* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/BayesERtools.Rcheck’
* using R Under development (unstable) (2026-06-25 r90191)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* current time: 2026-06-26 09:40:39 UTC
* checking for file ‘BayesERtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BayesERtools’ version ‘0.2.6’
* 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 ‘BayesERtools’ can be installed ... [22s/21s] 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 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/28s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking examples with --run-donttest ... [370s/284s] ERROR
Running examples in ‘BayesERtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot_er_exp_sel
> ### Title: Plot exposure metric selection comparison
> ### Aliases: plot_er_exp_sel
> 
> ### ** Examples
> 
> ## Don't show: 
> if (BayesERtools:::.if_run_ex_plot_er()) withAutoprint({ # examplesIf
+ ## End(Don't show)
+ ## No test: 
+ data(d_sim_binom_cov_hgly2)
+ 
+ ermod_bin_exp_sel <-
+   dev_ermod_bin_exp_sel(
+     data = d_sim_binom_cov_hgly2,
+     var_resp = "AEFLAG",
+     var_exp_candidates = c("AUCss_1000", "Cmaxss", "Cminss")
+   )
+ 
+ plot_er_exp_sel(ermod_bin_exp_sel) +
+   xgxr::xgx_scale_x_log10(guide = ggplot2::guide_axis(minor.ticks = TRUE))
+ ## End(No test)
+ ## Don't show: 
+ }) # examplesIf
> data(d_sim_binom_cov_hgly2)
> ermod_bin_exp_sel <- dev_ermod_bin_exp_sel(data = d_sim_binom_cov_hgly2, 
+     var_resp = "AEFLAG", var_exp_candidates = c("AUCss_1000", "Cmaxss", "Cminss"))
ℹ The exposure metric selected was: AUCss_1000
> plot_er_exp_sel(ermod_bin_exp_sel) + xgxr::xgx_scale_x_log10(guide = ggplot2::guide_axis(minor.ticks = TRUE))
Error in `tidyr::pivot_longer()`:
ℹ In argument: `dplyr::all_of(var_exp_order)`.
Caused by error in `dplyr::all_of()`:
! Can't subset elements that don't exist.
✖ Elements `1`, `2`, and `3` don't exist.
Backtrace:
     ▆
  1. ├─base::withAutoprint(...)
  2. │ └─base::source(...)
  3. │   ├─base::withVisible(eval(ei, envir))
  4. │   └─base::eval(ei, envir)
  5. │     └─base::eval(ei, envir)
  6. ├─BayesERtools::plot_er_exp_sel(ermod_bin_exp_sel)
  7. │ ├─dplyr::left_join(...)
  8. │ ├─tidyr::pivot_longer(...)
  9. │ └─tidyr:::pivot_longer.data.frame(...)
 10. │   └─tidyr::build_longer_spec(...)
 11. │     └─tidyselect::eval_select(...)
 12. │       └─tidyselect:::eval_select_impl(...)
 13. │         ├─tidyselect:::with_subscript_errors(...)
 14. │         │ └─base::withCallingHandlers(...)
 15. │         └─tidyselect:::vars_select_eval(...)
 16. │           └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 17. │             └─tidyselect:::eval_context(expr, context_mask, call = error_call)
 18. │               ├─tidyselect:::with_chained_errors(...)
 19. │               │ └─base::withCallingHandlers(...)
 20. │               └─rlang::eval_tidy(as_quosure(expr, env), context_mask)
 21. ├─dplyr::all_of(var_exp_order)
 22. │ └─tidyselect:::as_indices_impl(x, vars = vars, strict = TRUE)
 23. │   └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
 24. │     └─vctrs::vec_as_location(...)
 25. └─vctrs (local) `<fn>`() at vctrs/R/subscript-loc.R:84:3
 26.   └─vctrs:::stop_subscript_oob(...)
 27.     └─vctrs:::stop_subscript(...) at vctrs/R/subscript-loc.R:503:3
 28.       └─rlang::abort(...) at vctrs/R/subscript.R:150:3
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [259s/204s]
 [259s/204s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(BayesERtools)
  > 
  > test_check("BayesERtools")
  Loading required namespace: projpred
  Saving _problems/test-dev_ermod_lin-229.R
  Saving _problems/test-dev_ermod_lin-273.R
  
  Diagnostic flags present.
  See ?`loo-glossary` (sections `diag_diff` and `diag_elpd`)
  or https://mc-stan.org/loo/reference/loo-glossary.html.
  Loading required package: bayestestR
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 208 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-dev_ermod_emax.R:150:5'): plot_ermod ───────────────────────────
  Error in `tidyr::pivot_longer(extract_data(x), dplyr::all_of(var_exp_order), names_to = ".exp_metric", values_to = ".exposure")`: i In argument: `dplyr::all_of(var_exp_order)`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1` and `2` don't exist.
  ── Error ('test-dev_ermod_emax.R:194:5'): plot_ermod_bin_emax ──────────────────
  Error in `tidyr::pivot_longer(extract_data(x), dplyr::all_of(var_exp_order), names_to = ".exp_metric", values_to = ".exposure")`: i In argument: `dplyr::all_of(var_exp_order)`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1` and `2` don't exist.
  ── Error ('test-dev_ermod_lin.R:229:5'): Exposure metrics selection ────────────
  Error in `tidyr::pivot_longer(extract_data(x), dplyr::all_of(var_exp_order), names_to = ".exp_metric", values_to = ".exposure")`: i In argument: `dplyr::all_of(var_exp_order)`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1`, `2`, and `3` don't exist.
  ── Failure ('test-dev_ermod_lin.R:273:5'): Final model ─────────────────────────
  Expected `coef(ermod_bin_cov_sel)[[1]]` to equal `-10.9133063`.
  Differences:
    `actual`: -10.948
  `expected`: -10.913
  
  ── Error ('test-dev_ermod_lin.R:427:5'): plot.ermod_exp_sel calls plot_er_exp_sel ──
  Error in `tidyr::pivot_longer(extract_data(x), dplyr::all_of(var_exp_order), names_to = ".exp_metric", values_to = ".exposure")`: i In argument: `dplyr::all_of(var_exp_order)`.
  Caused by error in `dplyr::all_of()`:
  ! Can't subset elements that don't exist.
  x Elements `1`, `2`, and `3` don't exist.
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 208 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [11s/11s] OK
* checking PDF 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: 2 ERRORs
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/BayesERtools.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 11:14.31, 673.49 + 149.80