* using log directory ‘/data/localhost/ripley/R/packages/tests-donttest/crane.Rcheck’
* using R Under development (unstable) (2026-08-24 r90445)
* 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: 2026-08-25 01:07:31 UTC
* checking for file ‘crane/DESCRIPTION’ ... OK
* this is package ‘crane’ version ‘0.3.2’
* 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 ‘crane’ can be installed ... [11s/15s] 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 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 ... [18s/24s] 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 examples ... [72s/117s] OK
* checking examples with --run-donttest ... [80s/96s] ERROR
Running examples in ‘crane-Ex.R’ failed
The error most likely occurred in:

> ### Name: tbl_roche_subgroups
> ### Title: Subgroup Analyses
> ### Aliases: tbl_roche_subgroups
> 
> ### ** Examples
> 
> ## Don't show: 
> if (identical(Sys.getenv("NOT_CRAN"), "true")) withAutoprint({ # examplesIf
+ ## End(Don't show)
+ set.seed(1)
+ 
+ # prepare sample data
+ df_adtte <- data.frame(
+   time = rexp(100, rate = 0.1),
+   status = sample(c(0, 1), 100, replace = TRUE),
+   arm = sample(c("Arm A", "Arm B"), 100, replace = TRUE),
+   grade = sample(c("I", "II"), 100, replace = TRUE),
+   strata = sample(c("1", "2"), 100, replace = TRUE)
+ ) |>
+   mutate(arm = relevel(factor(arm), ref = "Arm A")) # Set Reference
+ 
+ # logistic regression -------------------------------------------------------
+ df_adtte |>
+   tbl_roche_subgroups(
+     rsp = "status",
+     by = "arm",
+     subgroups = c("grade"),
+     .tbl_fun =
+       ~ glm(status ~ arm, data = .x) |>
+         tbl_regression(
+           show_single_row = arm,
+           exponentiate = TRUE # , tidy_fun = broom.helpers::tidy_parameters
+         )
+   ) |>
+   modify_header(starts_with("estimate") ~ "**Odds Ratio**")
+ ## Don't show: 
+ }) # examplesIf
> ## End(Don't show)
> ## Don't show: 
> if (rlang::is_installed("survival")) withAutoprint({ # examplesIf
+ ## End(Don't show)
+ # coxph regression ----------------------------------------------------------
+ # please use browser() inside .tbl_fun to check if the coxph model throws an error
+ # and use tryCatch to modify the input/output accordingly
+ ## No test: 
+ df_adtte |>
+   tbl_roche_subgroups(
+     rsp = status,
+     by = arm,
+     time_to_event = time, # Specify time variable for time-to-event analyses (different mid table)
+     subgroups = c(grade, strata),
+     ~ survival::coxph( # Please use coxph for time-to-event analyses
+       survival::Surv(time, status) ~ arm,
+       data = .x,
+       ties = "exact"
+     ) |> # Exact Ties
+       tbl_regression(
+         show_single_row = arm,
+         exponentiate = TRUE # Get Hazard Ratios
+       )
+   ) |>
+   modify_header(starts_with("estimate") ~ "**Hazard Ratio**")
+ ## End(No test)
+ ## Don't show: 
+ }) # examplesIf
> modify_header(tbl_roche_subgroups(df_adtte, rsp = status, by = arm, time_to_event = time, 
+     subgroups = c(grade, strata), ~tbl_regression(survival::coxph(survival::Surv(time, 
+         status) ~ arm, data = .x, ties = "exact"), show_single_row = arm, exponentiate = TRUE)), 
+     starts_with("estimate") ~ "**Hazard Ratio**")
Error in eval(ei, envir) : object 'df_adtte' not found
Calls: withAutoprint ... tbl_roche_subgroups -> check_data_frame -> check_class
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [234s/138s]
 [235s/138s] OK
* checking PDF version of manual ... [6s/10s] 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
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/localhost/ripley/R/packages/tests-donttest/crane.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 8:40.52, 473.44 + 30.30