* using log directory ‘/data/localhost/ripley/R/packages/tests-donttest/hcruR.Rcheck’ * using R Under development (unstable) (2026-08-25 r90448) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2) GNU Fortran (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2) * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-08-26 17:54:48 UTC * checking for file ‘hcruR/DESCRIPTION’ ... OK * this is package ‘hcruR’ 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 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 ‘hcruR’ can be installed ... [5s/11s] 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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/15s] OK * checking Rd files ... 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 ... 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 ... OK * checking examples with --run-donttest ... ERROR Running examples in ‘hcruR-Ex.R’ failed The error most likely occurred in: > ### Name: estimate_hcru > ### Title: estimate_hcru > ### Aliases: estimate_hcru > > ### ** Examples > > ## No test: > df <- hcru_sample_data[sample(nrow(hcru_sample_data), 10), ] > estimate_hcru(data = df) Error in `purrr::map()`: ℹ In index: 1. Caused by error: ! The `update` argument of `modify_header()` was deprecated in gtsummary 2.0.0 and is now defunct. ℹ Use `modify_header(...)` input instead. Dynamic dots allow for syntax like `modify_header(!!!list(...))`. Backtrace: ▆ 1. └─hcruR::estimate_hcru(data = df) 2. └─hcruR::summarize_descriptives_gt(...) 3. └─purrr::map(...) 4. └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 5. ├─purrr:::with_indexed_errors(...) 6. │ └─base::withCallingHandlers(...) 7. ├─purrr:::call_with_cleanup(...) 8. └─hcruR (local) .f(.x[[i]], ...) 9. ├─gtsummary::bold_labels(...) 10. ├─gtsummary::modify_caption(...) 11. └─gtsummary::modify_header(tbl, update = header_map) 12. └─gtsummary:::.deprecate_modify_update_and_quiet_args(...) 13. └─lifecycle::deprecate_stop(...) 14. └─lifecycle:::deprecate_stop0(msg) 15. └─rlang::cnd_signal(...) Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [7s/16s] [7s/17s] ERROR 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(hcruR) > > test_check("hcruR") 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-estimate_hcru-20.R Saving _problems/test-estimate_hcru-41.R Saving _problems/test-utils-109.R [ FAIL 3 | WARN 24 | SKIP 0 | PASS 36 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-estimate_hcru.R:20:3'): estimate_hcru returns expected output without gt_summary ── Error in `purrr::map(settings, function(setting) { df_setting <- dplyr::filter(data, .data[[group_var_by]] == setting) vars_this <- var_list if (setting != "IP") { vars_this <- setdiff(vars_this, c("LOS", "Readmission")) } cohort_sym <- rlang::sym(group_var_main) n_df <- dplyr::mutate(dplyr::count(dplyr::distinct(df_setting, .data[[patient_id_col]], .data[[group_var_main]]), .data[[group_var_main]], name = "n"), colname = paste0("stat_", dplyr::row_number()), header = glue::glue("{.data[[group_var_main]]}, N = {n}")) header_map <- stats::setNames(n_df$header, n_df$colname) tbl <- gtsummary::tbl_summary(data = df_setting, by = !!cohort_sym, include = gtsummary::all_of(vars_this), missing = "no", type = list(all_continuous() ~ "continuous2"), statistic = list(all_continuous() ~ c(Total = "{sum}", `Mean (SD)` = "{mean} ({sd})", `Median (IQR)` = "{median} ({p25}, {p75})", Q1 = "{p25}", Q3 = "{p75}", Range = "{min} - {max}"))) if (length(unique(df_setting[[group_var_main]])) > 1) { tbl <- if (!is.null(test)) { gtsummary::add_p(tbl, test = test) } else { gtsummary::add_p(tbl) } } tbl <- gtsummary::bold_labels(gtsummary::modify_caption(gtsummary::modify_header(tbl, update = header_map), glue::glue("**Summary Table**"))) })`: i In index: 1. Caused by error: ! The `update` argument of `modify_header()` was deprecated in gtsummary 2.0.0 and is now defunct. i Use `modify_header(...)` input instead. Dynamic dots allow for syntax like `modify_header(!!!list(...))`. ── Error ('test-estimate_hcru.R:41:3'): estimate_hcru returns both summaries when gt_output = TRUE ── Error in `purrr::map(settings, function(setting) { df_setting <- dplyr::filter(data, .data[[group_var_by]] == setting) vars_this <- var_list if (setting != "IP") { vars_this <- setdiff(vars_this, c("LOS", "Readmission")) } cohort_sym <- rlang::sym(group_var_main) n_df <- dplyr::mutate(dplyr::count(dplyr::distinct(df_setting, .data[[patient_id_col]], .data[[group_var_main]]), .data[[group_var_main]], name = "n"), colname = paste0("stat_", dplyr::row_number()), header = glue::glue("{.data[[group_var_main]]}, N = {n}")) header_map <- stats::setNames(n_df$header, n_df$colname) tbl <- gtsummary::tbl_summary(data = df_setting, by = !!cohort_sym, include = gtsummary::all_of(vars_this), missing = "no", type = list(all_continuous() ~ "continuous2"), statistic = list(all_continuous() ~ c(Total = "{sum}", `Mean (SD)` = "{mean} ({sd})", `Median (IQR)` = "{median} ({p25}, {p75})", Q1 = "{p25}", Q3 = "{p75}", Range = "{min} - {max}"))) if (length(unique(df_setting[[group_var_main]])) > 1) { tbl <- if (!is.null(test)) { gtsummary::add_p(tbl, test = test) } else { gtsummary::add_p(tbl) } } tbl <- gtsummary::bold_labels(gtsummary::modify_caption(gtsummary::modify_header(tbl, update = header_map), glue::glue("**Summary Table**"))) })`: i In index: 1. Caused by error: ! The `update` argument of `modify_header()` was deprecated in gtsummary 2.0.0 and is now defunct. i Use `modify_header(...)` input instead. Dynamic dots allow for syntax like `modify_header(!!!list(...))`. ── Error ('test-utils.R:101:3'): timeline filter works as expected ───────────── Error in `purrr::map(settings, function(setting) { df_setting <- dplyr::filter(data, .data[[group_var_by]] == setting) vars_this <- var_list if (setting != "IP") { vars_this <- setdiff(vars_this, c("LOS", "Readmission")) } cohort_sym <- rlang::sym(group_var_main) n_df <- dplyr::mutate(dplyr::count(dplyr::distinct(df_setting, .data[[patient_id_col]], .data[[group_var_main]]), .data[[group_var_main]], name = "n"), colname = paste0("stat_", dplyr::row_number()), header = glue::glue("{.data[[group_var_main]]}, N = {n}")) header_map <- stats::setNames(n_df$header, n_df$colname) tbl <- gtsummary::tbl_summary(data = df_setting, by = !!cohort_sym, include = gtsummary::all_of(vars_this), missing = "no", type = list(all_continuous() ~ "continuous2"), statistic = list(all_continuous() ~ c(Total = "{sum}", `Mean (SD)` = "{mean} ({sd})", `Median (IQR)` = "{median} ({p25}, {p75})", Q1 = "{p25}", Q3 = "{p75}", Range = "{min} - {max}"))) if (length(unique(df_setting[[group_var_main]])) > 1) { tbl <- if (!is.null(test)) { gtsummary::add_p(tbl, test = test) } else { gtsummary::add_p(tbl) } } tbl <- gtsummary::bold_labels(gtsummary::modify_caption(gtsummary::modify_header(tbl, update = header_map), glue::glue("**Summary Table**"))) })`: i In index: 1. Caused by error: ! The `update` argument of `modify_header()` was deprecated in gtsummary 2.0.0 and is now defunct. i Use `modify_header(...)` input instead. Dynamic dots allow for syntax like `modify_header(!!!list(...))`. [ FAIL 3 | WARN 24 | SKIP 0 | PASS 36 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [10s/27s] ERROR Error(s) in re-building vignettes: --- re-building ‘hcruR.Rmd’ using rmarkdown Quitting from hcruR.Rmd:30-57 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `purrr::map()`: ℹ In index: 1. Caused by error: ! The `update` argument of `modify_header()` was deprecated in gtsummary 2.0.0 and is now defunct. ℹ Use `modify_header(...)` input instead. Dynamic dots allow for syntax like `modify_header(!!!list(...))`. --- Backtrace: ▆ 1. └─hcruR::estimate_hcru(...) 2. └─hcruR::summarize_descriptives_gt(...) 3. └─purrr::map(...) 4. └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 5. ├─purrr:::with_indexed_errors(...) 6. │ └─base::withCallingHandlers(...) 7. ├─purrr:::call_with_cleanup(...) 8. └─hcruR (local) .f(.x[[i]], ...) 9. ├─gtsummary::bold_labels(...) 10. ├─gtsummary::modify_caption(...) 11. └─gtsummary::modify_header(tbl, update = header_map) 12. └─gtsummary:::.deprecate_modify_update_and_quiet_args(...) 13. └─lifecycle::deprecate_stop(...) 14. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'hcruR.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error: ! The `update` argument of `modify_header()` was deprecated in gtsummary 2.0.0 and is now defunct. ℹ Use `modify_header(...)` input instead. Dynamic dots allow for syntax like `modify_header(!!!list(...))`. --- failed re-building ‘hcruR.Rmd’ SUMMARY: processing the following file failed: ‘hcruR.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... NOTE Found the following files/directories: ‘~/.cache/R/Require’ ‘~/.cache/R/Require/README’ ‘~/.cache/R/Require/packages’ ‘~/.cache/R/Require/packages/4.7’ * DONE Status: 3 ERRORs, 1 NOTE See ‘/data/localhost/ripley/R/packages/tests-donttest/hcruR.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 2:27.02, 60.45 + 9.42