* using log directory ‘/data/localhost/ripley/R/packages/tests-MKL/SimtablR.Rcheck’
* using R Under development (unstable) (2026-10-28 r90786)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)
    GNU Fortran (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)
* running under: Fedora Linux 44 (Server Edition)
* using session charset: UTF-8
* current time: 2026-10-29 16:59:50 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘SimtablR/DESCRIPTION’ ... OK
* this is package ‘SimtablR’ version ‘3.1.1’
* 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 ‘SimtablR’ can be installed ... [11s/11s] 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 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 ... [31s/34s] 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 for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [13s/14s]
 [14s/14s] 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(SimtablR)
  ── SimtablR 3.1.1 ────────────────── Publication-ready epidemiological tables ──
  ✔ Describe: tb(), table1()  Estimate: regtab(), survtab()
  ✔ Diagnose: diag_test(), roc()  Build: simtab() |> verbs, simtablr()
  ✔ Revise: adjust(), sensitivity(), e_value()
  ✔ Report: as_methods(), strobe(), codebook(), why()
  ✔ Export: export_docx(), as_flextable(), as_gt(), autoplot()
  ℹ Learning SimtablR? Use browseVignettes(package = 'SimtablR') for guides
  Use suppressPackageStartupMessages() to silence.
  
  Attaching package: 'SimtablR'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > 
  > test_check("SimtablR")
  ! Methodological warning
    A data-driven ROC cutpoint is reported from the same data used to estimate performance; its sensitivity and specificity are optimistic. Validate the threshold in external data or with resampling before treating it as a decision rule.
    2 additional methodological notes hidden. Run simtablr_guidance("teaching") separately before printing to show all advice.
  Table exported to: /tmp/RtmpINVIHe/working_dir/RtmpeS7bZv/file13f66678b2f5d.docx
  Table exported to: /tmp/RtmpINVIHe/working_dir/RtmpeS7bZv/file13f66641e9e533.xlsx
  ! Methodological warning
    Logistic model has low events per parameter (minimum EPV 0.0). Consider fewer predictors, penalisation, or a sample-size calculation.
    1 additional methodological note hidden. Run simtablr_guidance("teaching") separately before printing to show all advice.
  SimtablR explanation
  Status: computed result.
  Engine: bivariate
  Design: not recorded
  Measure: RR
  Measure source: user
  Ruleset version: downscale-2026-09-23
  i Methodological guidance
    Adjusted coefficients for covariates are conditional associations, not automatically total causal effects. Footnote covariate rows or present the pre-specified exposure estimate separately.
    Run simtablr_guidance("off") separately before printing to hide advice.
  Saving _problems/test-style-101.R
  Variable 'age' automatically treated as continuous because it is numeric. Use 'var.type' to override.
  Variable 'age' automatically treated as continuous because it is numeric. Use 'var.type' to override.
  Variable 'age' automatically treated as continuous because it is numeric. Use 'var.type' to override.
  Variable 'age' automatically treated as continuous because it is numeric. Use 'var.type' to override.
  Variable 'age' automatically treated as continuous because it is numeric. Use 'var.type' to override.
  ! Methodological warning
    Outcome is common (14.7%); odds ratios can overstate the prevalence/risk ratio. Consider measure = 'PR' for cross-sectional tables or Poisson/log-binomial models for adjusted estimates.
    Run simtablr_guidance("off") separately before printing to hide advice.
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 354 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-style.R:101:3'): GLM journal style applies through the spec grammar ──
  Expected `grammar$data` to be identical to `r$data`.
  Differences:
    `actual$lower`: 1.06011258227871363 0.98871414506353839
  `expected$lower`: 1.06011258227871341 0.98871414506353839
  
    `actual$p`: 0.008969375381723734 0.049887140863360546
  `expected$p`: 0.008969375381723745 0.049887140863360629
  
    `actual$gvif`: 1.21631811953083324 1.21631811953083324
  `expected$gvif`: 1.21631811953083302 1.21631811953083302
  
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 354 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [28s/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
See
  ‘/data/localhost/ripley/R/packages/tests-MKL/SimtablR.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:28.57, 128.65 + 10.98