• using R version 4.6.1 (2026-06-24)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-16 (Debian 16.2.0-1) 16.2.0     GNU Fortran (Debian 16.2.0-1) 16.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-08-29 14:17:36 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 ... 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/3s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the package can be unloaded cleanly ... [1s/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 ... [9s/12s] OK
• checking Rd files ... [0s/1s] 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 ... [3s/3s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [10s/12s] ERROR   Running ‘testthat.R’ [10s/12s] 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   The following errors were returned during `add_p()`:   x For variable `var1` (`cohort`) and "estimate", "std.error", "parameter", "statistic", "conf.low", "conf.high", and "p.value" statistics: The package "broom" (>= 1.0.8) is required.   x For variable `var2` (`cohort`) and "estimate", "std.error", "parameter", "statistic", "conf.low", "conf.high", and "p.value" statistics: The package "broom" (>= 1.0.8) is required.   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 ──   <purrr_error_indexed/rlang_error/error/condition>   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 ──   <purrr_error_indexed/rlang_error/error/condition>   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 ─────────────   <purrr_error_indexed/rlang_error/error/condition>   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 ... [6s/7s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘hcruR.Rmd’ using rmarkdown Quitting from hcruR.Rmd:30-57 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/purrr_error_indexed> 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 ... [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