Last updated on 2026-05-03 07:49:38 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 10.49 | 386.93 | 397.42 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 7.53 | 259.28 | 266.81 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 19.00 | 577.74 | 596.74 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 19.00 | 643.67 | 662.67 | OK | |
| r-devel-windows-x86_64 | 1.0.0 | 18.00 | 322.00 | 340.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.0 | 10.18 | 368.68 | 378.86 | OK | |
| r-release-linux-x86_64 | 1.0.0 | 9.70 | 364.39 | 374.09 | OK | |
| r-release-macos-arm64 | 1.0.0 | 3.00 | 77.00 | 80.00 | OK | |
| r-release-macos-x86_64 | 1.0.0 | 8.00 | 345.00 | 353.00 | OK | |
| r-release-windows-x86_64 | 1.0.0 | 13.00 | 315.00 | 328.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.0 | OK | ||||
| r-oldrel-macos-x86_64 | 1.0.0 | 6.00 | 339.00 | 345.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.0 | 18.00 | 471.00 | 489.00 | OK |
Version: 1.0.0
Check: tests
Result: ERROR
Running 'testthat.R' [203s]
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")
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Saving _problems/test-descriptive_table-122.R
Saving _problems/test-descriptive_table-123.R
# A tibble: 18 x 6
Variable Type `Missing (%)` Unique Levels Compatibility
<chr> <chr> <chr> <int> <chr> <chr>
1 pregnant numeric 0% 17 - compatible
2 glucose numeric 0.7% 135 - compatible
3 pressure numeric 4.6% 46 - compatible
4 triceps numeric 29.6% 50 - compatible
5 insulin numeric 48.7% 185 - compatible
6 mass numeric 1.4% 247 - compatible
7 pedigree numeric 0% 517 - compatible
8 age numeric 0% 52 - compatible
9 diabetes numeric 0% 2 - maybe
10 bmi factor 1.4% 3 Normal, Overweight, ~ compatible
11 age_cat factor 0% 3 Young, Middle-aged, ~ compatible
12 npreg_cat factor 0% 2 Low parity, High par~ compatible
13 glucose_cat factor 0.7% 2 Normal, High compatible
14 bp_cat factor 4.6% 2 Normal, High compatible
15 triceps_cat factor 29.6% 2 Normal, High compatible
16 insulin_cat factor 48.7% 3 Low, Normal, High compatible
17 dpf_cat factor 0% 3 Low Genetic Risk, Mo~ compatible
18 diabetes_cat factor 0% 2 Diabetes negative, D~ compatible
Interpretation notes:
- compatible: ready to use in regression
- maybe: require transformation to factor or check no of levels
- incompatible: not usable as-is (e.g., all NA, <2 levels)
------------------------------------------------------------
Crude Estimate: 2.961
Adjusted Estimate: 2.496
% Change from Crude: 15.69%
------------------------------------------------------------
Confounding: Yes
------------------------------------------------------------
Notes:
* Confounding is suggested if percent change >=10%.
* This method does not assess effect modification.
* Use DAGs or domain knowledge to support confounder identification.
# A tibble: 4 x 5
covariate crude_est adjusted_est pct_change is_confounder
<chr> <dbl> <dbl> <dbl> <lgl>
1 bmi 2.96 2.50 15.7 TRUE
2 age_cat 2.96 2.62 11.5 TRUE
3 npreg_cat 2.96 2.78 6.07 FALSE
4 bp_cat 2.96 NA NA NA
Notes:
* Confounding is suggested if percent change >=10%.
* This method does not assess effect modification.
* Use DAGs or domain knowledge to support confounder
identification.
------------------------------------------------------------
Crude Estimate: 2.961
Adjusted Estimate: NA
% Change from Crude: NA%
------------------------------------------------------------
Confounding: NA
------------------------------------------------------------
Notes:
* Confounding is suggested if percent change >=10%.
* This method does not assess effect modification.
* Use DAGs or domain knowledge to support confounder identification.
# A tibble: 4 x 5
covariate crude_est adjusted_est pct_change is_confounder
<chr> <dbl> <dbl> <dbl> <lgl>
1 bmi 2.96 NA NA NA
2 age_cat 2.96 NA NA NA
3 npreg_cat 2.96 NA NA NA
4 bp_cat 2.96 NA NA NA
Notes:
* Confounding is suggested if percent change >=10%.
* This method does not assess effect modification.
* Use DAGs or domain knowledge to support confounder
identification.
# A tibble: 3 x 5
covariate crude_est adjusted_est pct_change is_confounder
<chr> <dbl> <dbl> <dbl> <lgl>
1 Eth 1.18 1.24 4.98 FALSE
2 Age 1.18 1.01 14.5 TRUE
3 Lrn 1.18 1.21 2.37 FALSE
Notes:
* Confounding is suggested if percent change >=10%.
* This method does not assess effect modification.
* Use DAGs or domain knowledge to support confounder
identification.
---------------------------------------------------
Interaction Term Assessment usingLikelihood Ratio Test
Model without interaction:
diabetes ~ age_cat + glucose_cat
Model with interaction:
diabetes ~ age_cat + glucose_cat + age_cat:glucose_cat
-----------------------------------------------------
P-value:0.1741
Interaction is not statistically significant.
Simpler model may be preferred.
----------------------------------------------------
---------------------------------------------------
Interaction Term Assessment usingLikelihood Ratio Test
Model without interaction:
diabetes ~ age_cat + glucose_cat
Model with interaction:
diabetes ~ age_cat + glucose_cat + age_cat:glucose_cat
-----------------------------------------------------
P-value:0.0100
Interaction is statistically significant. Consider including it.
----------------------------------------------------
The number rows in the tables to be merged do not match, which may result in rows appearing out of order.
i See `tbl_merge()` (`?gtsummary::tbl_merge()`) help file for details. Use `quiet=TRUE` to silence message.
The number rows in the tables to be merged do not match, which may result in rows appearing out of order.
i See `tbl_merge()` (`?gtsummary::tbl_merge()`) help file for details. Use `quiet=TRUE` to silence message.
robpoisson: Implausible predicted probability >0.99999 occurred: 1.20967417078353
robpoisson: Implausible predicted probability >0.99999 occurred: 1.27352337518946
Table saved at: D:\temp\2026_04_30_01_50_01_32376\RtmpwN9SMb\regression_results.docx
`height` was translated to `width`.
Plot saved at: D:\temp\2026_04_30_01_50_01_32376\RtmpwN9SMb\plot_png.png
`height` was translated to `width`.
Plot saved at: D:\temp\2026_04_30_01_50_01_32376\RtmpwN9SMb\plot_pdf.pdf
`height` was translated to `width`.
Plot saved at: D:\temp\2026_04_30_01_50_01_32376\RtmpwN9SMb\plot_jpg.jpg
`height` was translated to `width`.
Word document saved at: D:\temp\2026_04_30_01_50_01_32376\RtmpwN9SMb\final_report.docx
If tables or plots extend beyond the page, consider switching to landscape layout in Word (Layout > Orientation > Landscape).
Attaching package: 'MASS'
The following object is masked from 'package:gtsummary':
select
The following object is masked from 'package:dplyr':
select
Running stratified multivariable regression by: glucose_cat
> Stratum: glucose_cat = High
> Stratum: glucose_cat = Normal
Running stratified multivariable regression by: glucose_cat
> Stratum: glucose_cat = Normal
> Stratum: glucose_cat = High
Running stratified multivariable regression by: glucose_cat
> Stratum: glucose_cat = High
> Stratum: glucose_cat = Normal
Running stratified multivariable regression by: glucose_cat
> Stratum: glucose_cat = High
x There was an error calling `tidy_fun()`. Most likely, this is because the
function supplied in `tidy_fun=` was misspelled, does not exist, is not
compatible with your object, or was missing necessary arguments (e.g. `conf.level=` or `conf.int=`). See error message below.
> Stratum: glucose_cat = Normal
Running stratified univariate regression by: glucose_cat
> Stratum: glucose_cat = High
> Stratum: glucose_cat = Normal
Running stratified univariate regression by: glucose_cat
> Stratum: glucose_cat = Normal
> Stratum: glucose_cat = High
Running stratified univariate regression by: glucose_cat
> Stratum: glucose_cat = High
> Stratum: glucose_cat = Normal
Running stratified univariate regression by: age_cat
> Stratum: age_cat = Older
> Stratum: age_cat = Middle-aged
> Stratum: age_cat = Young
Running stratified univariate regression by: glucose_cat
Call: glm(formula = formula, family = binomial("logit"), data = data)
Coefficients:
(Intercept) glucose
-6.09552 0.04242
Degrees of Freedom: 391 Total (i.e. Null); 390 Residual
Null Deviance: 498.1
Residual Deviance: 386.7 AIC: 390.7
[ FAIL 2 | WARN 21 | SKIP 2 | PASS 240 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test-dissect.R:1:1', 'test-multi_reg.R:62:7'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-descriptive_table.R:113:3'): descriptive_table works with row percentages ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-descriptive_table.R:113:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─gtregression::descriptive_table(...)
8. │ ├─gtsummary::add_overall(...)
9. │ └─gtsummary:::add_overall.tbl_summary(...)
10. │ └─gtsummary:::add_overall_generic(...)
11. │ ├─base::do.call(calling_fun, args_overall)
12. │ └─gtsummary::tbl_summary(...)
13. │ ├─cards::replace_null_statistic(...)
14. │ │ └─cards:::check_class(x, "card")
15. │ ├─... %>% structure(., class = c("card", class(.)))
16. │ ├─cards::bind_ard(...)
17. │ │ └─dplyr::bind_rows(...)
18. │ │ └─rlang::list2(...)
19. │ ├─cards::ard_tabulate(...)
20. │ └─cards:::ard_tabulate.data.frame(...)
21. │ └─cards:::.calculate_tabulation_statistics(...)
22. │ └─cards:::.process_denominator(...)
23. │ ├─stats::setNames(...)
24. │ └─base::lapply(...)
25. │ └─cards (local) FUN(X[[i]], ...)
26. │ ├─dplyr::summarise(...)
27. │ ├─tidyr::drop_na(...)
28. │ └─cards:::.table_as_df(...)
29. │ ├─dplyr::as_tibble(...)
30. │ └─tibble:::as_tibble.table(...)
31. │ ├─base::as.data.frame(x, stringsAsFactors = FALSE)
32. │ └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
33. │ ├─base::eval(ex)
34. │ │ └─base::eval(ex)
35. │ └─base::data.frame(...)
36. │ ├─base::as.data.frame(x[[i]], optional = TRUE)
37. │ └─base::as.data.frame.integer(x[[i]], optional = TRUE)
38. └─base::structure(., class = c("card", class(.)))
── Failure ('test-descriptive_table.R:123:3'): descriptive_table works with row percentages ──
Expected `tbl` to be an S3 object.
Actual OO type: none.
[ FAIL 2 | WARN 21 | SKIP 2 | PASS 240 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64