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Last updated on 2026-09-03 05:59:27 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 6.01 | 76.35 | 82.36 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.1 | 5.12 | 72.03 | 77.15 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.1 | 5.00 | 70.62 | 75.62 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.1 | 70.99 | OK | |||
| r-devel-windows-x86_64 | 1.0.1 | 9.00 | 108.00 | 117.00 | OK | |
| r-patched-linux-x86_64 | 1.0.1 | 6.48 | 91.63 | 98.11 | OK | |
| r-release-linux-x86_64 | 1.0.0 | 4.32 | 72.22 | 76.54 | ERROR | |
| r-release-macos-arm64 | 1.0.1 | 2.00 | 28.00 | 30.00 | OK | |
| r-release-macos-x86_64 | 1.0.1 | 5.00 | 117.00 | 122.00 | OK | |
| r-release-windows-x86_64 | 1.0.1 | 9.00 | 105.00 | 114.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.1 | 2.00 | 32.00 | 34.00 | OK | |
| r-oldrel-macos-x86_64 | 1.0.1 | 5.00 | 139.00 | 144.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.1 | 11.00 | 131.00 | 142.00 | OK |
Version: 1.0.0
Check: tests
Result: 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
Flavors: r-devel-linux-x86_64-debian-clang, r-release-linux-x86_64
Version: 1.0.0
Check: re-building of vignette outputs
Result: 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
Flavors: r-devel-linux-x86_64-debian-clang, r-release-linux-x86_64
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