* using log directory ‘/data/localhost/ripley/R/packages/tests-noLD/gtregression.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 09:56:53 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘gtregression/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gtregression’ version ‘1.1.0’ * 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 ‘gtregression’ can be installed ... [21s/48s] 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 ... [39s/54s] 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 ... [27s/28s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [140s/144s] [140s/144s] 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(gtregression) > > test_check("gtregression") Running stratified multivariable regression by: race > Stratum: race = White > Stratum: race = Black > Stratum: race = Other Running stratified multivariable regression by: race > Stratum: race = White > Stratum: race = Black > Stratum: race = Other Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Loading required package: shiny # A tibble: 2 x 7 Variable Type `Missing (%)` Unique Levels Compatibility Hint 1 x numeric 0% 3 - compatible Numeric variable c~ 2 y factor 0% 2 a, b compatible Factor variable ca~ Running stratified univariate regression by: race > Stratum: race = White > Stratum: race = Black > Stratum: race = Other Running stratified multivariable regression by: race > Stratum: race = White > Stratum: race = Black > Stratum: race = Other Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment a flextable object. col_keys: `Exposure`, `Potential confounder`, `Crude estimate`, `Adjusted estimate`, `MH estimate`, `% change model`, `% change MH`, `Confounder?`, `Interaction p`, `Effect modifier?`, `Decision`, `Recommendation` header has 1 row(s) body has 1 row(s) original dataset sample: 'data.frame': 1 obs. of 12 variables: $ Exposure : chr "smoke" $ Potential confounder: chr "race" $ Crude estimate : chr "2.022" $ Adjusted estimate : chr "3.053" $ MH estimate : chr "3.086" $ % change model : chr "50.98" $ % change MH : chr "52.64" $ Confounder? : chr "Yes" $ Interaction p : chr "0.206" $ Effect modifier? : chr "No" $ Decision : chr "Confounder" $ Recommendation : chr "Adjust for race." Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment uni_reg(): reference rows are hidden for dichotomous/categorical variables. To display Ref., use `show_ref = TRUE`. Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment uni_reg(): reference rows are hidden for dichotomous/categorical variables. To display Ref., use `show_ref = TRUE`. multi_reg(): reference rows are hidden for dichotomous/categorical variables. To display Ref., use `show_ref = TRUE`. Table saved at: /tmp/RtmpbLgTd2/working_dir/RtmpKQMgR1/gtregression-table-2737158.html Table saved at: /tmp/RtmpbLgTd2/working_dir/RtmpKQMgR1/gtregression-flex-2737158.docx Table saved at: /tmp/RtmpbLgTd2/working_dir/RtmpKQMgR1/gtregression-flex-2737158.rtf Table saved at: /tmp/RtmpbLgTd2/working_dir/RtmpKQMgR1/gtregression-flex-2737158.html Saving _problems/test-save_functions-116.R Saving _problems/test-save_functions-119.R Plot saved at: /tmp/RtmpbLgTd2/working_dir/RtmpKQMgR1/gtregression-plot-2737158.png Forest plot saved at: /tmp/RtmpbLgTd2/working_dir/RtmpKQMgR1/gtregression-forest-2737158.pdf Forest plot saved at: /tmp/RtmpbLgTd2/working_dir/RtmpKQMgR1/gtregression-forest-2737158-png.png Forest plot saved at: /tmp/RtmpbLgTd2/working_dir/RtmpKQMgR1/gtregression-forest-temp-2737158.pdf Word document saved at: /tmp/RtmpbLgTd2/working_dir/RtmpKQMgR1/gtregression-report-2737158.docx Word document saved at: /tmp/RtmpbLgTd2/working_dir/RtmpKQMgR1/gtregression-warning-2737158.docx Running stratified multivariable regression by: ht > Stratum: ht = No > Stratum: ht = Yes Running stratified univariate regression by: ht > Stratum: ht = No > Stratum: ht = Yes Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Running stratified survival regression by: trt > Stratum: trt = Standard treatment > Stratum: trt = Test treatment Saving _problems/test-uni_reg-167.R descriptive_table(): dichotomous variables are displayed as single rows for smoke, ht. To display all levels, use `show_dichotomous = "all_levels"`. [ FAIL 3 | WARN 2 | SKIP 0 | PASS 2202 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-save_functions.R:116:3'): docx flextables are fitted without unsafe font shrinking ── Expected `sum(flextable::flextable_dim(fitted)$widths)` <= 6.5. Actual comparison: 9.9 > 6.5 Difference: 3.4 > 0 ── Failure ('test-save_functions.R:118:3'): docx flextables are fitted without unsafe font shrinking ── Expected `sum(flextable::flextable_dim(natural)$widths)` > `sum(flextable::flextable_dim(fitted)$widths)`. Actual comparison: 9.9 <= 9.9 Difference: 0.0 <= 0 ── Error ('test-uni_reg.R:167:3'): uni_reg supports poisson and negative binomial count models ── Error: All models failed. Check data and exposure specifications. Backtrace: ▆ 1. └─gtregression::uni_reg(...) at test-uni_reg.R:167:3 [ FAIL 3 | WARN 2 | SKIP 0 | PASS 2202 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [110s/112s] 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-noLD/gtregression.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 8:00.04, 384.82 + 18.41