* using log directory ‘/data/localhost/ripley/R/packages/tests-ATLAS/tram.Rcheck’ * using R Under development (unstable) (2026-07-23 r90295) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2) GNU Fortran (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2) * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-07-24 09:59:31 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘tram/DESCRIPTION’ ... OK * this is package ‘tram’ version ‘1.4-4’ * 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 ‘tram’ 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 code 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [15s/15s] 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [24s/24s] ERROR Running examples in ‘tram-Ex.R’ failed The error most likely occurred in: > ### Name: tram-methods > ### Title: Methods for Stratified Linear Transformation Models > ### Aliases: as.mlt.tram model.frame.tram model.matrix.tram > ### model.matrix.stram coef.tram coef.Lm coef.Survreg vcov.tram > ### logLik.tram estfun.tram predict.tram predict.stram residuals.tram > ### plot.tram plot.ROCtram PI PI.tram PI.default OVL OVL.tram OVL.default > ### TV TV.tram TV.default L1 L1.tram L1.default ROC ROC.tram ROC.default > > ### ** Examples > > > data("BostonHousing2", package = "mlbench") > > ### fit non-normal Box-Cox type linear model with two > ### baseline functions (for houses near and off Charles River) > BC_BH_2 <- BoxCox(cmedv | 0 + chas ~ crim + zn + indus + nox + + rm + age + dis + rad + tax + ptratio + b + lstat, + data = BostonHousing2) > logLik(BC_BH_2) 'log Lik.' -1334.509 (df=26) > > ### classical likelihood inference > summary(BC_BH_2) (Stratified) Non-normal (Box-Cox-Type) Linear Regression Model Call: BoxCox(formula = cmedv | 0 + chas ~ crim + zn + indus + nox + rm + age + dis + rad + tax + ptratio + b + lstat, data = BostonHousing2) Coefficients: Estimate Std. Error z value Pr(>|z|) crim -0.0468291 0.0074131 -6.317 2.67e-10 *** zn 0.0061567 0.0029332 2.099 0.0358 * indus 0.0140535 0.0131135 1.072 0.2839 nox -4.9493303 0.8464101 -5.847 4.99e-09 *** rm 0.4367658 0.0948221 4.606 4.10e-06 *** age -0.0016586 0.0028369 -0.585 0.5588 dis -0.2992350 0.0437646 -6.837 8.07e-12 *** rad 0.0811996 0.0142694 5.690 1.27e-08 *** tax -0.0037182 0.0008041 -4.624 3.76e-06 *** ptratio -0.2183805 0.0285718 -7.643 2.11e-14 *** b 0.0026674 0.0005776 4.618 3.87e-06 *** lstat -0.1669489 0.0123201 -13.551 < 2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Log-Likelihood: -1334.509 (df = 26) Likelihood-ratio Test: Chisq = 817.2316 on 12 degrees of freedom; p = < 2.2e-16 > > ### coefficients of the linear predictor > coef(BC_BH_2) crim zn indus nox rm age -0.046829146 0.006156688 0.014053527 -4.949330334 0.436765796 -0.001658559 dis rad tax ptratio b lstat -0.299234981 0.081199628 -0.003718232 -0.218380515 0.002667439 -0.166948857 > > ### plot linear predictor (mean of _transformed_ response) > ### vs. observed values > plot(predict(BC_BH_2, type = "lp"), BostonHousing2$cmedv) > > ### all coefficients > coef(BC_BH_2, with_baseline = TRUE) Bs1(cmedv):chas0 Bs2(cmedv):chas0 Bs3(cmedv):chas0 Bs4(cmedv):chas0 -13.301606105 -11.573666201 -11.573666157 -4.412730205 Bs5(cmedv):chas0 Bs6(cmedv):chas0 Bs7(cmedv):chas0 Bs1(cmedv):chas1 -2.924911217 -2.924911219 -2.176156988 -17.458111771 Bs2(cmedv):chas1 Bs3(cmedv):chas1 Bs4(cmedv):chas1 Bs5(cmedv):chas1 -17.458085933 -8.209731436 -4.374264134 -4.374264187 Bs6(cmedv):chas1 Bs7(cmedv):chas1 crim zn -4.374264252 -3.376824818 -0.046829146 0.006156688 indus nox rm age 0.014053527 -4.949330334 0.436765796 -0.001658559 dis rad tax ptratio -0.299234981 0.081199628 -0.003718232 -0.218380515 b lstat 0.002667439 -0.166948857 > > ### compute predicted median along with 10% and 90% quantile for the first > ### observations > predict(BC_BH_2, newdata = BostonHousing2[1:3,], type = "quantile", + prob = c(.1, .5, .9)) prob [,1] [,2] [,3] 0.1 22.77286 19.83902 23.39701 0.5 27.98474 23.65864 29.08606 0.9 38.50994 29.55980 41.48675 > > ### plot the predicted density for these observations > plot(BC_BH_2, newdata = BostonHousing2[1:3, -1], + which = "distribution", type = "density", K = 1000) > > ### evaluate the two baseline transformations, with confidence intervals > nd <- model.frame(BC_BH_2)[1:2, -1] > nd$chas <- factor(c("0", "1")) > library("colorspace") > col <- diverge_hcl(2, h = c(246, 40), c = 96, l = c(65, 90)) > fill <- diverge_hcl(2, h = c(246, 40), c = 96, l = c(65, 90), alpha = .3) > plot(BC_BH_2, which = "baseline only", newdata = nd, col = col, + confidence = "interval", fill = fill, lwd = 2, + xlab = "Median Value", ylab = expression(h[Y])) > legend("bottomright", lty = 1, col = col, + title = "Near Charles River", legend = c("no", "yes"), bty = "n") > > ### cars data; with quantile functions > plot(dist ~ speed, data = cars) > m <- Colr(dist ~ speed, data = cars) > q <- predict(as.mlt(m), newdata = data.frame(speed = s <- 7:20), + type = "quantile", prob = c(1, 5, 9) / 10) > lines(s, q[1,]) > lines(s, q[2,]) > lines(s, q[3,]) > > nd <- data.frame(speed = s <- as.double(1:5 * 5)) > > # Prob(dist at speed s > dist at speed 0) > # speed 0 is reference, not a good choice here > PI(m, newdata = nd) [,1] [,2] [,3] [,4] [,5] [1,] 0.8592843 0.9783094 0.9975498 0.9997612 0.9999785 > > # Prob(dist at speed s > dist at speed 15) > lp15 <- c(predict(m, newdata = data.frame(speed = 15))) > PI(m, newdata = nd, reference = lp15) [,1] [,2] [,3] [,4] [,5] [1,] 0.02169061 0.1407157 0.5 0.8592843 0.9783094 > PI(m, newdata = nd, reference = nd[3,,drop = FALSE]) [,1] [,2] [,3] [,4] [,5] [1,] 0.02169061 0.1407157 0.5 0.8592843 0.9783094 > > # Prob(dist at speed s' > dist at speed s) > PI(m, newdata = nd, reference = nd) 1 2 3 4 2 0.8592843 3 0.9783094 0.8592843 4 0.9975498 0.9783094 0.8592843 5 0.9997612 0.9975498 0.9783094 0.8592843 > # essentially: > lp <- predict(m, newdata = nd) > PI(object = dist(lp)) 1 2 3 4 2 0.8592843 3 0.9783094 0.8592843 4 0.9975498 0.9783094 0.8592843 5 0.9997612 0.9975498 0.9783094 0.8592843 > # same, with simultaneous confidence intervals > PI(m, newdata = nd, reference = nd, conf.level = .95) Estimate lwr upr 1-2 0.8592843 0.7810205 0.9140831 1-3 0.9783094 0.9324163 0.9937064 2-3 0.8592843 0.7810205 0.9140831 1-4 0.9975498 0.9835292 0.9996734 2-4 0.9783094 0.9324163 0.9937064 3-4 0.8592843 0.7810205 0.9140831 1-5 0.9997612 0.9965051 0.9999853 2-5 0.9975498 0.9835292 0.9996734 3-5 0.9783094 0.9324163 0.9937064 4-5 0.8592843 0.7810205 0.9140831 attr(,"conf.level") [1] 0.95 attr(,"calpha") [1] 1.960362 > > # plot ROC curves + confidence bands > # compare speed 20 and 25 to speed 15 > plot(ROC(m, newdata = nd[4:5,,drop = FALSE], + reference = nd[3,,drop = FALSE], + conf.level = 0.95)) > > # Overlap of conditional densities at speed s' and s > OVL(m, newdata = nd, reference = nd) 1 2 3 4 2 0.419905083 3 0.131925884 0.419905083 4 0.036843326 0.131925884 0.419905083 5 0.009925244 0.036843326 0.131925884 0.419905083 > > ### ROC analysis (takes too long for CRAN Windows) > if (require("mlbench") && .Platform$OS.type != "windows") { + + layout(matrix(1:4, nrow = 2)) + data("PimaIndiansDiabetes2", package = "mlbench") + dia <- sort(unique(PimaIndiansDiabetes2$diabetes)) + nd <- data.frame(diabetes = dia, + age = 29, mass = 32) ### median values + + ### unconditional ROC analysis: glucose tolerance test + m0 <- Colr(glucose ~ diabetes, data = PimaIndiansDiabetes2) + # ROC curve + confidence band + plot(ROC(m0, newdata = nd[2,,drop = FALSE], conf.level = .95)) + # Wald interval for AUC + PI(m0, newdata = nd[2,,drop = FALSE], conf.level = .95) + # score interval for AUC + PI(-c(coef(m0), score_test(m0)$conf.int[2:1])) + + ### adjusted ROC analysis for age and mass + m1 <- Colr(glucose ~ diabetes + age + mass, data = PimaIndiansDiabetes2) + # ROC curve + confidence band (this is the same for all ages / + # masses) + plot(ROC(m1, newdata = nd[2,,drop = FALSE], + reference = nd[1,,drop = FALSE], + conf.level = .95)) + # Wald interval for adjusted AUC + PI(m1, newdata = nd[2,,drop = FALSE], reference = nd[1,,drop = FALSE], + conf.level = .95) + # Score interval for adjusted AUC + PI(-c(coef(m1)[1], score_test(m1, names(coef(m1))[1])$conf.int[2:1])) + + ### conditional ROC analysis: AUC regression ~ age + mass + m2 <- Colr(glucose ~ diabetes * (age + mass), data = PimaIndiansDiabetes2) + # ROC curve for a person with age = 29 and mass = 32 + plot(ROC(m2, newdata = nd[2,,drop = FALSE], + reference = nd[1,,drop = FALSE], + conf.level = .95)) + # AUC for persons ages 21:81, all with mass = 32 + nd1 <- data.frame(diabetes = nd[1,"diabetes"], age = 21:81, mass = 32) + nd2 <- data.frame(diabetes = nd[2,"diabetes"], age = 21:81, mass = 32) + auc <- PI(m2, newdata = nd2, reference = nd1, one2one = TRUE, + conf.level = 0.95) + plot(nd1$age, auc[, "Estimate"], xlab = "Age (in years)", ylab = + "AUC", ylim = c(0, 1), type = "l") + lines(nd1$age, auc[, "lwr"], lty = 3) + lines(nd1$age, auc[, "upr"], lty = 3) + } Loading required package: mlbench Warning in data("PimaIndiansDiabetes2", package = "mlbench") : data set ‘PimaIndiansDiabetes2’ not found Error: object 'PimaIndiansDiabetes2' not found Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘Coxph-Ex.R’ Comparing ‘Coxph-Ex.Rout’ to ‘Coxph-Ex.Rout.save’ ... OK Running ‘KaplanMeier-Ex.R’ Running ‘PI_OVL-Ex.R’ Running ‘Polr-Ex.R’ Comparing ‘Polr-Ex.Rout’ to ‘Polr-Ex.Rout.save’ ... OK Running ‘Survreg-Ex.R’ Comparing ‘Survreg-Ex.Rout’ to ‘Survreg-Ex.Rout.save’ ... OK Running ‘bugfixes.R’ [52s/52s] Running ‘intercepts-Ex.R’ Comparing ‘intercepts-Ex.Rout’ to ‘intercepts-Ex.Rout.save’ ... OK Running ‘mmlt-Ex.R’ [103s/104s] Comparing ‘mmlt-Ex.Rout’ to ‘mmlt-Ex.Rout.save’ ... OK Running ‘mmlt-interface.R’ [27s/28s] Running ‘mtram-Ex.R’ Comparing ‘mtram-Ex.Rout’ to ‘mtram-Ex.Rout.save’ ... OK Running ‘stram-Ex.R’ [19s/19s] Comparing ‘stram-Ex.Rout’ to ‘stram-Ex.Rout.save’ ... OK [231s/233s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [589s/591s] OK * checking PDF version of manual ... OK * checking HTML 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 See ‘/data/localhost/ripley/R/packages/tests-ATLAS/tram.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 15:19.54, 894.17 + 18.10