## PR 640 (diff.default computes an incorrect starting time) ## By: Laimonis Kavalieris library(ts) y <- ts(rnorm(24), freq=12) x <- ts(rnorm(24), freq=12) arima0(y,xreg=x, seasonal=list(order=c(0,1,0))) ## Comments: ## PR 644 (crash using fisher.test on Windows) ## By: Uwe Ligges library(ctest) x <- matrix(c(2, 2, 4, 8, 6, 0, 1, 1, 7, 8, 1, 3, 1, 3, 7, 4, 2, 2, 2, 1, 1, 0, 0, 0, 0, 0, 1, 1, 2, 0, 1, 1, 0, 2, 1, 0, 0, 0), nc = 2) fisher.test(x) ## Comments: (wasn't just on Windows) ## PR 653 (extrapolation in spline) ## By: Ian White x <- c(2,5,8,10) y <- c(1.2266,-1.7606,-0.5051,1.0390) fn <- splinefun(x, y, method="natural") xx1 <- fn(0:12) # should be the same if reflected fn <- splinefun(rev(-x),rev(y),method="natural") xx2 <- fn(0:-12) stopifnot(all.equal(xx1, xx2)) # should be the same as interpSpline library(splines) xx3 <- predict(interpSpline(x, y), 0:12) stopifnot(all.equal(xx1, xx3$y)) detach("package:splines") ## Comments: all three differed in 1.2.1. ## PR 698 (print problem with data frames) ## actually, a subsetting problem with data frames fred <- data.frame(happy=c(TRUE, FALSE, TRUE), sad=7:9) z <- try(tmp <- fred[c(FALSE, FALSE, TRUE, TRUE)]) stopifnot(class(z) == "try-error") ## Comments: No error before 1.2.1 ## PR 753 (step can't find variables) ## x <- data.frame(a=rnorm(10), b=rnorm(10), c=rnorm(10)) x0.lm <- lm(a ~ 1, data=x) step(x0.lm, ~ b + c) ## Comments: ## PR 796 (aic in binomial models is often wrong) ## data(esoph) a1 <- glm(cbind(ncases, ncontrols) ~ agegp + tobgp * alcgp, data = esoph, family = binomial())$aic a1 a2 <- glm(ncases/(ncases+ncontrols) ~ agegp + tobgp * alcgp, data = esoph, family = binomial(), weights=ncases+ncontrols)$aic a2 stopifnot(a1 == a2) ## Comments: # both should be 236.9645 ## Follow up: example from Lindsey, purportedly of inaccuracy in aic y <- matrix(c(2, 0, 7, 3, 0, 9), ncol=2) x <- gl(3, 1) a <- glm(y ~ x, family=binomial)$aic stopifnot(is.finite(a)) ## Comments: gave NaN prior to 1.2.1 ## PR 802 (crash with scan(..., what=list(,,))) ## m <- matrix(1:9, 3,3) write(m, "test.dat", 3) try(scan("test.dat", what=list(,,,))) unlink("test.dat") ## Comments: segfaulted in 1.2.0 ## Jonathan Rougier, 2001-01-30 [bug in 1.2.1 and earlier] tmp <- array(list(3), c(2, 3)) tmp[[2, 3]] <- "fred" all.equal(t(tmp), aperm(tmp)) ## PR 860 (Context problem with ... and rbind) Prof Brian D Ripley, 2001-03-03, f <- function(x, ...) { g <- function(x, ...) x rbind(numeric(), g(x, ...)) } f(1:3) ## Error in 1.2.2 f <- function(x, ...) h(g(x, ...)) g <- function(x, ...) x h <- function(...)substitute(list(...)) f(1) ## Error in 1.2.2 substitute(list(...)) ## Error in 1.2.2 ## Martin Maechler, 2001-03-07 [1.2.2 and in parts earlier] tf <- tempfile() cat(1:3,"\n", file = tf) for(line in list(4:6, "", 7:9)) cat(line,"\n", file = tf, append = TRUE) count.fields(tf) # 3 3 3 : ok {blank line skipped} z <- scan(tf, what=rep(list(""),3), nmax = 3) all(sapply(z, length) == 3) ## FALSE in 1.2.2 z <- as.data.frame(scan(tf, what=rep(list(""),3), n=9)) dim(z) ## should be 3 3. Was 2 3 in 1.2.2. read.table(tf) ## gave error in 1.2.2 unlink(tf) ## PR 870 (as.numeric and NAs) Harald Fekjær, 2001-03-08, is.na(as.numeric(" ")) is.na(as.integer(" ")) is.na(as.complex(" ")) ## all false in 1.2.2 ## PR 871 (deparsing of attribute names) Harald Fekjær, 2001-03-08, midl <- 4 attr(midl,"Object created") <- date() deparse(midl) dump("midl", "midl.R") source("midl.R") ## syntax error in 1.2.2 unlink("midl.R") ## PR 872 (surprising behavior of match.arg()) Woodrow Setzer, 2001-03-08, fun1 <- function(x, A=c("power","constant")) { arg <- match.arg(A) formals() } topfun <- function(x, Fun=fun1) { a1 <- fun1(x) print(a1) a2 <- Fun(x,A="power") stopifnot(all.equal(a1, a2)) print(a2) } topfun(2, fun1) ## a1 printed without defaults in 1.2.2 ## PR 873 (long formulas in terms()) Jerome Asselin, 2001-03-08, form <- cbind(log(inflowd1),log(inflowd2),log(inflowd3), log(inflowd4),log(inflowd5),log(inflowd6)) ~ precip*I(Tmax^2) terms(form) # error in 1.2.2 ## PR 881 Incorrect values in non-central chisq values on Linux, 2001-03-21 x <- dchisq(c(7.1, 7.2, 7.3), df=2, ncp=20) stopifnot(all(diff(x) > 0)) ## on 1.2.2 on RH6.2 i686 Linux x = 0.01140512 0.00804528 0.01210514 ## PR 882 eigen segfaults on 0-diml matrices, 2001-03-23 m <- matrix(1, 0, 0) # 1 to force numeric not logical try(eigen(m)) ## segfaults on 1.2.2 ## 1.3.0 had poor compression on gzfile() with lots of small pieces. if (capabilities("libz")) { zz <- gzfile("t1.gz", "w") write(1:1000, zz) close(zz) (sz <- file.info("t1.gz")$size) unlink("t1.gz") stopifnot(sz < 2000) } ## PR 1010: plot.mts (type="p") was broken in 1.3.0 and this call failed. plot(ts(matrix(runif(10), ncol = 2)), type = "p") ## in 1.3.0 readLines(ok=FALSE) failed. cat(file="foo", 1:10, sep="\n") x <- try(readLines("foo", 100, ok=FALSE)) unlink("foo") stopifnot(length(class(x)) == 1 &&class(x) == "try-error") ## PR 1047 [<-data.frame failure, BDR 2001-08-10 test <- df <- data.frame(x=1:10, y=11:20, row.names=letters[1:10]) test[] <- lapply(df, factor) test ## error in 1.3.0 in test[] ## PR 1048 bug in dummy.coef.lm, Adrian Baddeley, 2001-08-10 ## modified to give a sensible test old <- getOption("contrasts") options(contrasts=c("contr.helmert", "contr.poly")) DF <- data.frame(x=1:20,y=rnorm(20),z=factor(1:20 <= 10)) dummy.coef.lm(lm(y ~ z * I(x), data=DF)) dummy.coef.lm(lm(y ~ z * poly(x,1), data=DF)) ## failed in 1.3.0. Second one warns: deficiency of the method. options(contrasts=old) ## PR 1050 error in ksmooth C code + patch, Hsiu-Khuern Tang, 2001-08-12 library(modreg) x <- 1:4 y <- 1:4 z <- ksmooth(x, y, x.points=x) stopifnot(all.equal(z$y, y)) detach("package:modreg") ## did some smoothing prior to 1.3.1. ## The length of lines read by scan() was limited before 1.4.0 xx <- paste(rep(0:9, 2000), collapse="") zz <- file("foo.txt", "w") writeLines(xx, zz) close(zz) xxx <- scan("foo.txt", "", sep="\n") stopifnot(identical(xx, xxx)) unlink("foo.txt") ## as.character was truncating formulae: John Fox 2001-08-23 mod <- this ~ is + a + very + long + formula + with + a + very + large + number + of + characters zz <- as.character(mod) zz nchar(zz) stopifnot(nchar(zz)[3] == 83) ## truncated in 1.3.0 ## substr<-, Tom Vogels, 2001-09-07 x <- "abcdef" substr(x, 2, 3) <- "wx" stopifnot(x == "awxdef") x <- "abcdef" substr(x, 2, 3) <- "wxy" stopifnot(x == "awxdef") x <- "abcdef" substr(x, 2, 3) <- "w" stopifnot(x == "awcdef") ## last was "aw" in 1.3.1 ## reading bytes from a connection, Friedrich Leisch 2001-09-07 cat("Hello World", file="world.txt") con <- file("world.txt", "r") zz <- readChar(con, 100) close(con) unlink("world.txt") stopifnot(zz == "Hello World") ## was "" in 1.3.1. ## prediction was failing for intercept-only model as model frame ## has no columns. d <- data.frame(x=runif(50), y=rnorm(50)) d.lm <- lm(y ~ 1, data=d) predict(d.lm, data.frame(x=0.5)) ## error in 1.3.1 ## predict.arima0 needed a matrix newxreg: Roger Koenker, 2001-09-27 library(ts) u <- rnorm(120) s <- 1:120 y <- 0.3*s + 5*filter(u, c(.95,-.1), "recursive", init=rnorm(2)) fit0 <- arima0(y,order=c(2,0,0), xreg=s) fit1 <- arima0(y,order=c(2,1,0), xreg=s, include.mean=TRUE) fore0 <- predict(fit0 ,n.ahead=44, newxreg=121:164) fore1 <- predict(fit1, n.ahead=44, newxreg=121:164) par(mfrow=c(1,2)) ts.plot(y,fore0$pred, fore0$pred+2*fore0$se, fore0$pred-2*fore0$se, gpars=list(lty=c(1,2,3,3))) abline(fit0$coef[3:4], lty=2) ts.plot(y, fore1$pred, fore1$pred+2*fore1$se, fore1$pred-2*fore1$se, gpars=list(lty=c(1,2,3,3))) abline(c(0, fit1$coef[3]), lty=2) detach("package:ts") ## merging when NA is a level a <- data.frame(x = 1:4) b <- data.frame(x = 1:3, y = factor(c("NA", "a", "b"), exclude="")) (m <- merge(a, b, all.x = TRUE)) stopifnot(is.na(m[4, 2])) ## was level NA in 1.3.1 stopifnot(!is.na(m[1, 2])) ## PR 902 segfaults when warning string is too long, Ben Bolker 2001-04-09 provoke.bug <- function(n=9000) { warnmsg <- paste(LETTERS[sample(1:26,n,replace=TRUE)],collapse="") warning(warnmsg) } provoke.bug() ## segfaulted in 1.2.2, will also on machines without vsnprintf. ## ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ## and hence keep the above line at the end of this file