* using log directory ‘/data/localhost/ripley/R/packages/tests-clang-trunk/arm.Rcheck’ * using R Under development (unstable) (2026-09-04 r90492) * using platform: x86_64-pc-linux-gnu * R was compiled by clang version 23.1.0 flang version 23.1.0 * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-09-06 07:15:09 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘arm/DESCRIPTION’ ... OK * this is package ‘arm’ version ‘1.15-3’ * 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 ‘arm’ can be installed ... [10s/17s] OK * checking installed package size ... OK * checking package 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 whether startup messages can be suppressed ... 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/23s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... INFO Undeclared packages ‘survey’, ‘Matching’ in Rd xrefs * 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 data for ASCII and uncompressed saves ... OK * checking examples ... ERROR Running examples in ‘arm-Ex.R’ failed The error most likely occurred in: > ### Name: standardize > ### Title: Function for Standardizing Regression Predictors by Centering > ### and Dividing by 2 sd's > ### Aliases: standardize standardize,lm-method standardize,glm-method > ### standardize,merMod-method standardize,polr-method > ### Keywords: manip models methods > > ### ** Examples > > # Set up the fake data > n <- 100 > x <- rnorm (n, 2, 1) > x1 <- rnorm (n) > x1 <- (x1-mean(x1))/(2*sd(x1)) # standardization > x2 <- rbinom (n, 1, .5) > b0 <- 1 > b1 <- 1.5 > b2 <- 2 > y <- rbinom (n, 1, invlogit(b0+b1*x1+b2*x2)) > y2 <- sample(1:5, n, replace=TRUE) > M1 <- glm (y ~ x, family=binomial(link="logit")) > display(M1) glm(formula = y ~ x, family = binomial(link = "logit")) coef.est coef.se (Intercept) 1.37 0.66 x 0.07 0.29 --- n = 100, k = 2 residual deviance = 94.2, null deviance = 94.3 (difference = 0.1) > M1.1 <- glm (y ~ rescale(x), family=binomial(link="logit")) > display(M1.1) glm(formula = y ~ rescale(x), family = binomial(link = "logit")) coef.est coef.se (Intercept) 1.52 0.26 rescale(x) 0.12 0.52 --- n = 100, k = 2 residual deviance = 94.2, null deviance = 94.3 (difference = 0.1) > M1.2 <- standardize(M1) > display(M1.2) glm(formula = y ~ z.x, family = binomial(link = "logit")) coef.est coef.se (Intercept) 1.52 0.26 z.x 0.12 0.52 --- n = 100, k = 2 residual deviance = 94.2, null deviance = 94.3 (difference = 0.1) > # M1.1 & M1.2 should be the same > M2 <- polr(ordered(y2) ~ x) > display(M2) Re-fitting to get Hessian polr(formula = ordered(y2) ~ x) coef.est coef.se x -0.19 0.20 1|2 -2.32 0.55 2|3 -1.11 0.49 3|4 -0.11 0.47 4|5 0.88 0.48 --- n = 100, k = 5 (including 4 intercepts) residual deviance = 317.3, null deviance is not computed by polr > M2.1 <- polr(ordered(y2) ~ rescale(x)) > display(M2.1) Re-fitting to get Hessian polr(formula = ordered(y2) ~ rescale(x)) coef.est coef.se rescale(x) -0.34 0.37 1|2 -1.92 0.30 2|3 -0.72 0.21 3|4 0.29 0.20 4|5 1.27 0.24 --- n = 100, k = 5 (including 4 intercepts) residual deviance = 317.3, null deviance is not computed by polr > M2.2 <- standardize(M2.1) > display(M2.2) Re-fitting to get Hessian polr(formula = ordered(y2) ~ rescale(z.x)) coef.est coef.se rescale(z.x) -0.34 0.37 1|2 -1.92 0.30 2|3 -0.72 0.21 3|4 0.29 0.20 4|5 1.27 0.24 --- n = 100, k = 5 (including 4 intercepts) residual deviance = 317.3, null deviance is not computed by polr > # M2.1 & M2.2 should be the same > form <- y ~ x1 + x2 # input formula as an object > M3 <- glm(form, family=binomial) > M3.1 <- standardize(M3) Error in standardize.default(call = call, unchanged = unchanged, standardize.y = standardize.y, : Error: The object x1 must be either numeric or a factor. Calls: standardize -> standardize -> .local -> standardize.default Execution halted * 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-clang-trunk/arm.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 1:46.51, 65.27 + 6.98