* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/stdReg2.Rcheck’
* using R Under development (unstable) (2026-05-07 r90013)
* 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: 2026-05-08 06:06:27 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 ... [17s/25s] 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 ... [30s/49s] 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 ... [20s/22s] 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 ...
  Running ‘testthat.R’ [9s/10s]
 [10s/11s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* checking HTML version of manual ... [7s/10s] 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/gannet/ripley/R/packages/tests-Suggests/stdReg2.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:52.44, 153.47 + 13.63