## Up to PR#9999 for R < 3.0.0 pdf("reg-tests-1a.pdf", encoding = "ISOLatin1.enc") ## force standard handling for data frames options(stringsAsFactors=FALSE) # R >= 4.0.0 ## .Machine (Meps <- .Machine$double.eps)# and use it in this file ## Facilitate diagnosing of testing startup: envLst <- c(t(outer(c("R_ENVIRON","R_PROFILE"), c("","_USER"), paste0)), "R_CHECK_ENVIRON","R_LIBS") cbind(Sys.getenv(envLst)) .libPaths() (have_cat <- nzchar(Sys.which("cat"))) assertError <- tools::assertError ## regression test for PR#376 aggregate(ts(1:20), nfreq=1/3) ## Comments: moved from aggregate.Rd ## aperm # check the names x <- array(1:24, c(4, 6)) nms <- list(happy=letters[1:4], sad=LETTERS[1:6]) dimnames(x) <- nms tmp <- aperm(x, c(2, 1)) stopifnot(all.equal(dimnames(tmp), nms[c(2, 1)])) dimnames(x) <- c(nms[1], list(NULL)) tmp <- aperm(x, c(2, 1)) stopifnot(all.equal(dimnames(tmp), c(list(NULL), nms[1]))) names(nms) <- c("happy", "sad") dimnames(x) <- nms tmp <- aperm(x, c(2, 1)) stopifnot(all.equal(names(dimnames(tmp)), names(nms[c(2, 1)]))) dimnames(x) <- c(nms[1], list(NULL)) tmp <- aperm(x, c(2, 1)) stopifnot(all.equal(names(dimnames(tmp)), c("", names(nms)[1]))) # check resize stopifnot(dim(aperm(x, c(2, 1), FALSE)) == dim(x)) stopifnot(is.null(dimnames(aperm(x, c(2, 1), FALSE)))) # check the types x <- array(1:24, c(4, 6)) stopifnot(all.equal(aperm(x, c(2, 1)), t(x))) stopifnot(is.integer(aperm(x, c(2, 1)))) x <- x + 0.0 stopifnot(all.equal(aperm(x, c(2, 1)), t(x))) stopifnot(is.double(aperm(x, c(2, 1)))) x <- x + 0.0i stopifnot(all.equal(aperm(x, c(2, 1)), t(x))) x[] <- LETTERS[1:24] stopifnot(all.equal(aperm(x, c(2, 1)), t(x))) x <- array(list("fred"), c(4, 6)) x[[3, 4]] <- 1:10 stopifnot(all.equal(aperm(x, c(2, 1)), t(x))) ## end of moved from aperm.Rd ## append stopifnot(append(1:5, 0:1, after=3) == append(1:3, c(0:1, 4:5))) ## end of moved from append.Rd ## array # funny object, but whatever was the point of that? utils::str(array(1:3, 0)) ## end of moved from array.Rd ## as.POSIXlt z <- Sys.time() stopifnot(range(z) == z, min(z) == z, max(z) == z, mean(z) == z) ## end of moved from as.POSIXlt.Rd ## autoload stopifnot(ls("Autoloads") == ls(envir = .AutoloadEnv), allow.logical0=TRUE) ## end of moved from autoload.Rd ## axis Y <- c(10.50, 4.0, 13.75, 7.25) plot(1:4, Y, xlim=c(0,5), ylim=c(0,15)) axis(side=4, at=Y, labels=LETTERS[1:4]) ## end of moved from axis.Rd ## backsolve r <- rbind(c(1,2,3), c(0,1,1), c(0,0,2)) ( y <- backsolve(r, x <- c(8,4,2)) ) # -1 3 1 r %*% y # == x = (8,4,2) ( y2 <- backsolve(r, x, transpose = TRUE)) # 8 -12 -5 stopifnot(all.equal(drop(t(r) %*% y2), x)) stopifnot(all.equal(y, backsolve(t(r), x, upper = FALSE, transpose = TRUE))) stopifnot(all.equal(y2, backsolve(t(r), x, upper = FALSE, transpose = FALSE))) ## end of moved from backsolve.Rd ## basename dirname(character(0)) ## end of moved from basename.Rd ## Bessel ## Check the Scaling : nus <- c(0:5,10,20) x <- seq(0,40,len=801)[-1] for(nu in nus) stopifnot(abs(1- besselK(x,nu)*exp( x) / besselK(x,nu,expo=TRUE)) < 2e-15) for(nu in nus) stopifnot(abs(1- besselI(x,nu)*exp(-x) / besselI(x,nu,expo=TRUE)) < 1e-15) ## end of moved from Bessel.Rd ## c ll <- list(A = 1, c="C") stopifnot(identical(c(ll, d=1:3), c(ll, as.list(c(d=1:3))))) ## moved from c.Rd ## Cauchy stopifnot(all.equal(dcauchy(-1:4), 1 / (pi*(1 + (-1:4)^2)))) ## end of moved from Cauchy.Rd ## chol ( m <- matrix(c(5,1,1,3),2,2) ) ( cm <- chol(m) ) stopifnot(abs(m - t(cm) %*% cm) < 100* Meps) ## check with pivoting ( m <- matrix(c(5,1,1,3),2,2) ) ( cm <- chol(m, TRUE) ) stopifnot(abs(m - t(cm) %*% cm) < 100* Meps) x <- matrix(c(1:5, (1:5)^2), 5, 2) m <- crossprod(x) Q <- chol(m) stopifnot(all.equal(t(Q) %*% Q, m)) Q <- chol(m, pivot = TRUE) pivot <- attr(Q, "pivot") oo <- order(pivot) stopifnot(all.equal(t(Q[, oo]) %*% Q[, oo], m)) stopifnot(all.equal(t(Q) %*% Q, m[pivot, pivot])) # now for something positive semi-definite x <- cbind(x, x[, 1]+3*x[, 2]) m <- crossprod(x) qr(m)$rank # is 2, as it should be (Q <- chol(m, pivot = TRUE)) # NB wrong rank here ... see Warning section. pivot <- attr(Q, "pivot") oo <- order(pivot) stopifnot(all.equal(t(Q[, oo]) %*% Q[, oo], m)) stopifnot(all.equal(t(Q) %*% Q, m[pivot, pivot])) ## end of moved from chol.Rd ## chol2inv cma <- chol(ma <- cbind(1, 1:3, c(1,3,7))) stopifnot(all.equal(diag(3), ma %*% chol2inv(cma))) ## end of moved from chol2inv.Rd ## col2rgb pp <- palette(); names(pp) <- pp # add & use names : stopifnot(col2rgb(1:8) == print(col2rgb(pp))) stopifnot(col2rgb("#08a0ff") == c(8, 160, 255)) grC <- col2rgb(paste("gray",0:100,sep="")) stopifnot(grC["red",] == grC["green",], grC["red",] == grC["blue",], grC["red", 1:4] == c(0,3,5,8)) ## end of moved from col2rgb.Rd ## colnames m0 <- matrix(NA, 4, 0) rownames(m0, do.NULL = FALSE) colnames(m0, do.NULL = FALSE) ## end of moved from colnames.Rd ## Constants stopifnot( nchar(letters) == 1, month.abb == substr(month.name, 1, 3) ) stopifnot(all.equal(pi, 4*atan(1), tol= 2*Meps)) # John Machin (1705) computed 100 decimals of pi : stopifnot(all.equal(pi/4, 4*atan(1/5) - atan(1/239), 4*Meps)) ## end of moved from Constants.Rd ## cor stopifnot( is.na(var(1)), !is.nan(var(1))) zz <- c(-1.30167, -0.4957, -1.46749, 0.46927) r <- cor(zz,zz); r - 1 stopifnot(r <= 1) # fails in R <= 1.3.x, for versions of Linux and Solaris ## end of moved from cor.Rd ## Spearman correlations ranked missing values at end <= 1.8.1 X <- cbind(c(1,3,4,NA),c(1,4,2,NA)) X1 <- X[-4,] stopifnot(all.equal(cor(X,X,method="spearman",use="complete"), cor(X1,X1,method="spearman",use="complete"))) stopifnot(all.equal(cov(X,X,method="spearman",use="complete"), cov(X1,X1,method="spearman",use="complete"))) ## DateTimeClasses (dls <- .leap.seconds[-1] - .leap.seconds[-length(.leap.seconds)]) table(dls) stopifnot(sum(dls == 365) >= 11) ## end of moved from DateTimeClasses.Rd ## deriv trig.exp <- expression(sin(cos(x + y^2))) D.sc <- D(trig.exp, "x") dxy <- deriv(trig.exp, c("x", "y")) y <- 1 stopifnot(eval(D.sc) == attr(eval(dxy),"gradient")[,"x"]) ff <- y ~ sin(cos(x) * y) stopifnot(all.equal(deriv(ff, c("x","y"), func = TRUE ), deriv(ff, c("x","y"), func = function(x,y){ } ))) ## end of moved from deriv.Rd ## diff x <- cumsum(cumsum(1:10)) stopifnot(diff(x, lag = 2) == x[(1+2):10] - x[1:(10 - 2)], diff(x, lag = 2) == (3:10)^2, diff(diff(x)) == diff(x, differences = 2)) ## end of moved from diff.Rd ## duplicated x <- c(9:20, 1:5, 3:7, 0:8) ## extract unique elements (xu <- x[!duplicated(x)]) stopifnot(xu == unique(x), # but unique(x) is more efficient 0:20 == sort(x[!duplicated(x)])) stopifnot(duplicated(iris)[143] == TRUE) ## end of moved from duplicated.Rd ## eigen set.seed(321, kind = "default") # force a particular seed m <- matrix(round(rnorm(25),3), 5,5) sm <- m + t(m) #- symmetric matrix em <- eigen(sm); V <- em$vect print(lam <- em$values) # ordered DEcreasingly stopifnot( abs(sm %*% V - V %*% diag(lam)) < 60*Meps, abs(sm - V %*% diag(lam) %*% t(V)) < 60*Meps) ##------- Symmetric = FALSE: -- different to above : --- em <- eigen(sm, symmetric = FALSE); V2 <- em$vect print(lam2 <- em$values) # ordered decreasingly in ABSolute value ! print(i <- rev(order(lam2))) stopifnot(abs(lam - lam2[i]) < 100 * Meps) # comparing two solns zapsmall(Diag <- t(V2) %*% V2) stopifnot( abs(1- diag(Diag)) < 60*Meps) stopifnot(abs(sm %*% V2 - V2 %*% diag(lam2)) < 60*Meps, abs(sm - V2 %*% diag(lam2) %*% t(V2)) < 60*Meps) ## Re-ordered as with symmetric: sV <- V2[,i] slam <- lam2[i] stopifnot(abs(sm %*% sV - sV %*% diag(slam)) < 60*Meps) stopifnot(abs(sm - sV %*% diag(slam) %*% t(sV)) < 60*Meps) ## sV *is* now equal to V -- up to sign (+-) and rounding errors stopifnot(abs(c(1 - abs(sV / V))) < 1000*Meps) ## end of moved from eigen.Rd ## euro stopifnot(euro == signif(euro,6), euro.cross == outer(1/euro, euro)) ## end of moved from euro.Rd ## Exponential r <- rexp(100) stopifnot(abs(1 - dexp(1, r) / (r*exp(-r))) < 1e-14) ## end of moved from Exponential.Rd ## family gf <- Gamma() stopifnot(1:10 == gf$linkfun(gf$linkinv(1:10))) ## end of moved from family.Rd ## fft set.seed(123) eps <- 1e-10 # typically see around 1e-11 for(N in 1:130) { x <- rnorm(N) if(N %% 5 == 0) { m5 <- matrix(x,ncol=5) stopifnot(apply(m5,2,fft) == mvfft(m5)) } dd <- Mod(1 - (f2 <- fft(fft(x), inverse=TRUE)/(x*length(x)))) stopifnot(dd < eps) } ## end of moved from fft.Rd ## findint N <- 100 X <- sort(round(rt(N, df=2), 2)) tt <- c(-100, seq(-2,2, len=201), +100) it <- findInterval(tt, X) ## See that this is N * Fn(.) : tt <- c(tt,X) stopifnot(it[c(1,203)] == c(0, 100), all.equal(N * stats::ecdf(X)(tt), findInterval(tt, X), tol = 100 * Meps), findInterval(tt,X) == apply( outer(tt, X, ">="), 1, sum) ) ## end of moved from findint.Rd ## NA & Inf's : tt[ina <- c(2,3,5,7)] <- NA tt[300] <- Inf X <- c(-Inf, X, Inf) it <- findInterval(tt,X) stopifnot(identical(it, as.integer(rowSums(outer(tt, X, ">=")))), is.na(it[ina])) if (have_cat) { ## fix oo <- options(editor="cat") # not really changing anything fix(pi) if(!is.numeric(pi) || length(pi)!=1 || !is.null(attributes(pi)) || abs(pi - 3.1415) > 1e-4) stop("OOPS: fix() is broken ...") rm(pi); options(oo) ## end of moved from fix.Rd } ## format (dd <- sapply(1:10, function(i)paste((9:0)[1:i],collapse=""))) np <- nchar(pd <- prettyNum(dd, big.mark="'")) stopifnot(sapply(0:2, function(m) all(grep("'", substr(pd, 1, np - 4*m)) == (4+3*m):10))) ## end of moved from format.Rd ## Geometric pp <- sort(c((1:9)/10, 1 - .2^(2:8))) print(qg <- qgeom(pp, prob = .2)) ## test that qgeom is an inverse of pgeom print(qg1 <- qgeom(pgeom(qg, prob=.2), prob =.2)) stopifnot(identical(qg, qg1)) ## moved from Geometric.Rd ## glm ## these are the same -- example from Jim Lindsey y <- rnorm(20) y1 <- y[-1]; y2 <- y[-20] summary(g1 <- glm(y1 - y2 ~ 1)) summary(g2 <- glm(y1 ~ offset(y2))) Eq <- function(x,y) all.equal(x,y, tol = 1e-12) stopifnot(Eq(coef(g1), coef(g2)), Eq(deviance(g1), deviance(g2)), Eq(resid(g1), resid(g2))) ## from logLik.glm.Rd anorexia <- structure(list(Treat = factor(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), labels = c("CBT", "Cont", "FT")), Prewt = c(80.7, 89.4, 91.8, 74, 78.1, 88.3, 87.3, 75.1, 80.6, 78.4, 77.6, 88.7, 81.3, 78.1, 70.5, 77.3, 85.2, 86, 84.1, 79.7, 85.5, 84.4, 79.6, 77.5, 72.3, 89, 80.5, 84.9, 81.5, 82.6, 79.9, 88.7, 94.9, 76.3, 81, 80.5, 85, 89.2, 81.3, 76.5, 70, 80.4, 83.3, 83, 87.7, 84.2, 86.4, 76.5, 80.2, 87.8, 83.3, 79.7, 84.5, 80.8, 87.4, 83.8, 83.3, 86, 82.5, 86.7, 79.6, 76.9, 94.2, 73.4, 80.5, 81.6, 82.1, 77.6, 83.5, 89.9, 86, 87.3), Postwt = c(80.2, 80.1, 86.4, 86.3, 76.1, 78.1, 75.1, 86.7, 73.5, 84.6, 77.4, 79.5, 89.6, 81.4, 81.8, 77.3, 84.2, 75.4, 79.5, 73, 88.3, 84.7, 81.4, 81.2, 88.2, 78.8, 82.2, 85.6, 81.4, 81.9, 76.4, 103.6, 98.4, 93.4, 73.4, 82.1, 96.7, 95.3, 82.4, 72.5, 90.9, 71.3, 85.4, 81.6, 89.1, 83.9, 82.7, 75.7, 82.6, 100.4, 85.2, 83.6, 84.6, 96.2, 86.7, 95.2, 94.3, 91.5, 91.9, 100.3, 76.7, 76.8, 101.6, 94.9, 75.2, 77.8, 95.5, 90.7, 92.5, 93.8, 91.7, 98)), names = c("Treat", "Prewt", "Postwt" ), class = "data.frame", row.names = 1:72) anorex.1 <- glm(Postwt ~ Prewt + Treat + offset(Prewt), family = gaussian, data = anorexia) summary(anorex.1) Eq <- function(x,y) all.equal(x,y, tol = 1e-12) stopifnot(Eq(AIC(anorex.1), anorex.1$aic), Eq(AIC(g1), g1$aic), Eq(AIC(g2), g2$aic)) ## next was wrong in 1.4.1 x <- 1:10 lmx <- logLik(lm(x ~ 1)); glmx <- logLik(glm(x ~ 1)) stopifnot(all.equal(as.vector(lmx), as.vector(glmx)), all.equal(attr(lmx, 'df'), attr(glmx, 'df'))) ## end of moved from glm.Rd and logLik.glm.Rd ## Hyperbolic x <- seq(-3, 3, len=200) stopifnot( abs(cosh(x) - (exp(x) + exp(-x))/2) < 20*Meps, abs(sinh(x) - (exp(x) - exp(-x))/2) < 20*Meps, abs(tanh(x)*cosh(x) - sinh(x)) < 20*Meps ) stopifnot(abs(asinh(sinh(x)) - x) < 20*Meps) stopifnot(abs(acosh(cosh(x)) - abs(x)) < 1000*Meps) #- imprecise for small x stopifnot(abs(atanh(tanh(x)) - x) < 100*Meps) stopifnot(abs(asinh(x) - log(x + sqrt(x^2 + 1))) < 100*Meps) cx <- cosh(x) stopifnot(abs(acosh(cx) - log(cx + sqrt(cx^2 - 1))) < 1000*Meps) ## end of moved from Hyperbolic.Rd ## image ## Degenerate, should still work image(as.matrix(1)) image(matrix(pi,2,4)) x <- seq(0,1,len=100) image(x, 1, matrix(x), col=heat.colors(10)) image(x, 1, matrix(x), col=heat.colors(10), oldstyle = TRUE) image(x, 1, matrix(x), col=heat.colors(10), breaks = seq(0.1,1.1,len=11)) ## end of moved from image.Rd ## integrate (ii <- integrate(dnorm, -1.96, 1.96)) (i1 <- integrate(dnorm, -Inf, Inf)) stopifnot(all.equal(0.9500042097, ii$val, tol = ii$abs.err, scale=1), all.equal( 1, i1$val, tol = i1$abs.err, scale=1)) integrand <- function(x) {1/((x+1)*sqrt(x))} (ii <- integrate(integrand, lower = 0, upper = Inf, rel.tol = 1e-10)) stopifnot(all.equal(pi, ii$val, tol = ii$abs.err, scale=1)) ## end of moved from integrate.Rd ## is.finite ( weird.values <- c(-20.9/0, 1/0, 0/0, NA) ) Mmax <- .Machine$double.xmax Mmin <- .Machine$double.xmin ( X.val <- c(Mmin*c(2^(-10:3),1e5,1e10), Mmax*c(1e-10,1e-5,2^(-3:0),1.001)) ) ( tst.val <- sort(c(X.val, weird.values), na.last = TRUE) ) ( x2 <- c(-1:1/0,pi,1,NA) ) ( z2 <- c(x2, 1+1i, Inf -Inf* 1i) ) is.inf <- function(x) (is.numeric(x) || is.complex(x)) && !is.na(x) && !is.finite(x) for(x in list(tst.val, x2, z2)) print(cbind(format(x), is.infinite=format(is.infinite(x))), quote=FALSE) rbind(is.nan(tst.val), is.na (tst.val)) tst.val [ is.nan(tst.val) != is.na(tst.val) ] stopifnot( is.na(0/0), !is.na(Inf), is.nan(0/0), !is.nan(NA) && !is.infinite(NA) && !is.finite(NA), is.nan(NaN) && !is.infinite(NaN) && !is.finite(NaN), !is.nan(c(1,NA)), c(FALSE,TRUE,FALSE) == is.nan(c (1,NaN,NA)) ) assertError(is.nan(list(1,NaN,NA))) #-> result allowed but varies in older versions stopifnot(identical(lgamma(Inf), Inf)) stopifnot(identical(Inf + Inf, Inf)) stopifnot(identical(Inf - Inf, NaN)) stopifnot(identical((1/0) * (1/0), Inf)) stopifnot(identical((1/0) / (1/0), NaN)) stopifnot(identical(exp(-Inf), 0)) stopifnot(identical(log(0), -Inf)) stopifnot(identical((-1)/0, -Inf)) pm <- c(-1,1) # 'pm' = plus/minus stopifnot(atan(Inf*pm) == pm*pi/2) ## end of moved from is.finite.Rd ## kronecker ( M <- matrix(1:6, ncol=2) ) stopifnot(kronecker(4, M)==4 * M) # Block diagonal matrix: stopifnot(kronecker(diag(1, 3), M) == diag(1, 3) %x% M) ## end of moved from kronecker.Rd ## list str(pl <- as.pairlist(ps.options())) ## These are all TRUE: stopifnot(is.list(pl) && is.pairlist(pl), !is.null(list()), is.null(pairlist()), !is.list(NULL), is.pairlist(pairlist()), is.null(as.pairlist(list())), is.null(as.pairlist(NULL)) ) ## end of moved from list.Rd ## log stopifnot(all.equal(log(1:10), log(1:10, exp(1)))) stopifnot(all.equal(log10(30), log(30, 10))) stopifnot(all.equal(log2(2^pi), 2^log2(pi))) stopifnot(Mod(pi - log(exp(pi*1i)) / 1i) < 10* Meps) stopifnot(Mod(1+exp(pi*1i)) < 10* Meps) ## end of moved from Log.Rd ## logistic eps <- 100 * Meps x <- c(0:4, rlogis(100)) stopifnot(all.equal(plogis(x), 1 / (1 + exp(-x)), tol = eps)) stopifnot(all.equal(plogis(x, lower=FALSE), exp(-x)/ (1 + exp(-x)), tol = eps)) stopifnot(all.equal(plogis(x, lower=FALSE, log=TRUE), -log(1 + exp(x)), tol = eps)) stopifnot(all.equal(dlogis(x), exp(x) * (1 + exp(x))^-2, tol = eps)) ## end of moved from Logistic.Rd ## Lognormal x <- rlnorm(1000) # not yet always : stopifnot(abs(x - qlnorm(plnorm(x))) < 1e4 * Meps * x) ## end of moved from Lognormal.Rd ## lower.tri ma <- matrix(1:20, 4, 5) stopifnot(lower.tri(ma) == !upper.tri(ma, diag=TRUE)) ## end of moved from lower.tri.Rd ## make.names stopifnot(make.names(letters) == letters) ## end of make.names ## mean x <- c(0:10, 50) stopifnot(all.equal(mean(x, trim = 0.5), median(x))) ## moved from mean.Rd ## Multinom N <- 20 pr <- c(1,3,6,10) # normalization not necessary for generation set.seed(153) rr <- rmultinom(5000, N, prob = pr) stopifnot(colSums(rr) == N) (m <- rowMeans(rr)) all.equal(m, N * pr/sum(pr)) # rel.error ~0.003 stopifnot(max(abs(m/(N*pr/sum(pr)) - 1)) < 0.01) (Pr <- dmultinom(c(0,0,3), prob = c(1, 1, 14))) stopifnot(all.equal(Pr, dbinom(3, 3, p = 14/16))) X <- t(as.matrix(expand.grid(0:3, 0:3))) X <- X[, colSums(X) <= 3] X <- rbind(X, 3:3 - colSums(X)) for(p in list(c(1,2,5), 1:3, 3:1, 2:0, 0:2, c(1,2,1), c(0,0,1))) { px <- apply(X, 2, function(x) dmultinom(x, prob = p)) stopifnot(all.equal(sum(px), 1)) } ## end of moved from Multinom.Rd ## Poisson dpois(c(0, 1, 0.17, 0.77), 1) ## end of moved from Poisson.Rd ## qr ## tests of complex case set.seed(1) A <- matrix(rnorm(25), 5, 5, dimnames=list(1:5, letters[1:5])) qr.solve(A, 1:5) A[] <- as.complex(A) qr.coef(qr(A), 1:5) qr.solve(A, 1:5) ## check for rank-deficient cases X <- cbind(1:3, 1:3, 1) stopifnot(all.equal(qr.X(qr(X)), X)) ## end of moved from qr.Rd ## qraux p <- ncol(x <- LifeCycleSavings[,-1]) # not the `sr' qrstr <- qr(x) # dim(x) == c(n,p) Q <- qr.Q(qrstr) # dim(Q) == dim(x) R <- qr.R(qrstr) # dim(R) == ncol(x) X <- qr.X(qrstr) # X == x stopifnot(all.equal(X, as.matrix(x))) ## X == Q %*% R : stopifnot((1 - X /( Q %*% R))< 100*Meps) dim(Qc <- qr.Q(qrstr, complete=TRUE)) # Square: dim(Qc) == rep(nrow(x),2) stopifnot((crossprod(Qc) - diag(nrow(x))) < 10*Meps) QD <- qr.Q(qrstr, D=1:p) # QD == Q \%*\% diag(1:p) stopifnot(QD - Q %*% diag(1:p) < 8* Meps) dim(Rc <- qr.R(qrstr, complete=TRUE)) # == dim(x) dim(Xc <- qr.X(qrstr, complete=TRUE)) # square: nrow(x) ^ 2 dimnames(X) <- NULL stopifnot(all.equal(Xc[,1:p], X)) ## end of moved from qraux.Rd ## quantile x <- rnorm(1001) n <- length(x) ## the following is exact, because 1/(1001-1) is exact: stopifnot(sort(x) == quantile(x, probs = ((1:n)-1)/(n-1), names=FALSE)) n <- 777 ox <- sort(x <- round(rnorm(n),1))# round() produces ties ox <- c(ox, ox[n]) #- such that ox[n+1] := ox[n] p <- c(0,1,runif(100)) i <- floor(r <- 1 + (n-1)*p) f <- r - i stopifnot(abs(quantile(x,p) - ((1-f)*ox[i] + f*ox[i+1])) < 20*Meps) ## end of moved from quantile.Rd ## rep stopifnot(identical(rep(letters, 0), character(0)), identical(rep.int(1:2, 0), integer(0))) stopifnot(sum(1:8) == length(rep(1:4, 1:8, each=2))) ## end of moved from rep.Rd ## Round x1 <- seq(-2, 4, by = .5) non.int <- ceiling(x1) != floor(x1) stopifnot( trunc(x1) == as.integer(x1), non.int == (ceiling(x1) != trunc(x1) | trunc(x1) != floor(x1)), (signif(x1, 1) != round(x1,1)) == (non.int & abs(x1) > 1) ) ## end of moved from Round.Rd ## seq stopifnot( 3 == seq(3,3, by=pi), 3 == seq(3,3.1,by=pi), seq(1,6,by=3) == c(1,4), seq(10,4.05,by=-3) == c(10,7) ) ## end of moved from seq.Rd ## sort x <- swiss$Education[1:25] stopifnot(!is.unsorted(sort(x)), !is.unsorted(LETTERS), is.unsorted(c(NA,1:3,2), na.rm = TRUE)) for(n in 1:20) { z <- rnorm(n) for(x in list(z, round(z,1))) { ## 2nd one has ties qxi <- sort(x, method = "quick", index.return = TRUE) stopifnot(qxi$x == sort(x, method = "shell"), any(duplicated(x)) || all(qxi$ix == order(x)), x[qxi$ix] == qxi$x) } } ## end of moved from sort.Rd ## substr ss <- substring("abcdef",1:6,1:6) stopifnot(ss == strsplit ("abcdef",NULL)[[1]]) x <- c("asfef", "qwerty", "yuiop[", "b", "stuff.blah.yech") stopifnot(substr(x, 2, 5) == substring(x, 2, 5)) ## end of moved from substr.Rd ## svd hilbert <- function(n) { i <- 1:n; 1 / outer(i - 1, i, "+") } str(X <- hilbert(9)[,1:6]) str(s <- svd(X)) Eps <- 100 * Meps D <- diag(s$d) stopifnot(abs(X - s$u %*% D %*% t(s$v)) < Eps)# X = U D V' stopifnot(abs(D - t(s$u) %*% X %*% s$v) < Eps)# D = U' X V X <- cbind(1, 1:7) str(s <- svd(X)); D <- diag(s$d) stopifnot(abs(X - s$u %*% D %*% t(s$v)) < Eps)# X = U D V' stopifnot(abs(D - t(s$u) %*% X %*% s$v) < Eps)# D = U' X V ## end of moved from svd.Rd ## Trig ## many of these tested for machine accuracy, which seems a bit extreme set.seed(123) stopifnot(cos(0) == 1) stopifnot(sin(3*pi/2) == cos(pi)) x <- rnorm(99) stopifnot(all.equal( sin(-x), - sin(x))) stopifnot(all.equal( cos(-x), cos(x))) x <- abs(x); y <- abs(rnorm(x)) stopifnot(abs(atan2(y, x) - atan(y/x)) < 10 * Meps) stopifnot(abs(atan2(y, x) - atan(y/x)) < 10 * Meps) x <- 1:99/100 stopifnot(Mod(1 - (cos(x) + 1i*sin(x)) / exp(1i*x)) < 10 * Meps) ## error is about 650* at x=0.01: stopifnot(abs(1 - x / acos(cos(x))) < 1000 * Meps) stopifnot(abs(1 - x / asin(sin(x))) <= 10 * Meps) stopifnot(abs(1 - x / atan(tan(x))) <= 10 *Meps) ## end of moved from Trig.Rd ## Uniform u <- runif(20) stopifnot(punif(u) == u, dunif(u) == 1, runif(100, 2,2) == 2)#-> TRUE [bug in R version <= 0.63.1] ## end of moved from Uniform.Rd ## unique my.unique <- function(x) x[!duplicated(x)] for(i in 1:4) { x <- rpois(100, pi); stopifnot(unique(x) == my.unique(x)) } unique(iris) stopifnot(dim(unique(iris)) == c(149, 5)) ## end of moved from unique.Rd ## which.min stopifnot(length(which.min(numeric(0))) == 0) stopifnot(length(which.max( c(NA,NA) )) == 0) ## end of moved from which.min.Rd ## Wilcoxon x <- -1:(4*6 + 1) fx <- dwilcox(x, 4, 6) stopifnot(fx == dwilcox(x, 6, 4)) Fx <- pwilcox(x, 4, 6) stopifnot(abs(Fx - cumsum(fx)) < 10 * Meps) ## end of moved from Wilcoxon.Rd ## All the following relations must hold : stopifnot( 1 + Meps != 1, 1 + .5* Meps == 1, log2(.Machine$double.xmax) == .Machine$double.max.exp, log2(.Machine$double.xmin) == .Machine$double.min.exp ) # This test failed on HP-UX since pow(2,1024) returns DBL_MAX and sets # errno = ERANGE. Most other systems return Inf and set errno stopifnot(is.infinite(.Machine$double.base ^ .Machine$double.max.exp)) ## end of moved from zMachine.Rd ## PR 640 (diff.default computes an incorrect starting time) ## By: Laimonis Kavalieris 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 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$y)) unloadNamespace("splines") ## Comments: all three differed in 1.2.1. ## PR 698 (print problem with data frames) ## actually, a subsetting problem with data frames fred <- data.frame(happy=c(TRUE, FALSE, TRUE), sad=7:9) z <- try(tmp <- fred[c(FALSE, FALSE, TRUE, TRUE)]) stopifnot(class(z) == "try-error") ## Comments: No error before 1.2.1 ## PR 753 (step can't find variables) ## x <- data.frame(a=rnorm(10), b=rnorm(10), c=rnorm(10)) x0.lm <- lm(a ~ 1, data=x) step(x0.lm, ~ b + c) ## Comments: ## PR 796 (aic in binomial models is often wrong) ## a1 <- glm(cbind(ncases, ncontrols) ~ agegp + tobgp * alcgp, data = esoph, family = binomial())$aic a1 a2 <- glm(ncases/(ncases+ncontrols) ~ agegp + tobgp * alcgp, data = esoph, family = binomial(), weights=ncases+ncontrols)$aic a2 stopifnot(all.equal(a1, a2)) ## Comments: # both should be 236.9645 # changed to use all.equal rather than == in 2.1.0 -pd ## Follow up: example from Lindsey, purportedly of inaccuracy in aic y <- matrix(c(2, 0, 7, 3, 0, 9), ncol=2) x <- gl(3, 1) a <- glm(y ~ x, family=binomial)$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) stopifnot(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(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 ## PR 979 expand.model.frame() failed for models fitted with a subset df <- data.frame(y = 1:10, z = 1:10, m = 1:10) fit <- lm(y ~ 1, data = df, subset = m < 8) mf <- expand.model.frame(fit, ~ z) # failed in 1.2.3 stopifnot(identical(names(mf), c("y", "z")), identical(mf$z, 1:7)) ## 1.3.0 had poor compression on gzfile() with lots of small pieces. zz <- gzfile("t1.gz", "w") write(1:1000, zz) close(zz) (sz <- file.info("t1.gz")$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.txt", 1:10, sep="\n") x <- try(readLines("foo.txt", 100, ok=FALSE)) unlink("foo.txt") 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(y ~ z * I(x), data=DF)) dummy.coef(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 x <- 1:4 y <- 1:4 z <- ksmooth(x, y, x.points=x) stopifnot(all.equal(z$y, y)) ## did some smoothing prior to 1.3.1. ## The length of lines read by scan() was limited before 1.4.0 xx <- paste(rep(0:9, 2000), collapse="") zz <- file("foo.txt", "w") writeLines(xx, zz) close(zz) xxx <- scan("foo.txt", "", sep="\n") stopifnot(identical(xx, xxx)) unlink("foo.txt") ## as.character was truncating formulae: John Fox 2001-08-23 mod <- this ~ is + a + very + long + formula + with + a + very + large + number + of + characters zz <- as.character(mod) zz nchar(zz) stopifnot(nchar(zz)[3] == 83) ## truncated in 1.3.0 ## substr<-, Tom Vogels, 2001-09-07 x <- "abcdef" substr(x, 2, 3) <- "wx" stopifnot(x == "awxdef") x <- "abcdef" substr(x, 2, 3) <- "wxy" stopifnot(x == "awxdef") x <- "abcdef" substr(x, 2, 3) <- "w" stopifnot(x == "awcdef") ## last was "aw" in 1.3.1 ## reading bytes from a connection, Friedrich Leisch 2001-09-07 cat("Hello World", file="world.txt") con <- file("world.txt", "r") zz <- readChar(con, 100) close(con) unlink("world.txt") stopifnot(zz == "Hello World") ## was "" in 1.3.1. ## prediction was failing for intercept-only model ## as model frame has no columns. d <- data.frame(x=runif(50), y=rnorm(50)) d.lm <- lm(y ~ 1, data=d) predict(d.lm, data.frame(x=0.5)) ## error in 1.3.1 ## predict.arima0 needed a matrix newxreg: Roger Koenker, 2001-09-27 u <- rnorm(120) s <- 1:120 y <- 0.3*s + 5*filter(u, c(.95,-.1), "recursive", init=rnorm(2)) fit0 <- arima0(y,order=c(2,0,0), xreg=s) fit1 <- arima0(y,order=c(2,1,0), xreg=s, include.mean=TRUE) fore0 <- predict(fit0 ,n.ahead=44, newxreg=121:164) fore1 <- predict(fit1, n.ahead=44, newxreg=121:164) par(mfrow=c(1,2)) ts.plot(y,fore0$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$coef[3]), lty=2) ## merging when NA is a level a <- data.frame(x = 1:4) b <- data.frame(x = 1:3, y = factor(c("NA", "a", "b"), exclude="")) (m <- merge(a, b, all.x = TRUE)) stopifnot(is.na(m[4, 2])) ## was level NA in 1.3.1 stopifnot(!is.na(m[1, 2])) ## merging with POSIXct columns: x <- data.frame(a = as.POSIXct(Sys.time() + (1:3)*10000), b = LETTERS[1:3]) y <- data.frame(b = LETTERS[3:4], c = 1:2) stopifnot(1 == nrow(merge(x, y))) stopifnot(4 == nrow(merge(x, y, all = TRUE))) ## PR 1149. promax was returning the wrong rotation matrix. ability.FA <- factanal(factors = 2, covmat = ability.cov, rotation = "none") pm <- promax(ability.FA$loadings) tmp1 <- as.vector(ability.FA$loadings %*% pm$rotmat) tmp2 <- as.vector(pm$loadings) stopifnot(all.equal(tmp1, tmp2)) ## PR 1155. On some systems strptime was not setting the month or mday ## when yday was supplied. bv1 <- data.frame(day=c(346,346,347,347,347), time=c(2340,2350,0,10,20)) attach(bv1) tmp <- strptime(paste(day, time %/% 100, time %% 100), "%j %H %M") detach() stopifnot(tmp$mon == 11) # day of month will be different in a leap year on systems that default # to the current year, so test differences: stopifnot(diff(tmp$mday) == c(0, 1, 0, 0)) ## Comments: failed on glibc-based systems in 1.3.1, including Windows. ## PR 1004 (follow up). Exact Kolmogorov-Smirnov test gave incorrect ## results due to rounding errors (Charles Geyer, charlie@stat.umn.edu, ## 2001-10-25). ## Example 5.4 in Hollander and Wolfe (Nonparametric Statistical ## Methods, 2nd ed., Wiley, 1999, pp. 180-181). x <- c(-0.15, 8.6, 5, 3.71, 4.29, 7.74, 2.48, 3.25, -1.15, 8.38) y <- c(2.55, 12.07, 0.46, 0.35, 2.69, -0.94, 1.73, 0.73, -0.35, -0.37) stopifnot(round(ks.test(x, y)$p.value, 4) == 0.0524) ## PR 1150. Wilcoxon rank sum and signed rank tests did not return the ## Hodges-Lehmann estimators of the associated confidence interval ## (Charles Geyer, charlie@stat.umn.edu, 2001-10-25). ## One-sample test: Example 3.1 in Hollander & Wolfe (1973), 29f. x <- c(1.83, 0.50, 1.62, 2.48, 1.68, 1.88, 1.55, 3.06, 1.30) y <- c(0.878, 0.647, 0.598, 2.05, 1.06, 1.29, 1.06, 3.14, 1.29) we <- wilcox.test(y, x, paired = TRUE, conf.int = TRUE) ## NOTE order: y then x. ## Results from Hollander & Wolfe (1999), 2nd edition, page 40 and 53 stopifnot(round(we$p.value,4) == 0.0391) stopifnot(round(we$conf.int,3) == c(-0.786, -0.010)) stopifnot(round(we$estimate,3) == -0.46) ## Two-sample test: Example 4.1 in Hollander & Wolfe (1973), 69f. x <- c(0.80, 0.83, 1.89, 1.04, 1.45, 1.38, 1.91, 1.64, 0.73, 1.46) y <- c(1.15, 0.88, 0.90, 0.74, 1.21) we <- wilcox.test(y, x, conf.int = TRUE) ## NOTE order: y then x. ## Results from Hollander & Wolfe (1999), 2nd edition, page 111 and 126 stopifnot(round(we$p.value,4) == 0.2544) stopifnot(round(we$conf.int,3) == c(-0.76, 0.15)) stopifnot(round(we$estimate,3) == -0.305) ## range gave wrong length result for R < 1.4.0 stopifnot(length(range(numeric(0))) == 2) ## Comments: was just NA ## mishandling of integer(0) in R < 1.4.0 x1 <- integer(0) / (1:3) x2 <- integer(0) ^ (1:3) stopifnot(length(x1) == 0 & length(x2) == 0) ## Comments: were integer NAs in real answer in 1.3.1. ## PR#1138/9 rounding could give non-integer answer. x <- round(100000/3, -2) - 33300 stopifnot(x == 0) ## failed in 1.3.x on Solaris and Windows but not Debian Linux. ## PR#1160 finding midpoints in image x2 <- c(0, 0.002242152, 0.004484305, 0.006726457, 0.00896861, 0.01121076, 0.01345291, 0.01569507, 0.01793722, 0.02017937, 0.02242152, 0.02466368, 0.02690583, 0.02914798, 0.03139013, 0.03363229, 0.03587444, 0.03811659, 0.04035874, 0.04932735, 0.05156951, 0.05381166) z <- c(0, 0.067, NA, 0.167, 0.083, 0.05, 0.067, NA, 0, 0.1, 0, 0.05, 0.067, 0.067, 0.016, 0.117, 0.017, -0.017, 0.2, 0.35, 0.134, 0.15) image(x2, 1, as.matrix(z)) ## Comments: failed under R 1.3.1. ##PR 1175 and 1123## set.seed(123) ## We can't seem to get Pearson residuals right ## x <- 1:4 # regressor variable y <- c(2,6,7,8) # response binomial counts n <- rep(10,4) # number of binomial trials ym <- cbind(y,n-y) # response variable as a matrix glm1 <- glm(ym~x,binomial) # fit a generalized linear model f <- fitted(glm1) rp1 <- (y-n*f)/sqrt(n*f*(1-f)) # direct calculation of pearson residuals rp2 <- residuals(glm1,type="pearson") # should be pearson residuals stopifnot(all.equal(rp1,rp2)) # sign should be same as response residuals x <- 1:10 y <- rgamma(10,2)/x glm2 <- glm(y~x,family=Gamma) stopifnot(all.equal(sign(resid(glm2,"response")),sign(resid(glm2,"pearson")))) # shouldn't depend on link for a saturated model x<-rep(0:1,10) y<-rep(c(0,1,1,0,1),4) glm3<-glm(y~x,family=binomial(),control=glm.control(eps=1e-8)) glm4<-glm(y~x,family=binomial("log"),control=glm.control(eps=1e-8)) stopifnot(all.equal(resid(glm3,"pearson"),resid(glm4,"pearson"))) ## Torsten Hothorn, 2001-12-04 stopifnot(pt(-Inf, 3, ncp=0) == 0, pt(Inf, 3, ncp=0) == 1) ## Comments: were 0.5 in 1.3.1 ## Paul Gilbert, 2001-12-07 cancor(matrix(rnorm(100),100,1), matrix(rnorm(300),100,3)) ## Comments: failed in R-devel. ## PR#1201: incorrect values in qbeta x <- seq(0, 0.8, len=1000) xx <- pbeta(qbeta(x, 0.143891, 0.05), 0.143891, 0.05) stopifnot(max(abs(x - xx)) < 1e-6) ## Comments: Get a range of zeroes in 1.3.1 ## PR#1216: binomial null model y <- rbinom(20, 1, 0.5) glm(y ~ 0, family = binomial) ## Comments: 1.3.1 gave Error in any(n > 1) : Object "n" not found ## Integer overflow in type.convert res <- type.convert("12345689", as.is=FALSE) stopifnot(typeof(res) == "integer") res <- type.convert("12345689012", as.is=FALSE) stopifnot(typeof(res) == "double") ## Comments: was integer in 1.4.0 ## La.eigen() segfault #e1 <- La.eigen(m <- matrix(1:9,3)) #stopifnot(e1$values == La.eigen(m, only.values = TRUE)$values) ## 2.0.0: La.eigen is defunct ## Patrick Connelly 2001-01-22, prediction with offsets failed ## a simpler example counts <- c(18, 17, 15, 20, 10, 20, 25, 13, 12) outcome <- gl(3, 1, 9) treatment <- gl(3, 3) DF <- data.frame(counts = c(18, 17, 15, 20, 10, 20, 25, 13, 12), outcome = gl(3, 1, 9), treatment = gl(3, 3), exposure = c(1.17, 1.78, 1.00, 2.36, 2.58, 0.80, 2.51, 1.16, 1.77)) fit <- glm(counts ~ outcome + treatment + offset(log(exposure)), family = poisson, data = DF) p1 <- predict(fit) p2 <- predict(fit, se = TRUE) ## failed < 1.4.1 p3 <- predict(fit, newdata = DF) p4 <- predict(fit, newdata = DF, se = TRUE) stopifnot(all.equal(p1, p2$fit), all.equal(p1, p3), all.equal(p2, p4)) fit <- glm(counts ~ outcome + treatment, offset = log(exposure), family = poisson, data = DF) p1 <- predict(fit) p2 <- predict(fit, se = TRUE) ## failed < 1.4.1 p3 <- predict(fit, newdata = DF) p4 <- predict(fit, newdata = DF, se = TRUE) stopifnot(all.equal(p1, p2$fit), all.equal(p1, p3), all.equal(p2, p4)) ## PR#1267 hashing NaN load(file.path(Sys.getenv("SRCDIR"), "nanbug.rda")) bb <- b; bb[5] <- NaN identical(b, bb) # TRUE unique(c(NaN, bb)) #[1] NaN 0 1 2 3 NA stopifnot(identical(unique(c(NaN, b)), unique(c(NaN, bb)))) ## 1.4.0 gives [1] NaN 0 1 2 NaN 3 NA on most platforms ## reported by PD 2002-01-24 Y <- matrix(rnorm(20), , 2) fit <- manova(Y ~ 1) fit # failed print(fit, intercept = TRUE) summary(fit) # failed summary(fit, intercept = TRUE) ## Several qr.*() functions lose (dim)names. ## reported by MM 2002-01-26 ## the following should work both in R and S+ : q4 <- qr(X4 <- cbind(a = 1:9, b = c(1:6,3:1), c = 2:10, d = rep(1,9))) ##q2 <- qr(X4[,1:2]) y04 <- y4 <- cbind(A=1:9,B=2:10,C=3:11,D=4:12) dimnames(y4)[[1]] <- paste("c",1:9,sep=".") y1 <- y4[,2] y40 <- y4 ; dimnames(y40) <- list(dimnames(y4)[[1]], NULL) c1 <- qr.coef( q4, y4) # row- AND col-names c2 <- qr.coef( q4, y04)# ditto c3 <- qr.coef( q4, y40)# row--names dn3 <- dimnames(c3) stopifnot(identical(dimnames(c1), dimnames(c2)), identical(dimnames(c1), list(letters[1:4], LETTERS[1:4])), identical(dn3[[1]], letters[1:4]), length(dn3[[2]]) == 0, identical(names(qr.coef(q4,y1)), letters[1:4]), identical(dimnames(qr.R(q4))[[2]], letters[1:4]), identical(dimnames(qr.qty(q4,y4)), dimnames(y4)), identical(dimnames(qr.qty(q4,y40)), dimnames(y40)), identical(dimnames(qr.qy (q4,y04)), dimnames(y04)), all.equal(y1, qr.fitted(q4, y1 ), tol = 1e-12), all.equal(y4, qr.fitted(q4, y4 ), tol = 1e-12), all.equal(y40, qr.fitted(q4, y40), tol = 1e-12), all.equal(y04, qr.fitted(q4, y04), tol = 1e-12), all.equal(X4, qr.X(q4), tol = 1e-12) ) ## PR 1297 read.fwf() was interpreting `#' in 1.4.0/1 cat(file="test.fwf", "123ABC123", "123#3 123", "123XYZ123", sep="\n") (res <- read.fwf("test.fwf", widths=c(3,3,3), comment.char="")) unlink("test.fwf") stopifnot(res[2, 2] == "#3 ") ## abs was failing to dispatch as part of the Math group generic tmp <- data.frame(x = -5:5) abs(tmp) ## failed in 1.4.1. ## PR 1363 La.svd was not working for integer args m <- matrix(1:4, 2) (s1 <- svd(m)) (s2 <- La.svd(m)) stopifnot(all.equal(s1$d, s2$d), all.equal(s1$u, s2$u), all.equal(s1$v, t(s2$vt))) (e1 <- eigen(m)) # (e2 <- La.eigen(m)) # 2.0.0: La.eigen is defunct stopifnot(all.equal(e1$d, e1$d)) ## order/sort.list on NA_STRING x <- c("A", NA, "Z") stopifnot(identical(sort(x, na.last = TRUE), x[sort.list(x, na.last = TRUE)])) stopifnot(identical(sort(x, na.last = FALSE), x[sort.list(x, na.last = FALSE)])) ## 1.4.1 sorted NA correctly with sort but not sort.list. ## Don MacQueen 2002-03-26 stopifnot(length(seq(1024902010, 1024902025, by=1)) == 16) t0 <- ISOdatetime(2002,6,24,0,0,10) x <- seq.POSIXt(from=t0,to=t0+15,by='1 sec') stopifnot(length(x) == 16) ## whilst reading the code BDR 2002-03-31 z <- try(max(complex(0))) stopifnot(inherits(z, "try-error")) z <- try(min(complex(0))) stopifnot(inherits(z, "try-error")) ## 1.4.1 gave +-Inf + random imaginary part ## PR#1283 min/max(NULL) or (integer(0)) z <- min(NULL) stopifnot(!is.na(z), mode(z) == "numeric", z == Inf) z <- min(integer(0)) stopifnot(!is.na(z), mode(z) == "numeric", z == Inf) z <- max(NULL) stopifnot(!is.na(z), mode(z) == "numeric", z == -Inf) z <- max(integer(0)) stopifnot(!is.na(z), mode(z) == "numeric", z == -Inf) ## more reading the code BDR 2002-03-31 stopifnot(identical(range(), range(numeric(0)))) ## in 1.4.1 range() was c(1,1) stopifnot(is.null(c())) ## in 1.4.1 this was structure(TRUE, names="recursive") ## range(numeric(0)) was not as documented x <- numeric(0) (rx <- range(x)) stopifnot(identical(rx, c(min(x), max(x)))) ## 1.4.1 had c(NA, NA) ## PR 1431 persp() crashes with numeric values for [x,y,z]lab persp(1:2, 1:2, matrix(1:4, 2), xlab=1) ## segfaulted in 1.4.1 ## PR#1244 bug in det using method="qr" ## method argument is no longer used in det #m2 <- structure(c(9822616000, 3841723000, 79790.09, 3841723000, 1502536000, # 31251.82, 79790.09, 31251.82, 64156419.36), dim = c(3, 3)) #(d1 <- det(m2, method="eigenvalues")) #(d2 <- det(m2, method="qr")) #stopifnot(d2 == 0) ## 1.4.1 gave 9.331893e+19 #(d3 <- det(m2, method="qr", tol = 1e-10)) #stopifnot(all.equal(d1, d3, tol=1e-3)) ## PR#1422 glm start/offset bugs res <- try(data(ships, package = MASS)) if(!inherits(res, "try-error")) { ships.glm <- glm(incidents ~ type + year + period + offset(log(service)), family = poisson, data = ships, subset = (service != 0)) update(ships.glm, start = coef(ships.glm)) } ## failed in 1.4.1. ## PR#1439 file.info()$isdir was only partially logical (info <- file.info(".")) info$isdir stopifnot(info$isdir == TRUE) ## 1.4.1 had a TRUE value that was not internally integer 1. ## PR#1473 predict.*bSpline() bugs extrapolating for deriv >= 1 library(splines) x <- c(1:3,5:6) y <- c(3:1,5:6) (isP <- interpSpline(x,y))# poly-spline representation (isB <- interpSpline(x,y, bSpl = TRUE))# B-spline repr. xo <- c(0, x, 10)# x + outside points op <- options(digits = 4) for(der in 0:3) # deriv=3 fails! print(formatC(try(predict(isP, xo, deriv = der)$y), wid=7,format="f"), quote = FALSE) ## and for B-spline (instead of polynomial): for(der in 0:3) # deriv=3 failed print(formatC(try(predict(isB, xo, deriv = der)$y), wid=7,format="f"), quote = FALSE) options(op) unloadNamespace("splines") ## PR 902 segfaults when warning string is too long, Ben Bolker 2001-04-09 provoke.bug <- function(n=9000) { warnmsg <- paste(LETTERS[sample(1:26,n,replace=TRUE)],collapse="") warning(warnmsg) } provoke.bug() ## segfaulted in 1.2.2, will also on machines without vsnprintf (none now) ## PR#1510 merge with multiple match rows and different names. df1 <- data.frame(z = 1:10, m = letters[1:10], w = rnorm(10)) df2 <- data.frame(x = 1:10, y = rnorm(10), n = letters[1:10]) merge(df2, df1, by.x = c("x", "n"), by.y = c("z", "m")) ## failed in 1.5.0 ## PR 1524 Problems with paste/unlist l <- names(unlist(list(aa = list(bb = 1)))) l # this is exactly "aa.bb" stopifnot(identical(l, "aa.bb")) l2 <- paste(l, "this should be added") stopifnot(identical(l2, "aa.bb this should be added")) ## 1.5.0 gave l2 printing as l. ## PR 1530 drop inconsistency for data frames DF <- data.frame(x = 1:3, y = c("A","D","E"), z = c(6,9,10)) a1 <- DF[1,1:3] xx <- DF[1,] a2 <- xx[, 1:3] a3 <- DF[1,1:3, drop = TRUE] a4 <- xx[, 1:3, drop = TRUE] stopifnot(identical(a1, a2), identical(a3, a4)) ## <= 1.5.0 had a2 == a3. ## PR 1536 rbind.data.frame converts logical to factor df <- data.frame(a = 1:10) df$b <- df$a < 5 ddf <- rbind(df, df) stopifnot(!is.factor(ddf$b)) ## 1.5.0 had b as a factor. ## PR 1548 : prettyNum inserted leading commas stopifnot(prettyNum(123456, big.mark=",") == "123,456") ## PR 1552: cut.dendrogram hc <- hclust(dist(USArrests), "ave") cc <- cut(as.dendrogram(hc), h = 20)## error in 1.5.0 ## predict.smooth.spline(*, deriv > 0) : x <- (1:200)/32 ss <- smooth.spline(x, 10*sin(x)) stopifnot(length(x) == length(predict(ss,deriv=1)$x))# not yet in 1.5.0 ## pweibull(large, log=T): stopifnot(pweibull(seq(1,50,len=1001), 2,3, log = TRUE) < 0) ## part of PR 1662: fisher.test with total one fisher.test(cbind(0, c(0,0,0,1))) ## crashed in R <= 1.5.0 stopifnot(Mod(vector("complex", 7)) == 0) # contained garbage in 1.5.0 ## hist.POSIXt with numeric `breaks' hist(.leap.seconds, breaks = 5) ## error in 1.5.1 ##Jonathan Rougier 2002-06-18 x <- matrix(runif(30), 10, 3) poly(x, degree=2) ## failed in 1.5.1 ## PR#1694 cut with infinite values -> NA (Markus Jäntti) cut.off <- c(-Inf, 0, Inf) x <- c(-Inf, -10, 0, 10, Inf) (res <- cut(x, cut.off, include.lowest=TRUE)) stopifnot(!is.na(res)) (res <- cut(x, cut.off, include.lowest=TRUE, right=FALSE)) stopifnot(!is.na(res)) ## outer values were NA in 1.5.1 ## ls.str() for function environments: Fn <- ecdf(rnorm(50)) ls.str(envir = environment(Fn)) ## failed in 1.5.1 ## PR 1767 all.equal.character for non-matching NAs all.equal(c("A", "B"), c("A", NA)) ## failed in 1.5.1 ## failed since at least version 0.90: stopifnot(is.character(a12 <- all.equal(1,1:2)), length(a12) == 1,# was 2 till 1.6.2 a12 == "Numeric: lengths (1, 2) differ") ## a12 was *list* of length 3 ## related to PR 1577/1608, conversions to character DF <- data.frame(b = LETTERS[1:3]) sapply(DF, class) DF[[1]] <- LETTERS[1:3] stopifnot(is.character(DF$b)) ## was factor < 1.6.0 DF <- data.frame(b = LETTERS[1:3]) DF$b <- LETTERS[1:3] stopifnot(is.character(DF$b)) ## always was character. x <- data.frame(var = LETTERS[1:3]); x$var <- as.character(x$var) x[[1]][2] <- "3" x stopifnot(is.character(x$var)) is.na(x[[1]]) <- 2 stopifnot(is.character(x$var)) x <- data.frame(var = I(LETTERS[1:3])) x[[1]][2] <- "3" x stopifnot(is.character(x$var)) is.na(x[[1]]) <- 2 stopifnot(is.character(x$var)) x <- data.frame(var = factor(LETTERS[1:3])) x[[1]][2] <- "3" x stopifnot(is.factor(x$var)) is.na(x[[1]]) <- 2 stopifnot(is.factor(x$var)) x <- data.frame(a = 1:4) y <- data.frame(b = LETTERS[1:3]) y$b <- as.character(y$b) z <- merge(x, y, by = 0, all.x = TRUE) sapply(z, data.class) stopifnot(is.character(z$b)) ## end of `related to PR 1577/1608' ## logicals became factors < 1.6.0 stopifnot(sapply(as.data.frame(matrix((1:12)%% 4 == 1, 3,4)), is.logical)) ## recycling of factors in data.frame (wish from PR#1713) data.frame(x=c("A","B"), y="C") # failed to recycle in 1.5.1 X <- data.frame(x=c("A","B"), y=I("C")) # also failed XX <- data.frame(x=c("A","B"), y=I(rep("C", 2))) # fine stopifnot(identical(X, XX)) ## Last is false in some S variants. ## test of rank-deficient prediction, as various claims this did not work ## on R-help in June 2002 x1 <- rnorm(100) x3 <- rnorm(100) y <- rnorm(100) train <- data.frame(y=y, x1=x1, x2=x1, x3=x3) fit <- lm(y ~ ., train) stopifnot(all.equal(predict(fit), predict(fit, train))) ## warning added for 1.6.0 ## terms(y ~ .) on data frames with duplicate names DF <- data.frame(y = rnorm(10), x1 = rnorm(10), x2 = rnorm(10), x3 = rnorm(10)) names(DF)[3] <- "x1" fit <- try(lm(y ~ ., DF)) stopifnot(class(fit) == "try-error") ## had formula y ~ x1 + x1 + x3 in 1.5.1. ## PR#1759 as.character.octmode() (Henrik Bengtsson) x <- 0; class(x) <- "octmode" stopifnot(as.character(x) == "0") ## gave "" in 1.5.1 ## PR#1843 unsplit() with f a list g <- factor(round(10 * runif(1000))) x <- rnorm(1000) + sqrt(as.numeric(g)) xg <- split(x, list(g1=g,g2=g)) res <- unsplit(xg, list(g1=g, g2=g)) stopifnot(x == res) # can't have rounding error here ## gave incorrect result with warning in 1.5.1. ## matching NAs on Solaris (MM 2002-08-02) # x <- as.double(NA) # identical(x + 0, x) # stopifnot(match(x + 0, x, 0) == 1) ## match failed on Solaris with some compiler settings ## NA+0 is not guaranteed to be NA: could be NaN ## identical on specials (BDR 2002-08-02) stopifnot(identical(as.double(NA), NaN) == FALSE) ## was identical on 1.5.1 ## safe prediction (PR#1840) cars.1 <- lm(dist ~ poly(speed, degree = 1), data = cars) cars1 <- lm(dist ~ speed, data = cars) DF <- data.frame(speed=4) stopifnot(all.equal(predict(cars.1, DF), predict(cars1, DF))) ## error in 1.5.1 ## Ops.data.frame (PR#1889) d <- data.frame(1:10) d > list(5) ## failed in 1.5.1 ## order(na.last = NA) (PR#1913 / 1906 / 1981) x <- 1 order(x, na.last=NA) order(x, x, x, na.last=NA) ## failed in 1.5.1, since sapply simplified to a scalar. stopifnot(3:1 == order(c(1,2,3,NA), na.last=NA, decreasing=TRUE)) ## ignored `decreasing' in 1.5.1 order(c(NA, NA), na.last = NA) ## error in 1.5.1, now integer(0) ## as.list() coerced logical to integer (PR#1926) x <- c(TRUE,FALSE,NA) stopifnot(identical(x, unlist(as.list(x)))) ## the 2nd was (1,0,NA) before 1.6 ## test of long Error expression in aov(): PR#1315 and later, ## and also a cross-check of deparse(, cutoff = 500) AA <- structure(list(Y2 = c(10, 9, 0, 0, 5, 6, 0, 0, 8, 9, 0, 0, 4, 4, 0, 0, 12, 11, 2, 0, 6, 7, 0, 0), P2 = factor(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), labels = c("1", "2", "3")), AAAAAAAA = factor(c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L ), labels = c("E1", "E2")), B2 = factor(c(1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L), labels = c("Red", "Unred" )), C2 = factor(c(1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L), labels = c("Agent", "Patient"))), names = c("Y2", "P2", "AAAAAAAA", "B2", "C2"), class = "data.frame", row.names = 1:24) AK2anova.out <- aov(Y2 ~ AAAAAAAA * B2 * C2 + Error(P2 + P2:AAAAAAAA + P2:B2 + P2:C2 + P2:AAAAAAAA:B2 + P2:AAAAAAAA:C2 + P2:B2:C2 + P2:AAAAAAAA:B2:C2), data=AA) ## failed in 1.5.1 ## as.character was silently truncating expressions to 60 chars q2 <- expression(c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19)) (q3 <- as.character(q2)) stopifnot(nchar(q3) == 68) ## was 61 in 1.5.1 ## Ops wasn't using NextMethod correctly ## Ops.ordered: or <- ordered(c("a","b","c")) stopifnot( (or == "a") == c(TRUE,FALSE,FALSE)) stopifnot(or == or) stopifnot(or != "d") ## last was NA NA NA in 1.5.1 Ops.foo <- function(e1, e2) { NextMethod() } Ops.baz <- function(e1, e2) { NextMethod() } a <- b <- 1 class(a) <- c("foo","bar","baz") class(b) <- c("foo","baz") stopifnot(a == 1, b == a) ##(already worked in 1.5.1) ## t() wrongly kept "ts" class and "tsp" t(ts(c(a=1, d=2))) ## gave error while printing in 1.5.1 at <- attributes(t(ts(cbind(1, 1:20)))) stopifnot(length(at) == 2, at$dim == c(2, 20), at$dimnames[[1]] == paste("Series", 1:2)) ## failed in 1.5.1 ## Nextmethod from anonymous function (PR#1211) try( get("print.ts")(1) )# -> Error ## seg.faulted till 1.5.1 ## cbind/rbind should work with NULL only args stopifnot(is.null(cbind(NULL)), is.null(cbind(NULL,NULL)), is.null(rbind(NULL)), is.null(rbind(NULL,NULL))) ## gave error from 0.63 till 1.5.1 ## seq.POSIXt() had rounding problem: stopifnot(4 == length(seq(from=ISOdate(2000,1,1), to=ISOdate(2000,1,4), length.out=4))) ## length was 5 till 1.6.0 ## loess has a limit of 4 predictors (John Deke on R-help, 2002-09-16) data1 <- array(runif(500*5),c(500,5)) colnames(data1) <- c("x1","x2","x3","x4","x5") y <- 3+2*data1[,"x1"]+15*data1[,"x2"]+13*data1[,"x3"]-8*data1[,"x4"]+14*data1[,"x5"]+rnorm(500) data2 <- as.data.frame(cbind(y,data1)) result4 <- loess(y~x1+x2+x3+x4,data2) try(result5 <- loess(y~x1+x2+x3+x4+x5,data2)) ## segfaulted in 1.5.1 ## format.AsIs was not handling matrices jk <- data.frame(x1=2, x2=I(matrix(0,1,2))) jk ## printing failed in 1.5.1 ## eigenvectors got irrelevant names (PR#2116) set.seed(1) A <- matrix(rnorm(20), 5, 4); A <- A[,c(1:4,1)] # rank 4! dimnames(A) <- list(LETTERS[1:5], letters[1:5]) (ev <- eigen(A)$vectors) stopifnot(is.null(dimnames(ev))) ## had colnames in 1.6.0 ## pretty was not pretty {because seq() isn't} (PR#1032 and D.Brahm) stopifnot(pretty(c(-.1, 1))[2] == 0, ## [2] was -2.775558e-17 pretty(c(-.4,.8))[3] == 0, ## [3] was 5.551115e-17 pretty(100+ c(0, pi*1e-10))[4] > 100,# < not too much rounding! pretty(c(2.8,3))[1] == 2.8) ## last differed by 4.44e-16 in R 1.1.1 ## add1 was giving misleading message when scope was nonsensical. counts <- c(18,17,15,20,10,20,25,13,12) fit <- glm(counts ~ 1, family=poisson) res <- try(add1(fit, ~ .)) ## error in 1.6.0 was ## `Error in if (ncol(add) > 1) { : missing value where logical needed' stopifnot(length(grep("missing value", res)) == 0) ## stripchart with NAs (PR#2018) Sepal <- iris$Sepal.Length Sepal[27] <- NA stripchart(Sepal ~ iris$Species, method="stack") ## failed in 1.6.1 ## losing is.object bit internally (PR#2315) stopifnot(is.ts(log(as.ts(1:10)))) ## failed for integer original as here in 1.6.1. ## formatC ignored rounding up (PR#2299) stopifnot(formatC(99.9, 1, format="fg") == "100") stopifnot(formatC(99.9, 2, format="fg") == "100") stopifnot(formatC(99.9, 3, format="fg") == "99.9") ## gave exponential format on 1.6.1 ## full/partial matching in attr. tmp <- list(id=1) attr(tmp,"n.ch") <- 2 attr(tmp,"n") <- 1 attributes(tmp) (res <- attr(tmp, "n")) stopifnot(length(res) == 1 && res == 1) ## gave NULL in 1.6.1 if (have_cat) { ## Formerly undocumented line limit in system(intern=TRUE) ## Naoki Takebayashi 2002-12-07 tmp <- tempfile() long <- paste(rep("0123456789", 20L), collapse="") cat(long, "\n", sep="", file=tmp) junk <- system(paste("cat", shQuote(tmp)), intern = TRUE) stopifnot(length(junk) == 1L, nchar(junk[1]) == 200L) ## and split truncated on 1.6.1 } ## missing group generics for `difftime' (related to PR#2345) x <- as.difftime(c("0:3:20", "11:23:15")) y <- ISOdate(2001, 4, 26) - ISOdate(2001, 2, 26) x + x 2*x x < y x < 100 ## all but last failed in R < 1.7.0 ## PR 2358 (part) mm <- 1:2 names(mm)[2] <- 'y' (mm <- c(mm, 3)) stopifnot(is.na(names(mm)[1])) ## 1.6.1 had "NA" ## PR 2357 a <- matrix(c(1,2,3,-1,-2,3),2,3,dimnames=list(c("A","B"),NULL)) (z <- pmax(a, 0)) stopifnot(identical(dimnames(z), dimnames(a))) # further checks a <- matrix(c(1,2,3,-1,-2,3),2,3,dimnames=list(c("A","B"),1:3)) (z <- pmax(a, 0)) stopifnot(identical(dimnames(z), dimnames(a))) a <- matrix(c(1,2,3,-1,-2,3),2,3,dimnames=list(NULL, letters[1:3])) (z <- pmax(a, 0)) stopifnot(identical(dimnames(z), dimnames(a))) ## 1.6.1 only transferred dimnames if both components were non-null ## internal conversion to factor in type.convert was not right ## if a character string NA was involved. x <- c(NA, "NA", "foo") (z <- type.convert(x, as.is=FALSE)) stopifnot(identical(levels(z), "foo")) (z <- type.convert(x, na.strings=character(0), as.is=FALSE)) stopifnot(identical(levels(z), sort(c("foo", "NA")))) (z <- type.convert(x, na.strings="foo", as.is=FALSE)) stopifnot(identical(levels(z), "NA")) ## extra level in 1.6.1 ## related example tmp <- tempfile() cat(c("1", "foo", "\n", "2", "NA", "\n"), file = tmp) (z <- read.table(tmp, na.strings="foo", stringsAsFactors=TRUE)) unlink(tmp) stopifnot(identical(levels(z$V2), "NA"), identical(is.na(z$V2), c(TRUE, FALSE))) ## 1.6.1 had V2 as NA NA. ## PR#2396, parsing and pushbacks. tmp <- tempfile() cat( c( "1", "a+b", "2"), file=tmp, sep="\n") open(tcon <- file(tmp)) readLines(tcon, n=1) pushBack("a1+b1", tcon) parse(file=tcon, n=1) close(tcon) unlink(tmp) ## failed with syntax error in 1.6.1 ## NAs in max.col a <- matrix(1, 3, 3) a[1,2] <- NA (z <- max.col(a)) stopifnot(is.na(z[1])) ## gave (randomly) 1 or 3 in 1.6.1 ## PR#2469: read.table on Mac OS CR-terminated files. tmp <- tempfile() x <- c("aaa", "bbb", "ccc") cat(x, sep="\r", file=tmp) con <- file(tmp) open(con) line <- readLines(con, 1) pushBack(line, con) (y <- readLines(con)) close(con) unlink(tmp) stopifnot(identical(x, y)) ## pushback problems in 1.6.2 only ## dimnames in solve(): not a bug just an improvement in 1.7.0 A <- diag(3) dimnames(A) <- list(LETTERS[1:3], letters[1:3]) (B <- solve(A)) stopifnot(identical(colnames(B), rownames(A))) ## R < 1.7.0 had no colnames for B, and S has the colnames of A. stopifnot(all.equal(t(B), solve(t(A)))) ## test here is of dimnames ## PR#2507: extracting 0-length dimensions for arrays dn <- list(LETTERS[1:2], letters[1:3], paste("t",1:4,sep="")) A. <- array(1:24, dim = 2:4, dimnames = dn) str(A.[1, 0, 2 ]) str(A.[1, 0, 2, drop = FALSE]) ## both gave errors in 1.6.2 plot(sf <- stepfun(2, 3:4)) ## failed in 1.6.2 ## PR#2541, cbind (and rbind) with zero-length components y <- matrix(0,1,0) cbind(y, integer(0)) y <- matrix(0,0,1) rbind(y, integer(0)) ## gave fatal error in 1.6.2, since miscalculated no of rows/cols. ## PR#2518 multiple objects in AIC.default. lm1 <- lm(y ~ x, list(x=1:10, y=jitter(1:10))) lm2 <- lm(y ~ x, list(x=1:10, y=jitter(1:10))) AIC(lm1, lm2) AIC(lm1, lm2, k=2) ## second failed in 1.6.2 ## PR#2591 unique on ordered factor f <- ordered(month.name, levels=month.name) (uf <- unique(f)) stopifnot(is.ordered(uf)) ## gave factor in 1.6.2 ## PR#2587 coercion of length-0 vectors x <- numeric(0) x[1] <- NA stopifnot(identical(mode(x), "numeric")) ## ## coercion lost the object bit in [<- x <- I(TRUE) is.object(x) x[2] <- "N" stopifnot(is.object(x)) ## failed in 1.6.2 ## check inherits now works for basic classes: x <- 1:3 is.object(x) # FALSE stopifnot(inherits(x, "integer")) ## 2003-Mar-12 it did not ## rank() is numeric also for NA char vectors stopifnot(is.numeric(rk <- rank(c("ch","c", NA))), all(rk == c(2,1,3))) ## did not from R 1.2 -- 1.6 ## table() should by default keep NA levels of factors i <- c(1:2,NA); fi <- factor(i, exclude = NULL) stopifnot(identical(as.character(i), dimnames(table(fi))[[1]])) ## not in 2003-Mar-10 unstable ## [lm.]influence() for multivariate lm : n <- 32 Y0 <- matrix(rnorm(3 * n), n, 3) # and a version with named Y's Yn <- Y0; colnames(Yn) <- paste0("Y",1:3) X <- matrix(rnorm(5 * n), n, 5) for(Y in list(Y0, Yn)) { fmL <- lapply(1:3, function(j) lm(Y[,j] ~ X)) infL <- lapply(fmL, lm.influence) infm <- lm.influence(mod <- lm(Y ~ X)) if(interactive()) str(infL, give.attr=FALSE) # should match the 'infm' parts ## 1. "hat" are all the 3 the same hatL <- sapply(infL, `[[`, "hat") stopifnot(all.equal(hatL[,1], hatL[,2]), all.equal(hatL[,2], hatL[,3])) ## 2. the other 3 components should be "concatenated" to give same as mlm : for(nm in c("coefficients", "sigma", "wt.res")) { stopifnot(all.equal(unname(infm[[nm]]), unname(sapply(infL, `[[`, nm, simplify="array", USE.NAMES=FALSE)))) } ## failed up to 2003-03-29 (pre 1.7.0) im1 <- influence.measures(mod) dfbs <- dfbetas(mod) dimnames(dfbs)[[3]] <- dimnames(im1$infmat)[[3]][1:6] stopifnot(all.equal(im1$infmat[,,1:6], dfbs)) }# for both Y's ## lm.influence() did not work correctly for "mlm"s in R <= 3.5.1 ## rbind.data.frame with character and ordered columns A <- data.frame(a=1) A$b <- "A" B <- data.frame(a=2) B$b <- "B" AB <- rbind(A,B) (cl <- sapply(AB, class)) stopifnot(cl[2] == "character") # was factor in 1.6.2 A <- data.frame(a=1:3, b=ordered(letters[1:3])) B <- data.frame(a=7:9, b=ordered(letters[7:9])) AB <- rbind(A,B) (cl <- sapply(AB, class)) stopifnot(cl$b[1] == "ordered") # was factor in 1.6.2 C <- data.frame(a=4:6, b=factor(letters[4:6])) ABC <- rbind(AB, C) (cl <- sapply(ABC, class)) stopifnot(cl[2] == "factor") A <- data.frame(a=1) A$b <- "A" B <- data.frame(a=2, b=factor("B")) (AB <- rbind(A,B)) (cl <- sapply(AB, class)) stopifnot(cl[2] == "character") A <- data.frame(a=1, b=factor("A")) B <- data.frame(a=2) B$b <- "B" (AB <- rbind(A,B)) (cl <- sapply(AB, class)) stopifnot(cl[2] == "factor") A <- data.frame(a=factor(c("A", NA, "C"))) B <- data.frame(a=factor(c("B", NA, "C"))) (AB <- rbind(A,B)) stopifnot(levels(AB$a) == c("A", "C", "B")) A <- data.frame(a=I(c("A", NA, "C"))) B <- data.frame(a=I(c("B", NA, "C"))) (AB <- rbind(A,B)) (cl <- sapply(AB, class)) stopifnot(cl[1] == "AsIs") A <- data.frame(a=1) A$b <- "A" B <- data.frame(a=2, b=I("B")) (AB <- rbind(A,B)) (cl <- sapply(AB, class)) stopifnot(cl[2] == "character") A <- data.frame(a=1, b=factor("A")) B <- data.frame(a=2, b=I("B")) (AB <- rbind(A,B)) (cl <- sapply(AB, class)) stopifnot(cl[2] == "factor") ## ## hclust(), as.hclust.twins(), agnes() consistency x <- matrix(rnorm(30), ncol=3) # no observation names xn <- x; rownames(xn) <- letters[10:1]# has obs. names hc <- hclust(dist(x), method="complete") hcn <- hclust(dist(xn), method="complete") iC1 <- !names(hc) %in% c("labels", "call") stopifnot(identical(hc, hhc <- as.hclust(hc)), identical(hhc, as.hclust(hhc)), identical(hc[iC1], hcn[iC1]), identical(hcn$labels, rownames(xn)) ) if(require(cluster, quietly = TRUE)) { # required package ag <- agnes(x, method="complete") hcag <- as.hclust(ag) agn <- agnes(xn, method="complete") hcagn <- as.hclust(agn) iC2 <- !names(hcag) %in% c("labels", "call") stopifnot(identical(hcagn[iC2], hcag[iC2]), identical(hcagn$labels, hcn$labels), all.equal(hc$height, hcag$height, tol = 1e-12), all(hc$merge == hcag$merge | hc$merge == hcag$merge[ ,2:1]) ) detach("package:cluster") } ## as.hclust.twins() lost labels and more till (incl) 1.6.2 ## PR#2867 qr(LAPACK=TRUE) didn't always pivot in 1.7.0 set.seed(1) X <- matrix(rnorm(40),10,4) X[,1] <- X[,2] (qrx <- qr(X, LAPACK=TRUE)) stopifnot(any(qrx$pivot != 1:4)) # check for pivoting ## ## rownames<- did not work on an array with > 2 dims in 1.7.0 A <- array(1:12, dim=c(2, 3, 2)) rownames(A) <- letters[1:2] A <- array(1:12, dim=c(2, 3, 2)) colnames(A) <- 1:3 ## failed in 1.7.0 ## predict on constant model, PR#2958 res <- model.frame(~1, data.frame(x = 1:5)) stopifnot(nrow(res) == 5) res <- predict(lm(y ~ 1, data = data.frame(y = rep(0:3, c(5,9,7,1)))), newdata = data.frame(x = 1:5)) stopifnot(length(res) == 5) res <- predict(glm(y ~ 1, family = poisson, data = data.frame(y = rep(0:3, c(5,9,7,1)))), newdata = data.frame(x = 1:5), type = "r") stopifnot(length(res) == 5) ## all length one in 1.7.0 ## PR#2993 need to consider delta=NULL in power.t.test{ctest} power.t.test(n=10, delta=NULL, power=.9, alternative="two.sided") ## failed in 1.7.0 ## PR#3221 eigenvectors should be a matrix even in the 1x1 case A <- matrix(1) stopifnot(is.matrix(eigen(A)$vectors)) ## gave vector in 1.7.0 ## [[<-.data.frame testdata <- data.frame(a=1:2, b = c(TRUE, NA)) td <- strptime(c("31121991", "31121992"), "%d%m%Y") testdata[["a"]] <- td if(FALSE) stopifnot(inherits(.Last.value, "try-error")) ## succeeded in 1.7.0 and again in 2.11.x {should it not?} ## pacf on n x 1 matrix: Paul Gilbert, R-devel, 2003-06-18 z <- as.ts(matrix(rnorm(100), , 1)) class(z) # not "mts" is.matrix(z) # TRUE in 1.7.1 pacf(z) pacf(matrix(rnorm(100), , 1)) ## both failed in 1.7.1. ## lsfit was not setting residuals in the rank=0 case fit <- lsfit(matrix(0, 10, 1), 1:10, intercept=FALSE) stopifnot(fit$residuals == 1:10) ## zero residuals in 1.7.1. ## interval calculations on predict.lm x <- 1:10 y <- rnorm(10) predict(lm(y ~ x), type="terms", interval="confidence") ## ## 0-level factors f <- factor(numeric(0)) sort(f) unique(f) ## both failed in 1.7.1 ## data failed with some multiple inputs data(cars, women) ## failed in 1.7.1 ## body() and formals() looked in different places bar <- function(x=NULL) { foo <- function(y=3) testit() print(formals("foo")) print(body("foo")) } bar() ## the call to body() failed in 1.7.0 ## string NAs shouldn't have any internal structure.(PR#3078) a <- c("NA", NA, "BANANA") na <- NA_character_ a1 <- substr(a,1,1) stopifnot(is.na(a1)==is.na(a)) a2 <- substring(a,1,1) stopifnot(is.na(a2)==is.na(a)) a3 <- sub("NA","na",a) stopifnot(is.na(a3)==is.na(a)) a3 <- gsub("NA","na",a) stopifnot(is.na(a3)==is.na(a)) substr(a3, 1, 2) <- "na" stopifnot(is.na(a3)==is.na(a)) substr(a3, 1, 2) <- na stopifnot(all(is.na(a3))) stopifnot(agrep("NA", a) == c(1, 3)) stopifnot(grep("NA", a) == c(1, 3)) stopifnot(grep("NA", a, perl=TRUE) == c(1, 3)) stopifnot(all(is.na(agrep(na, a)))) stopifnot(all(is.na(grep(na, a)))) stopifnot(all(is.na(grep(na, a, perl=TRUE)))) a4 <- abbreviate(a) stopifnot(is.na(a4) == is.na(a)) a5 <- chartr("NA", "na", a) stopifnot(is.na(a5) == is.na(a)) a6 <- gsub(na, "na", a) stopifnot(all(is.na(a6))) a6a <- gsub("NANA", na, a) stopifnot(is.na(a6a)==c(FALSE, TRUE, TRUE)) a7 <- a; substr(a7, 1, 2) <- "na" stopifnot(is.na(a7) == is.na(a)) a8 <- a; substr(a8, 1, 2) <- na stopifnot(all(is.na(a8))) stopifnot(identical(a, toupper(tolower(a)))) a9 <- strsplit(a, "NA") stopifnot(identical(a9, list("", na ,c("BA","")))) a9 <- strsplit(a, "NA", fixed = TRUE) stopifnot(identical(a9, list("", na ,c("BA","")))) a9 <- strsplit(a, "NA", perl = TRUE) stopifnot(identical(a9, list("", na ,c("BA","")))) a10 <- strsplit(a, na) stopifnot(identical(a10, as.list(a))) ## nchar() differs a bit stopifnot(identical(is.na(a), is.na(nchar(a))), all(!is.na(nchar(a, type = "width")))) ## NA and "NA" were not distinguished in 1.7.x ## coercing 0-length generic vectors as.double(list()) as.integer(list()) as.logical(list()) as.complex(list()) as.character(list()) ## all but the last failed in 1.7.x ## help on reserved words ## if else repeat while function for in next break will fail if(.Platform$OS.type == "windows") options(pager="console") for(topic in c("TRUE", "FALSE", "NULL", "NA", "Inf", "NaN", "NA_integer_", "NA_real_", "NA_complex_", "NA_character_")) { eval(parse(text=paste("?", topic, sep=""))) eval(parse(text=paste("help(", topic, ")", sep=""))) } ## ?NULL and all the help calls fail in 1.7.x ## row names in data frames xx <- structure(1:3, names=letters[1:3]) data.frame(xx) data.frame(xx, yy=1:6) # failed with misleading message in 1.7.x data.frame(xx, yy=1:6, row.names=NULL) # no warning ## ## empty paste stopifnot(length(paste(character(0), character(0))) == 0) # was "" stopifnot(identical(paste(character(0), character(0), collapse="+"), "")) ## ## concatenation of make.names (Tom Minka, R-help, 2003-06-17) a1 <- make.names(c("a", "a", "a"), unique=TRUE) a2 <- make.names(c(make.names(c("a", "a"), unique=TRUE), "a"), unique=TRUE) stopifnot(identical(a1, a2)) df1 <- rbind(data.frame(x=1), data.frame(x=2), data.frame(x=3)) df2 <- rbind(rbind(data.frame(x=1), data.frame(x=2)), data.frame(x=3)) stopifnot(identical(df1, df2)) ## ## PR#3280 data.frame(check.name=FALSE) was not always respected DF <- data.frame(list("a*" = 3), check.names = FALSE) stopifnot(identical(names(DF), "a*")) ## gave "a." in 1.7.1 ## functions using get() were not always looking for functions or in the ## right place x <- factor(1:3) contrasts(x) <- "ctr" test <- function(x) { ctr <- contr.treatment contrasts(x) # failed in 1.7.1 } test(x) ## ## get/exists were ignoring mode in base stopifnot(exists(".Device")) stopifnot(!exists(".Device", mode="function")) # was true in 1.7.1 ## ## inadvertent recursive indexing bug (PR#3324) x <- list(a=1:3, b=2:4) try(x[[c("c", "d")]]) try(x[[c("c", "d")]] <- NA) ## both segfaulted in 1.7.1 ## empty indexing of data frames (PR#3532) x <- data.frame(x = "1.5") num <- numeric(0) x[num] <- list() x[, num] <- list() ## x[[num]] is rightly an error ## x[num] etc failed in 1.7.x. ## .Random.seed was searched for with inherits=TRUE rm(.Random.seed) attach(list(.Random.seed=c(0:4))) x <- runif(1) detach(2) (new <- RNGkind()) stopifnot(identical(new, c("Mersenne-Twister", "Inversion", "Rejection"))) stopifnot(identical(find(".Random.seed"), ".GlobalEnv")) ## took from and assigned to list in 1.7.x. ## PR#3750 y <- c(1, NA, NA, 7) identical(y, qqnorm(y, plot.it=FALSE)$y) ## qqnorm() used to drop NA's in its result till 1.7.x ## PR#3763 d0 <- ISOdate(2001,1,1)[0] # length 0 POSIX (rd0 <- round(d0, "day")) stopifnot(identical(rd0, as.POSIXlt(d0))) ## 2nd line gave floating point exception (in format(*)!) ## New det() function m <- cbind(1, c(1, 1)) stopifnot(det(m) == 0, determinant(m)$mod == -Inf, determinant(m, log=FALSE)$mod == 0) ## gave error for singular matrices in earlier Aug.2003 ## tests of model fitting in the presence of non-syntactic names names(swiss)[6] <- "Infant Mortality" (lm1 <- lm(Fertility ~ ., data = swiss)) formula(lm1) # is expanded out slm1 <- step(lm1) add1(lm1, ~ I(Education^2) + .^2) step(lm1, scope=~ I(Education^2) + .^2) Quine <- structure(list(Eth = factor(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), levels = 1:2, labels = c("A", "N")), Sex = factor(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), levels = 1:2, labels = c("F", "M")), Age = factor(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L), levels = 1:4, labels = c("F0", "F1", "F2", "F3")), `Slow or fast` = factor(c(2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), levels = 1:2, labels = c("AL", "SL")), Days = c(2, 11, 14, 5, 5, 13, 20, 22, 6, 6, 15, 7, 14, 6, 32, 53, 57, 14, 16, 16, 17, 40, 43, 46, 8, 23, 23, 28, 34, 36, 38, 3, 5, 11, 24, 45, 5, 6, 6, 9, 13, 23, 25, 32, 53, 54, 5, 5, 11, 17, 19, 8, 13, 14, 20, 47, 48, 60, 81, 2, 0, 2, 3, 5, 10, 14, 21, 36, 40, 6, 17, 67, 0, 0, 2, 7, 11, 12, 0, 0, 5, 5, 5, 11, 17, 3, 4, 22, 30, 36, 8, 0, 1, 5, 7, 16, 27, 0, 30, 10, 14, 27, 41, 69, 25, 10, 11, 20, 33, 5, 7, 0, 1, 5, 5, 5, 5, 7, 11, 15, 5, 14, 6, 6, 7, 28, 0, 5, 14, 2, 2, 3, 8, 10, 12, 1, 1, 9, 22, 3, 3, 5, 15, 18, 22, 37)), class = "data.frame", row.names = 1:146) step(aov(log(Days+2.5) ~ .^4, data=Quine)) set.seed(11) DF <- data.frame(y=rnorm(21), `x 1`=-10:10., check.names = FALSE) lm(y ~ ., data = DF) (fm <- lm(y ~ `x 1` + I(`x 1`^2), data = DF)) step(fm) N <- c(0,1,0,1,1,1,0,0,0,1,1,0,1,1,0,0,1,0,1,0,1,1,0,0) P <- c(1,1,0,0,0,1,0,1,1,1,0,0,0,1,0,1,1,0,0,1,0,1,1,0) K <- c(1,0,0,1,0,1,1,0,0,1,0,1,0,1,1,0,0,0,1,1,1,0,1,0) yield <- c(49.5,62.8,46.8,57.0,59.8,58.5,55.5,56.0,62.8,55.8,69.5,55.0, 62.0,48.8,45.5,44.2,52.0,51.5,49.8,48.8,57.2,59.0,53.2,56.0) npk <- data.frame(`block no`=gl(6,4), N=factor(N), P=factor(P), K=factor(K), yield=yield, check.names=FALSE) op <- options(contrasts=c("contr.helmert", "contr.treatment")) (npk.aovE <- aov(yield ~ N*P*K + Error(`block no`), npk)) summary(npk.aovE) model.tables(npk.aovE) model.tables(npk.aovE, "means") options(op)# reset to previous ## Didn't work before 1.8.0 ## cmdscale ## failed in versions <= 1.4.0 : cm1 <- cmdscale(eurodist, k=1, add=TRUE, x.ret = TRUE) cmdsE <- cmdscale(eurodist, k=20, add = TRUE, eig = TRUE, x.ret = TRUE) # FAILED on Debian testing just prior to 1.9.0! #stopifnot(identical(cm1$x, cmdsE$x), # identical(cm1$ac, cmdsE$ac)) stopifnot(all.equal(cm1$x, cmdsE$x), all.equal(cm1$ac, cmdsE$ac)) ## end of moved from cmdscale.Rd ## cutree hc <- hclust(dist(USArrests)) ct <- cutree(hc, h = c(0, hc$height[c(1,49)], 1000)) stopifnot(ct[,"0"]== 1:50, unique(ct[,2]) == 1:49, ct[,3] == ct[,4], ct[,4] == 1) ## end of moved from cutree.Rd ## princomp USArrests[1, 2] <- NA pc.cr <- princomp(~ Murder + Assault + UrbanPop, data = USArrests, na.action=na.exclude, cor = TRUE) update(pc.cr, ~ . + Rape) ## end of moved from princomp.Rd ## arima{0} (fit <- arima(lh, c(1,0,0))) tsdiag(fit) (fit <- arima0(lh, c(1,0,0))) tsdiag(fit) ## end of moved from arima{0}.Rd ## predict.arima predict(arima(lh, order=c(1,0,1)), n.ahead=5) predict(arima(lh, order=c(1,1,0)), n.ahead=5) predict(arima(lh, order=c(0,2,1)), n.ahead=5) ## end of moved from predict.arima.Rd library(splines) ## ns ## Consistency: x <- c(1:3,5:6) stopifnot(identical(ns(x), ns(x, df = 1)), !is.null(kk <- attr(ns(x), "knots")),# not true till 1.5.1 length(kk) == 0) ## end of moved from ns.Rd ## predict.bs ## Consistency: basis <- ns(women$height, df = 5) newX <- seq(58, 72, len = 51) wh <- women$height bbase <- bs(wh) nbase <- ns(wh) stopifnot(identical(predict(basis), predict(basis, newx=wh)), identical(predict(bbase), predict(bbase, newx=wh)), identical(predict(nbase), predict(nbase, newx=wh))) ## end of moved from predict.bs.Rd ## internal coerceVector() was too lenient plot(1) r <- try(strwidth(plot))## Error: cannot coerce stopifnot(inherits(r, "try-error"), grep("cannot coerce", r) == 1) ## gave seg.fault or memory allocation error before 1.8.0 ## rank sometimes kept and sometimes dropped names x2 <- c(3, 1, 4, 1, 5, NA, 9, 2, 6, 5, 3, 5) names(x2) <- letters[1:12] (y1 <- rank(x2)) (y2 <- rank(x2, na.last=FALSE)) (y3 <- rank(x2, na.last=NA)) (y4 <- rank(x2, na.last="keep")) stopifnot(identical(names(y1), names(x2)), identical(names(y2), names(x2)), identical(names(y4), names(x2)), identical(names(y3), names(x2)[-6])) ## ## as.dist(x) only obeyed `diag=TRUE' or `upper=TRUE' when x was "dist" already m <- as.matrix(dist(matrix(rnorm(100), nrow=5))) stopifnot(identical(TRUE, attr(as.dist(m, diag=TRUE), "Diag"))) ## failed previous to 1.8.0 stopifnot(1:2 == ave(1:2,factor(2:3,levels=1:3))) ## gave "2 NA" previous to 1.8.0, because unused levels weren't dropped ## PR#4092: arrays with length(dim(.)) = 1 z <- array(c(-2:1, 1.4),5) cz <- crossprod(as.vector(z)) dimnames(z) <- list(letters[1:5]) z0 <- z names(dimnames(z)) <- "D1" stopifnot(crossprod(z) == cz,# the first has NULL dimnames identical(crossprod(z), crossprod(z0)), identical(crossprod(z), crossprod(z,z0))) ## crossprod(z) segfaulted (or gave silly error message) before 1.8.0 ## PR#4431 stopifnot(!is.na(rmultinom(12,100, c(3, 4, 2, 0,0)))) ## 3rd line was all NA before 1.8.0 ## PR#4275: getAnywhere with extra "." g0 <- getAnywhere("predict.loess") g1 <- getAnywhere("as.dendrogram.hclust") g2 <- getAnywhere("predict.smooth.spline") g3 <- getAnywhere("print.data.frame") is.S3meth <- function(ga) any(substr(ga$where, 1,20) == "registered S3 method") stopifnot(is.S3meth(g0), is.S3meth(g1), is.S3meth(g2), is.S3meth(g3)) ## all but g0 failed until 1.8.0 (Oct 6) ## symnum(x) for length 0 and some logical arrays: sm <- symnum(m <- matrix(1:8 %% 3 == 0, 2)) stopifnot(identical(symnum(FALSE[FALSE]), noquote(""[FALSE])), identical(symnum(c(m)), c(symnum(m))), dim(sm) == dim(m), class(sm) == "noquote") ## symnum() gave noquote("()") before 1.8.1 ## abbreviate with leading (or trailing) space differences (PR#4564) abbreviate(c("A"," A"), 4) ## this gave infinite loop before 1.8.1 ## crossprod on 0-extent matrices a <- matrix(,0,5) stopifnot(crossprod(a) == 0) stopifnot(crossprod(a,a) == 0) stopifnot(crossprod(a+0i) == 0+0i) ## were random areas in <= 1.8.0 ## DF[[i, j]] should be row i, col j stopifnot(women[[2, 1]] == women[2, 1]) women[[2, 1]] <- 77 stopifnot(women[2, 1] == 77) ## was reversed from May 2002 to Oct 2003 ## merge.data.frame with a single-column df (PR#4299) x <- data.frame(x = 1:5, y = letters[1:5]) y <- data.frame(z = 1:2) z <- merge(x, y) stopifnot(identical(names(z), c("x", "y", "z"))) ## third name was wrong in 1.8.0 ## cor(mat, use = "pair") was plainly wrong # longley has no NA's -- hence all "use = " should give the same! X <- longley ep <- 32 * Meps for(meth in eval(formals(cor)$method)) { cat("method = ", meth,"\n") Cl <- cor(X, method = meth) stopifnot(all.equal(Cl, cor(X, method= meth, use= "complete"), tol=ep), all.equal(Cl, cor(X, method= meth, use= "pairwise"), tol=ep), all.equal(Cl, cor(X, X, method= meth), tol=ep), all.equal(Cl, cor(X, X, method= meth, use= "pairwise"), tol=ep), all.equal(Cl, cor(X, X, method= meth, use= "pairwise"), tol=ep) ) } ## "pairwise" failed in 1.8.0 ## regexpr(*, fixed=TRUE) had 0-index from C txt <- c("english", "french", "swiss") ir <- regexpr("en", txt, fixed = TRUE) stopifnot(ir == c(1, 3, -1), identical(ir, regexpr("en", txt))) ## (*, fixed=TRUE) gave 0 2 -1 before R 1.8.1 ## PR#5017: filter(init=) had the wrong time order xx <- filter(4:8, c(1, 0.5, 0.25), method="recursive", init=3:1) stopifnot(identical(xx[1:3], c(8.25, 15.25, 26.125))) ## 1.8.0 gave 6.75 12.75 22.375 ## PR#5090 user error with writeChar could segfault tf <- tempfile() zz <- file(tf, "wb") writeChar("", zz, nchars=10000000) close(zz) unlink(tf) ## segfaults in 1.8.0 ## PR#4710 round (and signif) dropped attributes x <- round(matrix(0, 0, 3)) stopifnot(identical(dim(x), as.integer(c(0, 3)))) ## numeric(0) in 1.8.0 ## PR#5405 try(stepfun(c(), 1)(2))# > Error ## segfaults in 1.8.1 and earlier ## PR#4955 now allow embedded newlines in quoted fields in read.table temp <- tempfile() data <- data.frame(a=c("c", "e\nnewline")) write.table(data, sep=",", row.names=FALSE, file=temp) data2 <- read.csv(temp) unlink(temp) # attributes get a different order here stopifnot(identical(data$a, data2$a)) ## not allowed prior to 1.9.0 ## scoping problems with model.frame methods foo <- c(1,1,0,0,1,1) rep <- 1:6 m <- lm(foo ~ rep, model=FALSE) model.matrix(m) n <- 1:6 m <- lm(foo ~ n, model=FALSE) model.matrix(m) ## failed in 1.8.0 because the wrong n or rep was found. rm(foo, rep) func <- function() { foo <- c(1,1,0,0,1,1) rep <- 1:6 m <- lm(foo ~ rep, model=FALSE) model.matrix(m) } func() ## ## broken strptime in glibc (and code used on Windows) # the spec says %d is allowed in 1-31, but it seems HP-UX thinks # the date is invalid. # stopifnot(!is.na(strptime("2003-02-30", format="%Y-%m-%d"))) stopifnot(is.na(strptime("2003-02-35", format="%Y-%m-%d"))) # this one is still wrong in glibc stopifnot(is.na(strptime("2003-02-40", format="%Y-%m-%d"))) stopifnot(is.na(strptime("2003-22-20", format="%Y-%m-%d"))) # and so is this one stopifnot(is.na(strptime("2003 22 20", format="%Y %m %d"))) stopifnot(is.na(ISOdate(year=2003, month=22, day=20))) ## several after the first gave non-NA values in 1.8.1 on some broken OSes ## PR#4688 reli <- cbind(Si = c(2121, 100, 27, 0), av = c(4700, 216, 67, 0), Nc = c(6234,2461,502,14)) stopifnot(inherits(try(fisher.test(reli, workspace=2000000)), "try-error")) ## gave p.value = Inf ; now gives FEXACT error 501 ## PR#5701 chisq.test(matrix(23171,2,2), simulate=TRUE) ## gave infinite loop in 1.8.1 and earlier ## as.matrix on an all-logical data frame ll <- data.frame(a = rpois(10,1) > 0, b = rpois(10,1) > 0) stopifnot(mode(as.matrix(ll)) == "logical") lll <- data.frame(a = LETTERS[1:10], b = rpois(10,1) > 0) stopifnot(mode(as.matrix(lll)) == "character") ## both were char before 1.9.0 ## outer called rep with a non-generic arg x <- .leap.seconds[1:6] outer(x, x, "<") outer(x, x, "-") (z <- outer(x, x, "difftime", units="days")) stopifnot(class(z) == "difftime") ## failed in 1.8.1 ## PR#5900 qbinom when probability is 1 stopifnot(qbinom(0.95, 10, 1) == 10) stopifnot(qbinom(0, 10, 1) == 0) # and for prob = 0 stopifnot(qbinom(0.95, 10, 0) == 0) stopifnot(qbinom(0, 10, 0) == 0) # and size = 0 stopifnot(qbinom(0.95, 0, 0.5) == 0) ## 1.8.1 was programmed to give NaN ## base:: and ::: were searching in the wrong places stopifnot(inherits(try(base::lm), "try-error")) stopifnot(inherits(try(graphics::log), "try-error")) ## equivalent constructs succeeded in 1.8.1 ## (PR#6452) princomp prediction without specifying centers should give NAs x <- matrix(rnorm(400), ncol=4) fit <- princomp(covmat=cov(x)) stopifnot(is.null(fit$scores)) stopifnot(is.na(predict(fit, newdata=x[1:10, ]))) ## failed in 1.8.1 ## (PR#6451) regex functions did not coerce args to character. sub(x=NA, pattern="x", replacement="y") ## failed in 1.8.1 ## length<- needed a factor method, and so needed to be generic aa <- factor(letters) length(aa) <- 20 aa stopifnot(is.factor(aa)) ## returned a vector in 1.8.1 ## spec.pgram() was too pAR <- c(2.7607, -3.82, 2.6535, -0.9238) N <- 1 + 2^14# 16385 set.seed(123) x <- arima.sim(model = list(ar = pAR), n = N) spP <- spec.pgram(x, spans = 41, plot=FALSE) spA <- spec.ar(x=list(ar=pAR, order=4, var.pred=1, frequency=1), n.freq = spP$n.used %/% 2, plot=FALSE) r <- spP$spec / spA$spec stopifnot(abs(mean(r) - 1) < 0.003) ## was 0.0268 in R 1.8.1 ## check for a Microsoft bug in timezones ahead of GMT stopifnot(!is.na(as.POSIXct("1970-01-01 00:00:00"))) ## ## PR#6672, split.default on factors x <- c(NA, 1, 2) y <- as.factor(x) split(x, y) split(y, y) # included NAs in 1.8.1 r1 <- tapply(x, y, length) r2 <- tapply(y, y, length) stopifnot(r1 == r2) ## ## PR#6652, points.formula with subset and extra arguments. roller <- data.frame(weight = c(1.9, 3.1, 3.3, 4.8, 5.3, 6.1, 6.4, 7.6, 9.8, 12.4), depression = c(2, 1, 5, 5, 20, 20, 23, 10, 30, 25)) plot(depression ~ weight, data=roller, type="n") with(roller, points( depression~weight, subset=8:10, col=2)) with(roller, points( depression~weight, subset=8:10, col=2:4)) plot(depression ~ weight, data=roller, type="n") points(depression~weight, subset=8:10, col=2:4, data=roller) ## first two gave error in 1.8.1 ## PR#4558 part 2 x <- seq(as.POSIXct("2004-03-25"), as.POSIXct("2004-03-31"), by="DSTdays") stopifnot(length(x) == 7) ## was length 6 in the UK time zone. ## PR#6702 c/rbind on list matrices A <- matrix(as.list(1:4), 2, 2) (res <- cbind(A, A)) stopifnot(typeof(res) == "list") (res <- rbind(A, A)) stopifnot(typeof(res) == "list") ## were not implemented in 1.8.1 ## Date objects with NA's (t1 <- strptime(c("6. Aug. 1930", "3. Nov. 1925", "28. Mar. 1959", NA, paste(1:29," Feb. 1960", sep=".")), format = "%d. %b. %Y")) stopifnot(6 == length(print(s1 <- summary(t1))), s1== summary(as.POSIXct(t1)), 6 == length(print(format(as.Date(s1)))) ) ## gave bizarre "NA's" entry in R 1.8.1 and 1.9.0alpha ## as.Date on a factor as.Date(factor("2000-01-02")) ## failed in 1.9.0 ## as.data.frame.list (PR#6782) xx <- list(row.names=1:2,foxglove=3:4,toadflax=5:6) foo <- as.data.frame(xx) stopifnot(identical(names(xx), names(foo))) ## 1.9.0 changed the last name to "x". ## type.convert quirk (PR#6781) res1 <- type.convert( c("abc","-"), as.is=TRUE, na.strings="-" ) stopifnot(identical(mode(res1), "character"), is.na(res1[2])) ## res1[2] was "-" <= 1.9.0. ## subsetting factor swaps order of attributes (PR#6799) af <- factor(c('A','B')) stopifnot(identical(af, af[1:2])) ## failed in 1.9.0 as the attributes were class, level for af[1:2] ## Comparison between lists and expressions stopifnot(inherits(try(list(1) <= list(2)), "try-error")) e <- expression(3 + 2 * 4) stopifnot(inherits(try(e == e), "try-error")) ## both were allowed but nonsense in 1.9.0 ## "nowhere" interpolation (PR#6809) try(approx(list(x=rep(NaN, 9), y=1:9), xout=NaN)) ## gave a seg.fault in 1.9.0 ## aggregate.data.frame failed if result would have one row ## Philippe Hupé, R-help, 2004-05-14 dat <- data.frame(a=rep(2,10),b=rep("a",10)) aggregate(dat$a, by=list(a1=dat$a, b1=dat$b), NROW) ## failed due to missing drop = FALSE ## [<-.data.frame with a data-frame value x <- data.frame(a=1:3, b=4:6, c=7:9) info <- x[1:2] x[, names(info)] <- info[1,] ## ## as.dendrogram.hclust() d <- as.dendrogram(hEU <- hclust(eurodist, "ave")) stopifnot(order.dendrogram(d) == hEU$order)# not new ##N require(gclus); hE1 <- reorder.hclust(hEU, dis) ## reconstruct without gclus (for R's testing) hE2 <- hEU; ii <- c(5,9:11, 13, 15:18); hE2$merge[ii,] <- hEU$merge[ii, 2:1] hE2$order <- as.integer(c(1,19,9,12,14,2,15,8,13,16,17,21,6,3,11,4,18,5,10,7,20)) ##N stopifnot(identical(hE1, hE2)) d1 <- as.dendrogram(hE2) stopifnot(order.dendrogram(d1) == hE2$order, identical(d1, rev(rev(d1)))) ## not true in 1.9.0 ## trunc on a Date trunc(xx <- Sys.Date()) # failed in 1.9.1 x <- xx + 0.9 stopifnot(identical(trunc(x), xx)) # gave next day in 1.9.1 xx <- as.Date("1960-02-02") x <- xx + 0.2 stopifnot(identical(trunc(x), xx)) # must not truncate towards 0. ## ### end of tests added in 1.9.1 ### ## 1.9.1 patched ## options(list('..', '..')) try(options(list('digits', 'width')))# give an error ## gave a segfault in 1.9.1 ## PR#7100 seg faulted or path too long error on ././././././. ... length( list.files('.', all.files = TRUE, recursive = TRUE) ) ## PR#7116 segfaulted on A, later versions segfaulted on B or gave different ## dims for the results. A <- cor(as.array(c(a=1,b=2)), cbind(1:2)) B <- cor(cbind(1:2), as.array(c(a=1,b=2))) stopifnot(identical(A, B)) ## regression test for PR#7108 ans <- gsub(" ", "", "b c + d | a * b", perl=TRUE) # NULL in 1.9.1 stopifnot(identical(ans, gsub(" ", "", "b c + d | a * b"))) gsub(" ", "", "a: 12345 :a", perl=TRUE) # segfaulted in 1.9.1 ## wrong answers, segfaults in 1.9.1. ## regression test for PR#7132 tmp <- data.frame(y=rnorm(8), aa=factor(c(1,1,1,1,2,2,2,2)), bb=factor(c(1,1,2,2,1,1,2,2)), cc=factor(c(1,2,3,4,1,2,3,4))) tmp.aov <- aov(y ~ cc + bb/aa, data=tmp) anova(tmp.aov) model.tables(tmp.aov, type="means") ## failed in 1.9.1. if(require(survival, quietly = TRUE)) { # required package a <- Surv(1:4, 2:5, c(0,1,1,0)) str(a) str(a[rep(1:4,3)], vec.len = 7) detach("package:survival") } ### end of tests added in 1.9.1 patched ### ## names in columns of data frames x <- 1:10 names(x) <- letters[x] DF <- data.frame(x=x) (nm <- names(DF$x)) stopifnot(is.null(nm)) DF$y1 <- x DF["y2"] <- x DF[, "y3"] <- x DF[["y4"]] <- x stopifnot(is.null(names(DF$y1)), is.null(names(DF$y2)), is.null(names(DF$y3)), is.null(names(DF$y4))) # names were preserved in 1.9.x # check factors xx <- as.factor(x) DF <- data.frame(x=xx) (nm <- names(DF$xx)) stopifnot(is.null(nm)) DF$y1 <- xx DF["y2"] <- xx DF[, "y3"] <- xx DF[["y4"]] <- xx stopifnot(is.null(names(DF$y1)), is.null(names(DF$y2)), is.null(names(DF$y3)), is.null(names(DF$y4))) # how about AsIs? This should preserve names DF <- data.frame(x=I(x)) (nm <- names(DF$x)) stopifnot(identical(nm, names(x))) DF2 <- rbind(DF, DF[7:8,, drop=FALSE]) (nm <- names(DF2$x)) stopifnot(identical(nm, c(names(x), names(x)[7:8]))) # and matrices? Ordinary matrices will be split into columns x <- 1:10 dim(x) <- c(5,2) dimnames(x) <- list(letters[1:5], c("i", "ii")) DF <- data.frame(x=I(x)) DF2 <- rbind(DF, DF) (rn <- rownames(DF2$x)) stopifnot(identical(rn, c(rownames(x), rownames(x)))) class(x) <- "model.matrix" DF <- data.frame(x=x) DF2 <- rbind(DF, DF) (rn <- rownames(DF2$x)) stopifnot(identical(rn, c(rownames(x), rownames(x)))) ## names were always preserved in 1.9.x, but rbind dropped names and dimnames. ## cumsum etc dropped names x <- rnorm(10) names(x) <- nm <- letters[1:10] stopifnot(identical(names(cumsum(x)), nm), identical(names(cumprod(x)), nm), identical(names(cummax(x)), nm), identical(names(cummin(x)), nm)) x <- x+1i stopifnot(identical(names(cumsum(x)), nm), identical(names(cumprod(x)), nm)) ## 1.9.x dropped names ## cumsum etc preserve NAs # double x <- c(1, NA, 3) r <- c(1, NA, NA) stopifnot(identical(cumsum(x), r)) stopifnot(identical(cumprod(x), r)) stopifnot(identical(cummin(x), r)) stopifnot(identical(cummax(x), r)) # complex x <- c(1+1i, NA, 3) r <- c(1+1i, NA, NA) stopifnot(identical(cumsum(x), r)) stopifnot(identical(cumprod(x), r)) # integer x <- c(1L, NA, 3L) r <- c(1L, NA, NA) stopifnot(identical(cumsum(x), r)) stopifnot(identical(cumprod(x), c(1, NA, NA))) # returns double stopifnot(identical(cummin(x), r)) stopifnot(identical(cummax(x), r)) ## complex superassignments e <- c(a=1, b=2) f <- c(a=1, b=2) g <- e h <- list(a=1, list(b=2, list(c=3, d=4), list(e=5))) j <- matrix(1, 2, 2) a <- "A" local({ eold <- e <- c(A=10, B=11) hold <- h <- 2 jold <- j <- 7 gold <- g <- e a <- "B" e[2] <<- e[2]+1 names(f)[2] <<- a g <<- 1 h[[2]][[h]][[ f[e==10] ]] <<- h names(h[[2]][[h]])[f[e==10] ] <<- a j[h, h] <<- h colnames(j)[2] <<- a stopifnot(identical(e, eold)) stopifnot(identical(h, hold)) stopifnot(identical(g, gold)) stopifnot(identical(j, jold)) }) stopifnot(identical(e, c(a=1, b=12))) stopifnot(identical(f, c(a=1, B=2))) stopifnot(identical(g, 1)) stopifnot(identical(h, list(a=1, list(b=2, list(B=2, d=4), list(e=5))))) stopifnot(identical(as.vector(j), c(1, 1, 1, 2))) stopifnot(identical(colnames(j), c(NA,"B"))) ## gave error 'subscript out of bounds' in 1.9.1 ## make sure we don't get cycles out of changes to subassign3. x <- list(a=1, y=2) x$a <- x print(x) x$d <- x print(x) y <- x x$b <- y print(x) x$f <- y print(x) ## ## model.frame incorrectly preserved ts attributes x1 <- ts(c(1:10, NA)) y1 <- ts(rnorm(11)) lm(y1 ~ x1) lm(y1 ~ x1 + I(x1^2)) # second term has two classes ## failed in 1.9.1 ## range checks missing in recursive assignments (PR#7196) l <- list() try(l[[2:3]] <- 1) l <- list(x=2) try(l[[2:3]] <- 1) l <- list(x=2, y=3) l[[2:3]] <- 1 ## first two segfaulted in 1.9.x ## apply() on an array of dimension >=3 AND when for each iteration ## the function returns a named vector of length >=2 (PR#7205) a <- array(1:24, dim=2:4) func1 <- function(x) c(a=mean(x), b=max(x)) apply(a, 1:2, func1) ## failed in 1.9.1 # col2rgb must return a matrix for a single colour stopifnot(is.matrix(col2rgb("red"))) ## was vector at one point in pre-2.0.0 ## Subscripting matrices with NA's AAA <- array(1:6, c(6,1,1)) idx <- c(1,2,NA,NA,5,6) B <- 10 AAA[idx,1,1] <- B stopifnot(all.equal(as.vector(AAA), c(10,10,3,4,10,10))) ## assigned only the first two elements in 1.9.1. ## Tests for >= 2.0.0 A <- c(1,2,3,4,5,6) A[idx] <- 27 # OK, one value stopifnot(identical(A, c(27,27,3,4,27,27))) try(A[idx] <- 6:1) # was 6 5 3 4 2 1 in 1.9.1 stopifnot(inherits(.Last.value, "try-error")) AA <- matrix(c(1,2,3,4,5,6), 6, 1) AA[idx,] <- 27 # OK, one value stopifnot(identical(AA, matrix(c(27,27,3,4,27,27), 6, 1))) try(AA[idx,] <- 6:1) # was 6 5 3 4 4 3 in 1.9.1 stopifnot(inherits(.Last.value, "try-error")) AAA <- array(c(1,2,3,4,5,6), c(6,1,1)) AAA[idx,,] <- 27 # OK, one value stopifnot(identical(AAA, array(c(27,27,3,4,27,27), c(6,1,1)))) try(AAA[idx,,] <- 6:1) # was 6 5 3 4 5 6 in 1.9.1 stopifnot(inherits(.Last.value, "try-error")) ## only length-1 values are allowed in >= 2.0.0. ## hist with infinite values (PR#7220) hist(log(-5:100), plot = FALSE) ## failed in 1.9.1: will warn, correctly. ## merge problem with names/not in rbind.data.frame x <- structure(c("a", "b", "2", "0.2-26", "O", "O"), dim = 2:3, dimnames = list(c("1", "2"), c("P", "V", "2"))) y <- structure(c("a", "b", "2", "0.2-25", "O", "O"), dim = 2:3, dimnames = list(c("1", "2"), c("P", "V", "1"))) merge(x, y, all.y = TRUE) ## failed for a while in pre-2.0.0 ## matrix responses in binomial glm lost names prior to 2.0.0 y <- rbinom(10, 10, 0.5) x <- 1:10 names(y) <- letters[1:10] ym <- cbind(y, 10-y) fit2 <- glm(ym ~ x, binomial) stopifnot(identical(names(resid(fit2)), names(y))) ## Note: fit <- glm(y/10 ~ x, binomial, weights=rep(10, 10)) ## Does not preserve names in R < 2.0.1, but does in S. fit <- glm(y/10 ~ x, binomial, weights=rep(10, 10)) stopifnot(identical(names(resid(fit)), names(y))) ## The problem was glm.fit assumed a vector response. ## dlogis(-2000) was NaN in <= 2.0.0. stopifnot(identical(dlogis(-2000), 0.0)) ## ## short vectors in spline[fun] (PR#7290) try(splinefun(1[0], 1[0])(1)) # segfault in <= 2.0.0 for(meth in c("fmm", "nat", "per")) stopifnot(all(splinefun(1, pi, method = meth)(0:2) == rep(pi, 3))) ## exactly constant for n=1; was NA for "periodic" in <= 2.0.0 ## ecdf with NAs (part of PR#7292). x <- c(1,2,2,4,7, NA, 10,12, 15,20) ecdf(x) ## failed in <= 2.0.0. ## Incorrect use of as.Date segfaulted on some x86_64 systems. as.Date("2001", "%Y") ## answer is usually current mon & day, but 2001-01-01 on Solaris. ## rank and order accepted invalid inputs (and gave nonsense) x1 <- as.list(10:1) x2 <- charToRaw("A test string") stopifnot(inherits(try(order(x1)), "try-error"), inherits(try(order(x2)), "try-error"), inherits(try(rank(x1)), "try-error"), inherits(try(rank(x2)), "try-error")) ## worked but gave 1:n in 2.0.0. stopifnot(inherits(try(sort(x1)), "try-error"), inherits(try(sort(x2)), "try-error"), inherits(try(sort(x1, partial=5)), "try-error"), inherits(try(sort(x2, partial=5)), "try-error")) ## ## pmax failed with NA inputs pmax(c(1,2,NA), c(3,4,NA), na.rm=TRUE) ## failed after for 2.0.0 change to subassignment ## subassigning expression could segfault (PR#7326) foo <- expression(alpha, beta, gamma) foo[2] foo[2] <- NA foo ## segfaulted in 2.0.0 ## incorrect arg matching in sum min max prod any all ## Pat Burns, R-devel 2004-11-19 stopifnot(identical(sum(1:4, NA, n = 78, na.rm = TRUE), 88)) ## was 11 in 2.0.1 ## segfault from text, P Ehlers, R-devel 2004-11-24 plot(1:10) loc <- list(5, 6) try(text(loc, labels = "a")) ## segfaulted in 2.0.1 ## automatic row.names can be number-like, MM, 2004-11-26 d0 <- data.frame(x=1:3, y=pi*2:0) row.names(d0)[3] <- c("01.00") write.table(d0, (tf <- tempfile())) d <- read.table(tf) ## gave error ("duplicate row.names") in 2.0.1 stopifnot(all.equal(d,d0)) unlink(tf) ## seq() should be more consistent in returning "integer" stopifnot(typeof(seq(length=0)) == "integer", identical(seq(length=0), seq(along.with=0[0])), identical(seq(length=3), 1:3), identical(seq(length=3), seq(along.with=1:3))) ## labels.lm was broken (PR#7417) # part of example(lm) ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14) trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69) group <- gl(2,10,20, labels=c("Ctl","Trt")) weight <- c(ctl, trt) lm.D9 <- lm(weight ~ group) stopifnot(labels(lm.D9) == "group") ## failed in 2.0.1, giving length 0 ## sprintf had no length check (PR#7554) a <- matrix (ncol=100, nrow=100, data=c(1,2,3,4,5)) a.serial <- rawToChar(serialize(a, NULL, ascii=TRUE)) try(sprintf('foo: %s\n', a.serial)) ## seqfaulted in 2.0.1 ## all/any did not coerce as the Blue Book described. for(x in c("F", "FALSE", "T", "TRUE", "NA")) { print(all(x)) print(any(x)) } all(list()) any(list()) ## all failed in 2.0.1 with 'incorrect argument type' ##---- named dimnames of %*% and crossprod() -- matrices and 1-d arrays: tst1 <- function(m) { stopifnot(identical(t(m) %*% (m), crossprod(m))) stopifnot(identical(m %*% t(m), crossprod(t(m)))) } tst2 <- function(x, y=x) { stopifnot(identical(t(x) %*% (y),(crossprod(x,y) -> C))) stopifnot(identical(t(y) %*% (x),(crossprod(y,x) -> tC))) stopifnot(identical(tC, t(C))) } {m1 <- array(1:2,1:2); dimnames(m1) <- list(D1="A", D2=c("a","b")); m1} tst1(m1) m2 <- m1; names(dimnames(m2)) <- c("", "d2"); tst1(m2) m3 <- m1; names(dimnames(m3)) <- c("", "") ; tst1(m3) m4 <- m1; names(dimnames(m4)) <- NULL ; tst1(m4) tst2(m1,m2) tst2(m1,m3) tst2(m1,m4) tst2(m2,m3) tst2(m2,m4) tst2(m3,m4) ## 2) Now the 'same' with 1-d arrays: a1 <- m1; dim(a1) <- length(a1); dimnames(a1) <- dimnames(m1)[2]; a1 # named dn a2 <- a1; names(dimnames(a2)) <- NULL ; a2 # unnamed dn a3 <- a1; dimnames(a3) <- NULL ; a3 # no dn stopifnot(identical(dimnames(t(a1))[2], dimnames(a1))) ## in version <= 2.0.1, t(.) was loosing names of dimnames() tst1(a1)# failed in 2.0.1 ("twice") tst1(a2)# failed in 2.0.1 tst1(a3)# ok ## these all three failed in (2.0.1) for more than one reason: tst2(a1,a2) tst2(a1,a3) tst2(a2,a3) ## end {testing named dimnames for %*% and crossprod()} ## -- coercing as.data.frame(NULL) to a pairlist didn't work y<-1:10 eval(quote(y), as.data.frame(NULL)) ## NULL as the second argument of eval should be treated ## like a list or data frame eval(quote(y), NULL) ## end ## data frame with nothing to replace A <- matrix(1:4, 2, 2) A[is.na(A)] <- 0 A <- as.data.frame(A) A[is.na(A)] <- 0 ## last not accepted prior to 2.1.0 ## scan on partial lines on an open connection cat("TITLE extra line", "235 335 535 735", "115 135 175", file="ex.data", sep="\n") cn.x <- file("ex.data", open="r") res <- scan(cn.x, skip=1, n=2) res <- c(res, scan(cn.x, n=2)) res <- c(res, scan(cn.x, n=2)) res <- c(res, scan(cn.x, n=2)) close(cn.x, sep=" ") unlink("ex.data") stopifnot(identical(res, c(235, 335, 535, 735, 115, 135, 175))) ## dropped some first chars < 2.1.0 ## PR#7686 formatC does not pick up on incorrect 'flag' inputs try(formatC(1, flag="s")) ## segfaulted in 2.0.1 ## PR#7695 contrasts needed coercion to double c <- matrix(c(0,1,2), nrow=3) storage.mode(c) <- "integer" f <- factor(1:3) contrasts(f, 1) <- c x <- model.matrix(~f) stopifnot(x == c(1,1,1,0,1,2)) ## gave machine-dependendent silly numbers in 2.0.1 ## extreme (de-normalized) axis range x <- 2^-seq(67, 1067, length=20) plot(x^.9, x, type="l", log="xy") # still warning and ugly labels because ## e.g., 10^-323 |==> 9.881313e-324 numerically ## gave error "log - axis(), 'at' creation, _LARGE_ range..." in 2.0.1 ## torture test of scan() with allowEscape=TRUE tf <- tempfile() x <- c('ABC', '"123"', "a'b") cat(shQuote(x, "cmd"), sep="\n", file=tf) (x2 <- scan(tf, "")) unlink(tf) stopifnot(identical(x, x2)) ## At one point pre-2.1.0 got confused ## se.contrast failed in 2.0.1 with some effectively one-stratum designs. old <- getOption("contrasts") options(contrasts = c("contr.helmert", "contr.poly")) Lab <- factor(rep(c("1","2","3"), each=12)) Material <- factor(rep(c("A","B","C","D"),each=3,times=3)) Measurement <- c(12.20,12.28,12.16,15.51,15.02,15.29,18.14,18.08,18.21, 18.54,18.36,18.45,12.59,12.30,12.67,14.98,15.46,15.22, 18.54,18.31,18.60,19.21,18.77,18.69,12.72,12.78,12.66, 15.33,15.19,15.24,18.00,18.15,17.93,18.88,18.12,18.03) testdata <- data.frame(Lab, Material, Measurement) (test.aov <- aov(Measurement ~ Material + Error(Lab/Material), data = testdata)) eff.aovlist(test.aov) (res <- se.contrast(test.aov, list(Material=="A", Material=="B", Material=="C", Material=="D"), coef = c(1, 1, -1, -1), data = testdata)) ## failed in 2.0.1 as a matrix was 1 x 1. ## 2.0.1 also failed to check for orthogonal contrasts ## in calculating the efficiencies (which are 1 here). options(contrasts = c("contr.treatment", "contr.poly")) (test2.aov <- aov(Measurement ~ Material + Error(Lab/Material), data = testdata)) (res2 <- se.contrast(test2.aov, list(Material=="A", Material=="B", Material=="C", Material=="D"), coef = c(1, 1, -1, -1), data = testdata)) stopifnot(all.equal(res, res2)) ## related checks on eff.aovlist # from example(eff.aovlist) # helmert contrasts Block <- gl(8, 4) A<-factor(c(0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1)) B<-factor(c(0,0,1,1,0,0,1,1,0,1,0,1,1,0,1,0,0,0,1,1,0,0,1,1,0,0,1,1,0,0,1,1)) C<-factor(c(0,1,1,0,1,0,0,1,0,0,1,1,0,0,1,1,0,1,0,1,1,0,1,0,0,0,1,1,1,1,0,0)) Yield <- c(101, 373, 398, 291, 312, 106, 265, 450, 106, 306, 324, 449, 272, 89, 407, 338, 87, 324, 279, 471, 323, 128, 423, 334, 131, 103, 445, 437, 324, 361, 302, 272) aovdat <- data.frame(Block, A, B, C, Yield) old <- getOption("contrasts") options(contrasts=c("contr.helmert", "contr.poly")) fit <- aov(Yield ~ A * B * C + Error(Block), data = aovdat) eff1 <- eff.aovlist(fit) options(contrasts = old) fit <- aov(Yield ~ A * B * C + Error(Block), data = aovdat) eff2 <- eff.aovlist(fit) stopifnot(all.equal(eff1, eff2)) # will have rounding-error differences ## Were different in earlier versions ## parts of PR#7742 and other examples sub('^','v_', 1:3, perl=TRUE) ## 2.0.1 did not coerce to character (nor was it documented to). x <- LETTERS[1:3] stopifnot(identical(paste('v_', x, sep=""), sub('^','v_', x, perl = TRUE))) ## 2.0.1 added random chars at the end stopifnot(identical(paste('v_', x, sep=""), sub('^','v_', x))) ## 2.0.1 did not substitute at all (x <- gsub("\\b", "|", "The quick brown fox", perl = TRUE)) stopifnot(identical(x, "|The| |quick| |brown| |fox|")) ## checked against sed: 2.0.1 infinite-looped. ## NB, the help page warns you not to do this one except in perl (x <- gsub("\\b", "|", "The quick brown fox", perl = TRUE)) stopifnot(identical(x, "|The| |quick| |brown| |fox|")) ## 2.0.1 gave wrong answer ## Another boundary case, same warning ## (x <- gsub("\\b", "|", " The quick ")) ## stopifnot(identical(x, " |The| |quick| ")) (x <- gsub("\\b", "|", " The quick ", perl = TRUE)) stopifnot(identical(x, " |The| |quick| ")) ## and some from a comment in the GNU sed code x <- gsub("a*", "x", "baaaac") stopifnot(identical(x, "xbxcx")) x <- gsub("a*", "x", "baaaac", perl = TRUE) stopifnot(identical(x, "xbxcx")) ## earlier versions got "bxc" or "xbxxcx" (x <- gsub("^12", "x", "1212")) # was "xx" stopifnot(identical(x, "x12")) (x <- gsub("^12", "x", "1212", perl = TRUE)) # was "xx" stopifnot(identical(x, "x12")) ## various fixes in 2.1.0 ## length(0) "dist": (d01. <- dist(matrix(0., 0,1))) ## failed in 2.0.1 and earlier ## Wish of PR#7775 x <- matrix(0, nrow=0, ncol=2) colSums(x); rowSums(x) x <- matrix(0, nrow=2, ncol=0) colSums(x); rowSums(x) ## not allowed in 2.0.1 ## infinite recursion in 2.0.1 (and R-beta 2005-04-11): summary(data.frame(mat = I(matrix(1:8, 2)))) summary(data.frame(x = gl(2,2), I(matrix(1:8, 4)))) ## ### fixes for 2.1.1 ### ## PR#7792: predict.glm dropped names nm <- names(predict(glm(y ~ x, family=binomial, data=data.frame(y=c(1, 0, 1, 0), x=c(1, 1, 0, 0))), newdata=data.frame(x=c(0, 0.5, 1)), type="response")) stopifnot(identical(nm, as.character(1:3))) ## no names in 2.1.0 ## PR#7808: as.data.frame: Error in "names<-.default" x1 <- array(1:9, c(3, 3, 3)) FUN <- function(x1, x2, x3, x4) cbind(x1[, 1, 1:2], x1[, 2, 1:2])[, 1] as.data.frame(FUN(x1[1:3,,], x2 = c("a", "b"), x3 = c("a", "b"), x4 = c("a", "b"))) ## failed in 2.1.0 ## PR#7797 citation() chops "Roeland " stopifnot(as.personList("Roeland Lastname")[[1]]$given[1] == "Roeland") ## was empty in 2.1.0. ## runmed()'s Turlach algorithm seg.faulted in rare cases: t2 <- c(-2,-7,5,2,-3, 0,1,3,2,-1,2,1,2,1,1,1,-2,4, 1,1,1, 32) rS <- runmed(t2, k=21, algorithm= "Stuetzle") rT <- runmed(t2, k=21, algorithm= "Turlach") stopifnot(identical(rS, rT)) ## seg.fault in 2.1.0 ## duplicated and unique on a list x <- list(1, 2, 3, 2) duplicated(x) unique(x) ## unique failed in 2.1.0 ## prog.aovlist on data with row.names N <- c(0,1,0,1,1,1,0,0,0,1,1,0,1,1,0,0,1,0,1,0,1,1,0,0) P <- c(1,1,0,0,0,1,0,1,1,1,0,0,0,1,0,1,1,0,0,1,0,1,1,0) K <- c(1,0,0,1,0,1,1,0,0,1,0,1,0,1,1,0,0,0,1,1,1,0,1,0) yield <- c(49.5,62.8,46.8,57.0,59.8,58.5,55.5,56.0,62.8,55.8,69.5, 55.0, 62.0,48.8,45.5,44.2,52.0,51.5,49.8,48.8,57.2,59.0,53.2,56.0) npk <- data.frame(block=gl(6,4), N=factor(N), P=factor(P), K=factor(K), yield=yield) row.names(npk) <- letters[2:25] npk.aovE <- aov(yield ~ N*P*K + Error(block), npk) pr <- proj(npk.aovE) ## failed in 2.1.0 ## PR#7894: Reversing axis in a log plot x <- 1:3 plot(x, exp(x), log = "y", ylim = c(30,1)) ## gave error (and warning) in log - axis(), 'at' creation ### end of tests added in 2.1.0 patched ### ## Multibyte character set regular expressions had buffer overrun regexpr("[a-z]", NA) ## crashed on 2.1.1 on Windows in MBCS build. ## PR#8033: density with 'Inf' in x: d <- density(1/0:2, kern = "rect", bw=1, from=0, to=1, n=2) stopifnot(all.equal(rep(1/sqrt(27), 2), d$y, tol=1e-14)) ## failed in R 2.1.1 (since about 1.9.0) stopifnot(all.equal(Arg(-1), pi)) ## failed in R <= 2.1.1 ## PR#7973: reversed log-scaled axis plot(1:100, log="y", ylim=c(100,10)) stopifnot(axTicks(2) == 10*c(10,5,2,1)) ## empty < 2.2.0 ## rounding errors in window.default (reported by Stefano Iacus) x <- ts(rnorm(50001), start=0, deltat=0.1) length(window(x, deltat=0.4)) length(window(x, deltat=1)) length(window(x, deltat=4.9)) length(window(x, deltat=5)) ## last failed in 2.1.1 ## incorrect sort in order with na.last != NA x <- c("5","6",NA,"4",NA) y <- x[order(x,na.last=FALSE)] stopifnot(identical(y, c(NA, NA, "4", "5", "6"))) ## 2.1.1 sorted "4" first: the fence was wrong. ## integer overflow in cor.test (PR#8087) n <- 46341 (z <- cor.test(runif(n), runif(n), method = "spearman")) stopifnot(!is.na(z$p.value)) ## ## seek on a file messed up in Windows (PR#7896) tf <- tempfile() f <- file(tf, "w+b") writeChar("abcdefghijklmnopqrstuvwxyz", f, eos=NULL) seek(f, 0, "end", rw="r") stopifnot(seek(f, NA, rw="r") == 26) # MinGW messed up seek to end of file that was open for writing close(f) f <- file(tf, "rb") seek(f, 12) stopifnot(readChar(f, 1) == "m") # First patch messed up on read-only files close(f) unlink(tf) ## ### end of tests added in 2.1.1 patched ### ## tests of hexadecimal constants x <- 0xAbc stopifnot(x == 2748) xx <- as.integer("0xAbc") stopifnot(x == xx) xx <- as.numeric("0xAbc") stopifnot(x == xx) stopifnot(as.integer("13.7") == 13) ## new in 2.2.0 ## save() of raw vector was incorrect on big-endian system (y <- x <- charToRaw("12345")) save(x, file="x.Rda") rm(x) load("x.Rda") x stopifnot(identical(x, y)) unlink("x.Rda") ## 00 00 00 00 00 in 2.1.0 on OS X (now macOS) ## fixed for 2.1.1, but test added only in 2.2.x ## PR#7922: Could not use expression() as an initial expression value setClass("test2", representation(bar = "expression")) new("test2", bar = expression()) ## failed ## Ops.data.frame had the default check.names=TRUE DF <- data.frame("100"=1:2, "200"=3:4, check.names=FALSE) DF/DF stopifnot(identical(names(DF), names(DF/DF))) ## DF/DF names had X prepended < 2.2.0 ## sum(T) was double x <- 1:10 stopifnot(typeof(sum(x)) == "integer") x <- c(TRUE, FALSE) stopifnot(typeof(sum(x)) == "integer") ## double < 2.2.0 ## Overflow in PrintGenericVector x <- paste(1:5000, collapse="+") as.matrix(list(a=1:2, b=2:3, c=x)) ## segfault in 2.1.1, silent truncation in 2.1.1 patched ## weighted.residuals for glm fits (PR#7961) set.seed(1) x <- runif(10) y <- x + rnorm(10) w <- 0:9 r1 <- weighted.residuals(lm(y ~ x, weights = w)) r2 <- weighted.residuals(glm(y ~ x, weights = w)) stopifnot(all.equal(r1, r2)) ## different in 2.1.1 ## errors in add1.{lm,glm} when adding vars with missing values(PR#8049) set.seed(2) y <- rnorm(10) x <- 1:10 is.na(x[9]) <- TRUE lm0 <- lm(y ~ 1) lm1 <- lm(y ~ 1, weights = rep(1, 10)) add1(lm0, scope = ~ x) add1(lm1, scope = ~ x) ## error in 2.1.1 glm0 <- glm(y ~ 1) glm1 <- glm(y ~ 1, weights = rep(1, 10)) glm2 <- glm(y ~ 1, offset = rep(0, 10)) add1(glm0, scope = ~ x) ## error in 2.1.1 add1(glm1, scope = ~ x) ## error in 2.1.1 add1(glm2, scope = ~ x) ## error in 2.1.1 ## ## levels<-.factor dropped other attributes. ## Heinz Tuechler, R-help, 2005-07-18 f1 <- factor(c("level c", "level b", "level a", "level c"), ordered=TRUE) attr(f1, "testattribute") <- "teststring" (old <- attributes(f1)) levels(f1) <- c("L-A", "L-B", "L-C") f1 (new <- attributes(f1)) new$levels <- old$levels <- NULL stopifnot(identical(old, new)) f2 <- factor(letters[1:4]) levels(f2) <- as.character(c(1:3, NA)) f2 stopifnot(nlevels(f2) == 3) ## dropped other attributes < 2.2.0. ## regressed at one point in pre-2.2.0 A <- matrix(pi, 0, 2) stopifnot(identical(dim(A), dim(format(A)))) ## dropped dim at one point ## ls.diag with missing values (PR#8139) x <- matrix(c(1,-1,1,-1,1,-1,1,-1,1,-1, 1,2,3,4,5,6,7,8,9,10), 10, 2) y <- as.matrix(c(1,2,3,NA,3,4,3,4,5,4)) wt <- c(1,1,1,1,1,1,1,1,1,0) regres <- lsfit(x, y, wt=wt) regdiag <- ls.diag(regres) ## failed < 2.2.0. ## window.default had an inappropriate tolerance a <- ts(1:5000, start = 0, freq = 10) b <- lag(a, 1) bb <- window(b, start = 0) stopifnot(length(bb) == length(a) - 1) ## was length(a) - 2 in 2.1.1, since the tolerance was abs(start) * ts.end ## subassignment of length zero vector to NULL gave garbage answer (PR#8157) x <- NULL x[[1]] <- numeric(0) stopifnot(length(x[[1]]) == 0) ## failed < 2.2.0 ## some checks for raw in data frames and lists x <- charToRaw("test") (z <- data.frame(x)) z$y <- x z[["y2"]] <- x z["y3"] <- x z ## lists use separate code z <- list(x=x) z$y <- x z[["y2"]] <- x z["y3"] <- list(x) z ## Not completely supported prior to 2.2.0 ### end of tests added in 2.2.0 ### ## summary.matrix failed on some classed objects surv <- structure(c(2.06, 2.13, 0.09, 0.27, 1, 0.36, 3.04, 0.67, 0.35, 0.24, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0), dim = c(10L, 2L), dimnames = list(NULL, c("time", "status")), type = "right", class = "Surv") summary(surv) ## Had infinite recursion (sometimes segfault) on 2.2.0. ## need fuzz even for ">=" : set.seed(1) stopifnot(all.equal(chisq.test(cbind(1:0, c(7,16)), simulate.p = TRUE)$p.value, 0.3368315842, tol = 1e-6)) ## some i686 platforms gave 0.00049975 ## PR#8228 image() failed on a matrix with all NAs image(z=matrix(NA, 1, 1), x=0:1, y=0:1) ## read.fwf(header=TRUE) failed (PR#8226) ff <- tempfile() cat(file=ff, "A\tB\tC", "123456", "987654", sep="\n") z <- read.fwf(ff, width=c(1,2,3), header=TRUE) stopifnot(identical(names(z), LETTERS[1:3])) unlink(ff) ## failed in <= 2.2.0 ## diag() failed if matrix had NA dimnames x <- matrix(1, 2, 2) dimnames(x) <- list(c("a", NA), c("a", NA)) diag(x) ## colnames in pivoted decompositions (PR#8258) A <- 1:10 X <- cbind(A,B=A^2, C=A^2-A, D=1) qrX <- qr(X) oo <- order(qrX$pivot) Q <- qr.Q(qrX) R <- qr.R(qrX) (z <- (Q%*%R)[,oo]) stopifnot(identical(colnames(X), colnames(z))) qrX <- qr(X, LAPACK=TRUE) oo <- order(qrX$pivot) Q <- qr.Q(qrX) R <- qr.R(qrX) (z <- (Q%*%R)[,oo]) stopifnot(identical(colnames(X), colnames(z))) Y <- crossprod(X) U <- chol(Y, pivot=TRUE) oo <- order(attr(U, "pivot")) (z <- t(U[,oo])%*% U[,oo]) stopifnot(identical(colnames(X), colnames(z))) ## unpivoted colnames in R <= 2.2.0 ## Im(-1) (PR#8272) stopifnot(all.equal(Im(c(1, 0, -1)), rep(0, 3))) ## R <= 2.2.0 had Im and Arg the same for non-complex numbers ## rounding errors in aggregate.ts aggregate(as.ts(c(1,2,3,4,5,6,7,8,9,10)),1/5,mean) ## failed in 2.2.0 ## prcomp(tol=1e-6) set.seed(16) x <- matrix(runif(30),ncol=10) s <- prcomp(x, tol=1e-6) stopifnot(length(s$sdev) == 3, ncol(s$rotation) == 2) summary(s) ## last failed in 2.2.0 ## mapply did not test type of MoreArgs try(mapply(rep,times=1:4, MoreArgs=42)) ## segfaulted in 2.2.0 ## qbinom had incorrect test for p with log=TRUE (z <- qbinom(-Inf, 1, 0.5, log.p = TRUE)) stopifnot(is.finite(z)) ## was NaN in 2.2.0 ## t(.) with NULL dimnames x <- diag(2) dimnames(x) <- list(NULL, NULL) stopifnot(identical(x, t(x)), identical(dimnames(x), dimnames(t(array(3, 1, dimnames=list(NULL))))))## dropped the length-2 list till 2.2.0 ## infinite influence measures (PR#8367) data(occupationalStatus) Diag <- as.factor(diag(1:8)) Rscore <- scale(as.numeric(row(occupationalStatus)), scale = FALSE) Cscore <- scale(as.numeric(col(occupationalStatus)), scale = FALSE) Uniform <- glm(Freq ~ origin + destination + Diag + Rscore:Cscore, family = poisson, data = occupationalStatus) Ind <- as.logical(diag(8)) residuals(Uniform)[Ind] #zero/near-zero stopifnot(is.nan(rstandard(Uniform)[Ind]), is.nan(rstudent (Uniform)[Ind]), is.nan(dffits (Uniform)[Ind]), is.nan(covratio (Uniform)[Ind]), is.nan(cooks.distance(Uniform)[Ind])) ## had infinities in 2.2.0 on some platforms ## plot.lm() on objects: plot(Uniform) # last plot gives warning on h_ii ~= 1 plot(Uniform, 6) # added 2006-01-10 plot(Uniform, 5:6)# failed for a few days 2008-05 plot(Uniform, 1:2, caption = "")# ditto ## ### end of tests added in 2.2.1 ### ## sub(fixed=TRUE), reported by Roger Peng 2005-12-21 x <- 0:10 v <- paste(x, "asdf", sep=".") (xx <- sub(".asdf", "", v, fixed = TRUE)) stopifnot(nchar(xx) == nchar(x), xx == x) ## had random trailing bytes from second element on in 2.2.1. ## identical reported true, fixed in 2.3.0. ## rbind on data frames with 0 rows (PR#8506) foo <- data.frame(x = 1:10, y = rnorm(10)) bar1 <- rbind.data.frame(foo[1:5,], foo[numeric(0),]) stopifnot(dim(bar1) == c(5,2)) bar2 <- rbind.data.frame(a = foo[1:5,], b = foo[numeric(0),]) stopifnot(dim(bar2) == c(5,2)) ## Last had 6 rows in 2.2.1, and was a corrupt data frame ## environments are recursive but cannot be indexed - all.equal.default() d <- data.frame(k=1:7, n=2:8, x=0:6) r <- glm(cbind(k, n-k) ~ x, family=binomial, data=d) stopifnot(all.equal(r,r)) ## failed in 2.2.1 ### end of tests added in 2.2.1 patched ### ## sort used to preserve inappropriate attributes and not always sort names. x <- runif(10) tsp(x) <- c(1,10,1) (z <- sort(x)) # kept tsp attribute stopifnot(is.null(attributes(z))) (z <- sort(x, method="quick")) # same stopifnot(is.null(attributes(z))) (z <- sort(x, partial = 1:10)) # same stopifnot(is.null(attributes(z))) names(x) <- letters[1:10] o <- sort.list(x) z2 <- structure(c(x)[o], names=names(x)[o]) (z <- sort(x)) # sorted names, dropped the tsp attribute stopifnot(identical(z, z2)) (z <- sort(x, method="quick")) # sorted names, kept the tsp attribute. stopifnot(identical(z, z2)) (z <- sort(x, partial = 1:10)) # did not sort names, kept tsp attribute stopifnot(is.null(attributes(z))) ## fixed for 2.3.0 to sort names (except partial), drop all other attributes. ## formatC on as.single (PR#8211) # not documented to work but someone tried it. (z <- formatC(as.single(1))) stopifnot(identical(z, "1")) ## was wrong < 2.3.0 ## outer on factors was broken in pre-2.3.0 x <- factor(1:3) outer(x, x, "!=") ## failed 2005-10-17 ## add tests for < 0 shape in [dpqr]gamma dgamma(1, -2) pgamma(1, -2) qgamma(0.95, -2) rgamma(3, -20) ## all errors < 2.1.1, now NaNs ## Make sure reference to local environment is serialized f <- function() { function(){} } serialize(f(), NULL) ## ## dummy_vfprintf with overlong format xx <- paste(rep("a", 10000), collapse="+") con <- gzfile("test.gz", "w") writeLines(xx, con) close(con) unlink("test.gz") ## segfaulted in 2.2.0 on some x86_64 systems. ## format() with *.marks: x <- 1.2345 + 10^(0:5) ff <- format(x, width = 11, big.mark = "'") stopifnot(nchar(ff) == 12) ## small marks test f2 <- format(x, big.mark = "'", small.mark="_", small.interval = 2) nc <- nchar(f2) stopifnot(substring(f2, nc,nc) != "_", # no traling small mark nc == nc[1])# all the same fc <- formatC(1.234 + 10^(0:8), format="fg", width=11, big.mark = "'") stopifnot(nchar(fc) == 11) ## had non-adjusted strings before 2.3.0 ## data.matrix on zero-length columns DF <- data.frame(x=c("a", "b"), y=2:3)[FALSE,] stopifnot(is.numeric(data.matrix(DF))) # was logical in 2.2.1. DF <- data.frame(a=I(character(0))) X <- data.matrix(DF) stopifnot(is.numeric(X)) ## gave logical matrix in 2.2.1. stopifnot(pbirthday(950, coincident=250) == 0, pbirthday(950, coincident=200) > 0) ## gave error before 2.3.0 ## raw matrices (PR#8529/30) v <- as.raw(c(1:6)) dim(v) <- c(2,3) dimnames(v) <- list(c("x","y"), c("P", "Q", "R")) v s <- as.raw(c(11:16)) dim(s) <- c(2,3) s rbind(s,v,v) (m <- cbind(s,v,v,s)) m[2,4] <- as.raw(254) m m[1:2,2:4] <- s m ## unimplemented before 2.3.0 ## window with non-overlapping ranges (PR#8545) test <- ts(1:144, start=c(1,1), frequency=12) window(test, start=c(15,1), end=c(17,1), extend=TRUE) ## failed < 2.3.0 ## pbinom(size=0) gave NaN (PR#8560) x <- c(-1,0,1,2) stopifnot(identical(pbinom(x, size = 0, p = 0.5), c(0,1,1,1))) ## 2.2.1 gave NaN in all cases (forced explicitly in C code). ## Limits on [dpqr]nbinom and [dqpr]geom stopifnot(is.nan(dnbinom(0, 1, 0)), dnbinom(0, 1, 1) == 1, pnbinom(c(-1, 0, 1), 1, 1) == c(0, 1, 1), is.nan(pnbinom(0, 1, 0)), qnbinom(0.5, 1, 1) == 0, is.nan(qnbinom(0.5, 1, 0)), is.finite(rnbinom(1, 1, 1)), !is.finite(rnbinom(1, 1, 0))) ## d allowed p=0, [pq] disallowed p=1 for R < 2.3.0, r gave NaN for p=1. stopifnot(is.nan(dgeom(0, 0)), dgeom(0, 1) == 1, pgeom(c(-1, 0, 1), 1) == c(0, 1, 1), is.nan(pgeom(0, 0)), qgeom(0.5, 1) == 0, is.nan(qgeom(0.5, 0)), is.finite(rgeom(1, 1)), !is.finite(rgeom(1, 0))) ## A response to PR#8528 incorrectly claimed these to be wrong. stopifnot(all.equal(df(0, 2, 2), 1)) stopifnot(is.infinite(df(0, 1.3, 2))) x <- 1e-170 stopifnot(all.equal(pbeta(x,x,x), 0.5)) ## just a regression check. ## This underflowed stopifnot(all.equal(dbeta(x,x,x), 0.5)) ## this was slow stopifnot(system.time(qnbinom(1e-10, 1e3, 1e-7))[3] < 0.1) ## but this failed qnbinom(0.5, 10000000000, 0.000000002) ## infinite-looped in 2.2.1 (answer is approx 4e18) qpois(0.9, 1e50) ## infinite-looped in 2.2.1 z <- 10^seq(10, 300, 10) stopifnot(all.equal(pt(-z, 1, log=TRUE), pcauchy(-z, 1, log=TRUE))) ## failed at about 1e150 in 2.2.1 stopifnot(pt(-1e200, 0.001) > 0) ## was 0 in 2.2.1, should be about 31% ## all.equal.numeric overflowed for large integers set.seed(1); r1 <- .Random.seed set.seed(2); r2 <- .Random.seed stopifnot(is.character(all.equal(r1, r2))) ## all.equal() gave NA in 2.2.1 ## support for raw indices in for() was added in 2.3.0 xx <- as.raw(40:48) for(i in xx) print(i) ## was error < 2.3.0 ## as.list on a symbol, for S-compatibility as.list(as.name("data.frame")) ## was error in 2.2.1 ## min ignored INT_MAX, (PR#8731) stopifnot(min(.Machine$integer.max) == .Machine$integer.max) stopifnot(max(-.Machine$integer.max) == -.Machine$integer.max) op <- options(warn=2) min(Inf) max(-Inf) options(op) ## were +/-Inf with warning in 2.2.1. ## PR#8718: invalid usage in R >= 2.7.0 #a <- matrix(2,2,2) #apply(a,1,"$","a") #apply(a,1,sum) ## first apply was corrupting apply() code in 2.2.1 ## NULL results in apply() apply(as.matrix(1), 1, function(x) NULL) ## was error in 2.2.1. ## sum on data frames (PR#8385) DF <- data.frame(m1=1:2, m2=3:4) sum(DF) sum(DF=DF) # needed arg named x sum(DF, DF) # failed DF[1, 1] <- NA stopifnot(is.na(sum(DF)), sum(DF, na.rm=TRUE) == 9) ## failures < 2.4.0 ## plot.lm # which=4 failed in R 1.0.1 par(mfrow=c(1,1), oma= rep(0,4)) summary(lm.fm2 <- lm(Employed ~ . - Population - GNP.deflator, data = longley)) for(wh in 1:6) plot(lm.fm2, which = wh) op <- par(mfrow = c(2,2), mar = .1+c(3,3,2,1), mgp = c(1.5, .6, 0)) y <- rt(200, df= 3) plot(lm(y ~ 1)) par(op) ## 4th plot (which = 5: "leverages") failed in 2.2.0 <= R <= 2.3.0 ## Re-fix PR#8506 z <- rbind(x = data.frame(a = 1, b = 2), y = data.frame(a = 1, b = 2)) stopifnot(row.names(z) == c("x", "y")) ## were NAs (and failed to print) in 2.3.0 dd <- data.frame(x = 3:4) stopifnot(identical(rownames(dd), row.names(dd)), identical(rownames(dd), c("1", "2"))) ## one was integer in an intermediate version of "pre 2.4.0" ## mean on integer vector ignored NAs stopifnot(is.na(mean(NA))) ## failed in R 2.3.0 ## title etc failed if passed col etc of length > 1 plot(1:2) title("foo", col=1:3) title("foo", cex=1:3) title("foo", lty=1:3) title("foo", lwd=1:3) title("foo", bg=4:7) ## threw errors in R <= 2.3.0 ## glm did not allow array offsets df1 <- data.frame(u=1:10, v=rpois(10,10), z=array(1,10, dimnames=list(1:10))) glm(v ~ u+offset(log(z)), data=df1, family=poisson) ## was error in R <= 2.3.0 ## invalid values of a logical vector from bindingIsLocked ## Martin Morgan, R-devel, 2006-05-14 e <- new.env() e$x <- 1 e$y <- 2 lockBinding("x", e) stopifnot(bindingIsLocked("x", e), bindingIsLocked("x", e)==TRUE, !bindingIsLocked("y", e), bindingIsLocked("y", e)==FALSE) ## on some systems in R <= 2.3.0, bindingIsLocked("x", e)==TRUE was false ## ccf on non-aligned time series x <- ts(rnorm(100), start=1) y <- ts(rnorm(120), start=3) ccf(x, y) ## needed na.action=na.contiguous in 2.3.0 ## merge.data.frame was not making column names unique when ## doing a Cartesian product. DF <- data.frame(col=1:3) DF2 <- merge(DF, DF, by=numeric(0)) stopifnot(identical(names(DF2), c("col.x", "col.y"))) ## both were 'col' in 2.3.0. ## [pq]unif were not consistent on infinite ranges. stopifnot(is.na(qunif(.5, 0, Inf))) ## was Inf in 2.3.1. stopifnot(is.na(punif(1, 0, Inf))) ## was 0 in 2.3.1 ## and failed on zero ranges despite the documentation. stopifnot(punif(c(0, 1, 2), 1, 1) == c(0, 1, 1)) stopifnot(qunif(c(0, 0.5, 1), 1, 1) == 1) ## were all NaN on 2.3.1 ## cbind segfaulted if coercion of the result to list failed. cbind(as.name("foo"), 1:3) # segfaulted in 2.3.1 (x <- cbind(y ~ x, 1)) x[,1] ## last is 3 x 2 list matrix ## empty point set r <- xy.coords(numeric(0)) ## gave an error with misleading message in 2.3.1 ## [<- could extend a ts but not change tsp. xx <- x <- ts(rnorm(6), frequency=7) try(x[8] <- NA) stopifnot(identical(x, xx)) ## Allowed in R < 2.4.0, but corrupted tsp. ## This only "works" by having an S3 generic use the registry ## of another S3 generic, which seems a very bad idea. ## ## Looking up generic in UseMethod ## mycoef <- function(object, ....) UseMethod("coef") ## x <- list(coefficients=1:3) ## mycoef(x) ## ## failed to find default method < 2.4.0 ## regression tests on changes to model.frame and model.matrix A <- data.frame(y = 1:10, z = 1:10+1i, x = rep(c("a", "b"), each = 5), r = as.raw(1:10), stringsAsFactors = FALSE) model.frame(z ~ x+y+r, data = A) # includes character, raw and complex lm(z ~ x+y, data = A) # complex response, character RHS # but we do not allow complex nor raw variables on the rhs stopifnot(inherits(try(model.matrix(y ~ x+z, data = A)), "try-error")) stopifnot(inherits(try(model.matrix(y ~ r, data = A)), "try-error")) ## new in 2.4.0 ## tests of stringsAsFactors a <- letters[1:8] aa <- matrix(a, 4, 2) aaa <- list(aaa=letters[20:23]) colnames(aa) <- paste("aa", 1:2, sep=".") (A <- data.frame(a=a[1:4], aa, aaa, stringsAsFactors = FALSE)) stopifnot(all(sapply(A, class) == "character")) stopifnot(class(as.data.frame(list(a=a), stringsAsFactors = TRUE)$a) == "factor") ## new in 2.4.0 ## failure to duplicate in environment<-(). ## Thomas Petzoldt, R-help, 2006-06-23. envfun <- function(L) { p <- parent.frame() assign("test", L$test, p) environment(p$test) <- p } solver <- function(L) envfun(L) L <- list(test = function() 1 + 2) environment(L$test) solver(L) (e <- environment(L$test)) stopifnot(identical(e, .GlobalEnv)) ## failed to look at NAMED ## sort.list(, method="radix") stopped working at some point x <- factor(sample(letters, 1000, replace=TRUE)) o <- sort.list(x, method = "radix") ## failed in 2.3.1 ## qt() bisection search: PR#9050 x <- -2:2 stopifnot(isTRUE(all.equal(x, qt(pt(x, df=20, ncp=1),df=20,ncp=1)))) ## failed in 2.3.1 ## poly() didn't pass 'raw' to polym() x <- -3:3 y <- 10*(1:7) stopifnot(identical(poly (x,y, degree = 2, raw = TRUE), polym(x,y, degree = 2, raw = TRUE))) ## failed in 2.3.1 ## plot.xy( type = "s" | "S" ) was missing an initial test: PR#9046 types <- c("p", "l", "b", "o", "h", "s", "S") p <- palette(hcl(h = seq(30,330, length= length(types)))) plot(c(1,6), c(-.4, 1.5), type="n", ann = FALSE); off <- 1:6 / 16 for(i in seq(types)) { lines(i*off /-1:4, type = types[i], col = i, pch = types[i]) mtext(types[i], 4, line= .5, at = i*off[6]/4, col = i, las = 1) } palette(p)# restored to previous ## failed in 2.3.1 ## qf for large df2 stopifnot(isTRUE(all.equal(qf(0.9,df1=1,df2=1e10,ncp=0), qf(0.9,df1=1,df2=1e10)))) ## failed in 2.3.1 ## some regression tests of as.vector() and as.list() x <- list(a=1, b=2) stopifnot(identical(x, as.list(x))) # was said to drop names x <- pairlist(a=1, b=2) stopifnot(is.list(x)) xx <- as.vector(x, "list") stopifnot(typeof(xx) == "list") stopifnot(!identical(x, xx)) stopifnot(identical(names(x), names(xx))) x <- expression(a=2+3, b=pi) xx <- as.vector(x, "list") # not allowed in 2.3.1 stopifnot(identical(names(x), names(xx))) xx <- as.list(x) # lost names in 2.3.1 stopifnot(identical(names(x), names(xx))) ## was incorrectly documented in 2.3.1 ## subsetting arrays preserved attributes, although it did not for matrices x <- structure(1:8, names=letters[1:8], comm="a comment", dim = c(2L,2L,2L)) stopifnot(is.null(attr(x[,,], "comm"))) x <- structure(1:8, names=letters[1:8], comm="a comment", dim = c(2L,4L)) stopifnot(is.null(attr(x[,], "comm"))) x <- structure(1:8, names=letters[1:8], comm="a comment") stopifnot(!is.null(attr(x[], "comm"))) # this does preserve stopifnot(is.null(attr(x[1:8], "comm"))) ## 2.3.1 preserved the first. ## diff() for POSIX(cl)t : ds1 <- diff(lsec <- .leap.seconds[1:12]) (ds2 <- diff(llsec <- as.POSIXlt(lsec))) # in days stopifnot(ds1 == ds2) ## gave different result for POSIXlt up to 2.3.1 ## format(trim = TRUE, big.mark=",") did not work correctly (PR#9118) (a <- format(c(-1,1,10,999,1e6), trim=TRUE)) (b <- format(c(-1,1,10,999,1e6), big.mark=",", trim=TRUE)) stopifnot(a[1:4] == b[1:4]) ## no trim in 2.3.1 if big.mark was used. ## residuals.glm needed 'y = TRUE' (PR#9124) # example for poisson GLM from ?glm d.AD <- data.frame(treatment = gl(3,3), outcome = gl(3,1,9), counts = c(18,17,15,20,10,20,25,13,12)) glm.D93 <- glm(counts ~ outcome + treatment, family = poisson, data = d.AD, y = FALSE) residuals(glm.D93, type = "working") residuals(glm.D93, type = "partial") residuals(glm.D93, type = "response") residuals(glm.D93, type = "deviance") residuals(glm.D93, type = "pearson") ## all failed in 2.3.1 ## anova.mlm failed dat<-matrix( c(9,7,8,8,12,11,8,13, 6,5,6,3,6,7,10,9, 10,13,8,13,12,14,14,16, 9,11,13,14,16,12,15,14), ncol = 4, dimnames = list(s=1:8, c=1:4)) mlmfit <- lm(dat ~ 1) anova(mlmfit, X = ~1) ## worked in 2.2.1, failed in 2.3.1 ## stopifnot() for a long expression (do not wrap the following line!!): r <- try(stopifnot(c("A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N", "O")), silent = TRUE) if(length(grep("TRUE.*TRUE",r))) stop("stopifnot() gives bad message for long expression") ## happened in 2.3.[01] ## rownames on 0-extent matrix (PR#9136) A <- matrix(NA, 0, 0) stopifnot(identical(rownames(A, do.NULL = FALSE), character(0))) stopifnot(identical(colnames(A, do.NULL = FALSE), character(0))) ## were 'row' etc in 2.3.1. ## grep(value = TRUE) sometimes preserved names, sometimes not x <- 1:3 xx <- letters[1:3] names(x) <- names(xx) <- xx z <- grep(1, x, value = TRUE) stopifnot(!is.null(names(z)), names(z) == xx[1]) z <- grep(1, x, value = TRUE, perl = TRUE) stopifnot(!is.null(names(z)), names(z) == xx[1]) z <- grep("a", xx, value = TRUE) stopifnot(!is.null(names(z)), names(z) == xx[1]) z <- grep("a", xx, value = TRUE, perl = TRUE) stopifnot(!is.null(names(z)), names(z) == xx[1]) z <- agrep("a", xx, value = TRUE) stopifnot(!is.null(names(z)), names(z) == xx[1:3]) ## perl=TRUE, agrep did not in 2.3.1, all did not for pre-2.4.0 x[2] <- xx[2] <- NA z <- grep(NA, x, value = TRUE) stopifnot(identical(names(z), names(xx))) z <- grep(NA, x, value = TRUE, perl = TRUE) stopifnot(identical(names(z), names(xx))) z <- grep(NA, xx, value = TRUE) stopifnot(identical(names(z), names(xx))) z <- grep(NA, xx, value = TRUE, perl = TRUE) stopifnot(identical(names(z), names(xx))) z <- agrep(NA, xx, value = TRUE) stopifnot(identical(names(z), names(xx))) ## always dropped names on NA matches < 2.4.0 oo <- options(max.print = 20) cc <- capture.output(women) options(oo) c2 <- capture.output(women[1:10,]) stopifnot(length(cc) == 1 + 20/2 + 1, identical(cc[-12], c2[1:11])) ## was wrong for some days in Aug.2006 ## errors in identical() stopifnot(!identical(pairlist(a=1, b=2), pairlist(a=1, aa=2))) stopifnot(!identical(structure(pi, a=1, b=2), structure(pi, a=1, aa=2))) stopifnot(identical(structure(pi, a=1, b=2), structure(pi, b=2, a=1))) ## ignored names of pairlists, but tested order of attributes < 2.4.0 ## failed subassign could leave '*tmp*' around ## Parlamis Franklin, R-devel, 2006-09-20 test <- 1:10 try(test[2:4] <- ls) # fails stopifnot(!exists("*tmp*", where=1)) ## was true < 2.4.0 ## merge on zero-row data frames L3 <- LETTERS[1:3] d <- data.frame(cbind(x=1, y=1), fac=sample(L3, 1, repl=TRUE)) e <- d[-1,] merge(d, e, by.x = "x", by.y = "x", all.x = TRUE) ## not allowed <= 2.4.0 ## PR#9313 library(stats4) g <- function(x, y) -cos(x) + abs(y) fit1 <- mle(g, start = list(x = 0, y = 7)) fit2 <- mle(g, start = list(y = 7, x = 0)) stopifnot(all.equal(coef(fit1), coef(fit2))) ## Found different solutions in 2.4.0, as names were not remapped in fit2 ## PR#9446 rbind( data.frame(x=1), list(x=2) ) ## was error in 2.4.0 as list gave double row names. ## extreme case bs <- boxplot.stats(c(1,Inf,Inf,Inf)) ## gave an error in 2.4.0 ## t.test with one group of size one x <- c(23,25,29,27,30,30) t.test(x=x[1], y=x[-1], var.equal=TRUE) t.test(y=x[1], x=x[-1], var.equal=TRUE) ## failed in 2.4.0 ## corrupted "ts" objects structure(1:3, class="ts") ## failed in print method < 2.4.1 ## PR#9399 x1 <- "x2" x2 <- pi rm(x1) # removes x1, not x2 stopifnot(!exists("x1", .GlobalEnv), exists("x2", .GlobalEnv)) rm("x2") # incorrectly documented <= 2.4.0 a <- b <- c <- 1 z <- try(rm(c("a", "b"))) stopifnot(inherits(z, "try-error")) ## removed 'a', 'b' and 'c' in 2.4.0 ### end of tests added in 2.4.1 ### ## translation error in optimize (PR#9438) ex2 <- function(x) log((18/41) * x - 2 * x^2) + 16 * log(4 * x^2 - (36/41) * x + (9/41)) + 24 * log((23/82) + (18/41) * x - 2 * x^2) opt <- optimise(ex2, lower = 0, upper = 9/41, maximum = TRUE)$maximum # there are two global maxima stopifnot(abs(opt - 0.187) < 0.01 || abs(opt - 0.033) < 0.01) ## changed both ends of interval at the first step, gave opt = 0.136 ## Needlessly failing subassignments e <- 1:10 e[2] <- expression(e) e <- pi e[2] <- expression(e) e <- letters e[2] <- expression(e) e <- as.raw(1:3) e[2] <- list(e=pi) ## all failed < 2.5.0 ## uniroot did not allow zero at the end of an interval f <- function(x) x-1 uniroot(f, c(0,2)) uniroot(f, c(0,1)) uniroot(f, c(1,2)) ## last two failed in 2.4.x ## PR#9360 and PR#9394 acf(1, lag.max=0, plot=FALSE) ## gave an error in 2.4.0 stopifnot( all.equal(ccf(1:3,-(1:3))$acf[2,1,1], -1) ) ## gave positive lag 0 cross-correlation after patching PR#9360 ## regression tests for complex sum/prod (briefly broken in Jan 2007) z <- rnorm(10) + rnorm(10)*(0+1i) sum(z) (x <- sum(pi, z)) stopifnot(all.equal(x, sum(pi,Re(z)) + sum(Im(z))*(0+1i))) prod(z) ## ## problems with 0-row data frames created by read.table x <- structure(list(one = NULL, two = NULL, three = NULL), names = c("one", "two", "three"), class = "data.frame") y <- data.frame(one=1,two=2,three=3) (z <- rbind(x,y)) stopifnot(dim(z) == c(1, 3)) (z <- rbind(y,x)) stopifnot(dim(z) == c(1, 3)) (z <- rbind(x,x)) stopifnot(dim(z) == c(0, 3)) ## variously failed or gave zero-column data frame in 2.4.1 ## tests of partial matching of attributes x <- 1:4 attr(x, "ab") <- 1 for(y in c("abc", "abcd", "abcde")) { attr(x, y) <- 1 stopifnot(is.null(attr(x, "a"))) } # second was '1' on 2.4.1. x <- 1:4 names(x) <- letters[x] stopifnot(identical(attr(x, "n"), names(x))) x <- as.pairlist(x) stopifnot(identical(attr(x, "n"), names(x))) ## worked for pairlists but not vectors in 2.4.1 ## which(arr.ind = TRUE) failed to give matrix on a 0-length input C <- matrix(1:16, 4) (ind <- which(C < 0, arr.ind = TRUE)) stopifnot(is.matrix(ind)) ## gave integer(0) in 2.4.1 ## plnorm wrong for out-of-range values (PR#9520) stopifnot(plnorm(0, lower.tail=FALSE) == 1, plnorm(0, lower.tail=TRUE) == 0) ## both lower tail in R < 2.5.0 ## supsmu with all NA values (PR#9519) x <- seq(0, 1, len = 100) y <- x + NA try(supsmu(x,y)) ## segfaulted < 2.5.0 ## which.max when max is Inf (PR#9522) which.min(c(NA, NA, Inf)) which.max(c(NA, NA, -Inf, -Inf)) ## were integer(0) in < 2.5.0 ## str.dendrogram did not work with 'max.level=NA' ## which has become default when called from str.default(): cm <- cor(USJudgeRatings) hm <- heatmap(cm, symm = TRUE, keep.dendro = TRUE) str(hm, max=2) # reasonable str(hm) # gave error (less reasonable than above) ## [<-.data.frame did not allow deleting the last column (PR#9565) DF <- data.frame(x = 1:3, y = 4:6, z = 7:9) DF[, "z"] <- NULL stopifnot(identical(dim(DF), c(3L, 2L))) ## 'subscript out of bounds' in 2.4.1. ## new tryCatch() based try() with anonymous function v <- try(do.call(function(x) stop("died"), list(1)), silent=TRUE) stopifnot(inherits(v, "try-error")) ## failed in some version of R-devel (2.5.0) ## choose(n,k) should be integer if n is stopifnot(choose(11,6) == 462) ## was < 462 on some AMD64 Linux ## fix up use of %j" format in strptime (PR#9577) x <- strptime(31:33, "%j") x stopifnot(!is.na(x)) ## day 32 was NA in R < 2.5.0 ## mosaicplot() broken by undocumented 'bug fix' r39655 x <- matrix(1:4,2,2) mosaicplot(x, sort = seq_len(dim(x))) ## failed in 2.4.1, fixed in 2.5.0 ## jitter failed in wierd case (PR#9580) stopifnot(is.finite( jitter(c(-1, 3)) )) ## was repeated NaN in 2.4.1 ## max.col() problems (PR#9542) x <- rep(0, 10) dim(x) <- c(1, 10) # max.col(x) should be random. ans <- numeric(100) for(i in 1:100) ans[i] <- max.col(x) table(ans) stopifnot(any(ans != 10)) ## always gave last in 2.4.1 ## rep could segfault: Hiroyuki Kawakatsu, R-help, 2007-03-30 try(rep(each = 0, length.out = 1)) # segfaulted in 2.4.1 ## readBin could read beyond the end of a raw vector. # Henrik Bengtsson, Rdevel, 2007-04-07 bfr <- as.raw(1:12) (x <- readBin(con=bfr, what="raw", n=20)) stopifnot(length(x) == 12) (x <- readBin(con=bfr, what="integer", n=20)) stopifnot(length(x) == 3) (x <- readBin(con=bfr, what="integer", size=4, n=20)) stopifnot(length(x) == 3) (x <- readBin(con=bfr, what="integer", size=2, n=20)) stopifnot(length(x) == 6) (x <- readBin(con=bfr, what="integer", size=1, n=20)) stopifnot(length(x) == 12) ## read too far where size-changing was involved in 2.4.x ## density() could give negative values by rounding error (PR#8876) x <- c(0.006, 0.002, 0.024, 0.02, 0.034, 0.09, 0.074, 0.072, 0.122, 0.048, 0.044, 0.168) result <- density(x, n = 20, from = -1, to = 1) stopifnot(result$y >= 0) ## slightly negative < 2.5.0 ## bw.SJ() used too small search interval in rare cases: bw.SJ(1:20) # error: "no solution in the specified range of bandwidths" in < 2.5.1 ## this is not ok when called as density(1:20, bw = "SJ") ## [that's a matter of opinion, since the example is ridiculous.] ## hexadecimal integer constants failed on some platforms (PR#9648) stopifnot(identical(0x10L, 16L)) ## first was 0L on Windows in 2.5.0 ## rbind failed if the only data frame had 0 rows (PR#9657) A <- data.frame(foo=character(0), bar=character(0)) rbind(A, c(foo="a", bar="b")) ## failed in 2.5.0 ## factor() with NA in dimnames(): x <- matrix(1:2, 2) rownames(x) <- factor(c("A", NA)) ## segfaulted <= 2.5.0 ## return value of median. z <- median(integer(0)) stopifnot(identical(z, NA_integer_)) z <- median(numeric(0)) stopifnot(identical(z, NA_real_)) ## returned logical NA in 2.5.0 ## seq.int on small reversed 'by' stopifnot(inherits(try(seq.int(1.2, 1, by=1)), "try-error")) ## was '1.2' in 2.5.0 ## subassignment on pairlists: Uwe Ligges on R-help, 2007-05-29 Call <- call("round", 10.5) try({Call[] <- NULL; Call}) ## seqgfaulted in 2.5.0 ## Bessel bugs for nu < 0: x <- seq(0., 3, length = 101) nu <- -0.4 stopifnot(all.equal(besselI(x,nu, TRUE), exp(-x)*besselI(x,nu, FALSE), tol = 1e-13)) ## wrong in 2.5.0 stopifnot(all.equal(besselY(seq(0.5, 3, 0.5), nu), c(0.309568577942, 0.568866844337, 0.626095631907, 0.544013906248, 0.366321150943, 0.141533189246), tol = 1e-11)) ## wrong numbers in 2.5.0 ### end of tests added in 2.5.1 ### ## regression tests for unlink and wildcards owd <- setwd(tempdir()) f <- c("ftest1", "ftest2", "ftestmore", "ftest&more") file.create(f) stopifnot(file.exists(f)) unlink("ftest?") stopifnot(file.exists(f) == c(FALSE, FALSE, TRUE, TRUE)) unlink("ftest*", recursive = TRUE) stopifnot(!file.exists(f)) stopifnot(unlink("no_such_file") == 0) # not an error dd <- c("dir1", "dir2", "dirs", "moredirs") for(d in dd) dir.create(d) dir(".") file.create(file.path(dd, "somefile")) dir(".", recursive=TRUE) stopifnot(unlink("dir?") == 1) # not an error unlink("dir?", recursive = TRUE) stopifnot(file.exists(dd) == c(FALSE, FALSE, FALSE, TRUE)) unlink("*dir*", recursive = TRUE) stopifnot(!file.exists(dd)) # Windows needs short path names for leading spaces dir.create(" test") dir(".", recursive=TRUE) unlink(" test", recursive = TRUE) stopifnot(!file.exists(" test")) setwd(owd) ## wildcards were broken in 2.5.0 on Unix, and always on Windows ## duplicated columns in a data frame x <- matrix(seq(1:12),ncol=3) colnames(x) <- c("A","B","A") #a redundant name for column 2 x.df <- as.data.frame(x) stopifnot(x.df[4,3] == x[4,3]) ## wrong column in 2.5.0 ## it really is unclear if this should work as the fit is to a ## numeric variable with levels, and the prediction does not have ## levels. But some people expected it to. worms <- data.frame(sex=gl(2,6), Dose=factor(rep(2^(0:5),2)), deaths=c(1,4,9,13,18,20,0,2,6,10,12,16)) worms$doselin <- unclass(worms$Dose) worms.glm <- glm(cbind(deaths, (20-deaths)) ~ sex+ doselin, data=worms, family=binomial) predict(worms.glm, new=data.frame(sex="1", doselin=6)) ## failed < 2.6.0 ## regression test for changes in aggregate.data.frame z <- aggregate(state.x77, list(Region = state.region, Cold = state.x77[,"Frost"] > 130), mean) stopifnot(sapply(z, class)[1:2] == c("factor", "logical"), identical(levels(z[[1]]), levels(state.region)) ) f1 <- c("a","b","a","b") f2 <- factor(f1, levels=c("b","c","a"), ordered=TRUE) z <- aggregate(1:4, list(groups=f1), sum) stopifnot(sapply(z, class) == c("character", "integer")) z <- aggregate(1:4, list(groups=f2), sum) stopifnot(identical(sapply(z, class), list(groups=class(f2), x="integer")), identical(levels(z[[1]]), levels(f2)), is.ordered(z[[1]]) ) ## converted to factors < 2.6.0 ## formals<- on function with NULL body (PR#9758) f <- function() NULL g <- alist(a=, b=4, c=) formals(f) <- g # identical(formals(f), g) is false as g has names attribute stopifnot(is.null(body(f)), identical(names(formals(f)), names(g))) ## was function(a, b=4) before 2.6.0 ## subsetting R.version stopifnot(identical("simple.list", class(R.version[1:7]))) ## [[, j]] swiss[["Broye", "Agriculture"]] swiss[[7, "Agriculture"]] swiss[["Broye", 2]] swiss[[7, 2]] ## first and third failed < 2.6.0 ## load of raw vector from ASCII save s1 <- "this is a test string 123" r0 <- r1 <- charToRaw(s1) save(r1, file="r1-ascii.rda", ascii=TRUE) save(r1, file="r1.rda", ascii=FALSE) rm(r1)# really prove... load("r1.rda") unlink("r1.rda") stopifnot(identical(r1, r0)) # was OK, but add regression test load("r1-ascii.rda") unlink("r1-ascii.rda") stopifnot(identical(r1, r0)) ## wrong < 2.5.1 patched ## match.arg with multiple values (PR#9859) x <- letters[1:3] y <- c('aa','bb') try(match.arg(x,y)) # gave spurious warning res <- match.arg(x,y, several.ok = TRUE) # error stopifnot(identical(res, y)) ## failed in 2.5.1 ## sweep() must work with 0-extent matrix/STATS : m <- matrix(1:5, 5,0) stopifnot(identical(m, sweep(m, 2, apply(m,2, min)))) ## failed in R-devel around 2007-08-31 ## julian with POSIXlt origin (PR#9908) julian(as.POSIXlt("1999-2-1"), origin=as.POSIXlt("1999-1-1")) ## failed < 2.6.0 ### continued in reg-tests-1b.R ### proc.time()