Last updated on 2026-08-04 02:50:43 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 10.06 | 155.26 | 165.32 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 7.80 | 112.39 | 120.19 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 18.00 | 235.50 | 253.50 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 112.28 | ERROR | |||
| r-devel-windows-x86_64 | 1.0.0 | 13.00 | 144.00 | 157.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.0 | 9.38 | 142.83 | 152.21 | ERROR | |
| r-release-linux-x86_64 | 1.0.0 | 9.88 | 141.62 | 151.50 | ERROR | |
| 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 | 146.00 | 159.00 | ERROR | |
| 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 | 198.00 | 216.00 | ERROR |
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in ‘gtregression-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: check_collinearity
> ### Title: Check Collinearity Using VIF for Fitted Models
> ### Aliases: check_collinearity
>
> ### ** Examples
>
> if (requireNamespace("gtregression", quietly = TRUE) &&
+ requireNamespace("mlbench", quietly = TRUE) &&
+ getRversion() >= "4.1.0") {
+ data(PimaIndiansDiabetes2, package = "mlbench")
+ pima <- PimaIndiansDiabetes2 |> dplyr::filter(!is.na(diabetes))
+ pima$diabetes <- ifelse(pima$diabetes == "pos", 1, 0)
+ fit <- multi_reg(pima,
+ outcome = "diabetes",
+ exposures = c("age", "mass", "glucose"),
+ approach = "logit"
+ )
+ check_collinearity(fit)
+ }
Warning in data(PimaIndiansDiabetes2, package = "mlbench") :
data set ‘PimaIndiansDiabetes2’ not found
Error: object 'PimaIndiansDiabetes2' not found
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [62s/76s]
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-check_collinearity-9.R
Saving _problems/test-check_collinearity-29.R
Saving _problems/test-check_convergence-19.R
Saving _problems/test-check_convergence-113.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)
Saving _problems/test-fit_multi_model-23.R
Saving _problems/test-fit_uni_model-17.R
Saving _problems/test-fit_uni_model-59.R
Saving _problems/test-identify_confounder-27.R
Saving _problems/test-interaction_models-32.R
Saving _problems/test-interaction_models-64.R
Saving _problems/test-interaction_models-96.R
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.
Saving _problems/test-multi_reg-50.R
Saving _problems/test-plot_reg-43.R
Saving _problems/test-plot_reg_combine-56.R
Table saved at: /home/hornik/tmp/scratch/Rtmp4HawDJ/regression_results.docx
`height` was translated to `width`.
Plot saved at: /home/hornik/tmp/scratch/Rtmp4HawDJ/plot_png.png
`height` was translated to `width`.
Plot saved at: /home/hornik/tmp/scratch/Rtmp4HawDJ/plot_pdf.pdf
`height` was translated to `width`.
Plot saved at: /home/hornik/tmp/scratch/Rtmp4HawDJ/plot_jpg.jpg
`height` was translated to `width`.
Word document saved at: /home/hornik/tmp/scratch/Rtmp4HawDJ/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
Saving _problems/test-select_models-25.R
Saving _problems/test-stratified_multi_reg-32.R
Saving _problems/test-stratified_multi_reg-75.R
Saving _problems/test-stratified_multi_reg-120.R
Saving _problems/test-stratified_multi_reg-167.R
Saving _problems/test-stratified_uni_reg-21.R
Saving _problems/test-stratified_uni_reg-46.R
Saving _problems/test-stratified_uni_reg-71.R
Saving _problems/test-stratified_uni_reg-106.R
Saving _problems/test-stratified_uni_reg-142.R
Saving _problems/test-stratified_uni_reg-167.R
Saving _problems/test-uni_reg-10.R
Saving _problems/test-uni_reg-70.R
[ FAIL 27 | WARN 29 | SKIP 1 | PASS 92 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-dissect.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-check_collinearity.R:7:3'): check_collinearity works correctly for multivariable models ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-check_collinearity.R:7:3
2. └─dplyr::filter(PimaIndiansDiabetes2, !is.na(diabetes))
── Error ('test-check_collinearity.R:27:3'): check_collinearity throws error for univariate models ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-check_collinearity.R:27:3
2. └─dplyr::filter(PimaIndiansDiabetes2, !is.na(diabetes))
── Error ('test-check_convergence.R:4:3'): check_convergence runs correctly for valid approaches ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-check_convergence.R:4:3
── Error ('test-check_convergence.R:98:3'): check_convergence handles model fitting failure ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-check_convergence.R:98:3
── Error ('test-fit_multi_model.R:7:3'): .fit_multi_model returns correct model class for each approach ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-fit_multi_model.R:7:3
2. └─dplyr::mutate(...)
── Error ('test-fit_uni_model.R:7:3'): .fit_uni_model returns correct model class (PimaIndiansDiabetes2) ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-fit_uni_model.R:7:3
2. └─dplyr::mutate(...)
── Error ('test-fit_uni_model.R:55:3'): .fit_uni_model handles model fitting failure gracefully ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-fit_uni_model.R:55:3
── Error ('test-identify_confounder.R:6:3'): identify_confounder works across approaches using
change-in-estimate method ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-identify_confounder.R:6:3
── Error ('test-interaction_models.R:6:3'): interaction_models returns a list with expected names ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:6:3
2. └─dplyr::mutate(...)
── Error ('test-interaction_models.R:52:3'): interaction_models handles robpoisson approach ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:52:3
2. └─dplyr::mutate(...)
── Error ('test-interaction_models.R:84:3'): interaction_models errors with invalid approach ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:84:3
2. └─dplyr::mutate(...)
── Error ('test-multi_reg.R:11:3'): multi_reg computes estimates correctly across approaches ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-multi_reg.R:11:3
── Error ('test-plot_reg.R:9:3'): plot_reg works with default settings and correct X-axis labels ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-plot_reg.R:9:3
2. └─dplyr::mutate(...)
── Error ('test-plot_reg_combine.R:9:3'): plot_reg_combine works with various options ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-plot_reg_combine.R:9:3
── Error ('test-select_models.R:8:3'): select_models works for valid approaches and directions ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-select_models.R:8:3
── Error ('test-stratified_multi_reg.R:9:3'): stratified_multi_reg returns a gtsummary tbl_merge object ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:9:3
── Error ('test-stratified_multi_reg.R:61:3'): stratified_multi_reg excludes NA values in stratifier ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:61:3
── Error ('test-stratified_multi_reg.R:109:3'): stratified_multi_reg runs with robpoisson and produces estimates ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:109:3
── Error ('test-stratified_multi_reg.R:153:3'): stratified_multi_reg works with negbin ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-stratified_multi_reg.R:153:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:4:3'): stratified_uni_reg returns a gtsummary tbl_merge object with logit ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-stratified_uni_reg.R:4:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:40:3'): stratified_uni_reg excludes NA values in stratifier ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:40:3
── Error ('test-stratified_uni_reg.R:67:3'): stratified_uni_reg errors for invalid inputs ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:67:3
── Error ('test-stratified_uni_reg.R:100:3'): stratified_uni_reg works with robpoisson ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:100:3
── Error ('test-stratified_uni_reg.R:126:3'): stratified_uni_reg works with negbin ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-stratified_uni_reg.R:126:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:163:3'): stratified_uni_reg errors when no valid strata exist ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:163:3
── Error ('test-uni_reg.R:6:3'): uni_reg returns a gtsummary object and works with binary data ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─tidyr::drop_na(...) at test-uni_reg.R:6:3
2. └─dplyr::mutate(...)
── Error ('test-uni_reg.R:70:3'): uni_reg$ accessors return correct components ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─tidyr::drop_na(PimaIndiansDiabetes2) at test-uni_reg.R:70:3
[ FAIL 27 | WARN 29 | SKIP 1 | PASS 92 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [44s/58s]
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-check_collinearity-9.R
Saving _problems/test-check_collinearity-29.R
Saving _problems/test-check_convergence-19.R
Saving _problems/test-check_convergence-113.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)
Saving _problems/test-fit_multi_model-23.R
Saving _problems/test-fit_uni_model-17.R
Saving _problems/test-fit_uni_model-59.R
Saving _problems/test-identify_confounder-27.R
Saving _problems/test-interaction_models-32.R
Saving _problems/test-interaction_models-64.R
Saving _problems/test-interaction_models-96.R
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.
Saving _problems/test-multi_reg-50.R
Saving _problems/test-plot_reg-43.R
Saving _problems/test-plot_reg_combine-56.R
Table saved at: /home/hornik/tmp/scratch/RtmpcvO4Fb/regression_results.docx
`height` was translated to `width`.
Plot saved at: /home/hornik/tmp/scratch/RtmpcvO4Fb/plot_png.png
`height` was translated to `width`.
Plot saved at: /home/hornik/tmp/scratch/RtmpcvO4Fb/plot_pdf.pdf
`height` was translated to `width`.
Plot saved at: /home/hornik/tmp/scratch/RtmpcvO4Fb/plot_jpg.jpg
`height` was translated to `width`.
Word document saved at: /home/hornik/tmp/scratch/RtmpcvO4Fb/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
Saving _problems/test-select_models-25.R
Saving _problems/test-stratified_multi_reg-32.R
Saving _problems/test-stratified_multi_reg-75.R
Saving _problems/test-stratified_multi_reg-120.R
Saving _problems/test-stratified_multi_reg-167.R
Saving _problems/test-stratified_uni_reg-21.R
Saving _problems/test-stratified_uni_reg-46.R
Saving _problems/test-stratified_uni_reg-71.R
Saving _problems/test-stratified_uni_reg-106.R
Saving _problems/test-stratified_uni_reg-142.R
Saving _problems/test-stratified_uni_reg-167.R
Saving _problems/test-uni_reg-10.R
Saving _problems/test-uni_reg-70.R
[ FAIL 27 | WARN 29 | SKIP 1 | PASS 92 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-dissect.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-check_collinearity.R:7:3'): check_collinearity works correctly for multivariable models ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-check_collinearity.R:7:3
2. └─dplyr::filter(PimaIndiansDiabetes2, !is.na(diabetes))
── Error ('test-check_collinearity.R:27:3'): check_collinearity throws error for univariate models ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-check_collinearity.R:27:3
2. └─dplyr::filter(PimaIndiansDiabetes2, !is.na(diabetes))
── Error ('test-check_convergence.R:4:3'): check_convergence runs correctly for valid approaches ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-check_convergence.R:4:3
── Error ('test-check_convergence.R:98:3'): check_convergence handles model fitting failure ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-check_convergence.R:98:3
── Error ('test-fit_multi_model.R:7:3'): .fit_multi_model returns correct model class for each approach ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-fit_multi_model.R:7:3
2. └─dplyr::mutate(...)
── Error ('test-fit_uni_model.R:7:3'): .fit_uni_model returns correct model class (PimaIndiansDiabetes2) ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-fit_uni_model.R:7:3
2. └─dplyr::mutate(...)
── Error ('test-fit_uni_model.R:55:3'): .fit_uni_model handles model fitting failure gracefully ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-fit_uni_model.R:55:3
── Error ('test-identify_confounder.R:6:3'): identify_confounder works across approaches using
change-in-estimate method ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-identify_confounder.R:6:3
── Error ('test-interaction_models.R:6:3'): interaction_models returns a list with expected names ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:6:3
2. └─dplyr::mutate(...)
── Error ('test-interaction_models.R:52:3'): interaction_models handles robpoisson approach ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:52:3
2. └─dplyr::mutate(...)
── Error ('test-interaction_models.R:84:3'): interaction_models errors with invalid approach ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:84:3
2. └─dplyr::mutate(...)
── Error ('test-multi_reg.R:11:3'): multi_reg computes estimates correctly across approaches ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-multi_reg.R:11:3
── Error ('test-plot_reg.R:9:3'): plot_reg works with default settings and correct X-axis labels ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-plot_reg.R:9:3
2. └─dplyr::mutate(...)
── Error ('test-plot_reg_combine.R:9:3'): plot_reg_combine works with various options ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-plot_reg_combine.R:9:3
── Error ('test-select_models.R:8:3'): select_models works for valid approaches and directions ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-select_models.R:8:3
── Error ('test-stratified_multi_reg.R:9:3'): stratified_multi_reg returns a gtsummary tbl_merge object ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:9:3
── Error ('test-stratified_multi_reg.R:61:3'): stratified_multi_reg excludes NA values in stratifier ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:61:3
── Error ('test-stratified_multi_reg.R:109:3'): stratified_multi_reg runs with robpoisson and produces estimates ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:109:3
── Error ('test-stratified_multi_reg.R:153:3'): stratified_multi_reg works with negbin ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-stratified_multi_reg.R:153:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:4:3'): stratified_uni_reg returns a gtsummary tbl_merge object with logit ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-stratified_uni_reg.R:4:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:40:3'): stratified_uni_reg excludes NA values in stratifier ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:40:3
── Error ('test-stratified_uni_reg.R:67:3'): stratified_uni_reg errors for invalid inputs ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:67:3
── Error ('test-stratified_uni_reg.R:100:3'): stratified_uni_reg works with robpoisson ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:100:3
── Error ('test-stratified_uni_reg.R:126:3'): stratified_uni_reg works with negbin ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-stratified_uni_reg.R:126:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:163:3'): stratified_uni_reg errors when no valid strata exist ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:163:3
── Error ('test-uni_reg.R:6:3'): uni_reg returns a gtsummary object and works with binary data ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─tidyr::drop_na(...) at test-uni_reg.R:6:3
2. └─dplyr::mutate(...)
── Error ('test-uni_reg.R:70:3'): uni_reg$ accessors return correct components ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─tidyr::drop_na(PimaIndiansDiabetes2) at test-uni_reg.R:70:3
[ FAIL 27 | WARN 29 | SKIP 1 | PASS 92 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.0
Check: for new files in some other directories
Result: NOTE
Found the following files/directories:
‘~/tmp/scratch/Rtmp049YRX’ ‘~/tmp/scratch/Rtmp0MULzL’
‘~/tmp/scratch/Rtmp0UKM26’ ‘~/tmp/scratch/Rtmp15sC26’
‘~/tmp/scratch/Rtmp1ML9CZ’ ‘~/tmp/scratch/Rtmp1NOzMo’
‘~/tmp/scratch/Rtmp2sLW6d’ ‘~/tmp/scratch/Rtmp35PNIK’
‘~/tmp/scratch/Rtmp3ERtdr’ ‘~/tmp/scratch/Rtmp3FN2kr’
‘~/tmp/scratch/Rtmp3NT3Wk’ ‘~/tmp/scratch/Rtmp3cS34r’
‘~/tmp/scratch/Rtmp4MRFqn’ ‘~/tmp/scratch/Rtmp5cfczi’
‘~/tmp/scratch/Rtmp5gGBgV’ ‘~/tmp/scratch/Rtmp5n7VpS’
‘~/tmp/scratch/Rtmp6Q6h7w’ ‘~/tmp/scratch/Rtmp6dhiLK’
‘~/tmp/scratch/Rtmp6r0DV0’ ‘~/tmp/scratch/Rtmp6sqcuN’
‘~/tmp/scratch/Rtmp8BfNXD’ ‘~/tmp/scratch/Rtmp8Uze5H’
‘~/tmp/scratch/Rtmp95Glwl’ ‘~/tmp/scratch/Rtmp97l0zd’
‘~/tmp/scratch/Rtmp9AU52G’ ‘~/tmp/scratch/Rtmp9bRB4B’
‘~/tmp/scratch/Rtmp9nOeJo’ ‘~/tmp/scratch/RtmpA1kIeW’
‘~/tmp/scratch/RtmpAdBGFd’ ‘~/tmp/scratch/RtmpBHMRD1’
‘~/tmp/scratch/RtmpBSfDRP’ ‘~/tmp/scratch/RtmpBT6xrp’
‘~/tmp/scratch/RtmpBiuqfO’ ‘~/tmp/scratch/RtmpBk6EKH’
‘~/tmp/scratch/RtmpBwYgs1’ ‘~/tmp/scratch/RtmpCFHxJG’
‘~/tmp/scratch/RtmpCKoWAH’ ‘~/tmp/scratch/RtmpCmoeCH’
‘~/tmp/scratch/RtmpCvNSXr’ ‘~/tmp/scratch/RtmpDlJ2uS’
‘~/tmp/scratch/RtmpDluCRi’ ‘~/tmp/scratch/RtmpEAFsq4’
‘~/tmp/scratch/RtmpELroEw’ ‘~/tmp/scratch/RtmpEttzbS’
‘~/tmp/scratch/RtmpF0nsjV’ ‘~/tmp/scratch/RtmpF63wNZ’
‘~/tmp/scratch/RtmpFcUvOP’ ‘~/tmp/scratch/RtmpHGBJnG’
‘~/tmp/scratch/RtmpIL9m7u’ ‘~/tmp/scratch/RtmpIQDLM5’
‘~/tmp/scratch/RtmpJCuoo6’ ‘~/tmp/scratch/RtmpJMjYSU’
‘~/tmp/scratch/RtmpJeG9M5’ ‘~/tmp/scratch/RtmpKGBoHc’
‘~/tmp/scratch/RtmpKeoTv1’ ‘~/tmp/scratch/RtmpKsWd99’
‘~/tmp/scratch/RtmpKypHDa’ ‘~/tmp/scratch/RtmpL8e3Ab’
‘~/tmp/scratch/RtmpLdkovJ’ ‘~/tmp/scratch/RtmpMQ2FLg’
‘~/tmp/scratch/RtmpMZ8eLm’ ‘~/tmp/scratch/RtmpMyY8AS’
‘~/tmp/scratch/RtmpNEcnh6’ ‘~/tmp/scratch/RtmpOA8pCs’
‘~/tmp/scratch/RtmpP29bPO’ ‘~/tmp/scratch/RtmpPJ0VWw’
‘~/tmp/scratch/RtmpPOv7Cl’ ‘~/tmp/scratch/RtmpPo1E5H’
‘~/tmp/scratch/RtmpQBm91S’ ‘~/tmp/scratch/RtmpQOi8I5’
‘~/tmp/scratch/RtmpQodGVx’ ‘~/tmp/scratch/RtmpSwTmpT’
‘~/tmp/scratch/RtmpT8HEci’ ‘~/tmp/scratch/RtmpTdj0QB’
‘~/tmp/scratch/RtmpTj6AOf’ ‘~/tmp/scratch/RtmpUJg0V3’
‘~/tmp/scratch/RtmpUYPj9Q’ ‘~/tmp/scratch/RtmpUiULWo’
‘~/tmp/scratch/RtmpUr1MWK’ ‘~/tmp/scratch/RtmpVcmI58’
‘~/tmp/scratch/RtmpX0e8kN’ ‘~/tmp/scratch/RtmpXPQ6zR’
‘~/tmp/scratch/RtmpY96afh’ ‘~/tmp/scratch/RtmpYVOd7v’
‘~/tmp/scratch/RtmpZIMnRo’ ‘~/tmp/scratch/RtmpZJdInv’
‘~/tmp/scratch/RtmpaYZllS’ ‘~/tmp/scratch/RtmpaqyOeD’
‘~/tmp/scratch/RtmpbykHDC’ ‘~/tmp/scratch/RtmpchDNsk’
‘~/tmp/scratch/Rtmpci0flc’ ‘~/tmp/scratch/RtmpcpAcx6’
‘~/tmp/scratch/Rtmpd4JH9o’ ‘~/tmp/scratch/Rtmpd4Qcw9’
‘~/tmp/scratch/RtmpdUQOrW’ ‘~/tmp/scratch/RtmpecXUZD’
‘~/tmp/scratch/RtmpfRia1U’ ‘~/tmp/scratch/Rtmpg24006’
‘~/tmp/scratch/RtmpgHJmoV’ ‘~/tmp/scratch/RtmpgvXnQP’
‘~/tmp/scratch/Rtmpgw6i5v’ ‘~/tmp/scratch/Rtmph15RMR’
‘~/tmp/scratch/RtmphOC8HG’ ‘~/tmp/scratch/Rtmphield9’
‘~/tmp/scratch/RtmphkMrZg’ ‘~/tmp/scratch/RtmphxHnGT’
‘~/tmp/scratch/Rtmpi7gDTH’ ‘~/tmp/scratch/Rtmpia6BRE’
‘~/tmp/scratch/RtmpjD9AcK’ ‘~/tmp/scratch/RtmpjZQv60’
‘~/tmp/scratch/Rtmpjh8BsI’ ‘~/tmp/scratch/Rtmpk2nD80’
‘~/tmp/scratch/RtmplJf4T1’ ‘~/tmp/scratch/Rtmple6MoU’
‘~/tmp/scratch/Rtmpm1RAzv’ ‘~/tmp/scratch/RtmpmQTUeD’
‘~/tmp/scratch/RtmpmodVZa’ ‘~/tmp/scratch/Rtmpmt3EAq’
‘~/tmp/scratch/Rtmpn35knB’ ‘~/tmp/scratch/RtmpnLymIx’
‘~/tmp/scratch/Rtmpnq0NBK’ ‘~/tmp/scratch/RtmpoLfS9P’
‘~/tmp/scratch/Rtmpp9K4dV’ ‘~/tmp/scratch/RtmppkBVKR’
‘~/tmp/scratch/RtmppuZXhe’ ‘~/tmp/scratch/RtmpqhTkFe’
‘~/tmp/scratch/RtmpqlgCmR’ ‘~/tmp/scratch/RtmpqvSRra’
‘~/tmp/scratch/RtmpqxTZ6O’ ‘~/tmp/scratch/Rtmpqzy6nQ’
‘~/tmp/scratch/Rtmpr0FK14’ ‘~/tmp/scratch/RtmprGtduD’
‘~/tmp/scratch/Rtmps8mjSQ’ ‘~/tmp/scratch/RtmpsHVso2’
‘~/tmp/scratch/RtmpsdVxTU’ ‘~/tmp/scratch/Rtmpsg9M5N’
‘~/tmp/scratch/RtmpshdHtR’ ‘~/tmp/scratch/Rtmpsn2Bwg’
‘~/tmp/scratch/RtmptBPqEx’ ‘~/tmp/scratch/RtmptKKO7a’
‘~/tmp/scratch/RtmpuD6weL’ ‘~/tmp/scratch/Rtmpuut0t3’
‘~/tmp/scratch/RtmpvDpkI5’ ‘~/tmp/scratch/RtmpvZE6Um’
‘~/tmp/scratch/Rtmpvolgrw’ ‘~/tmp/scratch/Rtmpw5DSQw’
‘~/tmp/scratch/RtmpwJWkNn’ ‘~/tmp/scratch/RtmpwOdg93’
‘~/tmp/scratch/RtmpwPvmlK’ ‘~/tmp/scratch/RtmpwpFuJ8’
‘~/tmp/scratch/RtmpxYqnto’ ‘~/tmp/scratch/RtmpyLxgD0’
‘~/tmp/scratch/RtmpyXsxIU’ ‘~/tmp/scratch/RtmpycvqFc’
‘~/tmp/scratch/Rtmpyu3t1z’ ‘~/tmp/scratch/RtmpzqHkpM’
‘~/tmp/scratch/xvfb-run.29mIo9’ ‘~/tmp/scratch/xvfb-run.5llI3b’
‘~/tmp/scratch/xvfb-run.7glSzJ’ ‘~/tmp/scratch/xvfb-run.9FeXwa’
‘~/tmp/scratch/xvfb-run.CTMcSL’ ‘~/tmp/scratch/xvfb-run.Ce0BLt’
‘~/tmp/scratch/xvfb-run.Cjckiq’ ‘~/tmp/scratch/xvfb-run.ExjfHN’
‘~/tmp/scratch/xvfb-run.EyKjpo’ ‘~/tmp/scratch/xvfb-run.F9fl7q’
‘~/tmp/scratch/xvfb-run.GIt79f’ ‘~/tmp/scratch/xvfb-run.HqjH1M’
‘~/tmp/scratch/xvfb-run.ItIAF3’ ‘~/tmp/scratch/xvfb-run.IyXWMK’
‘~/tmp/scratch/xvfb-run.JP5Fxz’ ‘~/tmp/scratch/xvfb-run.Lyn2Fk’
‘~/tmp/scratch/xvfb-run.Lys0rd’ ‘~/tmp/scratch/xvfb-run.MLmkKr’
‘~/tmp/scratch/xvfb-run.PN84ti’ ‘~/tmp/scratch/xvfb-run.PpVwSU’
‘~/tmp/scratch/xvfb-run.Qt8y0E’ ‘~/tmp/scratch/xvfb-run.SSeNxP’
‘~/tmp/scratch/xvfb-run.SmpTmI’ ‘~/tmp/scratch/xvfb-run.U0kxcT’
‘~/tmp/scratch/xvfb-run.V0nOR9’ ‘~/tmp/scratch/xvfb-run.VOBMLQ’
‘~/tmp/scratch/xvfb-run.WWdVof’ ‘~/tmp/scratch/xvfb-run.XHx9wh’
‘~/tmp/scratch/xvfb-run.YciqPv’ ‘~/tmp/scratch/xvfb-run.Z7N4Dc’
‘~/tmp/scratch/xvfb-run.ZRCHgE’ ‘~/tmp/scratch/xvfb-run.a84JOn’
‘~/tmp/scratch/xvfb-run.aDvJwX’ ‘~/tmp/scratch/xvfb-run.aFGAXo’
‘~/tmp/scratch/xvfb-run.aGciHH’ ‘~/tmp/scratch/xvfb-run.anj5El’
‘~/tmp/scratch/xvfb-run.awP46E’ ‘~/tmp/scratch/xvfb-run.c3fNgP’
‘~/tmp/scratch/xvfb-run.cccslh’ ‘~/tmp/scratch/xvfb-run.dSWC14’
‘~/tmp/scratch/xvfb-run.ebDatd’ ‘~/tmp/scratch/xvfb-run.fmyu4w’
‘~/tmp/scratch/xvfb-run.nMm27c’ ‘~/tmp/scratch/xvfb-run.nXquVr’
‘~/tmp/scratch/xvfb-run.ni09KN’ ‘~/tmp/scratch/xvfb-run.q0Es5x’
‘~/tmp/scratch/xvfb-run.qu54tI’ ‘~/tmp/scratch/xvfb-run.rQetLO’
‘~/tmp/scratch/xvfb-run.tMnM9i’ ‘~/tmp/scratch/xvfb-run.tlTPBV’
‘~/tmp/scratch/xvfb-run.u3eEqI’ ‘~/tmp/scratch/xvfb-run.uS7WWs’
‘~/tmp/scratch/xvfb-run.vHLmSs’ ‘~/tmp/scratch/xvfb-run.vN9KOn’
‘~/tmp/scratch/xvfb-run.vRiA61’ ‘~/tmp/scratch/xvfb-run.w5GHyX’
‘~/tmp/scratch/xvfb-run.wt9huF’ ‘~/tmp/scratch/xvfb-run.x3UKde’
‘~/tmp/scratch/xvfb-run.xLrGtC’ ‘~/tmp/scratch/xvfb-run.xe3Fdf’
‘~/tmp/scratch/xvfb-run.yDj6tb’ ‘~/tmp/scratch/xvfb-run.yQJdnX’
‘~/tmp/scratch/xvfb-run.yhJtr1’ ‘~/tmp/scratch/xvfb-run.zBcgCc’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in ‘gtregression-Ex.R’ failed
The error most likely occurred in:
> ### Name: check_collinearity
> ### Title: Check Collinearity Using VIF for Fitted Models
> ### Aliases: check_collinearity
>
> ### ** Examples
>
> if (requireNamespace("gtregression", quietly = TRUE) &&
+ requireNamespace("mlbench", quietly = TRUE) &&
+ getRversion() >= "4.1.0") {
+ data(PimaIndiansDiabetes2, package = "mlbench")
+ pima <- PimaIndiansDiabetes2 |> dplyr::filter(!is.na(diabetes))
+ pima$diabetes <- ifelse(pima$diabetes == "pos", 1, 0)
+ fit <- multi_reg(pima,
+ outcome = "diabetes",
+ exposures = c("age", "mass", "glucose"),
+ approach = "logit"
+ )
+ check_collinearity(fit)
+ }
Warning in data(PimaIndiansDiabetes2, package = "mlbench") :
data set ‘PimaIndiansDiabetes2’ not found
Error: object 'PimaIndiansDiabetes2' not found
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [100s/136s]
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-check_collinearity-9.R
Saving _problems/test-check_collinearity-29.R
Saving _problems/test-check_convergence-19.R
Saving _problems/test-check_convergence-113.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)
Saving _problems/test-fit_multi_model-23.R
Saving _problems/test-fit_uni_model-17.R
Saving _problems/test-fit_uni_model-59.R
Saving _problems/test-identify_confounder-27.R
Saving _problems/test-interaction_models-32.R
Saving _problems/test-interaction_models-64.R
Saving _problems/test-interaction_models-96.R
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.
Saving _problems/test-multi_reg-50.R
Saving _problems/test-plot_reg-43.R
Saving _problems/test-plot_reg_combine-56.R
Table saved at: /tmp/RtmpOZhzjs/working_dir/RtmprX43pI/regression_results.docx
`height` was translated to `width`.
Plot saved at: /tmp/RtmpOZhzjs/working_dir/RtmprX43pI/plot_png.png
`height` was translated to `width`.
Plot saved at: /tmp/RtmpOZhzjs/working_dir/RtmprX43pI/plot_pdf.pdf
`height` was translated to `width`.
Plot saved at: /tmp/RtmpOZhzjs/working_dir/RtmprX43pI/plot_jpg.jpg
`height` was translated to `width`.
Word document saved at: /tmp/RtmpOZhzjs/working_dir/RtmprX43pI/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
Saving _problems/test-select_models-25.R
Saving _problems/test-stratified_multi_reg-32.R
Saving _problems/test-stratified_multi_reg-75.R
Saving _problems/test-stratified_multi_reg-120.R
Saving _problems/test-stratified_multi_reg-167.R
Saving _problems/test-stratified_uni_reg-21.R
Saving _problems/test-stratified_uni_reg-46.R
Saving _problems/test-stratified_uni_reg-71.R
Saving _problems/test-stratified_uni_reg-106.R
Saving _problems/test-stratified_uni_reg-142.R
Saving _problems/test-stratified_uni_reg-167.R
Saving _problems/test-uni_reg-10.R
Saving _problems/test-uni_reg-70.R
[ FAIL 27 | WARN 29 | SKIP 1 | PASS 92 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-dissect.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-check_collinearity.R:7:3'): check_collinearity works correctly for multivariable models ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-check_collinearity.R:7:3
2. └─dplyr::filter(PimaIndiansDiabetes2, !is.na(diabetes))
── Error ('test-check_collinearity.R:27:3'): check_collinearity throws error for univariate models ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-check_collinearity.R:27:3
2. └─dplyr::filter(PimaIndiansDiabetes2, !is.na(diabetes))
── Error ('test-check_convergence.R:4:3'): check_convergence runs correctly for valid approaches ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-check_convergence.R:4:3
── Error ('test-check_convergence.R:98:3'): check_convergence handles model fitting failure ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-check_convergence.R:98:3
── Error ('test-fit_multi_model.R:7:3'): .fit_multi_model returns correct model class for each approach ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-fit_multi_model.R:7:3
2. └─dplyr::mutate(...)
── Error ('test-fit_uni_model.R:7:3'): .fit_uni_model returns correct model class (PimaIndiansDiabetes2) ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-fit_uni_model.R:7:3
2. └─dplyr::mutate(...)
── Error ('test-fit_uni_model.R:55:3'): .fit_uni_model handles model fitting failure gracefully ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-fit_uni_model.R:55:3
── Error ('test-identify_confounder.R:6:3'): identify_confounder works across approaches using
change-in-estimate method ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-identify_confounder.R:6:3
── Error ('test-interaction_models.R:6:3'): interaction_models returns a list with expected names ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:6:3
2. └─dplyr::mutate(...)
── Error ('test-interaction_models.R:52:3'): interaction_models handles robpoisson approach ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:52:3
2. └─dplyr::mutate(...)
── Error ('test-interaction_models.R:84:3'): interaction_models errors with invalid approach ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:84:3
2. └─dplyr::mutate(...)
── Error ('test-multi_reg.R:11:3'): multi_reg computes estimates correctly across approaches ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-multi_reg.R:11:3
── Error ('test-plot_reg.R:9:3'): plot_reg works with default settings and correct X-axis labels ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-plot_reg.R:9:3
2. └─dplyr::mutate(...)
── Error ('test-plot_reg_combine.R:9:3'): plot_reg_combine works with various options ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-plot_reg_combine.R:9:3
── Error ('test-select_models.R:8:3'): select_models works for valid approaches and directions ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-select_models.R:8:3
── Error ('test-stratified_multi_reg.R:9:3'): stratified_multi_reg returns a gtsummary tbl_merge object ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:9:3
── Error ('test-stratified_multi_reg.R:61:3'): stratified_multi_reg excludes NA values in stratifier ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:61:3
── Error ('test-stratified_multi_reg.R:109:3'): stratified_multi_reg runs with robpoisson and produces estimates ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:109:3
── Error ('test-stratified_multi_reg.R:153:3'): stratified_multi_reg works with negbin ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-stratified_multi_reg.R:153:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:4:3'): stratified_uni_reg returns a gtsummary tbl_merge object with logit ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-stratified_uni_reg.R:4:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:40:3'): stratified_uni_reg excludes NA values in stratifier ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:40:3
── Error ('test-stratified_uni_reg.R:67:3'): stratified_uni_reg errors for invalid inputs ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:67:3
── Error ('test-stratified_uni_reg.R:100:3'): stratified_uni_reg works with robpoisson ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:100:3
── Error ('test-stratified_uni_reg.R:126:3'): stratified_uni_reg works with negbin ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-stratified_uni_reg.R:126:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:163:3'): stratified_uni_reg errors when no valid strata exist ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:163:3
── Error ('test-uni_reg.R:6:3'): uni_reg returns a gtsummary object and works with binary data ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─tidyr::drop_na(...) at test-uni_reg.R:6:3
2. └─dplyr::mutate(...)
── Error ('test-uni_reg.R:70:3'): uni_reg$ accessors return correct components ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─tidyr::drop_na(PimaIndiansDiabetes2) at test-uni_reg.R:70:3
[ FAIL 27 | WARN 29 | SKIP 1 | PASS 92 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [41s/42s]
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-check_collinearity-9.R
Saving _problems/test-check_collinearity-29.R
Saving _problems/test-check_convergence-19.R
Saving _problems/test-check_convergence-113.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)
Saving _problems/test-fit_multi_model-23.R
Saving _problems/test-fit_uni_model-17.R
Saving _problems/test-fit_uni_model-59.R
Saving _problems/test-identify_confounder-27.R
Saving _problems/test-interaction_models-32.R
Saving _problems/test-interaction_models-64.R
Saving _problems/test-interaction_models-96.R
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.
Saving _problems/test-multi_reg-50.R
Saving _problems/test-plot_reg-43.R
Saving _problems/test-plot_reg_combine-56.R
Table saved at: /tmp/Rtmp9zmVob/working_dir/RtmpGxvJNK/regression_results.docx
`height` was translated to `width`.
Plot saved at: /tmp/Rtmp9zmVob/working_dir/RtmpGxvJNK/plot_png.png
`height` was translated to `width`.
Plot saved at: /tmp/Rtmp9zmVob/working_dir/RtmpGxvJNK/plot_pdf.pdf
`height` was translated to `width`.
Plot saved at: /tmp/Rtmp9zmVob/working_dir/RtmpGxvJNK/plot_jpg.jpg
`height` was translated to `width`.
Word document saved at: /tmp/Rtmp9zmVob/working_dir/RtmpGxvJNK/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
Saving _problems/test-select_models-25.R
Saving _problems/test-stratified_multi_reg-32.R
Saving _problems/test-stratified_multi_reg-75.R
Saving _problems/test-stratified_multi_reg-120.R
Saving _problems/test-stratified_multi_reg-167.R
Saving _problems/test-stratified_uni_reg-21.R
Saving _problems/test-stratified_uni_reg-46.R
Saving _problems/test-stratified_uni_reg-71.R
Saving _problems/test-stratified_uni_reg-106.R
Saving _problems/test-stratified_uni_reg-142.R
Saving _problems/test-stratified_uni_reg-167.R
Saving _problems/test-uni_reg-10.R
Saving _problems/test-uni_reg-70.R
[ FAIL 27 | WARN 29 | SKIP 1 | PASS 92 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-dissect.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-check_collinearity.R:7:3'): check_collinearity works correctly for multivariable models ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-check_collinearity.R:7:3
2. └─dplyr::filter(PimaIndiansDiabetes2, !is.na(diabetes))
── Error ('test-check_collinearity.R:27:3'): check_collinearity throws error for univariate models ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-check_collinearity.R:27:3
2. └─dplyr::filter(PimaIndiansDiabetes2, !is.na(diabetes))
── Error ('test-check_convergence.R:4:3'): check_convergence runs correctly for valid approaches ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-check_convergence.R:4:3
── Error ('test-check_convergence.R:98:3'): check_convergence handles model fitting failure ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-check_convergence.R:98:3
── Error ('test-fit_multi_model.R:7:3'): .fit_multi_model returns correct model class for each approach ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-fit_multi_model.R:7:3
2. └─dplyr::mutate(...)
── Error ('test-fit_uni_model.R:7:3'): .fit_uni_model returns correct model class (PimaIndiansDiabetes2) ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-fit_uni_model.R:7:3
2. └─dplyr::mutate(...)
── Error ('test-fit_uni_model.R:55:3'): .fit_uni_model handles model fitting failure gracefully ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-fit_uni_model.R:55:3
── Error ('test-identify_confounder.R:6:3'): identify_confounder works across approaches using
change-in-estimate method ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-identify_confounder.R:6:3
── Error ('test-interaction_models.R:6:3'): interaction_models returns a list with expected names ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:6:3
2. └─dplyr::mutate(...)
── Error ('test-interaction_models.R:52:3'): interaction_models handles robpoisson approach ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:52:3
2. └─dplyr::mutate(...)
── Error ('test-interaction_models.R:84:3'): interaction_models errors with invalid approach ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:84:3
2. └─dplyr::mutate(...)
── Error ('test-multi_reg.R:11:3'): multi_reg computes estimates correctly across approaches ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-multi_reg.R:11:3
── Error ('test-plot_reg.R:9:3'): plot_reg works with default settings and correct X-axis labels ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-plot_reg.R:9:3
2. └─dplyr::mutate(...)
── Error ('test-plot_reg_combine.R:9:3'): plot_reg_combine works with various options ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-plot_reg_combine.R:9:3
── Error ('test-select_models.R:8:3'): select_models works for valid approaches and directions ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-select_models.R:8:3
── Error ('test-stratified_multi_reg.R:9:3'): stratified_multi_reg returns a gtsummary tbl_merge object ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:9:3
── Error ('test-stratified_multi_reg.R:61:3'): stratified_multi_reg excludes NA values in stratifier ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:61:3
── Error ('test-stratified_multi_reg.R:109:3'): stratified_multi_reg runs with robpoisson and produces estimates ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:109:3
── Error ('test-stratified_multi_reg.R:153:3'): stratified_multi_reg works with negbin ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-stratified_multi_reg.R:153:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:4:3'): stratified_uni_reg returns a gtsummary tbl_merge object with logit ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-stratified_uni_reg.R:4:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:40:3'): stratified_uni_reg excludes NA values in stratifier ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:40:3
── Error ('test-stratified_uni_reg.R:67:3'): stratified_uni_reg errors for invalid inputs ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:67:3
── Error ('test-stratified_uni_reg.R:100:3'): stratified_uni_reg works with robpoisson ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:100:3
── Error ('test-stratified_uni_reg.R:126:3'): stratified_uni_reg works with negbin ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-stratified_uni_reg.R:126:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:163:3'): stratified_uni_reg errors when no valid strata exist ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:163:3
── Error ('test-uni_reg.R:6:3'): uni_reg returns a gtsummary object and works with binary data ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─tidyr::drop_na(...) at test-uni_reg.R:6:3
2. └─dplyr::mutate(...)
── Error ('test-uni_reg.R:70:3'): uni_reg$ accessors return correct components ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─tidyr::drop_na(PimaIndiansDiabetes2) at test-uni_reg.R:70:3
[ FAIL 27 | WARN 29 | SKIP 1 | PASS 92 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.0.0
Check: tests
Result: ERROR
Running 'testthat.R' [49s]
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-check_collinearity-9.R
Saving _problems/test-check_collinearity-29.R
Saving _problems/test-check_convergence-19.R
Saving _problems/test-check_convergence-113.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)
Saving _problems/test-fit_multi_model-23.R
Saving _problems/test-fit_uni_model-17.R
Saving _problems/test-fit_uni_model-59.R
Saving _problems/test-identify_confounder-27.R
Saving _problems/test-interaction_models-32.R
Saving _problems/test-interaction_models-64.R
Saving _problems/test-interaction_models-96.R
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.
Saving _problems/test-multi_reg-50.R
Saving _problems/test-plot_reg-43.R
Saving _problems/test-plot_reg_combine-56.R
Table saved at: D:\temp\2026_07_29_01_50_00_30317\RtmpYTVAcH\regression_results.docx
`height` was translated to `width`.
Plot saved at: D:\temp\2026_07_29_01_50_00_30317\RtmpYTVAcH\plot_png.png
`height` was translated to `width`.
Plot saved at: D:\temp\2026_07_29_01_50_00_30317\RtmpYTVAcH\plot_pdf.pdf
`height` was translated to `width`.
Plot saved at: D:\temp\2026_07_29_01_50_00_30317\RtmpYTVAcH\plot_jpg.jpg
`height` was translated to `width`.
Word document saved at: D:\temp\2026_07_29_01_50_00_30317\RtmpYTVAcH\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
Saving _problems/test-select_models-25.R
Saving _problems/test-stratified_multi_reg-32.R
Saving _problems/test-stratified_multi_reg-75.R
Saving _problems/test-stratified_multi_reg-120.R
Saving _problems/test-stratified_multi_reg-167.R
Saving _problems/test-stratified_uni_reg-21.R
Saving _problems/test-stratified_uni_reg-46.R
Saving _problems/test-stratified_uni_reg-71.R
Saving _problems/test-stratified_uni_reg-106.R
Saving _problems/test-stratified_uni_reg-142.R
Saving _problems/test-stratified_uni_reg-167.R
Saving _problems/test-uni_reg-10.R
Saving _problems/test-uni_reg-70.R
[ FAIL 27 | WARN 29 | SKIP 1 | PASS 92 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-dissect.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-check_collinearity.R:7:3'): check_collinearity works correctly for multivariable models ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-check_collinearity.R:7:3
2. └─dplyr::filter(PimaIndiansDiabetes2, !is.na(diabetes))
── Error ('test-check_collinearity.R:27:3'): check_collinearity throws error for univariate models ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-check_collinearity.R:27:3
2. └─dplyr::filter(PimaIndiansDiabetes2, !is.na(diabetes))
── Error ('test-check_convergence.R:4:3'): check_convergence runs correctly for valid approaches ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-check_convergence.R:4:3
── Error ('test-check_convergence.R:98:3'): check_convergence handles model fitting failure ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-check_convergence.R:98:3
── Error ('test-fit_multi_model.R:7:3'): .fit_multi_model returns correct model class for each approach ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-fit_multi_model.R:7:3
2. └─dplyr::mutate(...)
── Error ('test-fit_uni_model.R:7:3'): .fit_uni_model returns correct model class (PimaIndiansDiabetes2) ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-fit_uni_model.R:7:3
2. └─dplyr::mutate(...)
── Error ('test-fit_uni_model.R:55:3'): .fit_uni_model handles model fitting failure gracefully ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-fit_uni_model.R:55:3
── Error ('test-identify_confounder.R:6:3'): identify_confounder works across approaches using
change-in-estimate method ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-identify_confounder.R:6:3
── Error ('test-interaction_models.R:6:3'): interaction_models returns a list with expected names ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:6:3
2. └─dplyr::mutate(...)
── Error ('test-interaction_models.R:52:3'): interaction_models handles robpoisson approach ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:52:3
2. └─dplyr::mutate(...)
── Error ('test-interaction_models.R:84:3'): interaction_models errors with invalid approach ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:84:3
2. └─dplyr::mutate(...)
── Error ('test-multi_reg.R:11:3'): multi_reg computes estimates correctly across approaches ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-multi_reg.R:11:3
── Error ('test-plot_reg.R:9:3'): plot_reg works with default settings and correct X-axis labels ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-plot_reg.R:9:3
2. └─dplyr::mutate(...)
── Error ('test-plot_reg_combine.R:9:3'): plot_reg_combine works with various options ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-plot_reg_combine.R:9:3
── Error ('test-select_models.R:8:3'): select_models works for valid approaches and directions ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-select_models.R:8:3
── Error ('test-stratified_multi_reg.R:9:3'): stratified_multi_reg returns a gtsummary tbl_merge object ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:9:3
── Error ('test-stratified_multi_reg.R:61:3'): stratified_multi_reg excludes NA values in stratifier ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:61:3
── Error ('test-stratified_multi_reg.R:109:3'): stratified_multi_reg runs with robpoisson and produces estimates ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:109:3
── Error ('test-stratified_multi_reg.R:153:3'): stratified_multi_reg works with negbin ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-stratified_multi_reg.R:153:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:4:3'): stratified_uni_reg returns a gtsummary tbl_merge object with logit ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-stratified_uni_reg.R:4:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:40:3'): stratified_uni_reg excludes NA values in stratifier ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:40:3
── Error ('test-stratified_uni_reg.R:67:3'): stratified_uni_reg errors for invalid inputs ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:67:3
── Error ('test-stratified_uni_reg.R:100:3'): stratified_uni_reg works with robpoisson ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:100:3
── Error ('test-stratified_uni_reg.R:126:3'): stratified_uni_reg works with negbin ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-stratified_uni_reg.R:126:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:163:3'): stratified_uni_reg errors when no valid strata exist ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:163:3
── Error ('test-uni_reg.R:6:3'): uni_reg returns a gtsummary object and works with binary data ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─tidyr::drop_na(...) at test-uni_reg.R:6:3
2. └─dplyr::mutate(...)
── Error ('test-uni_reg.R:70:3'): uni_reg$ accessors return correct components ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─tidyr::drop_na(PimaIndiansDiabetes2) at test-uni_reg.R:70:3
[ FAIL 27 | WARN 29 | SKIP 1 | PASS 92 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [60s/78s]
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-check_collinearity-9.R
Saving _problems/test-check_collinearity-29.R
Saving _problems/test-check_convergence-19.R
Saving _problems/test-check_convergence-113.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)
Saving _problems/test-fit_multi_model-23.R
Saving _problems/test-fit_uni_model-17.R
Saving _problems/test-fit_uni_model-59.R
Saving _problems/test-identify_confounder-27.R
Saving _problems/test-interaction_models-32.R
Saving _problems/test-interaction_models-64.R
Saving _problems/test-interaction_models-96.R
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.
Saving _problems/test-multi_reg-50.R
Saving _problems/test-plot_reg-43.R
Saving _problems/test-plot_reg_combine-56.R
Table saved at: /home/hornik/tmp/scratch/Rtmpambp9M/regression_results.docx
`height` was translated to `width`.
Plot saved at: /home/hornik/tmp/scratch/Rtmpambp9M/plot_png.png
`height` was translated to `width`.
Plot saved at: /home/hornik/tmp/scratch/Rtmpambp9M/plot_pdf.pdf
`height` was translated to `width`.
Plot saved at: /home/hornik/tmp/scratch/Rtmpambp9M/plot_jpg.jpg
`height` was translated to `width`.
Word document saved at: /home/hornik/tmp/scratch/Rtmpambp9M/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
Saving _problems/test-select_models-25.R
Saving _problems/test-stratified_multi_reg-32.R
Saving _problems/test-stratified_multi_reg-75.R
Saving _problems/test-stratified_multi_reg-120.R
Saving _problems/test-stratified_multi_reg-167.R
Saving _problems/test-stratified_uni_reg-21.R
Saving _problems/test-stratified_uni_reg-46.R
Saving _problems/test-stratified_uni_reg-71.R
Saving _problems/test-stratified_uni_reg-106.R
Saving _problems/test-stratified_uni_reg-142.R
Saving _problems/test-stratified_uni_reg-167.R
Saving _problems/test-uni_reg-10.R
Saving _problems/test-uni_reg-70.R
[ FAIL 27 | WARN 29 | SKIP 1 | PASS 92 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-dissect.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-check_collinearity.R:7:3'): check_collinearity works correctly for multivariable models ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-check_collinearity.R:7:3
2. └─dplyr::filter(PimaIndiansDiabetes2, !is.na(diabetes))
── Error ('test-check_collinearity.R:27:3'): check_collinearity throws error for univariate models ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-check_collinearity.R:27:3
2. └─dplyr::filter(PimaIndiansDiabetes2, !is.na(diabetes))
── Error ('test-check_convergence.R:4:3'): check_convergence runs correctly for valid approaches ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-check_convergence.R:4:3
── Error ('test-check_convergence.R:98:3'): check_convergence handles model fitting failure ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-check_convergence.R:98:3
── Error ('test-fit_multi_model.R:7:3'): .fit_multi_model returns correct model class for each approach ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-fit_multi_model.R:7:3
2. └─dplyr::mutate(...)
── Error ('test-fit_uni_model.R:7:3'): .fit_uni_model returns correct model class (PimaIndiansDiabetes2) ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-fit_uni_model.R:7:3
2. └─dplyr::mutate(...)
── Error ('test-fit_uni_model.R:55:3'): .fit_uni_model handles model fitting failure gracefully ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-fit_uni_model.R:55:3
── Error ('test-identify_confounder.R:6:3'): identify_confounder works across approaches using
change-in-estimate method ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-identify_confounder.R:6:3
── Error ('test-interaction_models.R:6:3'): interaction_models returns a list with expected names ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:6:3
2. └─dplyr::mutate(...)
── Error ('test-interaction_models.R:52:3'): interaction_models handles robpoisson approach ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:52:3
2. └─dplyr::mutate(...)
── Error ('test-interaction_models.R:84:3'): interaction_models errors with invalid approach ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:84:3
2. └─dplyr::mutate(...)
── Error ('test-multi_reg.R:11:3'): multi_reg computes estimates correctly across approaches ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-multi_reg.R:11:3
── Error ('test-plot_reg.R:9:3'): plot_reg works with default settings and correct X-axis labels ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-plot_reg.R:9:3
2. └─dplyr::mutate(...)
── Error ('test-plot_reg_combine.R:9:3'): plot_reg_combine works with various options ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-plot_reg_combine.R:9:3
── Error ('test-select_models.R:8:3'): select_models works for valid approaches and directions ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-select_models.R:8:3
── Error ('test-stratified_multi_reg.R:9:3'): stratified_multi_reg returns a gtsummary tbl_merge object ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:9:3
── Error ('test-stratified_multi_reg.R:61:3'): stratified_multi_reg excludes NA values in stratifier ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:61:3
── Error ('test-stratified_multi_reg.R:109:3'): stratified_multi_reg runs with robpoisson and produces estimates ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:109:3
── Error ('test-stratified_multi_reg.R:153:3'): stratified_multi_reg works with negbin ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-stratified_multi_reg.R:153:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:4:3'): stratified_uni_reg returns a gtsummary tbl_merge object with logit ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-stratified_uni_reg.R:4:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:40:3'): stratified_uni_reg excludes NA values in stratifier ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:40:3
── Error ('test-stratified_uni_reg.R:67:3'): stratified_uni_reg errors for invalid inputs ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:67:3
── Error ('test-stratified_uni_reg.R:100:3'): stratified_uni_reg works with robpoisson ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:100:3
── Error ('test-stratified_uni_reg.R:126:3'): stratified_uni_reg works with negbin ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-stratified_uni_reg.R:126:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:163:3'): stratified_uni_reg errors when no valid strata exist ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:163:3
── Error ('test-uni_reg.R:6:3'): uni_reg returns a gtsummary object and works with binary data ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─tidyr::drop_na(...) at test-uni_reg.R:6:3
2. └─dplyr::mutate(...)
── Error ('test-uni_reg.R:70:3'): uni_reg$ accessors return correct components ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─tidyr::drop_na(PimaIndiansDiabetes2) at test-uni_reg.R:70:3
[ FAIL 27 | WARN 29 | SKIP 1 | PASS 92 ]
Error:
! Test failures.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [60s/74s]
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-check_collinearity-9.R
Saving _problems/test-check_collinearity-29.R
Saving _problems/test-check_convergence-19.R
Saving _problems/test-check_convergence-113.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)
Saving _problems/test-fit_multi_model-23.R
Saving _problems/test-fit_uni_model-17.R
Saving _problems/test-fit_uni_model-59.R
Saving _problems/test-identify_confounder-27.R
Saving _problems/test-interaction_models-32.R
Saving _problems/test-interaction_models-64.R
Saving _problems/test-interaction_models-96.R
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.
Saving _problems/test-multi_reg-50.R
Saving _problems/test-plot_reg-43.R
Saving _problems/test-plot_reg_combine-56.R
Table saved at: /home/hornik/tmp/scratch/RtmpQrj0t6/regression_results.docx
`height` was translated to `width`.
Plot saved at: /home/hornik/tmp/scratch/RtmpQrj0t6/plot_png.png
`height` was translated to `width`.
Plot saved at: /home/hornik/tmp/scratch/RtmpQrj0t6/plot_pdf.pdf
`height` was translated to `width`.
Plot saved at: /home/hornik/tmp/scratch/RtmpQrj0t6/plot_jpg.jpg
`height` was translated to `width`.
Word document saved at: /home/hornik/tmp/scratch/RtmpQrj0t6/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
Saving _problems/test-select_models-25.R
Saving _problems/test-stratified_multi_reg-32.R
Saving _problems/test-stratified_multi_reg-75.R
Saving _problems/test-stratified_multi_reg-120.R
Saving _problems/test-stratified_multi_reg-167.R
Saving _problems/test-stratified_uni_reg-21.R
Saving _problems/test-stratified_uni_reg-46.R
Saving _problems/test-stratified_uni_reg-71.R
Saving _problems/test-stratified_uni_reg-106.R
Saving _problems/test-stratified_uni_reg-142.R
Saving _problems/test-stratified_uni_reg-167.R
Saving _problems/test-uni_reg-10.R
Saving _problems/test-uni_reg-70.R
[ FAIL 27 | WARN 29 | SKIP 1 | PASS 92 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-dissect.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-check_collinearity.R:7:3'): check_collinearity works correctly for multivariable models ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-check_collinearity.R:7:3
2. └─dplyr::filter(PimaIndiansDiabetes2, !is.na(diabetes))
── Error ('test-check_collinearity.R:27:3'): check_collinearity throws error for univariate models ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-check_collinearity.R:27:3
2. └─dplyr::filter(PimaIndiansDiabetes2, !is.na(diabetes))
── Error ('test-check_convergence.R:4:3'): check_convergence runs correctly for valid approaches ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-check_convergence.R:4:3
── Error ('test-check_convergence.R:98:3'): check_convergence handles model fitting failure ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-check_convergence.R:98:3
── Error ('test-fit_multi_model.R:7:3'): .fit_multi_model returns correct model class for each approach ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-fit_multi_model.R:7:3
2. └─dplyr::mutate(...)
── Error ('test-fit_uni_model.R:7:3'): .fit_uni_model returns correct model class (PimaIndiansDiabetes2) ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-fit_uni_model.R:7:3
2. └─dplyr::mutate(...)
── Error ('test-fit_uni_model.R:55:3'): .fit_uni_model handles model fitting failure gracefully ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-fit_uni_model.R:55:3
── Error ('test-identify_confounder.R:6:3'): identify_confounder works across approaches using
change-in-estimate method ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-identify_confounder.R:6:3
── Error ('test-interaction_models.R:6:3'): interaction_models returns a list with expected names ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:6:3
2. └─dplyr::mutate(...)
── Error ('test-interaction_models.R:52:3'): interaction_models handles robpoisson approach ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:52:3
2. └─dplyr::mutate(...)
── Error ('test-interaction_models.R:84:3'): interaction_models errors with invalid approach ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:84:3
2. └─dplyr::mutate(...)
── Error ('test-multi_reg.R:11:3'): multi_reg computes estimates correctly across approaches ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-multi_reg.R:11:3
── Error ('test-plot_reg.R:9:3'): plot_reg works with default settings and correct X-axis labels ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-plot_reg.R:9:3
2. └─dplyr::mutate(...)
── Error ('test-plot_reg_combine.R:9:3'): plot_reg_combine works with various options ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-plot_reg_combine.R:9:3
── Error ('test-select_models.R:8:3'): select_models works for valid approaches and directions ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-select_models.R:8:3
── Error ('test-stratified_multi_reg.R:9:3'): stratified_multi_reg returns a gtsummary tbl_merge object ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:9:3
── Error ('test-stratified_multi_reg.R:61:3'): stratified_multi_reg excludes NA values in stratifier ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:61:3
── Error ('test-stratified_multi_reg.R:109:3'): stratified_multi_reg runs with robpoisson and produces estimates ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:109:3
── Error ('test-stratified_multi_reg.R:153:3'): stratified_multi_reg works with negbin ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-stratified_multi_reg.R:153:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:4:3'): stratified_uni_reg returns a gtsummary tbl_merge object with logit ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-stratified_uni_reg.R:4:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:40:3'): stratified_uni_reg excludes NA values in stratifier ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:40:3
── Error ('test-stratified_uni_reg.R:67:3'): stratified_uni_reg errors for invalid inputs ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:67:3
── Error ('test-stratified_uni_reg.R:100:3'): stratified_uni_reg works with robpoisson ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:100:3
── Error ('test-stratified_uni_reg.R:126:3'): stratified_uni_reg works with negbin ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-stratified_uni_reg.R:126:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:163:3'): stratified_uni_reg errors when no valid strata exist ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:163:3
── Error ('test-uni_reg.R:6:3'): uni_reg returns a gtsummary object and works with binary data ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─tidyr::drop_na(...) at test-uni_reg.R:6:3
2. └─dplyr::mutate(...)
── Error ('test-uni_reg.R:70:3'): uni_reg$ accessors return correct components ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─tidyr::drop_na(PimaIndiansDiabetes2) at test-uni_reg.R:70:3
[ FAIL 27 | WARN 29 | SKIP 1 | PASS 92 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-linux-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running 'testthat.R' [49s]
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-check_collinearity-9.R
Saving _problems/test-check_collinearity-29.R
Saving _problems/test-check_convergence-19.R
Saving _problems/test-check_convergence-113.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)
Saving _problems/test-fit_multi_model-23.R
Saving _problems/test-fit_uni_model-17.R
Saving _problems/test-fit_uni_model-59.R
Saving _problems/test-identify_confounder-27.R
Saving _problems/test-interaction_models-32.R
Saving _problems/test-interaction_models-64.R
Saving _problems/test-interaction_models-96.R
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.
Saving _problems/test-multi_reg-50.R
Saving _problems/test-plot_reg-43.R
Saving _problems/test-plot_reg_combine-56.R
Table saved at: D:\temp\2026_08_01_01_50_00_24787\RtmpKWzu64\regression_results.docx
`height` was translated to `width`.
Plot saved at: D:\temp\2026_08_01_01_50_00_24787\RtmpKWzu64\plot_png.png
`height` was translated to `width`.
Plot saved at: D:\temp\2026_08_01_01_50_00_24787\RtmpKWzu64\plot_pdf.pdf
`height` was translated to `width`.
Plot saved at: D:\temp\2026_08_01_01_50_00_24787\RtmpKWzu64\plot_jpg.jpg
`height` was translated to `width`.
Word document saved at: D:\temp\2026_08_01_01_50_00_24787\RtmpKWzu64\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
Saving _problems/test-select_models-25.R
Saving _problems/test-stratified_multi_reg-32.R
Saving _problems/test-stratified_multi_reg-75.R
Saving _problems/test-stratified_multi_reg-120.R
Saving _problems/test-stratified_multi_reg-167.R
Saving _problems/test-stratified_uni_reg-21.R
Saving _problems/test-stratified_uni_reg-46.R
Saving _problems/test-stratified_uni_reg-71.R
Saving _problems/test-stratified_uni_reg-106.R
Saving _problems/test-stratified_uni_reg-142.R
Saving _problems/test-stratified_uni_reg-167.R
Saving _problems/test-uni_reg-10.R
Saving _problems/test-uni_reg-70.R
[ FAIL 27 | WARN 29 | SKIP 1 | PASS 92 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-dissect.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-check_collinearity.R:7:3'): check_collinearity works correctly for multivariable models ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-check_collinearity.R:7:3
2. └─dplyr::filter(PimaIndiansDiabetes2, !is.na(diabetes))
── Error ('test-check_collinearity.R:27:3'): check_collinearity throws error for univariate models ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-check_collinearity.R:27:3
2. └─dplyr::filter(PimaIndiansDiabetes2, !is.na(diabetes))
── Error ('test-check_convergence.R:4:3'): check_convergence runs correctly for valid approaches ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-check_convergence.R:4:3
── Error ('test-check_convergence.R:98:3'): check_convergence handles model fitting failure ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-check_convergence.R:98:3
── Error ('test-fit_multi_model.R:7:3'): .fit_multi_model returns correct model class for each approach ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-fit_multi_model.R:7:3
2. └─dplyr::mutate(...)
── Error ('test-fit_uni_model.R:7:3'): .fit_uni_model returns correct model class (PimaIndiansDiabetes2) ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-fit_uni_model.R:7:3
2. └─dplyr::mutate(...)
── Error ('test-fit_uni_model.R:55:3'): .fit_uni_model handles model fitting failure gracefully ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-fit_uni_model.R:55:3
── Error ('test-identify_confounder.R:6:3'): identify_confounder works across approaches using
change-in-estimate method ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-identify_confounder.R:6:3
── Error ('test-interaction_models.R:6:3'): interaction_models returns a list with expected names ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:6:3
2. └─dplyr::mutate(...)
── Error ('test-interaction_models.R:52:3'): interaction_models handles robpoisson approach ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:52:3
2. └─dplyr::mutate(...)
── Error ('test-interaction_models.R:84:3'): interaction_models errors with invalid approach ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:84:3
2. └─dplyr::mutate(...)
── Error ('test-multi_reg.R:11:3'): multi_reg computes estimates correctly across approaches ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-multi_reg.R:11:3
── Error ('test-plot_reg.R:9:3'): plot_reg works with default settings and correct X-axis labels ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-plot_reg.R:9:3
2. └─dplyr::mutate(...)
── Error ('test-plot_reg_combine.R:9:3'): plot_reg_combine works with various options ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-plot_reg_combine.R:9:3
── Error ('test-select_models.R:8:3'): select_models works for valid approaches and directions ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-select_models.R:8:3
── Error ('test-stratified_multi_reg.R:9:3'): stratified_multi_reg returns a gtsummary tbl_merge object ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:9:3
── Error ('test-stratified_multi_reg.R:61:3'): stratified_multi_reg excludes NA values in stratifier ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:61:3
── Error ('test-stratified_multi_reg.R:109:3'): stratified_multi_reg runs with robpoisson and produces estimates ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:109:3
── Error ('test-stratified_multi_reg.R:153:3'): stratified_multi_reg works with negbin ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-stratified_multi_reg.R:153:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:4:3'): stratified_uni_reg returns a gtsummary tbl_merge object with logit ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-stratified_uni_reg.R:4:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:40:3'): stratified_uni_reg excludes NA values in stratifier ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:40:3
── Error ('test-stratified_uni_reg.R:67:3'): stratified_uni_reg errors for invalid inputs ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:67:3
── Error ('test-stratified_uni_reg.R:100:3'): stratified_uni_reg works with robpoisson ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:100:3
── Error ('test-stratified_uni_reg.R:126:3'): stratified_uni_reg works with negbin ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-stratified_uni_reg.R:126:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:163:3'): stratified_uni_reg errors when no valid strata exist ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:163:3
── Error ('test-uni_reg.R:6:3'): uni_reg returns a gtsummary object and works with binary data ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─tidyr::drop_na(...) at test-uni_reg.R:6:3
2. └─dplyr::mutate(...)
── Error ('test-uni_reg.R:70:3'): uni_reg$ accessors return correct components ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─tidyr::drop_na(PimaIndiansDiabetes2) at test-uni_reg.R:70:3
[ FAIL 27 | WARN 29 | SKIP 1 | PASS 92 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-windows-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running 'testthat.R' [76s]
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-check_collinearity-9.R
Saving _problems/test-check_collinearity-29.R
Saving _problems/test-check_convergence-19.R
Saving _problems/test-check_convergence-113.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)
Saving _problems/test-fit_multi_model-23.R
Saving _problems/test-fit_uni_model-17.R
Saving _problems/test-fit_uni_model-59.R
Saving _problems/test-identify_confounder-27.R
Saving _problems/test-interaction_models-32.R
Saving _problems/test-interaction_models-64.R
Saving _problems/test-interaction_models-96.R
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.
Saving _problems/test-multi_reg-50.R
Saving _problems/test-plot_reg-43.R
Saving _problems/test-plot_reg_combine-56.R
Table saved at: D:\temp\2026_07_31_12_46_36_2361\RtmpAxsADp\regression_results.docx
`height` was translated to `width`.
Plot saved at: D:\temp\2026_07_31_12_46_36_2361\RtmpAxsADp\plot_png.png
`height` was translated to `width`.
Plot saved at: D:\temp\2026_07_31_12_46_36_2361\RtmpAxsADp\plot_pdf.pdf
`height` was translated to `width`.
Plot saved at: D:\temp\2026_07_31_12_46_36_2361\RtmpAxsADp\plot_jpg.jpg
`height` was translated to `width`.
Word document saved at: D:\temp\2026_07_31_12_46_36_2361\RtmpAxsADp\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
Saving _problems/test-select_models-25.R
Saving _problems/test-stratified_multi_reg-32.R
Saving _problems/test-stratified_multi_reg-75.R
Saving _problems/test-stratified_multi_reg-120.R
Saving _problems/test-stratified_multi_reg-167.R
Saving _problems/test-stratified_uni_reg-21.R
Saving _problems/test-stratified_uni_reg-46.R
Saving _problems/test-stratified_uni_reg-71.R
Saving _problems/test-stratified_uni_reg-106.R
Saving _problems/test-stratified_uni_reg-142.R
Saving _problems/test-stratified_uni_reg-167.R
Saving _problems/test-uni_reg-10.R
Saving _problems/test-uni_reg-70.R
[ FAIL 27 | WARN 29 | SKIP 1 | PASS 92 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-dissect.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-check_collinearity.R:7:3'): check_collinearity works correctly for multivariable models ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-check_collinearity.R:7:3
2. └─dplyr::filter(PimaIndiansDiabetes2, !is.na(diabetes))
── Error ('test-check_collinearity.R:27:3'): check_collinearity throws error for univariate models ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-check_collinearity.R:27:3
2. └─dplyr::filter(PimaIndiansDiabetes2, !is.na(diabetes))
── Error ('test-check_convergence.R:4:3'): check_convergence runs correctly for valid approaches ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-check_convergence.R:4:3
── Error ('test-check_convergence.R:98:3'): check_convergence handles model fitting failure ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-check_convergence.R:98:3
── Error ('test-fit_multi_model.R:7:3'): .fit_multi_model returns correct model class for each approach ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-fit_multi_model.R:7:3
2. └─dplyr::mutate(...)
── Error ('test-fit_uni_model.R:7:3'): .fit_uni_model returns correct model class (PimaIndiansDiabetes2) ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-fit_uni_model.R:7:3
2. └─dplyr::mutate(...)
── Error ('test-fit_uni_model.R:55:3'): .fit_uni_model handles model fitting failure gracefully ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-fit_uni_model.R:55:3
── Error ('test-identify_confounder.R:6:3'): identify_confounder works across approaches using
change-in-estimate method ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-identify_confounder.R:6:3
── Error ('test-interaction_models.R:6:3'): interaction_models returns a list with expected names ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:6:3
2. └─dplyr::mutate(...)
── Error ('test-interaction_models.R:52:3'): interaction_models handles robpoisson approach ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:52:3
2. └─dplyr::mutate(...)
── Error ('test-interaction_models.R:84:3'): interaction_models errors with invalid approach ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-interaction_models.R:84:3
2. └─dplyr::mutate(...)
── Error ('test-multi_reg.R:11:3'): multi_reg computes estimates correctly across approaches ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-multi_reg.R:11:3
── Error ('test-plot_reg.R:9:3'): plot_reg works with default settings and correct X-axis labels ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-plot_reg.R:9:3
2. └─dplyr::mutate(...)
── Error ('test-plot_reg_combine.R:9:3'): plot_reg_combine works with various options ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-plot_reg_combine.R:9:3
── Error ('test-select_models.R:8:3'): select_models works for valid approaches and directions ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-select_models.R:8:3
── Error ('test-stratified_multi_reg.R:9:3'): stratified_multi_reg returns a gtsummary tbl_merge object ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:9:3
── Error ('test-stratified_multi_reg.R:61:3'): stratified_multi_reg excludes NA values in stratifier ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:61:3
── Error ('test-stratified_multi_reg.R:109:3'): stratified_multi_reg runs with robpoisson and produces estimates ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_multi_reg.R:109:3
── Error ('test-stratified_multi_reg.R:153:3'): stratified_multi_reg works with negbin ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-stratified_multi_reg.R:153:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:4:3'): stratified_uni_reg returns a gtsummary tbl_merge object with logit ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::mutate(...) at test-stratified_uni_reg.R:4:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:40:3'): stratified_uni_reg excludes NA values in stratifier ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:40:3
── Error ('test-stratified_uni_reg.R:67:3'): stratified_uni_reg errors for invalid inputs ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:67:3
── Error ('test-stratified_uni_reg.R:100:3'): stratified_uni_reg works with robpoisson ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:100:3
── Error ('test-stratified_uni_reg.R:126:3'): stratified_uni_reg works with negbin ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─dplyr::filter(...) at test-stratified_uni_reg.R:126:3
2. └─dplyr::mutate(...)
── Error ('test-stratified_uni_reg.R:163:3'): stratified_uni_reg errors when no valid strata exist ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─dplyr::mutate(...) at test-stratified_uni_reg.R:163:3
── Error ('test-uni_reg.R:6:3'): uni_reg returns a gtsummary object and works with binary data ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. ├─tidyr::drop_na(...) at test-uni_reg.R:6:3
2. └─dplyr::mutate(...)
── Error ('test-uni_reg.R:70:3'): uni_reg$ accessors return correct components ──
Error in `eval(code, test_env)`: object 'PimaIndiansDiabetes2' not found
Backtrace:
▆
1. └─tidyr::drop_na(PimaIndiansDiabetes2) at test-uni_reg.R:70:3
[ FAIL 27 | WARN 29 | SKIP 1 | PASS 92 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-windows-x86_64