* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/FitAR.Rcheck’ * using R Under development (unstable) (2022-04-26 r82260) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘FitAR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘FitAR’ version ‘1.94’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘FitAR’ can be installed ... [18s/47s] OK * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘lattice’ ‘leaps’ ‘ltsa’ A package should be listed in only one of these fields. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘bestglm’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [26s/70s] NOTE ARSdf: no visible global function definition for ‘fft’ AcfPlot: no visible global function definition for ‘lines’ BICqLL: no visible global function definition for ‘qchisq’ BICqSelect: no visible global function definition for ‘qchisq’ Boot.FitAR: no visible global function definition for ‘ts’ BoxCox.Arima: no visible global function definition for ‘optimize’ BoxCox.Arima: no visible global function definition for ‘spline’ BoxCox.Arima: no visible global function definition for ‘abline’ BoxCox.Arima: no visible global function definition for ‘text’ BoxCox.FitAR: no visible global function definition for ‘optimize’ BoxCox.FitAR: no visible global function definition for ‘spline’ BoxCox.FitAR: no visible global function definition for ‘abline’ BoxCox.FitAR: no visible global function definition for ‘text’ BoxCox.numeric: no visible global function definition for ‘optimize’ BoxCox.numeric: no visible global function definition for ‘spline’ BoxCox.numeric: no visible binding for global variable ‘data’ BoxCox.numeric: no visible global function definition for ‘abline’ BoxCox.numeric: no visible global function definition for ‘text’ ChampernowneD: no visible global function definition for ‘toeplitz’ FitARp: no visible global function definition for ‘acf’ FitARp: no visible global function definition for ‘tsp’ FitARz: no visible global function definition for ‘tsp’ FitARz: no visible global function definition for ‘acf’ GetB: no visible global function definition for ‘acf’ GetFitARpLS: no visible global function definition for ‘embed’ GetFitARpLS: no visible global function definition for ‘lm’ GetFitARpLS: no visible global function definition for ‘resid’ GetFitARpLS: no visible global function definition for ‘coef’ GetFitARpLS: no visible global function definition for ‘vcov’ GetFitARpMLE: no visible global function definition for ‘arima’ GetFitARpMLE: no visible global function definition for ‘resid’ GetFitARpMLE: no visible global function definition for ‘coef’ GetFitARz: no visible global function definition for ‘ar.burg’ GetFitARz: no visible global function definition for ‘optim’ GetLeapsAR: no visible global function definition for ‘qchisq’ InformationMatrixAR: no visible global function definition for ‘toeplitz’ InformationMatrixARp: no visible global function definition for ‘toeplitz’ JarqueBeraTest: no visible global function definition for ‘pchisq’ LBQPlot: no visible global function definition for ‘abline’ LjungBoxTest: no visible global function definition for ‘acf’ LjungBoxTest: no visible global function definition for ‘pchisq’ PacfPlot: no visible global function definition for ‘ar.burg’ PacfPlot: no visible global function definition for ‘lines’ PacfPlot: no visible global function definition for ‘segments’ PacfPlot: no visible global function definition for ‘title’ RacfPlot: no visible global function definition for ‘residuals’ RacfPlot: no visible global function definition for ‘acf’ RacfPlot: no visible global function definition for ‘qnorm’ RacfPlot: no visible global function definition for ‘lines’ RacfPlot: no visible global function definition for ‘title’ Readts: no visible global function definition for ‘ts’ SelectModel: no visible global function definition for ‘ar.burg’ SelectModel: no visible global function definition for ‘qchisq’ SimulateGaussianAR: no visible global function definition for ‘rnorm’ SimulateGaussianAR: no visible global function definition for ‘toeplitz’ TimeSeriesPlot: no visible global function definition for ‘par’ UnitRootTest: no visible global function definition for ‘rnorm’ cts: no visible global function definition for ‘is.ts’ cts: no visible global function definition for ‘end’ cts: no visible global function definition for ‘start’ cts: no visible global function definition for ‘tsp’ cts: no visible global function definition for ‘window’ plot.FitAR: no visible global function definition for ‘resid’ plot.FitAR: no visible global function definition for ‘layout’ plot.FitAR: no visible global function definition for ‘title’ plot.FitAR: no visible global function definition for ‘lines’ plot.FitAR: no visible global function definition for ‘lowess’ plot.FitAR: no visible global function definition for ‘acf’ plot.FitAR: no visible global function definition for ‘var’ plot.Selectmodel: no visible global function definition for ‘par’ plot.Selectmodel: no visible global function definition for ‘abline’ plot.Selectmodel: no visible global function definition for ‘title’ plot.Selectmodel: no visible global function definition for ‘axis’ plot.Selectmodel: no visible global function definition for ‘mtext’ summary.FitAR: no visible global function definition for ‘var’ Undefined global functions or variables: abline acf ar.burg arima axis coef data embed end fft is.ts layout lines lm lowess mtext optim optimize par pchisq qchisq qnorm resid residuals rnorm segments spline start text title toeplitz ts tsp var vcov window Consider adding importFrom("graphics", "abline", "axis", "layout", "lines", "mtext", "par", "segments", "text", "title") importFrom("stats", "acf", "ar.burg", "arima", "coef", "embed", "end", "fft", "is.ts", "lm", "lowess", "optim", "optimize", "pchisq", "qchisq", "qnorm", "resid", "residuals", "rnorm", "spline", "start", "toeplitz", "ts", "tsp", "var", "vcov", "window") importFrom("utils", "data") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'GetLeapsAR.Rd': \usage lines wider than 90 characters: GetLeapsAR(z, lag.max = 15, Criterion = "UBIC", Best = 3, Candidates=5, t="default", ExactQ=FALSE) Rd file 'PlotARSdf.Rd': \usage lines wider than 90 characters: PlotARSdf(phi = NULL, theta = NULL, units = "radial", logSdf = FALSE, InnovationVariance = 1, main = NULL, sub = NULL, lwd=3, col="blue ... [TRUNCATED] Rd file 'SelectModel.Rd': \usage lines wider than 90 characters: SelectModel(z, lag.max = 15, ARModel = c("AR", "ARz", "ARp"), Criterion = "default", Best = 3, Candidates = 5, t="default") Rd file 'UnitRootTest.Rd': \usage lines wider than 90 characters: UnitRootTest(z, method = c("MLE", "ExactMLE", "LS", "All"), statistic = c("Z", "T"), NumBoot = 1000, PValueMethod = c("DH", "ET")) These lines will be truncated in the PDF manual. * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... NOTE File ‘FitAR/libs/FitAR.so’: Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’ It is good practice to register native routines and to disable symbol search. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking examples ... [5s/15s] ERROR Running examples in ‘FitAR-Ex.R’ failed The error most likely occurred in: > ### Name: AcfPlot > ### Title: Basic ACF Plotting > ### Aliases: AcfPlot > ### Keywords: ts > > ### ** Examples > > # > #Simple example, plot acf for AR(1) > phi<-0.8 > maxLag<-20 > g<-phi^(1:maxLag) > AcfPlot(g) > AcfPlot(g, LagZeroQ=FALSE) > # > # Plot the sample inverse partial autocorrelations. > # On the basis of this plot, Cleveland (1972) suggested an ARp(1,2,7) > # for this data > "InverseAcf" <- + function(z, p=15){ + g<-TacvfMA(GetFitARpLS(z-mean(z),1:p)$phiHat, lag.max=p) + g/g[1] + } > # > data(SeriesA) > AcfPlot(InverseAcf(SeriesA),LagZeroQ=FALSE) ----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref --- : --- package (from environment) --- FitAR --- call from context --- GetFitARpLS(z - mean(z), 1:p) --- call from argument --- length(pvec) == 0 || pvec == 0 --- R stacktrace --- where 1: GetFitARpLS(z - mean(z), 1:p) where 2: TacvfMA(GetFitARpLS(z - mean(z), 1:p)$phiHat, lag.max = p) where 3: InverseAcf(SeriesA) where 4: plot(1:length(g), g, type = "h", ylim = c(-1, 1), xlab = "lag", ylab = ylab, main = main) where 5: AcfPlot(InverseAcf(SeriesA), LagZeroQ = FALSE) --- value of length: 15 type: logical --- [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [13] FALSE FALSE FALSE --- function from context --- function (z, pvec) { stopifnot(length(z) > 0) if (length(pvec) == 0 || pvec == 0) { phiHat <- numeric(0) constantTerm <- mean(z) res <- z - constantTerm yX <- matrix(z, ncol = 1) Iq <- TRUE LL <- LoglikelihoodAR(0, z, MeanValue = constantTerm) covHat <- numeric(0) } else { PMAX <- max(pvec) stopifnot(PMAX < length(z)) Xy <- embed(z, PMAX + 1) y <- Xy[, 1] if (length(pvec) == 1 && pvec == 1) X <- matrix(Xy[, -1], ncol = 1) else X <- (Xy[, -1])[, pvec] yX <- cbind(y, X) ans <- lm(y ~ X) res <- resid(ans) betaHat <- as.vector(coef(ans)[-1]) constantTerm <- as.vector(coef(ans)[1]) phiHat <- numeric(PMAX) phiHat[pvec] <- betaHat covHat <- vcov(ans) } Iq <- InvertibleQ(phiHat) if (Iq) LL <- LoglikelihoodAR(phiHat, z, MeanValue = mean(z)) else LL <- -1e+30 list(loglikelihood = LL, phiHat = phiHat, constantTerm = constantTerm, res = res, pvec = pvec, InvertibleQ = Iq, yX = yX, covHat = covHat) } --- function search by body --- Function GetFitARpLS in namespace FitAR has this body. ----------- END OF FAILURE REPORT -------------- Fatal error: length > 1 in coercion to logical * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 5 NOTEs See ‘/data/gannet/ripley/R/packages/tests-LENGTH1/FitAR.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 5:32.43, 120.36 + 11.78