• using R Under development (unstable) (2026-07-23 r90295)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-16 (Debian 16.1.0-2) 16.1.0     GNU Fortran (Debian 16.1.0-2) 16.1.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-07-24 15:14:34 UTC
• checking for file ‘gtregression/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘gtregression’ version ‘1.0.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/2s] OK
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘gtregression’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [2s/4s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the package can be unloaded cleanly ... [2s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
• checking loading without being on the library search path ... [2s/2s] 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 ... [12s/13s] OK
• checking Rd files ... [0s/0s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [0s/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 ... [2s/2s] 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
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [41s/47s] ERROR   Running ‘testthat.R’ [40s/47s] 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/RtmpZbSUEI/regression_results.docx   `height` was translated to `width`.   Plot saved at: /home/hornik/tmp/scratch/RtmpZbSUEI/plot_png.png   `height` was translated to `width`.   Plot saved at: /home/hornik/tmp/scratch/RtmpZbSUEI/plot_pdf.pdf   `height` was translated to `width`.   Plot saved at: /home/hornik/tmp/scratch/RtmpZbSUEI/plot_jpg.jpg   `height` was translated to `width`.   Word document saved at: /home/hornik/tmp/scratch/RtmpZbSUEI/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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [1s/2s] OK
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs