40:1); pp[17:19] <- NA ppa <- p.adjust(pp, "holm") # worked always but was not strictly tested stopifnot(all.equal(c(3.365e-11, 6.548e-11, 1.273e-10, 2.474e-10, 4.802e-10, 9.313e-10, 1.804e-09), ppa[1:7])) n0 <- numeric() stopifnot(identical(n0, p.adjust(n0, n = length(n0)))) ## errored in R <= 4.0.3 ## show() where it has package ".GlobalEnv" f <- function(x) x setGeneric("f") f # failed for a while (in R-devel only) ## all.equal.function() in case the env contains '...' -- PR#18010 a <- (function(...) function() NULL)(1) b <- (function(...) function() NULL)(1) # want "a .eq. b" D <- (function(...) function() NULL)(1:2 < 3) # want "D .NE. b" e.. <- (function(...) environment())(1) ##' General creator of "..." (DOTSXP) objects (short form by Suharto Anggono): ...maker <- function(...) get("...") ## fails if called without argument ...maker <- function(...) (function(...) environment())(...)[["..."]] str( ddd <- ...maker(1) ) str( Ddd <- environment(D)[["..."]] ) # length 1, mode "...": str( D2 <- ...maker(TRUE,TRUE)) # length 2, mode "...": str( D3n <- ...maker(ch = {cat("HOO!\n"); "arg1"}, 2, three=1+2) ) ## These all worked "accidentally" in R <= 4.0.x assertErrV(lD2 <- D2[]) # type '...' is not subsettable assertErrV(D3n[]) # (ditto) assertErrV(D3n[][["three"]]) # (ditto) assertErrV(D3n $ ch) # (ditto) str( D3n <- ...maker(ch = {cat("HOO!\n"); "arg1"}, 2, three=1+2) ) stopifnot(exprs = { identical(alist(a=)$a, ...maker())# "*the* missing", the empty symbol identical(ddd, ...maker(1)) identical(Ddd, ...maker(1:2 < 3)) is.character(aeLD <- all.equal(quote(x+1), ddd)) grepl("Mode", aeLD[1]) grepl("deparse", aeLD[2]) all.equal(a, b) # failed with "Component “...”: target is not list-like" since r79585 (2020-12-07) all.equal(e.., environment(a)) ## all.equal() dispatch for "..." objects ('ddd') directly: typeof(ddd) == "..." typeof(D2) == "..." length(D2) == 2 is.character(aeD <- all.equal(a, D) ) grepl("same length", aeD) grepl("...", aeD, fixed=TRUE) grepl("not identical", aeD) ## ## names(): is.null(names(ddd)) identical(c("ch", "", "three"), names(D3n)) }) ## for identical() ==> ./reg-tests-2.R -- as it's about "output" op <- options(keep.source = FALSE) # don't keep "srcref" etc ## Qlis <- list(NULL ## Next 4 now must work as identical(X,X) is true: , ddd = ddd , Ddd = Ddd , D2 = D2 , D3n = D3n , Qass = quote(x <- 1) , Qbrc = quote({1}) , Qparen = quote((1)) , Qif = quote(if(1)2) , Qif2 = quote(if(1)2 else 3) , Qwhile = quote(while(1) 2) ) ## sapply(Qlis, class) stopifnot( sapply(Qlis, function(obj) all.equal(obj, obj)) ) ## only the first failed in R <= 4.0.3 ## See PR#18012 -- may well change aS <- (function(x) function() NULL)(stop('hello')) bS <- (function(x) function() NULL)(stop('hello')) try( all.equal(aS, bS) ) ## now (check.environment=TRUE) triggers the promise .. ## Now have a way *not* to evaluate aka force the promise: (aeS <- all.equal(aS, bS, evaluate=FALSE)) # no promises forced stopifnot(grepl("same names.* not identical", aeS)) ## PR#18032: identical(,*) ddd <- ...maker(47) DDD <- ...maker(ch = {cat("Hu hu!\n"); "arg1"}, two = 1+1, pi, ABC="A") stopifnot(exprs = { identical(ddd,ddd) identical(DDD,DDD) identical (ddd, ...maker(47)) ! identical(ddd, ...maker(7 )) # these *are* different ! identical(ddd, DDD) }) options(op) ## PR#18034 : explicit and implicit row.names=NULL for as.data.frame.list() data(mtcars, package="datasets") lmtcars <- as.list(mtcars) names(lmtcars[[3]]) <- RN <- c(letters[1:26], LETTERS[1:6]) dfcars1 <- as.data.frame.list(lmtcars)# default: missing(row.names); uses RN dfcarsN <- as.data.frame.list(lmtcars, row.names = NULL)# does *not* use RN stopifnot(identical(RN, rownames (dfcars1)) , identical(-32L, .row_names_info(dfcarsN))) # now has "automatic" (integer) row names ## dfcarsN == dfcars1 in R <= 4.0.3 ## str(x) when x has "unusal" length() semantics such that lapply() / vapply() fails: length.Strange4 <- function(x) 4 `[[.Strange4` <- function(x, i) { stopifnot(length(i) == 1) if(i %in% 1:4) paste(sprintf("content of x[[%d]]", i)) else stop("invalid [[-index, partly out of 1..4") } `[.Strange4` <- function(x, i) { isM <- length(i) > 1 if(all(i %in% 1:4)) paste(sprintf("content of x[%s]", if(isM) paste0("c(", i, collapse=", ", ")") else paste0(i, collapse=", "))) else stop("invalid indices, partly out of 1..4") } L <- structure(as.list(1:6), class="Strange4") stopifnot(is.list(L), length(L) == 4, length(unclass(L)) == 6) assertErrV(lapply(L, length)) assertErrV(vapply(L, typeof, "")) lns <- capture.output(str(L)) # no longer fails stopifnot(length(lns) == 1+6, grepl("hidden list", lns[1])) ## str() failed for these and similar in R <= 4.0.x ## PR#18041: checkRdaFiles() $ version save(pi, file = rda2 <- tempfile(fileext = ".rda"), version = 2) save(pi, file = rda3 <- tempfile(fileext = ".rda"), version = 3) stopifnot(identical(2:3, tools::checkRdaFiles(c(rda2, rda3))$version)) ## gave '3 3' in R <= 4.0.3 ## constructing the names() of quantile(): str(L <- lapply(c(2,3,5,7), function(dig) { options(digits = dig) names(quantile(lynx, probs = 1 - 10^(-1:-5))) })) stopifnot(length(unique(L)) == 1) ## in R <= 4.0.x, L contained 3 different results ## PR#18079: sub() & gsub(patt, repl, x) -- when patt is NA (x <- c(a="abc", b="bd", d=NA, foo="babar")) stopifnot(exprs = { identical(names(x1 <- sub("a", "_", x)), names(x)) ; x1[["foo"]] == "b_bar" identical(names(x2 <- gsub("a", "_", x)), names(x)) ; x2[["foo"]] == "b_b_r" identical(names(xN2 <- gsub(NA , "_", x)), names(x)) ; is.na(xN2) identical(names(xN1 <- sub(NA , "_", x)), names(x)) ; is.na(xN1) }) ## NA-pattern did not keep any attributes in R <= 4.0 ## svn c80082/80141's change to grep.R broke several of these -- the PR#18063 saga check_regexetc <- function(txt, fx.ptn, s.ptn, gr.ptn, msg = stop) { stopifnot(is.character(txt)) chkString <- function(ch) { if(!is.character(ch)) { str(ch); stop("is not a character") } if(length(ch) != 1) { str(ch); stop("is not of length 1") } } chkString(fx.ptn) chkString( s.ptn) chkString(gr.ptn) ## ref: result using "character"; ## x : from as.character(.) w/ "lost" attributes identC <- function(x, ref) { attributes(ref) <- attributes(ref)[names(attributes(x))] identical(x, ref) } a2_fns <- expression(grepl, regexpr, gregexpr, regexec) # plus possibly: if(getRversion() >= "4.1") a2_fns <- c(a2_fns, expression(gregexec)) exclude <- NA # (the default, used in factor(.., exclude=*) ## for (txt_i in 1:3) { if (txt_i == 2) { # txt_i \in {2, 3} will have NA in 'txt' txt <- c(NA_character_, txt, NA_character_) } else if (txt_i == 3) { exclude <- NULL } txt_fkt <- factor(txt, exclude = exclude) cat("txt_i = ", txt_i,"; str():\n", sep="") ; str(txt_fkt) if(chkpre <- !is.null(names(txt_fkt)) && length(levels(txt_fkt)) < length(txt_fkt)) { txt_fkt_pre <- txt_fkt[seq(levels(txt_fkt))] cat("str(txt_fkt_pre):\n") ; str(txt_fkt_pre) } for (ptn in c(fx.ptn, s.ptn, gr.ptn, NA_character_)) { fixed <- (!is.na(ptn) && ptn == fx.ptn) perl <- (!is.na(ptn) && ptn == gr.ptn) ptn_ch <- if(is.na(ptn)) ptn else dQuote(ptn, q=NULL) cat(sprintf(" pattern=%16s, fixed=%s, perl=%s: ", ptn_ch, fixed, perl)) for (e_2 in a2_fns) { f_2 <- eval(e_2) f_2s <- as.character(e_2) ## when ptn == NA_character_ only test grep() & grepl() : if(is.na(ptn) && !(f_2s %in% c("grep", "grepl"))) next cat(f_2s,"") if(!identical( f_2(ptn, txt_fkt, fixed = fixed, perl = perl), f_2(ptn, txt, fixed = fixed, perl = perl) )) msg(sprintf( "not identical: %s(%s, txt*, fixed=%s, perl=%s)", f_2s, ptn_ch, fixed, perl)) } cat("\n\t grep(*, invert=F/T, value = F/T): ") for(iv in list(c(FALSE,FALSE), c(TRUE,FALSE), c(FALSE,TRUE), c(TRUE,TRUE))) if(!identical( grep(ptn, txt_fkt, fixed = fixed, perl = perl, invert=iv[1], value = iv[2]), grep(ptn, txt, fixed = fixed, perl = perl, invert=iv[1], value = iv[2]) )) msg(sprintf( "not identical: grep(%s, txt*, fixed=%s, perl=%s, invert=%s, value=%s)", ptn_ch, fixed, perl, iv[1], iv[2])) cat("f_3, i.e. *sub() :") for (e_3 in expression(sub, gsub)) { ## --- ----- f_3 <- eval(e_3) f_3s <- as.character(e_3) cat(f_3s,"") if(!identC(##identical( res <- f_3(ptn, "@@", txt_fkt, fixed = fixed, perl = perl), f_3(ptn, "@@", txt, fixed = fixed, perl = perl) )) msg(sprintf( "not identical: %s(%s, \"@@\", txt*, fixed=%s, perl=%s)", f_3s, ptn_ch, fixed, perl)) if(chkpre && is.null(names(f_3(ptn, "@@", txt_fkt_pre, fixed = fixed, perl = perl))) != is.null(names(res)) ) msg(sprintf( "not identical pre: names(%s(%s, \"@@\", txt_fkt*, fixed=%s, perl=%s))", f_3s, ptn_ch, fixed, perl)) } cat("\n") } cat("--------- finished txt_i = ", txt_i,"\n") } } ## end{ check_regexetc } if(requireNamespace("codetools", quietly = TRUE)) codetools::findGlobals(check_regexetc, merge=FALSE) ## "default check" txt <- c( "The", "licenses", "for", "most", "software", "are", "designed", "to", "take", "away", "your", "freedom", "to", "share", "and", "change", "it.", "", "By", "contrast,", "the", "GNU", "General", "Public", "License", "is", "intended", "to", "guarantee", "your", "freedom", "to", "share", "and", "change", "free", "software", "--", "to", "make", "sure", "the", "software", "is", "free", "for", "all", "its", "users") names(txt) <- paste0("c", seq_along(txt)) if(FALSE) system.time(check_regexetc(txt, fx.ptn = "e", s.ptn = "e.", gr.ptn = "(?e)(?.)", msg=warning)) check_regexetc(txt, fx.ptn = "e", s.ptn = "e.", gr.ptn = "(?e)(?.)") ##============ x <- c("e", "\xe7") Encoding(x) <- "UTF-8" x <- factor(c(1, 1, 2), c(1, 2), x) tools::assertWarning(grep("e", x, fixed = TRUE)) ## broken by svn c80136 ## "difftime" objects pmin() .. & modifications when "units" differ -- PR#18066 x_hr <- as.difftime(1:10, units = "hours") y_hr <- as.difftime( 5, units = "hours") y_mi <- `units<-`(y_hr, "mins") x_na <- `[<-`(x_hr, 2L, NA_real_) stopifnot(exprs = { ## these all are FALSE in R <= 4.0.* inherits(rep(y_hr, 5L), "difftime") identical(`[<-`(x_hr, 1L, y_hr), `[<-`(x_hr, 1L, y_mi)) identical(pmin(x_hr, y_hr), pmin(x_hr, y_mi)) identical(pmin(x_na, y_hr, na.rm = TRUE), pmin(x_na, y_mi, na.rm = TRUE)) }) ## objects became wrong without warning in R <= 4.0.x ## Bytes Enc may be unset directly to unknown (impossible R <= 4.0.x) x <- "fa\xE7ile" Encoding(x) <- "bytes" xu <- x Encoding(xu) <- "unknown" stopifnot(identical(Encoding(c(x, xu)), c("bytes", "unknown"))) proc.time() - .pt; .pt <- proc.time() ## Correctness tests for sorted ALTREP handling of unique/duplicated (PR#17993) ------ altrep_dup_test <- function(vec, nalast, fromlast, s3class) { svec_ar <- sort(vec, na.last = nalast) svec_std <- svec_ar svec_std[1] <- svec_std[1] ## this clobbers ALTREP-ness if(!is.null(s3class)) { class(svec_ar) <- s3class class(svec_std) <- s3class } stopifnot(identical(duplicated(svec_ar, fromLast = fromlast), duplicated(svec_std, fromLast = fromlast)), identical(unique(svec_ar, fromLast = fromlast), unique(svec_std, fromLast = fromlast)), identical(anyDuplicated(svec_ar, fromLast = fromlast), anyDuplicated(svec_std, fromLast = fromlast)) ) } altint_dup_check <- function(vec, numna, nalast, fromlast, s3class = NULL) { if(length(vec) > 0 && numna > 0) { vec[1:numna] = NA_integer_ } altrep_dup_test(vec, nalast = nalast, fromlast = fromlast, s3class = s3class) } altint_dup_multicheck <- function(vec, numna, s3class = NULL) { altint_dup_check(ivec, numna, FALSE, FALSE, s3class = s3class) altint_dup_check(ivec, numna, FALSE, TRUE, s3class = s3class) altint_dup_check(ivec, numna, TRUE, FALSE, s3class = s3class) altint_dup_check(ivec, numna, TRUE, TRUE, s3class = s3class) } altreal_dup_check <- function(vec, numna, numnan, numinf, nalast, fromlast, s3class = NULL) { if(length(vec) > 0) { ## on Intel adding 0 changes the NA_real_ NaN from signaling ## to non-signaling if(numna > 0) { vec[1:numna] <- rep(c(NA_real_, NA_real_ + 0), length.out = numna) } if(numnan > 0) { vec[seq(1 + numna, numna + numnan)] <- rep(c(NaN, NaN + 0), length.out = numnan) } if(numinf > 0) { infstrt <- 1 + numna + numnan vec[seq(infstrt, infstrt + numinf - 1)] <- rep(c(Inf, -Inf), length.out = numinf) } } ## end length(vec) > 0 altrep_dup_test(vec, nalast = nalast, fromlast = fromlast, s3class = s3class) } altreal_dup_multicheck <- function(vec, numna, numnan, numinf, s3class = NULL) { altreal_dup_check(ivec, numna, numnan, numinf, FALSE, FALSE, s3class = s3class) altreal_dup_check(ivec, numna, numnan, numinf, FALSE, TRUE, s3class = s3class) altreal_dup_check(ivec, numna, numnan, numinf, TRUE, FALSE, s3class = s3class) altreal_dup_check(ivec, numna, numnan, numinf, TRUE, TRUE, s3class = s3class) } ## NB buffer size used by ITERATE_BY_REGION macros is 512, so we need to test ## handling of NAs, NaNs, and Infs around/past that barrier. set.seed(83); dvec <- round(runif(2000, 1, 20), 1) ivec <- ceiling(dvec) altint_dup_multicheck(ivec, 0) ## just before buffer break altint_dup_multicheck(ivec, 512) ## just after buffer break altint_dup_multicheck(ivec, 513) ## all nas altint_dup_multicheck(ivec, 2000) altreal_dup_multicheck(dvec, 0, 0, 0) ## NA/NaN up to edge of 1 buffer altreal_dup_multicheck(dvec, 256, 256, 0) ## NA/NaN crossing buffer barrier altreal_dup_multicheck(dvec, 256, 257, 0) ## all NA/NaN altreal_dup_multicheck(dvec, 1000, 1000, 0) ## non-finite filling exactly one buffer on each side altreal_dup_multicheck(dvec, 0, 0, 1024) ## non-finite across more than one buffer on both sides altreal_dup_multicheck(dvec, 0, 0, 1026) ## all non-finite altreal_dup_multicheck(dvec, 0, 0, 2000) ## sanity checks ## no breakage on length 0 vectors altint_dup_multicheck(integer(0), 0) altreal_dup_multicheck(numeric(0), 0, 0, 0) ## works on on length 1 vectors altint_dup_multicheck(1L, 0) altreal_dup_multicheck(1.0, 0, 0, 0) ## s3 methods take precedence over altrep methods ## these methods are (very) wrong on purpose so there can be ## no doubt they are hit rather than the altrep code even in the sorted case duplicated.fake_class <- function(x, incomparables = FALSE, ...) { rep(c(TRUE, FALSE), length.out = length(x)) } unique.fake_class <- function(x, incomparables = FALSE, ...) { x[c(1, 5, length(x))] } altint_dup_multicheck(ivec, 0, s3class = "fake_class") altreal_dup_multicheck(dvec, 0, 0, 0, s3class = "fake_class") ##----------------------------------- end of tests for sorted ALTREP ... (PR#17993) ------ proc.time() - .pt; .pt <- proc.time() ## seq(from, to, *) i.e. seq.default() *and* seq.int(..) in case of large ## from & to, notably *infinite (to - from) : seq (-1.5e308, 1e308, by=1e307) # gave error in R <= 4.1.0 seq (-1.5e308, 1.6e308, length.out=33)# all Inf apart from first & last ## and these two where identical to seq(), aka seq.default() seq.int(-1.5e308, 1e308, by=1e307) seq.int(-1.5e308, 1.6e308, length.out=33) ## more systematically: ------------------------------------------------------ ## test a series B <- .Machine$double.xmax; B. <- 1.79769e308 Lby <- lapply(1:25, function(N) seq.int(-.99*B, B , by = N*2e306) / B) LbyR <- lapply(1:25, function(N) seq.default(-.99*B, B , by = N*2e306) / B) Llen <- lapply(2:26, function(N) seq.int(- B, B., length.out = N) / B) LleR <- lapply(2:26, function(N) seq.default(- B, B., length.out = N) / B) ## first diff should be constant relE <- function(x) { m <- mean(x); max(abs(x - m) / m) } relEdiff <- function(L) vapply(lapply(L, diff), relE, 1.23) by <- 1e307 stopifnot(exprs = { ## C = R : seq.int() <==> seq.default : all.equal(Lby , LbyR, tol=1e-15) all.equal(Llen, LleR, tol=1e-15) ## by : abs(diff(s <- seq.int(-1.5e308, 1e308, by=by))/by - 1) < 1e-14 is.matrix(rng <- vapply(Lby, range, numeric(2))) all.equal(rep(-.99, 25), rng[1,]) 0.79 <= rng[2,] ; rng[2,] <= 0.991 ## length.out is.matrix(rng <- vapply(Llen, range, numeric(2))) all.equal(rep( -1, 25), rng[1,]) all.equal(rep(B./B, 25), rng[2,]) ## first diff s: abs(relEdiff(Llen) / lengths(Llen)^1.5) < 2e-16 # see max ~3e-17 abs(relEdiff(Llen) / lengths(Llen)^1.5) < 2e-16 # (ditto) }) ## cosmetic: suppress warning that was never intended (from *this* call): op <- options(warn = 2)# no warnings aP <- .axisPars((1:2)* 777, log=TRUE) stopifnot(identical(aP, list(axp = c(Inf, Inf), n = 1L))) ## gave warning (turned into error) in R <= 4.1.0 ## all.equal(x,y) when 'x' or 'y' are close to overflowing to +/- Inf: set.seed(7); x <- c(outer(pi^(-4*(-3:4)), 1:7)); y <- x*(1+rt(x, 3)/1e9) stopifnot(all.equal(x,y, tol=8e-8)) for(f in c(10^c(-308:-300, 300:308), rlnorm(2^9, 3, 4))) stopifnot(all.equal(f*x, f*y, tol=8e-8)) ## failed for 1e301 (and larger) in R <= 4.1.0 ## check that some primitives don't increment reference counts x <- c(1); old_xr <- .Internal(refcnt(x)) sum(x) range(x) round(x) (nxr <- .Internal(refcnt(x))) stopifnot(nxr == old_xr) x <- logical(1); old_xr <- .Internal(refcnt(x)) all(x) stopifnot(.Internal(refcnt(x)) == old_xr) ## the counts were 6 and 2 instead of 1 in R <= 4.1.0 ## Value stored in .Last.value needs to count at least one reference c(1) stopifnot(1 + .Last.value + .Last.value == 3) ## c79505 made match() possibly convert NA_character_ to "NA" (PR#18126). stopifnot(is.na(match(c("NA", "\u{e0}"), NA))) ## pretty(x) when range(x) is finite but diff(range(x)) is +/- Inf: B <- 1e308; 2*B; (s <- seq(-B,B,length.out = 3)) options(warn=1) # => warnings *as they happen* (ps <- pretty(c(-B,B))) ## Warning in pretty.default(c(-B, B)) : ## Internal(pretty()): very large range 4e+307, corrected to 2.24712e+307 nps <- length(ps) dd <- sum((dps <- diff(ps))/length(dps)) # mean w/o overflow epsC <- .Machine$double.eps relD <- (dps/dd - 1)/epsC relEr <- function(f, y) abs((f-y)/(f+y)*2) # cheap relative error, |f| > 0 ! stopifnot(is.finite(mean(ps)), ## these all failed without "long-double" is.finite(mdp <- mean(dps)), all.equal(dd, mdp, tolerance=1e-15)) stopifnot(relEr(c(-B,B), ps[c(1L,nps)]) <= 4*epsC, -8 <= relD, relD <= 8) # seen [-1.5,.., 3.0]; w/o long-double: [-5, .., 4] ## ps was 0 Inf Inf Inf Inf Inf Inf Inf Inf Inf 0 , in R <= 4.1.0 f. <- c(-1.797, -1.79, -1.75, seq(-1.7, -1, by=.1)) stopifnot(!is.unsorted(f.)) ; f.nm <- setNames(, f.) fmtRng <- function(x) paste(format(range(x)), collapse=", ") ns <- c(2:12, 15, 20, 30, 51, 100, 2001, 1e5) nms.n <- formatC(ns, digits=0, format="f") nmsRng <- c(t(outer(paste0("r",1:2), c("lo","hi"), paste, sep="."))) rr <- matrix(NA, length(ns), 4, dimnames=list(nms.n, nmsRng)) for(i.n in seq_along(ns)) { n <- ns[i.n] cat("n = ", n,":\n--------\n") pBL <- lapply(f., function(f) structure(pretty(c(f*1e308, 2^1023.9), n), f=f)) ## -> a warning per f n.s <- lengths(pBL) # how close to target 'n' ?? cat("lengths(.) in [", fmtRng(n.s), "]\n") if(n <= 15) stopifnot(n.s <= 20)# seen {14,..,17} else stopifnot(abs(n.s/n - 1) <= 1/2) if(n) cat("length(.) <> n relative err in [", fmtRng(n.s/n - 1), "]\n") ## .pretty(*, bounds=FALSE) : prM <- t(sapply(f.nm, function(f) unlist( .pretty(c(f*1e308, 2^1023.9), n, bounds=FALSE) ))) print(prM) luM <- prM[,c("ns","nu")] * prM[,"unit"] # the pretty-scaled unit r1 <- luM[,"ns"] / (f.nm*1e308) rr[i.n, 1:2] <- r1 <- range(r1) cat(sprintf("range(r1): [%g, %g]\n", r1[1], r1[2])) r2 <- luM[,"nu"] / 2^1023.9 rr[i.n, 3:4] <- r2 <- range(r2) cat(sprintf("range(r2): [%g, %g]\n", r2[1], r2[2])) stopifnot(exprs = { is.matrix(prM) prM[,"nu"] - prM[,"ns"] == prM[,"n"] # could differ, but not for this data identical(colnames(prM), c("ns", "nu", "n", "unit")) ## These bounds depend on 'n' : r1 >= if(n <= 12) 0.55 else 0.89 r1 <= if(n <= 15) 1.4 else 1.1 r2 >= if(n <= 12) 0.58 else 0.95 r2 <= if(n <= 15) 1 else 1.025 }) invisible(lapply(pBL, function(ps) { mdB <- sum((dB <- diff(ps))/length(dB)) rd <- dB/mdB - 1 # relative differences ## print(range(rd)) x <- c(attr(ps,"f")*1e308, 2^1023.9) stopifnot(if(n >= 1) abs(rd) <= n * 3e-15 else TRUE, ps[1] <= x[1] , x[2] <= ps[length(ps)]) })) } ## stopifnot(abs(rr-1) < 3.3/ns) ## many of these pretty() calls errored (because internally gave Inf) in R <= 4.1.0 ## ##---------------- very small ranges ------------------ ## The really smallest positive number (unless subnormals do "not exist"): mm <- with(.Machine, double.xmin * double.eps) log2(mm) == -1074 # T ## "of course", this an extreme *sub normal* number, e.g. mm == c(0.50001, 1.49999) * mm # TRUE TRUE (!) (1.5*mm) / mm # 2 (!!) ## nns0 <- setNames(,0:28) # n=0,1 give often warnings (and make no difference!) nns <- setNames(,2:30) fs <- c(.05, .1, .25, .375, .5, .75, .9, .95, .99, .995, .999, .9999, .99999) names(fs) <- sub("^0", "", formatC(fs)) h.u <- c(.5, 1, 1.5, 2, 2.5, 3, 4, 6, 10); names(h.u) <- formatC(h.u); h.u ## for mm/f, *sub*normal: fsS <- fs[fs <= 0.75] options(warn=0) # (collect warnings) psmm <- lapply(h.u, function(hu) lapply(fsS, function(f) lapply(nns, pretty, x = c(0, mm/f), high.u=hu, eps.correction = 2))) summary(warnings())## many; mostly "very small range 'cell'=0, corrected to 2.122e-314" (T <- table(psA <- unlist(psmm))) # is this portable? (nT <- as.numeric(names(T))) range(rEd <- abs(2e-314/diff(nT) - 1)) stopifnot(nT >= 0, length(nT) == 11, rEd <= 2^-50) # only seen rEd == 0 ## psmm.o <- lapply(h.u, function(hu) lapply(fsS, function(f) # older R: f.min = 20 hardwired: lapply(nns, pretty, x = c(0, mm/f), high.u=hu, f.min = 20) )) summary(warnings())## many; mostly "very small range 'cell'=0, corrected to 4.45015e-307" (To <- table(psAo <- signif(unlist(psmm.o), 13))) (nTo <- as.numeric(names(To))) range(rEdo <- abs(5e-307/diff(nTo) - 1)) stopifnot(nTo >= 0, length(nTo) == 11, rEdo <= 2^-44) # seen max of 2^-51 on Lnx_64; 2^-44.5 on Win64 ## graphics::axis(), but also *engine* GScale() / GPretty() etc ## when range(.) is finite, but diff(range(.)) is Inf: mplot <- function(..., pch=20, col=2, type="o") { plot(..., pch=pch, col=col, type=type, axes=FALSE) list(a1 = axis(1), a2 = axis(2)) } options(warn=2) # (*no* warnings anymore !) summary(LL <- 2^(994:1024 - 1e-12)) ## simple unproblematic (not in all cases!) a <- mplot(log2(LL), sin(LL)) stopifnot(all.equal(list(a1= seq(995, 1025, by=5), a2= (-2:2)/2), a)) a <- mplot(LL, sin(LL)) # gave infinite axis extents [GEPretty(-7.19077e+306,inf,5)] ## then warning .. plot.window(): Internal(pretty()): very large range, but no longer! al <- mplot(LL, sin(LL), log="x") ## gave Error in axis(1): ## log - axis(), 'at' creation, _LARGE_ range: invalid {xy}axp or par; nint=5 ## axp[0:1]=(1e+299,1e+308), usr[0:1]=(7.28752e+298,inf); i=9, ni=1 stopifnot(exprs = { all.equal(a, list(a1=5e307 * 0:3, a2=(-2:2)/2)) all.equal(al$a1, 10^(299:308)) }) parUAx <- function(pua = par(c("usr", "xaxp"))) { rbind(M <- sapply(pua, `[`, 1:2), D = diff(M)) } mE <- 1024 - 1e-12 if(dev.interactive()) opa <- par(ask=TRUE, xaxs = par("xaxs")) for(xaxs in c("r","i")) { cat(sprintf('xaxs = "%s"\n==========\n', xaxs)); par(xaxs = xaxs) for(e2Min in c(-1074, -1070, -1060, -1050)) { cat("\ne2Min=",e2Min,":\n------------\n") sL <- 2^seq(e2Min, mE, length=128) mplot(sL, sin(sL))# was Error plot.window(): infinite axis extents [GEPretty(-7.19e306,inf,5)] print(puaxN <- parUAx()) mplot(sL, sin(sL), log="x") ## gave Error in axis(side... log - axis(), 'at' creation, _LARGE_ range: .... ## axp[0:1]=(1e-307,1e+308), usr[0:1]=(8.28905e-317,inf); i=615, ni=123 print(puax <- parUAx()) u <- puax[1:2, "usr"] print(axu <- axisTicks(u, log=TRUE)) stopifnot(exprs = { all.equal(puaxN, list("r" = cbind(usr= c(-7.19077254e+306, 2^mE, Inf), xaxp=c(0, rep(1.5e+308,2))), "i" = cbind(usr= 2^c(e2Min, mE, mE), xaxp=c(0, rep(1.5e+308,2))))[[xaxs]]) all.equal(10^cumsum(c(-307, rep(123, 5))), axu, tol=1e-12)# 3.4e-14 {Win64} all.equal(puax[1:2,"xaxp"], c(1e-307, 1e308)) { cat("1 - u / ... : ") abs(print(1 - u / c(c(r=-1022, i=e2Min)[[xaxs]], mE) * log2(10))) < 5e-5 } ## all.equal(u, log10(sL[c(1,length(sL))])) }) } } ## gave warnings: plot.window() .. pretty(): very large range .. corrected to .. if(dev.interactive()) par(opa) ## Just the range: -------------------------------------------------- sL <- 2^c(-1074, mE) mplot(sL, 1:2, yaxt="n")# was Error plot.window(): infinite axis extents [GEPretty(*)] ## works ok now (2nd point: partly clipped off) (puax <- parUAx()) # usr *and* axp where = Inf, now axp is finite! ## stopifnot(all.equal( c(0, rep(1.6e308, 2)), puax[,"xaxp"] )) ## for now: stopifnot( all.equal(rep(1.5e308,2), puax[-1,"xaxp"]) ) all.equal(5e307*(0:3), grid::grid.pretty(range(sL))) # <==> GEPretty() is fine ##============================================================================ ## ## Using LL is *harder*: large on both sides! ==> diff(LL) == Inf (LL <- c(-1,1)* 2^mE) # similarly bad as 'sL' (cut-off points to the very left..) a <- mplot(LL, 0:1) # (no warning) (puax <- parUAx()) ## diff(usr) = Inf, but xaxp is ok ==> axis labels "fine" stopifnot(exprs = { all.equal(a$a1, axTicks(1)) all.equal(a$a1, (-3:3)*5e307) all.equal(LL, puax[1:2,"usr"], tol=1e-10) puax[3,] == Inf }) ## These are even a bit better (no partial clipping) {gave error in R <= 4.1.0}: a2 <- mplot(LL/2, 1:2, yaxt="n") a75 <- mplot(LL/1.75, 1:2, yaxt="n") (puax <- parUAx()) stopifnot(exprs = { all.equal(a2 $a1, (-1:1)*5e307) all.equal(a75$a1, (-2:2)*5e307) all.equal(a75$a1, axTicks(1)) puax[3,] == Inf all.equal(c(-1,1)*1e308, puax[1:2,"xaxp"]) }) ## axisTicks(), axis() -- graphics *engine* & {graphics} -- "unpretty" in R <= 4.1.x for(yMin in c(0, 5e-324, 1e-318, 1e-312, 1e-306)) { W <- NULL withCallingHandlers( plot(1:2, (1:2)/16, ylim = c(yMin, 1), log="y", main= sprintf("ylim = c(%g, 1)", yMin)) , warning = function(w){ W <<- w ; invokeRestart("muffleWarning") }) if(englishMsgs && yMin == 0 && !is.null(W)) stopifnot(grepl("nonfinite axis=2 limits [GScale(-inf,", conditionMessage(W), fixed=TRUE)) atx <- axisTicks(par("usr")[3:4], log=TRUE, axp=par("yaxp")) # ditto if(yMin > 0) { print(axT <- axTicks(2)) # 1e-307 1e-244 1e-181 1e-118 1e-55 1e+08 stopifnot(all.equal(axT, atx, tol = 1e-15)) } stopifnot(all.equal(atx, 10^cumsum(c(-307, rep(63, 5))), tol=1e-13)) # Win64: 3.3e-14 } ## the *first* plot looked ugly in R <= 4.1.0 and failed for a few days in R-devel proc.time() - .pt; .pt <- proc.time() ## Error message for missing weave outputs, PR#18154: d.doc <- system.file("doc", package = "utils") (msg <- tryCatch(tools:::find_vignette_product("Sweeeeeave", engine = tools::vignetteEngine("Sweave"), dir = d.doc), error = conditionMessage)) (patt <- paste0(rep("\\([0-9]+ bytes\\)", length(list.files(d.doc))), collapse=".*")) stopifnot(grepl(patt, msg)) ## contained all "(NA bytes)" in R <= 4.1.0 ## density(x_with_NA, weights = *, na.rm=TRUE) -- PR#18151 x <- c(1, 2, NA, 4) w <- rep(1/4, 4) # summing to one ! dxw <- density(x, weights=w, na.rm=TRUE) ## gave Error dx3 <- density(x[-3], weights=w[-3], subdensity = TRUE) dx3w <- density(x[-3], weights=w[-3]*4/3) dx3. <- density(x[-3]) (cmpN <- setdiff(names(dxw), c("call","data.name"))) stopifnot(exprs = { all.equal(dxw[cmpN], dx3.[cmpN]) all.equal(dxw[cmpN], dx3w[cmpN]) all.equal(dxw$bw, dx3$bw) all.equal(dxw$y, dx3$y * 4/3) }) ## in R <= 4.1.0, Error in density..: 'x' and 'weights' have unequal length ## residuals() were is.object(.) & failed in qqline() x <- sort(runif(20)) y <- (2*x^(1/3) + rnorm(x)/16)^3 summary(fit <- lm(I(y ^ (1/3)) ~ I(x ^ (1/3)))) ## only `which = 2` (QQ plot) failed here plot(fit, which = 2) # gave Error: $ operator is invalid for atomic vectors stopifnot(class(r <- residuals(fit)) == "numeric", # was "AsIs" names(r) == as.character(seq_along(r))) ## in R <= 4.1.1, plot.lm() -->> qqline() -->> abline() wrongly chose coef(.) ## qqline(, *) - also from PR#18190 qqline(I(1:12)) ## --> $ operator is invalid for atomic vectors (from coef() in abline()) ## More "rational" as.character() for and , ## fulfilling the "law" as.(x)[j] === as.(x[j]) i <- matrix(0:21, 2) FT <- c(FALSE,TRUE); names(FT) <- c("F", "T") hiL <- lapply(FT, function(kp) as.character(as.hexmode(i), keepStr = kp)) oiL <- lapply(FT, function(kp) as.character(as.octmode(i), keepStr = kp)) stopifnot(exprs = { identical(dim (hiL[["T"]]), dim(i)) identical(nrow(oiL[["T"]]), nrow(i)) identical(hi <- hiL[["F"]], as.vector(hiL[["T"]])) ; is.null(dim(hi)) identical(oi <- oiL[["F"]], as.vector(oiL[["T"]])) ; is.null(dim(oi)) hi[1:8] == as.character(0:7) oi[1:8] == hi[1:8] c(nchar(hi)) == rep(1:2, c(16,6)) c(nchar(oi)) == rep(1:2, c(8,14)) }) ## as.character.*() methods had used format() previously; now by default drop, dim() etc ## within.list() & within.data.frame() assumed setdiff(a, b) to always eval 'b' stopifnot(exprs = { identical(list(1, let="abc"), within(list(1), let <- "abc")) identical(data.frame(let = character()), within(data.frame(), let <- character())) })# failed for ~ 40 hours in R-devel ## mapply() & Map() follow usual "max-or-0-if" recycling rule and keeps ## returning a named list in the "empty" case. nL0 <- setNames(list(), character()) # named empty list stopifnot(exprs = { identical(list(), mapply(`+`, 1:3, NULL)) identical(nL0, mapply(paste, character(), NULL)) identical(nL0, mapply(paste, character(), letters)) identical(nL0, mapply(paste, "A", character()) ) identical(nL0, mapply(paste, character(), letters) ) }) ## zero-length argument with non-zero one errored in R <= 4.1.x ## substr(ch, beg, end) <- CH preserving attributes incl. names ch <- c("one", "two", "three", "four", "5") Ch <- setNames(,ch); attr(Ch, "foo") <- "bar" at <- attributes(Ch) substring(ch, 2) <- c("||", "+++"); ch # recycling along ch substring(Ch, 2) <- c("||", "+++") stopifnot(Ch == ch, identical(at, attributes(Ch))) ## Ch had lost all attributes in R <= 4.1.x ## ## negative `stop` values stopifnot(identical(`substr<-`("A", 1, -1, "_"), "A")) ## were treated as `(size_t) stop` in R <= 4.1.2 ## dimnames(table(.)) in the 1D list/data.frame case: (dnn <- dimnames(table(warpbreaks[3]))) dn <- dimnames(table(warpbreaks[2], dnn = "abc")) stopifnot(identical(dnn, list(tension = levels(warpbreaks[[3]]))), identical(dn, list(abc = c("A","B")))) # not ok in R-devel only ## dnn had no names() in R <= 4.1.x ## ## table(<1-column data frame>), #c3 in PR#18224 stopifnot({ names(dimnames(t1 <- table(FOO = list(warpbreaks[[2]])))) == "FOO" names(dimnames(t2 <- table( list(warpbreaks[[2]])))) == "" }) ## had a trailing ".1" for a while in R-devel only ## ## table(, ) now signals an error (PR#18224): options(warn=0) -> op2 r <- tryCid( table(warpbreaks[2], warpbreaks[3]) ) stopifnot(inherits(r, "error"), getOption("warn") == 0, grepl("cannot\\b.* data frame", conditionMessage(r))) m1 <- tryCmsg(table(exclude=NA, warpbreaks[2], warpbreaks[3])) m2 <- tryCmsg(table(data.frame(a = 1, d = I(data.frame(x = 1))))) stopifnot(exprs = { is.character(m1) identical(m1, m2) !englishMsgs || grepl("cannot xtfrm data frames", m1) }) options(op2) ## factor() works fine, hence table(), does too: tm <- as.POSIXlt(c("1990-07-01", "1990-07-01", "1991-01-01")) stopifnot(exprs = { is.table(t2 <- table(mon = tm$mon, time = tm)) t2 == c(0L,2:0) is.table(t1 <- table(list(time = tm))) t1 == 2:1 }) ## Wrong deparse()ing: not setting parens around ' if(..) .. else .. ' --- PR#18232 ## from Duncan Murdoch -- e1 and e2 are obviously different expressions : e1 <- quote(5 * if (TRUE) 2 else 3 /4) e2 <- quote(5 * (if (TRUE) 2 else 3)/4) # evaluating differently stopifnot(eval(e1) == 10, eval(e2) == 2.5) ## an equivalent version of e2 (same parse tree, but ..): ie <- 2:3; e2[[ie]] # (if (TRUE) 2 else 3) e3 <- e2 ; (e3[[ie]] <- e3[[c(2,3,2)]]) # missing the parens '( . )' e3 ## e3 behaves *still* like e2: stopifnot(eval(e3) == 2.5, deparse(e3) == deparse(e2)) ## in R <= 4.1.x, e3 looked (i.e. was deparsed) like e1 -- wrongly ## remove.packages( is.vector(as.vector(d.f)) stopifnot(exprs = { ! is.vector(data.frame(a=1)) is.vector(as.vector(d.f) -> l.df) identical(as.vector(d.f, mode="list"), l.df) identical(as.list(d.f), l.df) }) ## PR#18244: [ ] m <- matrix(1:9, 3) i <- cbind(letters, letters) ul <- unique(replicate(1e4, tryCid(m[i]), simplify = FALSE)) (msg <- conditionMessage(ul[[1]])) a4 <- array(1:10, dim=c(2,5,1,1)) u4.<- unique(replicate(1e4, tryCid(a4[i]), simplify = FALSE)) i4 <- cbind(i,i) u4 <- unique(replicate(1e4, tryCmsg(a4[i4]), simplify = FALSE)) stopifnot(exprs = { length(ul) == 1 inherits(ul[[1]], "error") !englishMsgs || identical(msg, "no 'dimnames' attribute for array") identical(u4., list(rep(NA_integer_, length(i)))) length(u4) == 1 ; is.list(u4) !englishMsgs || identical(u4[[1]], msg) }) ## gave "random" results in R <= 4.1.2 ## PR#17977 --- x[] behavior should fulfill x[i] === x[as.integer(i)] x <- 1:3 stopifnot(exprs = { identical(x[-3.5], x[-3]) identical(x[-0.5], x[0]) ; identical(x[0], integer()) identical(x[c(-.5, .5)], x[0]) identical(x[c(-1, .5)], x[-1:0]) }) ## Now for `[[` : x <- 1:3 (e05 <- tryCmsg(x[[0.5]])) if(englishMsgs) stopifnot(grepl("attempt to select less than one element", e05)) eN <- tryCmsg(x[[-0.5]]) stopifnot(identical(e05, eN)) (e2 <- tryCmsg((1:2)[[-0.5]])) stopifnot(identical(e05, eN), identical(e05, e2), identical((1:2)[[-1.5]], 2L)) (s <- (1:2)[[-1.5]]) stopifnot(identical(s, (1:2)[[-1L]]), identical(s, 2L)) ## check.bounds: op <- options(warn = 2, check.bounds=TRUE) x <- NA; x[1.5] <- 3.3 ; options(op) stopifnot(identical(x, 3.3)) ## gave a wrong warning in R <= 4.1.x ## all.equal.numeric(*, scale=s) where length(s) > 1 -- PR#18272 stopifnot( identical("Mean scaled difference: 1", all.equal(c(1, 1), c(1.01, 1.01), scale = c(.01, .01)))) ## gave error when _R_CHECK_LENGTH_1_LOGIC2_ was set and length 2 answer otherwise one <- rep(1,5) stopifnot(all.equal(one, one+(-1:3)/1e9, scale=1:5)) ## gave Error .. (converted from warning) longer object length is not a multiple .. ## all.equal() no longer wrongly warns stopifnot(all.equal(SSfol, SSfol)) ## gave Error .. from warning 'all.equal.default()' is deprecated ## reformulate() error msg [part of PR#18281]: (msg <- tryCmsg(reformulate(paste0("x", 1:8), response = c("y","z")))) if(englishMsgs) stopifnot(grepl("must be a character string", msg)) ## was 'Error in doWithOneRestart(return(expr), restart) : bad error message' ### globalCallingHandlers() when being called inside withCallingHandlers(), PR#18257 globalCallingHandlers(NULL) stopifnot(identical(globalCallingHandlers(), list())) ## Register a global calling handler for messages globalCallingHandlers(message = function(m) { cat("Hey, message :", conditionMessage(m)) invokeRestart("muffleMessage") }) h1 <- globalCallingHandlers() ## Confirm that it is registered stopifnot(is.list(h1), length(h1) == 1, is.function(h1$message)) ## and verify it works stopifnot(identical(capture.output(message("boom")), "Hey, message : boom")) ## Now try to remove all global calling handlers while having active ## calling handlers; gives a non-tryCatch()able (!) error, hence: op <- options(catch.script.errors = TRUE) # careful!! ## ... "should not be called with handlers on the stack" [as expected] withCallingHandlers(globalCallingHandlers(NULL), foo = identity) options(op)# revert to sanity. Then: h2 <- globalCallingHandlers() globalCallingHandlers(NULL)# unregister all stopifnot(identical(h1, h2)) ## h2 was empty list() erronously in R versions <= 4.1.x ## PR#18246: par() should warn about invalid/unused arguments tools::assertWarning({usr <- par("usr"); par(usr)}, verbose = TRUE) tools::assertWarning(par(las = 1, list(cex = 2))) ## silently did not have the "intended" effect; eventually may become errors ## window(x, *) now uses fuzz also for 'start < end' -- PR#17527 & PR#18291 ## Start the time series from CE 1: (x2 <- ts(1:20, start = 1, frequency = 12)) stopifnot(identical(end(x2), c(2,8))) (wx2 <- window(x2, start = c(2, 8), end = c(2, 8))) # always fine wxs <- window(x2, start = c(2, 8)) ## gave error ...: 'start' cannot be after 'end' stopifnot(identical(wxs, wx2), as.numeric(wx2) == 20) ## PR#18291 x <- ts(1:8434, start=c(1999,4,1), frequency=366) s0 <- start(x); stopifnot(identical(s0, c(1999, 4))) e0 <- end(x); stopifnot(identical(e0, c(2022,19))) s <- c(2022, 1) y1 <- window(x, start=s) stopifnot(identical(y1, window(x, start=s, end=e0))) ## now, with 'end' clearly *beyond* end(x): tools::assertWarning(y3 <- window(x, start=s, end=c(2022,24), verbose=TRUE)) ## -> Warning: 'end' *not* changed -- indeed: stopifnot(identical(end(y3), end(x))) ## this *also* gives the warning as it should, but wrongly errored tools::assertWarning(y2 <- window(x, start=c(2022,19), end=c(2022,20))) stopifnot(identical(end(y2), end(x)), y2 == x[length(x)]) ## in R <= 4.1.2, wrongly signalled Error: 'start' cannot be after 'end' ## print(smooth.spline()) failure when using special call f <- function(..., cv=FALSE) smooth.spline(..., cv=cv) x <- (1:23)/4 (f(x, y=sin(x))) ## gave an error in R <= 4.1.2 ## smooth.spline(x, y, [w, ], *)$cv.crit depending on sort()ed x -- PR#18294 x <- 1:10 e <- c(12, -16, 2:0, -49, -32, -9, -64, 60)/16 y <- x^2 + e sspline_ <- function(x, y, w=NULL, cv=TRUE, ...) smooth.spline(x, y, w=w, cv=cv, # see more: control.spar = list(trace=TRUE), keep.stuff=TRUE, keep.data=FALSE) noC <- function(x) { x$call <- NULL; x } # as the 'call's often differ i <- c(8:5, 3:4, 2:1, 9:10)# 10:1 is too special (a permutation which is its own inverse) ss <- sspline_(x=x, y=y ) ss.u <- sspline_(x=x[i], y=y[i]) ## was "Component “cv.crit”: Mean relative difference: 3099.013" : all.equal(noC(ss), noC(ss.u), tol=0) # TRUE (!) stopifnot(all.equal(noC(ss), noC(ss.u), tol=1e-14)) ## now fixed ## The same with __weights__ some of which exactly 0 table(w <- pmax(0, abs(16*e)-1)) # 2 x 0 ssw <- sspline_(x=x, y=y, w=w ) ssw.u <- sspline_(x=x[i], y=y[i], w=w[i]) all.equal(noC(ssw), noC(ssw.u), tol=0) # TRUE (!) stopifnot(all.equal(noC(ssw), noC(ssw.u), tol=1e-14)) ## now fixed ## was "Component “cv.crit”: Mean relative difference: 60.05904" ## Now with GCV instead of CV ==================== ## 1) no weights ssg <- sspline_(x=x, y=y , cv=FALSE) ssg.u <- sspline_(x=x[i], y=y[i], cv=FALSE) all.equal(noC(ssg), noC(ssg.u), tol=0) # TRUE (!) stopifnot(all.equal(noC(ssg), noC(ssg.u), tol=1e-14)) ## now fixed ## 2) with weights sswg <- sspline_(x=x, y=y, w=w , cv=FALSE) sswg.u <- sspline_(x=x[i], y=y[i], w=w[i], cv=FALSE) all.equal(noC(sswg), noC(sswg.u), tol=0) # TRUE (!) stopifnot(all.equal(noC(sswg), noC(sswg.u), tol=1e-14)) ## now fixed ## the same with 'x' that are almost identical so will be collapsed (and weighted): x. <- c(1:2, (1- 1e-7)*4, 4:6, (1- 1e-9)*8, 8:10) ss3w <- getVaW(sspline_(x=x., y=y , w=w )) ss3w.u <- getVaW(sspline_(x=x.[i], y=y[i], w=w[i])) all.equal(noC(ss3w), noC(ss3w.u), tol=0) # TRUE (also previously) stopifnot(all.equal(noC(ss3w), noC(ss3w.u), tol=1e-14)) ## was "Component “cv.crit”: Mean relative difference: 60.05904" if(englishMsgs) stopifnot(attr(ss3w,"warning") == "cross-validation with non-unique 'x' values seems doubtful") ## now with GCV : ss3gw <- sspline_(x=x., y=y , w=w , cv=FALSE) ss3gw.u <- sspline_(x=x.[i], y=y[i], w=w[i], cv=FALSE) all.equal(noC(ss3gw), noC(ss3gw.u), tol=0) # TRUE (also previously) stopifnot(all.equal(noC(ss3gw), noC(ss3gw.u), tol=1e-14)) ## non-ordered 'x' gave wrong $cv.crit in the nx=n case in R <= 4.1.2 ## aggregate(, *) method in lapply() etc -- ## PR18299 L1 <- lapply(X = list(mtcars), FUN = aggregate, x = mpg ~ cyl, mean) mtcars |> aggregate(x = mpg ~ cyl, FUN = mean) -> m stopifnot(identical(L1[[1]], aggregate(mpg ~ cyl, mtcars, mean)), is.data.frame(m), dim(m) == 3:2) ## formula method different 1st arg than generic such that ## both examples failed in R <= 4.1.2 ## rbind.data.frame() : should warn when it does not fully recycle: df <- data.frame(a = 1, b = 2) d22 <- data.frame(a = c(1, 3), b = c(2, 4)) tools::assertWarning(r <- rbind(df, c(3, 4, 5)), verbose=TRUE) L <- FN <- c(cbind, data.frame) # <==> rbind() for matrix and data.frame LC <- lapply(seq_along(FN), function(i) tools::assertWarning( L[[i]] <<- rbind((FN[[i]])(a=1, b=2, c=3, d=4), 5:7, -1, 8:9, integer(), 11:14, NULL, 21:28), verbose=TRUE))# 2 3 4 5 6 7 8 stopifnot(exprs = { all.equal(r, d22) identical(lapply(L, class), list(c("matrix","array"), "data.frame")) identical(dim(L[[1]]), dim(L[[2]])) L[[1]] == L[[2]] # a matrix of TRUE unlist(lapply(LC, function(x) vapply(print(x), inherits, what="warning", NA))) identical(lengths(LC), 1:2) # ^^^^^ 2 warnings in data.frame case }) ## rbind.data.frame(.) did not warn in R <= 4.1.x ## match.arg("",*) etc; PR#17959 (m1 <- tryCmsg(match.arg("", choices = c("", "a")))) (m2 <- tryCmsg(match.arg("", choices = c("", "a", "b")))) stopifnot(!grepl(dQuote(""), m1), !grepl(dQuote(""), m2)) if(englishMsgs) stopifnot(grepl("'arg' should be ", m1), grepl("'arg' should be one ", m2)) ## was 'arg' should be one of “”, “a” ( , “b” ) ## 'R CMD Sweave --clean' / tools::buildVignette(clean = TRUE) ## should only remove *newly created* files/directories -- PR#18242 owd <- setwd(tempdir()) dir.create("subdir") writeLines(c('<<>>=', 'file.create("subdir/dummyfile")', '@'), "Sweave-test-2.Rnw") utils:::.Sweave(c("--clean", "Sweave-test-2.Rnw"), no.q = TRUE) stopifnot(dir.exists("subdir")) setwd(owd) ## the pre-existing directory was removed in R <= 4.1.x ## as.list(): PR#18309 f <- gl(3,2,12, letters[1:3]) nf <- LETTERS[seq_along(f)] names(f) <- nf ; f str(lf <- as.list(f)) stopifnot(identical(nf, names(f)), identical(nf, names(lf))) ## In R <= 4.1.x, the length-1 factor components were named instead ## More accurate tanpi() {calling R's API Rtanpi()}: k <- -999:999 tools::assertWarning(m <- cbind(k/4, tanpi(k/4), deparse.level=2), verbose=TRUE) # NaNs produced for the half integers head(m, 12) ## the non-half quarters give +/- 1; integers give exact 0 : pm1 <- c(1,-1) # +/- 1 stopifnot(tanpi(outer(pm1/4, k, `+`)) == pm1, m[k %% 4 == 0, "tanpi(k/4)"] == 0) ## in R <= 4.1.x, tanpi( +- 1/4 ) values typically were off (by +/- 2^-53) ## plot.lm(which = 5), when leverages are constant -- PR#17840 dd <- expand.grid(a = factor(1:3), b = factor(1:2), c = as.character(1:2), stringsAsFactors = FALSE) dd$y <- rnorm(nrow(dd)) plot(lm(y~a+b+c, dd), which = 5) # gave Error: non-conformable arguments plot(lm(y~ b+c, dd), which = 5) # gave Error: 'x' and 'y' lengths differ r <- tryCatch( plot(lm(y~ c, dd), which = 5) # gave empty plot, noting missing factors , message = conditionMessage) stopifnot("plot(, which=5) gave message and no plot" = is.null(r)) ## failed for character predictors in R <= 4.1.x ### contined in reg-tests-1e.R for R >- 4.3.0 ## keep at end rbind(last = proc.time() - .pt, total = proc.time())