• using R Under development (unstable) (2026-05-10 r90032)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)     GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8 * current time: 2026-05-10 13:10:04 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘stdReg2/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘stdReg2’ version ‘1.0.3’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘AF’
• 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 ‘stdReg2’ can be installed ... [16s/21s] OK See the install log for details.
• 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 ... [28s/31s] 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [17s/18s] ERROR Running examples in ‘stdReg2-Ex.R’ failed The error most likely occurred in: > ### Name: standardize_glm > ### Title: Get regression standardized estimates from a glm > ### Aliases: standardize_glm > > ### ** Examples > > > # basic example > # needs to correctly specify the outcome model and no unmeasered confounders > # (+ standard causal assunmptions) > set.seed(6) > n <- 100 > Z <- rnorm(n) > X <- cut(rnorm(n, mean = Z), breaks = c(-Inf, 0, Inf), labels = c("low", "high")) > Y <- rbinom(n, 1, prob = (1 + exp(as.numeric(X) + Z))^(-1)) > dd <- data.frame(Z, X, Y) > x <- standardize_glm( + formula = Y ~ X * Z, + family = "binomial", + data = dd, + values = list(X = c("low", "high")), + contrasts = c("difference", "ratio"), + reference = "low" + ) > x Outcome formula: Y ~ X * Z Outcome family: quasibinomial Outcome link function: logit Exposure: X Tables:      X Estimate Std.Error lower.0.95 upper.0.95 1 low 0.286 0.0556 0.17676 0.395 2 high 0.198 0.1007 0.00035 0.395 Reference level: X = low Contrast: difference      X Estimate Std.Error lower.0.95 upper.0.95 1 low 0.000 0.000 0.000 0.000 2 high -0.088 0.113 -0.309 0.133 Reference level: X = low Contrast: ratio      X Estimate Std.Error lower.0.95 upper.0.95 1 low 1.000 0.000 1.000 1.00 2 high 0.692 0.372 -0.037 1.42 > # different transformations of causal effects > > # example from Sjölander (2016) with case-control data > # here the matching variable needs to be passed as an argument > singapore <- AF::singapore Error in loadNamespace(x) : there is no package called ‘AF’ Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... OK   Running ‘testthat.R’
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [27s/29s] 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