* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/boxcoxmix.Rcheck’ * using R Under development (unstable) (2022-03-11 r81877) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘boxcoxmix/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘boxcoxmix’ version ‘0.28’ * package encoding: UTF-8 * 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 ‘boxcoxmix’ can be installed ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [13s/13s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * 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 LazyData ... NOTE 'LazyData' is specified without a 'data' directory * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking examples with --run-donttest ... [49s/50s] ERROR Running examples in ‘boxcoxmix-Ex.R’ failed The error most likely occurred in: > ### Name: optim.boxcox > ### Title: Response Transformations for Random Effect and Variance > ### Component Models > ### Aliases: optim.boxcox > ### Keywords: boxcox optim > > ### ** Examples > > # The strength Data > data(strength, package = "mdscore") > maxlam <- optim.boxcox(y ~ cut*lot, data = strength, K = 3, + start = "gq" , find.in.range = c(-2, 2), s = 5) Maximum profile log-likelihood: 33.6795 at lambda= -0.4 > # Maximum profile log-likelihood: 33.6795 at lambda= -0.4 > > ## No test: > data(Oxboys, package = "nlme") > Oxboys$boy <- gl(26,9) > maxlamvc <- optim.boxcox(height ~ age, groups = Oxboys$boy, + data = Oxboys, K = 2, start = "gq", + find.in.range=c(-1.2,1), s=6, plot.opt = 0) > maxlamvc$Maximum [1] -0.8333333 > #[1] -0.8333333 > plot(maxlamvc,8) ----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref --- : --- package (from environment) --- boxcoxmix --- call from context --- plot.boxcoxmix(maxlamvc, 8) --- call from argument --- x$kind %in% c(1, 3) && !x$fitted == "none" --- R stacktrace --- where 1: plot.boxcoxmix(maxlamvc, 8) where 2: plot(maxlamvc, 8) --- value of length: 234 type: logical --- [,1] 1 TRUE 2 TRUE 3 TRUE 4 TRUE 5 TRUE 6 TRUE 7 TRUE 8 TRUE 9 TRUE 10 TRUE 11 TRUE 12 TRUE 13 TRUE 14 TRUE 15 TRUE 16 TRUE 17 TRUE 18 TRUE 19 TRUE 20 TRUE 21 TRUE 22 TRUE 23 TRUE 24 TRUE 25 TRUE 26 TRUE 27 TRUE 28 TRUE 29 TRUE 30 TRUE 31 TRUE 32 TRUE 33 TRUE 34 TRUE 35 TRUE 36 TRUE 37 TRUE 38 TRUE 39 TRUE 40 TRUE 41 TRUE 42 TRUE 43 TRUE 44 TRUE 45 TRUE 46 TRUE 47 TRUE 48 TRUE 49 TRUE 50 TRUE 51 TRUE 52 TRUE 53 TRUE 54 TRUE 55 TRUE 56 TRUE 57 TRUE 58 TRUE 59 TRUE 60 TRUE 61 TRUE 62 TRUE 63 TRUE 64 TRUE 65 TRUE 66 TRUE 67 TRUE 68 TRUE 69 TRUE 70 TRUE 71 TRUE 72 TRUE 73 TRUE 74 TRUE 75 TRUE 76 TRUE 77 TRUE 78 TRUE 79 TRUE 80 TRUE 81 TRUE 82 TRUE 83 TRUE 84 TRUE 85 TRUE 86 TRUE 87 TRUE 88 TRUE 89 TRUE 90 TRUE 91 TRUE 92 TRUE 93 TRUE 94 TRUE 95 TRUE 96 TRUE 97 TRUE 98 TRUE 99 TRUE 100 TRUE 101 TRUE 102 TRUE 103 TRUE 104 TRUE 105 TRUE 106 TRUE 107 TRUE 108 TRUE 109 TRUE 110 TRUE 111 TRUE 112 TRUE 113 TRUE 114 TRUE 115 TRUE 116 TRUE 117 TRUE 118 TRUE 119 TRUE 120 TRUE 121 TRUE 122 TRUE 123 TRUE 124 TRUE 125 TRUE 126 TRUE 127 TRUE 128 TRUE 129 TRUE 130 TRUE 131 TRUE 132 TRUE 133 TRUE 134 TRUE 135 TRUE 136 TRUE 137 TRUE 138 TRUE 139 TRUE 140 TRUE 141 TRUE 142 TRUE 143 TRUE 144 TRUE 145 TRUE 146 TRUE 147 TRUE 148 TRUE 149 TRUE 150 TRUE 151 TRUE 152 TRUE 153 TRUE 154 TRUE 155 TRUE 156 TRUE 157 TRUE 158 TRUE 159 TRUE 160 TRUE 161 TRUE 162 TRUE 163 TRUE 164 TRUE 165 TRUE 166 TRUE 167 TRUE 168 TRUE 169 TRUE 170 TRUE 171 TRUE 172 TRUE 173 TRUE 174 TRUE 175 TRUE 176 TRUE 177 TRUE 178 TRUE 179 TRUE 180 TRUE 181 TRUE 182 TRUE 183 TRUE 184 TRUE 185 TRUE 186 TRUE 187 TRUE 188 TRUE 189 TRUE 190 TRUE 191 TRUE 192 TRUE 193 TRUE 194 TRUE 195 TRUE 196 TRUE 197 TRUE 198 TRUE 199 TRUE 200 TRUE 201 TRUE 202 TRUE 203 TRUE 204 TRUE 205 TRUE 206 TRUE 207 TRUE 208 TRUE 209 TRUE 210 TRUE 211 TRUE 212 TRUE 213 TRUE 214 TRUE 215 TRUE 216 TRUE 217 TRUE 218 TRUE 219 TRUE 220 TRUE 221 TRUE 222 TRUE 223 TRUE 224 TRUE 225 TRUE 226 TRUE 227 TRUE 228 TRUE 229 TRUE 230 TRUE 231 TRUE 232 TRUE 233 TRUE 234 TRUE --- function from context --- function (x, plot.opt = 1, ...) { K <- length(x$mass.point) if (plot.opt %in% c(7, 8, 9, 10)) { graphics::par(mfrow = c(1, 1)) } else if (plot.opt %in% c(1, 4, 5)) { graphics::par(mfrow = c(2, 1), cex = 0.5, cex.axis = 1.5, cex.lab = 1.5) } else { graphics::par(mfrow = c(1, 2), cex = 0.5, cex.axis = 1.5, cex.lab = 1.5) } if (x$kind %in% c(1, 3) && K > 1 && plot.opt == 1) { graphics::plot(1:x$EMiteration, x$Disparities, , col = 1, type = "l", xlab = "EM iterations", ylab = "-2logL") } if (x$kind %in% c(1, 3) && K > 1 && plot.opt == 1) { ylim <- x$ylim followmass <- x$masses graphics::plot(1:x$EMiteration, followmass[, 1], col = 1, type = "l", ylim = ylim, ylab = "mass points", xlab = "EM iterations") for (k in 1:K) { graphics::lines(1:x$EMiteration, followmass[, k], col = k) } } if (x$kind %in% c(1, 3) && !x$fitted == "none" && plot.opt == 2) { class.col <- masspoint.class(x) graphics::plot(x$y, x$fitted, xlab = "True response", ylab = "fitted", col = class.col) graphics::abline(0, 1) graphics::plot(x$yt, x$fitted.transformed, xlab = "Transformed response", ylab = "fitted.transformed", col = class.col) graphics::abline(0, 1) } if (x$kind %in% c(1, 3) && plot.opt == 3) { R <- x$residuals RT <- x$residuals.transformed graphics::par(mfrow = c(1, 2)) stats::qqnorm(R, main = "Q-Q plot of Original data") stats::qqline(R, col = "red", lwd = 3) stats::qqnorm(RT, main = "Q-Q plot of Transformed data") stats::qqline(RT, col = "red", lwd = 3) } if (x$kind %in% c(1, 3) && x$mform == "1" && K > 1 && plot.opt == 4) { if (is.infinite(abs(max(x$residuals)))) { return(c("Posterior probabilty plot not applicable for this object.")) } pmax <- max(x$w) graphics::plot(x$residuals, x$w[, 1], col = 1, type = "p", ylim = c(0, pmax), ylab = "post.prob", xlab = "Residuals") for (k in 2:K) { graphics::points(x$residuals, x$w[, k], col = k, pch = k, type = "p") } graphics::plot(x$residuals.transformed, x$w[, 1], col = 1, type = "p", ylim = c(0, pmax), ylab = "post.prob", xlab = "Residuals transformed") for (k in 2:K) { graphics::points(x$residuals.transformed, x$w[, k], col = k, pch = k, type = "p") } } if (x$kind %in% c(1, 3) && plot.opt == 5) { qicharts::qic(x$residuals, chart = "i", cex = 1.3, xlab = NULL, ylab = NULL, main = "Control Chart of Original Data") qicharts::qic(x$residuals.transformed, chart = "i", cex = 1.3, xlab = NULL, ylab = NULL, main = "Control Chart of Transformed Data") } if (x$kind %in% c(1, 3) && plot.opt == 6) { r <- x$residuals rt <- x$residuals.transformed graphics::hist(r, main = "Original data", xlab = NULL, ylab = NULL, col = "lightblue") graphics::hist(rt, main = "Transformed data", xlab = NULL, ylab = NULL, col = "pink") } if (x$kind == "2" && plot.opt == 7) { npc <- x$npcolors graphics::plot(x$Alltol, x$AllDisparities, type = "o", xlab = "tol", ylab = "Disparity", col = npc) graphics::segments(x$tol.min, x$min.Disp, x$tol.min, 1.1 * x$min.Disp, col = 4) } if (x$kind == "3" && plot.opt == 8) { plims <- graphics::par("usr") y0 <- plims[3] npc0 <- x$npcolor result <- x$ylim1 graphics::plot(x$All.lambda, x$profile.loglik, type = "l", xlab = expression(lambda), ylab = "Profile log-likelihood", ylim = result, col = npc0, main = x$maxl) graphics::segments(x$Maximum, y0, x$Maximum, x$objective, lty = 1, col = "red", lwd = 2) } if (x$kind == "4" && plot.opt == 9) { plims <- graphics::par("usr") y0 <- plims[3] if (x$mselect == "1") { graphics::plot(x$All.K, x$Allaic, type = "o", xlab = "K", ylab = "AIC", col = "green", main = x$md) graphics::segments(x$Best.K, y0, x$Best.K, x$MinAIC, lty = 2, col = "red", lwd = 2) } else { graphics::plot(x$All.K, x$Allbic, type = "o", xlab = "K", ylab = "BIC", col = "green", main = x$md) graphics::segments(x$Best.K, y0, x$Best.K, x$MinBIC, lty = 2, col = "red", lwd = 2) } } if (x$kind == "5" && plot.opt == 10) { graphics::plot(x$All.lam, x$profile.loglik, type = "l", xlab = expression(lambda), ylab = "Profile log-likelihood", ylim = x$ylim1, col = "green", main = x$ml) graphics::segments(x$Maximum, x$y0, x$Maximum, x$objective, lty = 1, col = "red", lwd = 3) } invisible(x) } --- function search by body --- Function plot.boxcoxmix in namespace boxcoxmix has this body. ----------- END OF FAILURE REPORT -------------- Fatal error: length > 1 in coercion to logical * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [32s/32s] OK * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/data/blackswan/ripley/R/packages/tests-devel/boxcoxmix.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 2:30.70, 139.44 + 9.85