* using log directory ‘/home/hornik/tmp/CRAN_special_noSuggests/BayesERtools.Rcheck’ * using R Under development (unstable) (2025-02-10 r87710) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (Debian 14.2.0-12) 14.2.0 GNU Fortran (Debian 14.2.0-12) 14.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘BayesERtools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BayesERtools’ version ‘0.2.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [6s/7s] NOTE Maintainer: ‘Kenta Yoshida ’ Days since last update: 1 * 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 ‘BayesERtools’ can be installed ... [4s/4s] OK * 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] 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 ... [6s/6s] 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 ... [10s/9s] ERROR Running examples in ‘BayesERtools-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: edit_spec_coveff > ### Title: Customize specifications for covariate effect > ### simulations/visualizations > ### Aliases: edit_spec_coveff build_spec_coveff_one_variable > ### replace_spec_coveff > > ### ** Examples > > set.seed(1234) > data(d_sim_binom_cov_hgly2) > > ermod_bin <- suppressWarnings(dev_ermod_bin( + data = d_sim_binom_cov_hgly2, var_resp = "AEFLAG", + var_exposure = "AUCss_1000", var_cov = c("BGLUC", "RACE"), + verbosity_level = 0, + # Below option to make the example run fast + chains = 2, iter = 1000 + )) > > spec_coveff <- build_spec_coveff(ermod_bin) > spec_new_bgluc <- build_spec_coveff_one_variable( + "BGLUC", seq(4, 8, by = 0.1), + qi_width_cov = 0.8, show_ref_value = FALSE + ) > spec_coveff_new <- replace_spec_coveff(spec_coveff, spec_new_bgluc) > plot_coveff(ermod_bin, spec_coveff = spec_coveff_new) Error in sim_coveff(ermod = x, data = data, spec_coveff = spec_coveff, : The package "ggforce" is required. Calls: plot_coveff -> plot_coveff.ermod -> sim_coveff -> Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed dev_ermod_bin 5.694 0.251 5.177 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [37s/36s] ERROR Running ‘testthat.R’ [37s/36s] 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(BayesERtools) > > test_check("BayesERtools") [ FAIL 12 | WARN 0 | SKIP 0 | PASS 61 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-build_spec_coveff.R:34:1'): (code run outside of `test_that()`) ── Error in `sim_coveff(ermod_bin, spec_coveff = spec_coveff_new)`: The package "ggforce" is required. Backtrace: ▆ 1. └─BayesERtools::sim_coveff(ermod_bin, spec_coveff = spec_coveff_new) at test-build_spec_coveff.R:34:1 2. └─rlang::check_installed("ggforce") ── Error ('test-coveff.R:25:1'): (code run outside of `test_that()`) ─────────── Error in `sim_coveff(ermod_bin)`: The package "ggforce" is required. Backtrace: ▆ 1. └─BayesERtools::sim_coveff(ermod_bin) at test-coveff.R:25:1 2. └─rlang::check_installed("ggforce") ── Error ('test-dev_ermod_emax.R:188:3'): plot_ermod_bin_emax ────────────────── Error in `loadNamespace(x)`: there is no package called 'xgxr' Backtrace: ▆ 1. ├─testthat::expect_silent(plot(plot_er(ersim_bin_med_qi, show_orig_data = TRUE))) at test-dev_ermod_emax.R:188:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. ├─base::plot(plot_er(ersim_bin_med_qi, show_orig_data = TRUE)) 10. ├─BayesERtools::plot_er(ersim_bin_med_qi, show_orig_data = TRUE) 11. ├─BayesERtools:::plot_er.ersim_med_qi(ersim_bin_med_qi, show_orig_data = TRUE) 12. │ └─BayesERtools:::.plot_er_binary(...) 13. └─base::loadNamespace(x) 14. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 15. └─base (local) withOneRestart(expr, restarts[[1L]]) 16. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test-dev_ermod_emax.R:197:3'): Convert factor as response variable into number ── Error in `loadNamespace(x)`: there is no package called 'xgxr' Backtrace: ▆ 1. ├─testthat::expect_silent(plot_er_gof(mod_mtcars_emax, n_bins = 2)) at test-dev_ermod_emax.R:197:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. ├─BayesERtools::plot_er_gof(mod_mtcars_emax, n_bins = 2) 10. │ ├─BayesERtools::plot_er(...) 11. │ └─BayesERtools:::plot_er.ermod(...) 12. │ ├─BayesERtools::plot_er(...) 13. │ └─BayesERtools:::plot_er.ersim_med_qi(...) 14. │ └─BayesERtools:::.plot_er_binary(...) 15. └─base::loadNamespace(x) 16. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 17. └─base (local) withOneRestart(expr, restarts[[1L]]) 18. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test-dev_ermod_lin.R:77:1'): (code run outside of `test_that()`) ──── Error in `loadNamespace(x)`: there is no package called 'projpred' Backtrace: ▆ 1. ├─BayesERtools::.dev_ermod_refmodel(...) at test-dev_ermod_lin.R:77:1 2. └─base::loadNamespace(x) 3. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 4. └─base (local) withOneRestart(expr, restarts[[1L]]) 5. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test-eval_ermod.R:4:1'): (code run outside of `test_that()`) ──────── Error in `loadNamespace(x)`: there is no package called 'rsample' Backtrace: ▆ 1. └─base::loadNamespace(x) at test-eval_ermod.R:4:1 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 3. └─base (local) withOneRestart(expr, restarts[[1L]]) 4. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test-kfold_cv.R:13:1'): (code run outside of `test_that()`) ───────── Error in `run_kfold_cv(ermod_bin, k = 3, seed = 123)`: The package "rsample" is required. Backtrace: ▆ 1. └─BayesERtools::run_kfold_cv(ermod_bin, k = 3, seed = 123) at test-kfold_cv.R:13:1 2. └─rlang::check_installed("rsample") ── Error ('test-plot_ermod.R:111:3'): plot_er.ermod ──────────────────────────── Error in `loadNamespace(x)`: there is no package called 'xgxr' Backtrace: ▆ 1. ├─BayesERtools::plot_er(ermod_bin, show_orig_data = TRUE) at test-plot_ermod.R:111:3 2. ├─BayesERtools:::plot_er.ermod(ermod_bin, show_orig_data = TRUE) 3. │ ├─BayesERtools::plot_er(...) 4. │ └─BayesERtools:::plot_er.ersim_med_qi(...) 5. │ └─BayesERtools:::.plot_er_binary(...) 6. └─base::loadNamespace(x) 7. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 8. └─base (local) withOneRestart(expr, restarts[[1L]]) 9. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test-plot_ermod.R:127:3'): plot_er.ersim ──────────────────────────── Error in `loadNamespace(x)`: there is no package called 'xgxr' Backtrace: ▆ 1. ├─BayesERtools::plot_er(ersim_curve_med_qi, show_orig_data = TRUE) at test-plot_ermod.R:127:3 2. ├─BayesERtools:::plot_er.ersim_med_qi(ersim_curve_med_qi, show_orig_data = TRUE) 3. │ └─BayesERtools:::.plot_er_binary(...) 4. └─base::loadNamespace(x) 5. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 6. └─base (local) withOneRestart(expr, restarts[[1L]]) 7. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test-plot_ermod.R:147:3'): plot_er with groups ────────────────────── Error in `loadNamespace(x)`: there is no package called 'xgxr' Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-plot_ermod.R:147:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. ├─BayesERtools::plot_er(ermod_bin, show_orig_data = TRUE, options_orig_data = list(var_group = "Dose_mg")) 10. ├─BayesERtools:::plot_er.ermod(...) 11. │ ├─BayesERtools::plot_er(...) 12. │ └─BayesERtools:::plot_er.ersim_med_qi(...) 13. │ └─BayesERtools:::.plot_er_binary(...) 14. └─base::loadNamespace(x) 15. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 16. └─base (local) withOneRestart(expr, restarts[[1L]]) 17. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test-plot_ermod.R:169:3'): plot_er show caption ───────────────────── Error in `loadNamespace(x)`: there is no package called 'xgxr' Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-plot_ermod.R:169:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. ├─BayesERtools::plot_er(...) 10. ├─BayesERtools:::plot_er.ersim_med_qi(...) 11. │ └─BayesERtools:::.plot_er_binary(...) 12. └─base::loadNamespace(x) 13. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 14. └─base (local) withOneRestart(expr, restarts[[1L]]) 15. └─base (local) doWithOneRestart(return(expr), restart) ── Error ('test-plot_ermod.R:189:3'): plot_er_gof ────────────────────────────── Error in `loadNamespace(x)`: there is no package called 'xgxr' Backtrace: ▆ 1. ├─testthat::expect_silent(plot_er_gof(ermod_bin)) at test-plot_ermod.R:189:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. ├─BayesERtools::plot_er_gof(ermod_bin) 10. │ ├─BayesERtools::plot_er(...) 11. │ └─BayesERtools:::plot_er.ermod(...) 12. │ ├─BayesERtools::plot_er(...) 13. │ └─BayesERtools:::plot_er.ersim_med_qi(...) 14. │ └─BayesERtools:::.plot_er_binary(...) 15. └─base::loadNamespace(x) 16. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 17. └─base (local) withOneRestart(expr, restarts[[1L]]) 18. └─base (local) doWithOneRestart(return(expr), restart) [ FAIL 12 | WARN 0 | SKIP 0 | PASS 61 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [2s/2s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘basic_workflow_bin.Rmd’ using rmarkdown Quitting from lines 21-26 [setup] (basic_workflow_bin.Rmd) Error: processing vignette 'basic_workflow_bin.Rmd' failed with diagnostics: The package "xgxr" is required. --- failed re-building ‘basic_workflow_bin.Rmd’ --- re-building ‘overview_of_the_package.Rmd’ using rmarkdown Quitting from lines 29-82 [unnamed-chunk-2] (overview_of_the_package.Rmd) Error: processing vignette 'overview_of_the_package.Rmd' failed with diagnostics: there is no package called 'readr' --- failed re-building ‘overview_of_the_package.Rmd’ SUMMARY: processing the following files failed: ‘basic_workflow_bin.Rmd’ ‘overview_of_the_package.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 3 ERRORs, 1 NOTE