* using log directory 'd:/Rcompile/CRANpkg/local/4.6/gtregression.Rcheck' * using R version 4.6.1 (2026-06-24 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 * current time: 2026-08-12 06:36:18 UTC * 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 ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [3s] OK * checking whether the package can be loaded with stated dependencies ... [2s] OK * checking whether the package can be unloaded cleanly ... [2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s] OK * checking whether the namespace can be unloaded cleanly ... [3s] OK * checking loading without being on the library search path ... [3s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [8s] OK * checking Rd files ... [1s] OK * checking Rd metadata ... 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 ... [3s] 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 ... [50s] 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 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_12_01_50_00_15434\RtmpkTAElm\regression_results.docx `height` was translated to `width`. Plot saved at: D:\temp\2026_08_12_01_50_00_15434\RtmpkTAElm\plot_png.png `height` was translated to `width`. Plot saved at: D:\temp\2026_08_12_01_50_00_15434\RtmpkTAElm\plot_pdf.pdf `height` was translated to `width`. Plot saved at: D:\temp\2026_08_12_01_50_00_15434\RtmpkTAElm\plot_jpg.jpg `height` was translated to `width`. Word document saved at: D:\temp\2026_08_12_01_50_00_15434\RtmpkTAElm\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 ... [2s] OK * checking PDF version of manual ... [19s] OK * checking HTML version of manual ... [8s] OK * DONE Status: 2 ERRORs Check process probably crashed or hung up for 20 minutes ... killed Most likely this happened in the example checks (?), if not, ignore the following last lines of example output: > base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv') > cleanEx() > nameEx("check_collinearity") > ### * check_collinearity > > flush(stderr()); flush(stdout()) > > ### 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 ======== End of example output (where/before crash/hang up occured ?) ========