* using log directory 'd:/Rcompile/CRANpkg/local/4.5/gtregression.Rcheck' * using R version 4.5.3 (2026-03-11 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'gtregression/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'gtregression' version '1.0.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'gtregression' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... 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OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... [0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [4s] 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 * checking for unstated dependencies in 'tests' ... OK * checking tests ... [78s] ERROR Running 'testthat.R' [77s] 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 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_27_01_50_00_23081\RtmpwrhwgA\regression_results.docx `height` was translated to `width`. Plot saved at: D:\temp\2026_07_27_01_50_00_23081\RtmpwrhwgA\plot_png.png `height` was translated to `width`. Plot saved at: D:\temp\2026_07_27_01_50_00_23081\RtmpwrhwgA\plot_pdf.pdf `height` was translated to `width`. Plot saved at: D:\temp\2026_07_27_01_50_00_23081\RtmpwrhwgA\plot_jpg.jpg `height` was translated to `width`. Word document saved at: D:\temp\2026_07_27_01_50_00_23081\RtmpwrhwgA\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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [3s] OK * checking PDF version of manual ... [17s] OK * checking HTML version of manual ... [6s] OK * DONE Status: 2 ERRORs