Package: cardx Check: examples New result: ERROR Running examples in ‘cardx-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: ard_incidence_rate > ### Title: ARD Incidence Rate > ### Aliases: ard_incidence_rate > > ### ** Examples > > set.seed(1) > data <- data.frame( + USUBJID = 1:100, + TRTA = sample(LETTERS[1:3], 100, replace = TRUE), + AETTE1 = abs(rnorm(100, mean = 0.5)), + AETOT1 = sample(0:20, 100, replace = TRUE) + ) > > data |> + ard_incidence_rate(time = AETTE1, count = AETOT1, id = USUBJID, by = TRTA, unit_label = "years") Error: ! `any_of()` must be used within a *selecting* function. ℹ See for details. Backtrace: ▆ 1. └─cardx::ard_incidence_rate(...) 2. ├─cards::tidy_ard_row_order(...) 3. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 4. ├─cards::tidy_ard_column_order(...) 5. │ ├─dplyr::pull(...) 6. │ ├─dplyr::arrange(...) 7. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 8. │ └─dplyr::select(x, all_ard_groups()) 9. ├─cards::as_card(...) 10. │ └─cards:::check_class(x, cls = "data.frame") 11. ├─dplyr::mutate(...) 12. ├─dplyr::left_join(...) 13. ├─dplyr::select(...) 14. ├─cards::ard_mvsummary(...) 15. ├─cards:::ard_mvsummary.data.frame(...) 16. └─tidyselect::any_of(by) 17. ├─vars %||% peek_vars(fn = "any_of") 18. └─tidyselect::peek_vars(fn = "any_of") 19. └─cli::cli_abort(...) 20. └─rlang::abort(...) Execution halted Package: cardx Check: tests New result: ERROR Running ‘testthat.R’ [84s/44s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > test_check("cardx", stop_on_warning = TRUE) Loading required package: cardx Starting 2 test processes. Saving _problems/test-ard_categorical_ci.survey.design-28.R > test-ard_categorical_ci.data.frame.R: 5 missing observations in the "am" column have been removed. Saving _problems/test-ard_continuous_ci.survey.design-39.R > test-ard_effectsize_cohens_d.R: For paired samples, 'repeated_measures_d()' provides more options. Saving _problems/test-ard_categorical_ci.data.frame-202.R Saving _problems/test-ard_categorical_ci.data.frame-224.R Saving _problems/test-ard_categorical_ci.data.frame-287.R Saving _problems/test-ard_categorical_ci.data.frame-309.R > test-ard_effectsize_hedges_g.R: For paired samples, 'repeated_measures_d()' provides more options. Saving _problems/test-ard_incidence_rate-12.R Saving _problems/test-ard_incidence_rate-48.R Saving _problems/test-ard_missing.survey.design-14.R Saving _problems/test-ard_missing.survey.design-15.R Saving _problems/test-ard_missing.survey.design-113.R Saving _problems/test-ard_missing.survey.design-146.R > test-ard_stats_oneway_test.R: Multiple parameters; naming those columns num.df and den.df. Saving _problems/test-ard_stats_t_test_onesample-49.R Saving _problems/test-ard_stats_wilcox_test_onesample-51.R Saving _problems/test-ard_summary.survey.design-18.R Saving _problems/test-ard_summary.survey.design-19.R Saving _problems/test-ard_summary.survey.design-90.R Saving _problems/test-ard_summary.survey.design-91.R Saving _problems/test-ard_summary.survey.design-256.R Saving _problems/test-ard_summary.survey.design-262.R Saving _problems/test-ard_summary.survey.design-302.R Saving _problems/test-ard_summary.survey.design-315.R Saving _problems/test-ard_summary.survey.design-331.R Saving _problems/test-ard_summary.survey.design-346.R Saving _problems/test-ard_summary.survey.design-374.R Saving _problems/test-ard_summary.survey.design-406.R Saving _problems/test-ard_summary.survey.design-519.R Saving _problems/test-ard_summary.survey.design-540.R Saving _problems/test-ard_tabulate_abnormal-14.R > test-ard_tabulate_max.R: `AESEV`: "MILD" < "MODERATE" < "SEVERE" Saving _problems/test-ard_tabulate_max-194.R Saving _problems/test-ard_tabulate_max-244.R Saving _problems/test-ard_tabulate.survey.design-21.R Saving _problems/test-ard_tabulate.survey.design-22.R Saving _problems/test-ard_tabulate.survey.design-484.R Saving _problems/test-ard_tabulate.survey.design-485.R Saving _problems/test-ard_tabulate.survey.design-780.R Saving _problems/test-ard_tabulate.survey.design-781.R Saving _problems/test-ard_tabulate.survey.design-1071.R Saving _problems/test-ard_tabulate.survey.design-1072.R Saving _problems/test-ard_tabulate.survey.design-1229.R Saving _problems/test-ard_tabulate.survey.design-1310.R Saving _problems/test-ard_tabulate.survey.design-1325.R Saving _problems/test-ard_tabulate.survey.design-1343.R Saving _problems/test-ard_tabulate.survey.design-1387.R Saving _problems/test-ard_tabulate_value.survey.design-21.R Saving _problems/test-ard_tabulate_value.survey.design-25.R Saving _problems/test-ard_tabulate_value.survey.design-640.R Saving _problems/test-ard_tabulate_value.survey.design-644.R Saving _problems/test-ard_tabulate_value.survey.design-799.R Saving _problems/test-ard_total_n.survey.design-7.R Saving _problems/test-ard_total_n.survey.design-15.R Saving _problems/test-ard_total_n.survey.design-37.R [ FAIL 52 | WARN 35 | SKIP 56 | PASS 315 ] ══ Skipped tests (56) ══════════════════════════════════════════════════════════ • On CRAN (56): 'test-ard_attributes.survey.design.R:3:1', 'test-ard_aod_wald_test.R:3:1', 'test-ard_car_vif.R:3:1', 'test-ard_car_vif.R:28:1', 'test-ard_car_anova.R:3:1', 'test-ard_car_anova.R:15:1', 'test-ard_categorical_ci.survey.design.R:6:1', 'test-ard_continuous_ci.survey.design.R:6:1', 'test-ard_continuous_ci.survey.design.R:193:1', 'test-ard_effectsize_cohens_d.R:3:1', 'test-ard_effectsize_hedges_g.R:3:1', 'test-ard_emmeans_contrast.R:3:1', 'test-ard_emmeans_contrast.R:100:1', 'test-ard_incidence_rate.R:66:1', 'test-ard_emmeans_emmeans.R:3:1', 'test-ard_emmeans_emmeans.R:93:1', 'test-ard_proportion_ci.R:62:1', 'test-ard_proportion_ci.R:112:1', 'test-ard_regression_basic.R:3:1', 'test-ard_regression.R:3:1', 'test-ard_regression.R:40:1', 'test-ard_stats_aov.R:3:1', 'test-ard_stats_kruskal_test.R:3:1', 'test-ard_stats_mantelhaen_test.R:3:1', 'test-ard_stats_mood_test.R:3:1', 'test-ard_stats_oneway_test.R:3:1', 'test-ard_stats_poisson_test.R:73:1', 'test-ard_survey_svychisq.R:3:1', 'test-ard_survey_svyranktest.R:3:1', 'test-ard_survival_survfit.R:3:1', 'test-ard_survival_survfit.R:16:1', 'test-ard_survival_survfit.R:29:1', 'test-ard_survival_survfit.R:42:1', 'test-ard_survival_survfit.R:64:1', 'test-ard_survival_survfit.R:90:1', 'test-ard_survival_survfit.R:120:1', 'test-ard_survival_survfit.R:191:1', 'test-ard_survival_survfit.R:201:1', 'test-ard_survival_survfit.R:221:1', 'test-ard_survival_survfit.R:231:1', 'test-ard_survival_survfit_diff.R:36:1', 'test-ard_tabulate_abnormal.R:41:1', 'test-ard_tabulate_max.R:1:1', 'test-ard_tabulate_max.R:60:1', 'test-ard_tabulate_max.R:75:1', 'test-ard_tabulate_max.R:115:1', 'test-ard_tabulate_max.R:210:1', 'test-ard_tabulate_max.R:258:1', 'test-ard_tabulate.survey.design.R:421:1', 'test-ard_tabulate.survey.design.R:1176:1', 'test-ard_tabulate.survey.design.R:1410:1', 'test-ard_tabulate_value.survey.design.R:736:1', 'test-proportion_ci.R:3:1', 'test-proportion_ci.R:122:1', 'test-construction_helpers.R:3:1', 'test-construction_helpers.R:103:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-ard_categorical_ci.survey.design.R:25:3'): ard_categorical_ci(variables) ── Error in `ard_categorical_ci(dclus1, variables = starts_with("xxxxxx"))`: The following columns are not present: "variable", "stat_name", "stat_label", "stat", "fmt_fun", "warning", and "error". Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-ard_categorical_ci.survey.design.R:25:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─cardx::ard_categorical_ci(dclus1, variables = starts_with("xxxxxx")) 5. └─cardx:::ard_categorical_ci.survey.design(dclus1, variables = starts_with("xxxxxx")) 6. └─cards::as_card(dplyr::tibble()) 7. └─cards::check_ard_structure(...) 8. └─cards:::.message_or_error(...) 9. └─cli::cli_abort(msg, call = call, .envir = envir) 10. └─rlang::abort(...) ── Error ('test-ard_continuous_ci.survey.design.R:36:3'): ard_continuous_ci(variables) ── Error in `ard_continuous_ci(dclus1, variables = starts_with("xxxxxx"))`: The following columns are not present: "variable", "stat_name", "stat_label", "stat", "fmt_fun", "warning", and "error". Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-ard_continuous_ci.survey.design.R:36:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─cardx::ard_continuous_ci(dclus1, variables = starts_with("xxxxxx")) 5. └─cardx:::ard_continuous_ci.survey.design(dclus1, variables = starts_with("xxxxxx")) 6. └─cards::as_card(dplyr::tibble()) 7. └─cards::check_ard_structure(...) 8. └─cards:::.message_or_error(...) 9. └─cli::cli_abort(msg, call = call, .envir = envir) 10. └─rlang::abort(...) ── Failure ('test-ard_categorical_ci.data.frame.R:188:3'): ard_continuous_ci.data.frame(denominator='row') ── Expected `dplyr::arrange(...)` to equal `dplyr::arrange(...)`. Differences: `attr(actual, 'args')` is absent `attr(expected, 'args')` is a list ── Failure ('test-ard_categorical_ci.data.frame.R:205:3'): ard_continuous_ci.data.frame(denominator='row') ── Expected `dplyr::arrange(...)` to equal `dplyr::arrange(...)`. Differences: `attr(actual, 'args')` is absent `attr(expected, 'args')` is a list ── Failure ('test-ard_categorical_ci.data.frame.R:273:3'): ard_continuous_ci.data.frame(denominator='cell') ── Expected `dplyr::arrange(...)` to equal `dplyr::arrange(...)`. Differences: `attr(actual, 'args')` is absent `attr(expected, 'args')` is a list ── Failure ('test-ard_categorical_ci.data.frame.R:290:3'): ard_continuous_ci.data.frame(denominator='cell') ── Expected `dplyr::arrange(...)` to equal `dplyr::arrange(...)`. Differences: `attr(actual, 'args')` is absent `attr(expected, 'args')` is a list ── Error ('test-ard_incidence_rate.R:9:3'): ard_incidence_rate() works ───────── Error: `any_of()` must be used within a *selecting* function. i See for details. Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-ard_incidence_rate.R:9:3 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. └─cardx::ard_incidence_rate(...) 10. ├─cards::tidy_ard_row_order(...) 11. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 12. ├─cards::tidy_ard_column_order(...) 13. │ ├─dplyr::pull(...) 14. │ ├─dplyr::arrange(...) 15. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 16. │ └─dplyr::select(x, all_ard_groups()) 17. ├─cards::as_card(...) 18. │ └─cards:::check_class(x, cls = "data.frame") 19. ├─dplyr::mutate(...) 20. ├─dplyr::left_join(...) 21. ├─dplyr::select(...) 22. ├─cards::ard_mvsummary(...) 23. ├─cards:::ard_mvsummary.data.frame(...) 24. └─tidyselect::any_of(by) 25. ├─vars %||% peek_vars(fn = "any_of") 26. └─tidyselect::peek_vars(fn = "any_of") 27. └─cli::cli_abort(...) 28. └─rlang::abort(...) ── Error ('test-ard_incidence_rate.R:45:3'): ard_incidence_rate(conf.type) works ── Error: `any_of()` must be used within a *selecting* function. i See for details. Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-ard_incidence_rate.R:45:3 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. └─cardx::ard_incidence_rate(...) 10. ├─cards::tidy_ard_row_order(...) 11. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 12. ├─cards::tidy_ard_column_order(...) 13. │ ├─dplyr::pull(...) 14. │ ├─dplyr::arrange(...) 15. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 16. │ └─dplyr::select(x, all_ard_groups()) 17. ├─cards::as_card(...) 18. │ └─cards:::check_class(x, cls = "data.frame") 19. ├─dplyr::mutate(...) 20. ├─dplyr::left_join(...) 21. ├─dplyr::select(...) 22. ├─cards::ard_mvsummary(...) 23. ├─cards:::ard_mvsummary.data.frame(...) 24. └─tidyselect::any_of(by) 25. ├─vars %||% peek_vars(fn = "any_of") 26. └─tidyselect::peek_vars(fn = "any_of") 27. └─cli::cli_abort(...) 28. └─rlang::abort(...) ── Failure ('test-ard_missing.survey.design.R:11:3'): ard_missing.survey.design() works ── Expected `... <- NULL` not to throw any errors. Actually got a with message: The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-ard_missing.survey.design.R:11:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─cards::ard_missing(svy_titanic, variables = c(Class, Age), by = NULL) 8. └─cardx:::ard_missing.survey.design(svy_titanic, variables = c(Class, Age), by = NULL) 9. ├─dplyr::mutate(...) 10. ├─cards::ard_tabulate(...) 11. └─cardx:::ard_tabulate.survey.design(...) 12. ├─cards::tidy_ard_row_order(...) 13. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 14. ├─cards::tidy_ard_column_order(...) 15. │ ├─dplyr::pull(...) 16. │ ├─dplyr::arrange(...) 17. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 18. │ └─dplyr::select(x, all_ard_groups()) 19. ├─cards::as_card(...) 20. │ └─cards:::check_class(x, cls = "data.frame") 21. ├─dplyr::mutate(...) 22. └─cardx:::.restore_original_column_types(cards, data = data$variables) 23. └─cards::as_card(...) 24. └─cards::check_ard_structure(...) 25. └─cards:::.message_or_error(...) 26. └─cli::cli_abort(msg, call = call, .envir = envir) 27. └─rlang::abort(...) ── Error ('test-ard_missing.survey.design.R:15:3'): ard_missing.survey.design() works ── Error in `eval(code, test_env)`: object 'ard_svy_missing' not found Backtrace: ▆ 1. ├─testthat::expect_invisible(...) at test-ard_missing.survey.design.R:15:3 2. │ └─base::withVisible(call) 3. └─cards::check_ard_structure(ard_svy_missing, method = FALSE) ── Error ('test-ard_missing.survey.design.R:110:3'): ard_missing.survey.design() follows ard structure ── Error in `cards::check_ard_structure(ard_missing(svy_titanic, variables = c(Class, Age), by = NULL), method = FALSE)`: The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-ard_missing.survey.design.R:110:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. ├─cards::check_ard_structure(...) 10. ├─cards::ard_missing(svy_titanic, variables = c(Class, Age), by = NULL) 11. └─cardx:::ard_missing.survey.design(...) 12. ├─dplyr::mutate(...) 13. ├─cards::ard_tabulate(...) 14. └─cardx:::ard_tabulate.survey.design(...) 15. ├─cards::tidy_ard_row_order(...) 16. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 17. ├─cards::tidy_ard_column_order(...) 18. │ ├─dplyr::pull(...) 19. │ ├─dplyr::arrange(...) 20. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 21. │ └─dplyr::select(x, all_ard_groups()) 22. ├─cards::as_card(...) 23. │ └─cards:::check_class(x, cls = "data.frame") 24. ├─dplyr::mutate(...) 25. └─cardx:::.restore_original_column_types(cards, data = data$variables) 26. └─cards::as_card(...) 27. └─cards::check_ard_structure(...) 28. └─cards:::.message_or_error(...) 29. └─cli::cli_abort(msg, call = call, .envir = envir) 30. └─rlang::abort(...) ── Error ('test-ard_missing.survey.design.R:118:3'): ard_missing.survey.design() works on design columns ── Error in `ard_missing(dplyr::tribble(~region, ~year, ~weights, 3, 1972, 0.663196271930943, 3, 1972, 0.917370028585327, 3, 1972, 0.897412512251031, 3, 1972, 1.06634082743438, 3, 1972, 0.94432371066466, 3, 1972, 0.526887241987567, 3, 1972, 0.526887241987567, 3, 1972, 0.546578869586901, 7, 1972, 0.283198307048893, 7, 1972, 0.494322145606406) %>% survey::svydesign(data = ., ids = ~region, strata = ~year, weights = ~weights, nest = TRUE), variables = weights)`: The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-ard_missing.survey.design.R:118:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─base::suppressWarnings(...) 5. │ └─base::withCallingHandlers(...) 6. ├─base::getElement(...) 7. ├─dplyr::pull(...) 8. ├─dplyr::filter(...) 9. ├─cards::ard_missing(...) 10. └─cardx:::ard_missing.survey.design(...) 11. ├─dplyr::mutate(...) 12. ├─cards::ard_tabulate(...) 13. └─cardx:::ard_tabulate.survey.design(...) 14. ├─cards::tidy_ard_row_order(...) 15. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 16. ├─cards::tidy_ard_column_order(...) 17. │ ├─dplyr::pull(...) 18. │ ├─dplyr::arrange(...) 19. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 20. │ └─dplyr::select(x, all_ard_groups()) 21. ├─cards::as_card(...) 22. │ └─cards:::check_class(x, cls = "data.frame") 23. ├─dplyr::mutate(...) 24. └─cardx:::.restore_original_column_types(cards, data = data$variables) 25. └─cards::as_card(...) 26. └─cards::check_ard_structure(...) 27. └─cards:::.message_or_error(...) 28. └─cli::cli_abort(msg, call = call, .envir = envir) 29. └─rlang::abort(...) ── Error ('test-ard_stats_t_test_onesample.R:43:3'): ard_stats_t_test_onesample() works ── Error in `ard_stats_t_test_onesample(cards::ADSL, variables = character(0))`: The following columns are not present: "variable", "stat_name", "stat_label", "stat", "fmt_fun", "warning", and "error". Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-ard_stats_t_test_onesample.R:43:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─cardx::ard_stats_t_test_onesample(cards::ADSL, variables = character(0)) 5. └─cards::as_card(dplyr::tibble()) 6. └─cards::check_ard_structure(...) 7. └─cards:::.message_or_error(...) 8. └─cli::cli_abort(msg, call = call, .envir = envir) 9. └─rlang::abort(...) ── Error ('test-ard_stats_wilcox_test_onesample.R:45:3'): ard_stats_wilcox_test_onesample() works ── Error in `ard_stats_wilcox_test_onesample(cards::ADSL, variables = character(0))`: The following columns are not present: "variable", "stat_name", "stat_label", "stat", "fmt_fun", "warning", and "error". Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-ard_stats_wilcox_test_onesample.R:45:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─cardx::ard_stats_wilcox_test_onesample(cards::ADSL, variables = character(0)) 5. └─cards::as_card(dplyr::tibble()) 6. └─cards::check_ard_structure(...) 7. └─cards:::.message_or_error(...) 8. └─cli::cli_abort(msg, call = call, .envir = envir) 9. └─rlang::abort(...) ── Failure ('test-ard_summary.survey.design.R:7:3'): unstratified ard_summary.survey.design() works ── Expected `... <- NULL` not to throw any errors. Actually got a with message: The following columns are not present: "stat_label" and "fmt_fun". Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-ard_summary.survey.design.R:7:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─cards::ard_summary(...) 8. └─cardx:::ard_summary.survey.design(...) 9. └─cardx:::.restore_original_column_types(...) 10. └─cards::as_card(...) 11. └─cards::check_ard_structure(...) 12. └─cards:::.message_or_error(...) 13. └─cli::cli_abort(msg, call = call, .envir = envir) 14. └─rlang::abort(...) ── Error ('test-ard_summary.survey.design.R:19:3'): unstratified ard_summary.survey.design() works ── Error in `eval(code, test_env)`: object 'ard_uni_svy_cont' not found Backtrace: ▆ 1. ├─testthat::expect_invisible(cards::check_ard_structure(ard_uni_svy_cont)) at test-ard_summary.survey.design.R:19:3 2. │ └─base::withVisible(call) 3. └─cards::check_ard_structure(ard_uni_svy_cont) ── Failure ('test-ard_summary.survey.design.R:78:3'): stratified ard_summary.survey.design() works ── Expected `... <- NULL` not to throw any errors. Actually got a with message: The following columns are not present: "stat_label" and "fmt_fun". Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-ard_summary.survey.design.R:78:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─cards::ard_summary(...) 8. └─cardx:::ard_summary.survey.design(...) 9. └─cardx:::.restore_original_column_types(...) 10. └─cards::as_card(...) 11. └─cards::check_ard_structure(...) 12. └─cards:::.message_or_error(...) 13. └─cli::cli_abort(msg, call = call, .envir = envir) 14. └─rlang::abort(...) ── Error ('test-ard_summary.survey.design.R:91:3'): stratified ard_summary.survey.design() works ── Error in `eval(code, test_env)`: object 'ard_svy_cont' not found Backtrace: ▆ 1. ├─testthat::expect_invisible(cards::check_ard_structure(ard_svy_cont)) at test-ard_summary.survey.design.R:91:3 2. │ └─base::withVisible(call) 3. └─cards::check_ard_structure(ard_svy_cont) ── Failure ('test-ard_summary.survey.design.R:245:3'): ard_summary.survey.design() NA handling ── Expected `... <- NULL` not to throw any errors. Actually got a with message: The following columns are not present: "stat_label" and "fmt_fun". Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-ard_summary.survey.design.R:245:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─cards::ard_summary(...) 8. └─cardx:::ard_summary.survey.design(...) 9. └─cardx:::.restore_original_column_types(...) 10. └─cards::as_card(...) 11. └─cards::check_ard_structure(...) 12. └─cards:::.message_or_error(...) 13. └─cli::cli_abort(msg, call = call, .envir = envir) 14. └─rlang::abort(...) ── Error ('test-ard_summary.survey.design.R:258:3'): ard_summary.survey.design() NA handling ── Error in `eval(code, test_env)`: object 'ard_uni_NA_svy_cont' not found Backtrace: ▆ 1. ├─testthat::expect_true(...) at test-ard_summary.survey.design.R:258:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─cardx:::map_lgl(...) 5. └─cardx:::.rlang_purrr_map_mold(.x, .f, logical(1), ...) 6. └─base::vapply(.x, .f, .mold, ..., USE.NAMES = FALSE) ── Failure ('test-ard_summary.survey.design.R:292:3'): ard_summary.survey.design() error handling ── Expected `ard_summary(...)` not to throw any errors. Actually got a with message: The following columns are not present: "stat_label" and "fmt_fun". Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-ard_summary.survey.design.R:292:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─cards::ard_summary(...) 8. └─cardx:::ard_summary.survey.design(...) 9. └─cardx:::.restore_original_column_types(...) 10. └─cards::as_card(...) 11. └─cards::check_ard_structure(...) 12. └─cards:::.message_or_error(...) 13. └─cli::cli_abort(msg, call = call, .envir = envir) 14. └─rlang::abort(...) ── Failure ('test-ard_summary.survey.design.R:304:3'): ard_summary.survey.design() error handling ── Expected `ard_summary(...)` not to throw any errors. Actually got a with message: The following columns are not present: "stat_label" and "fmt_fun". Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-ard_summary.survey.design.R:304:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─cards::ard_summary(...) 8. └─cardx:::ard_summary.survey.design(...) 9. └─cardx:::.restore_original_column_types(...) 10. └─cards::as_card(...) 11. └─cards::check_ard_structure(...) 12. └─cards:::.message_or_error(...) 13. └─cli::cli_abort(msg, call = call, .envir = envir) 14. └─rlang::abort(...) ── Error ('test-ard_summary.survey.design.R:322:3'): ard_summary.survey.design(fmt_fun) ── Error in `ard_summary(dclus1, variables = c(api99, api00), statistic = ~c("mean", "median", "min", "max"), fmt_fun = list(api00 = list(mean = 2, median = "xx.xx", min = as.character)))`: The following columns are not present: "stat_label" and "fmt_fun". Backtrace: ▆ 1. ├─base::as.data.frame(...) 2. ├─dplyr::select(...) 3. ├─cards::ard_summary(...) 4. └─cardx:::ard_summary.survey.design(...) 5. └─cardx:::.restore_original_column_types(...) 6. └─cards::as_card(...) 7. └─cards::check_ard_structure(...) 8. └─cards:::.message_or_error(...) 9. └─cli::cli_abort(msg, call = call, .envir = envir) 10. └─rlang::abort(...) ── Error ('test-ard_summary.survey.design.R:338:3'): ard_summary.survey.design(stat_label) ── Error in `ard_summary(dclus1, variables = c(api00, api99), statistic = ~c("mean", "median", "min", "max"), stat_label = list(api00 = list(mean = "MeAn", median = "MEDian", min = "MINimum")))`: The following columns are not present: "stat_label" and "fmt_fun". Backtrace: ▆ 1. ├─base::as.data.frame(...) 2. ├─cards::ard_summary(...) 3. └─cardx:::ard_summary.survey.design(...) 4. └─cardx:::.restore_original_column_types(...) 5. └─cards::as_card(...) 6. └─cards::check_ard_structure(...) 7. └─cards:::.message_or_error(...) 8. └─cli::cli_abort(msg, call = call, .envir = envir) 9. └─rlang::abort(...) ── Error ('test-ard_summary.survey.design.R:363:3'): ard_summary.survey.design(by) unobserved levels/combinations ── Error in `ard_summary(dclus1, variables = api00, by = both, statistic = ~c("mean", "median", "min", "max"))`: The following columns are not present: "stat_label" and "fmt_fun". Backtrace: ▆ 1. ├─testthat::expect_setequal(...) at test-ard_summary.survey.design.R:363:3 2. │ └─testthat::quasi_label(enquo(expected)) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─base::unique(...) 5. ├─cardx:::map_chr(...) 6. │ └─cardx:::.rlang_purrr_map_mold(.x, .f, character(1), ...) 7. │ └─base::vapply(.x, .f, .mold, ..., USE.NAMES = FALSE) 8. ├─dplyr::pull(...) 9. ├─cards::ard_summary(...) 10. └─cardx:::ard_summary.survey.design(...) 11. └─cardx:::.restore_original_column_types(...) 12. └─cards::as_card(...) 13. └─cards::check_ard_structure(...) 14. └─cards:::.message_or_error(...) 15. └─cli::cli_abort(msg, call = call, .envir = envir) 16. └─rlang::abort(...) ── Error ('test-ard_summary.survey.design.R:403:3'): ard_summary.survey.design() works when using generic names ── Error in `ard_summary(dclus1, variables = c(cds, stype), by = dnum)`: The following columns are not present: "stat_label" and "fmt_fun". Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-ard_summary.survey.design.R:403:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─dplyr::select(...) 5. ├─cards::ard_summary(dclus1, variables = c(cds, stype), by = dnum) 6. └─cardx:::ard_summary.survey.design(dclus1, variables = c(cds, stype), by = dnum) 7. └─cardx:::.restore_original_column_types(...) 8. └─cards::as_card(...) 9. └─cards::check_ard_structure(...) 10. └─cards:::.message_or_error(...) 11. └─cli::cli_abort(msg, call = call, .envir = envir) 12. └─rlang::abort(...) ── Error ('test-ard_summary.survey.design.R:516:3'): ard_summary.survey.design() follows ard structure ── Error in `cards::check_ard_structure(ard_summary(dclus1, variables = c(cds, stype), by = snum), method = FALSE)`: The following columns are not present: "stat_label" and "fmt_fun". Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-ard_summary.survey.design.R:516:3 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. ├─cards::check_ard_structure(...) 10. ├─cards::ard_summary(dclus1, variables = c(cds, stype), by = snum) 11. └─cardx:::ard_summary.survey.design(...) 12. └─cardx:::.restore_original_column_types(...) 13. └─cards::as_card(...) 14. └─cards::check_ard_structure(...) 15. └─cards:::.message_or_error(...) 16. └─cli::cli_abort(msg, call = call, .envir = envir) 17. └─rlang::abort(...) ── Error ('test-ard_summary.survey.design.R:533:3'): ard_summary.survey.design() original types are retained ── Error in `ard_summary(data = dclus1, variables = c(api00, api99), by = c(stype, sch.wide_int, sch.wide_dbl))`: The following columns are not present: "stat_label" and "fmt_fun". Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-ard_summary.survey.design.R:533:3 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. ├─cards::ard_summary(...) 10. └─cardx:::ard_summary.survey.design(...) 11. └─cardx:::.restore_original_column_types(...) 12. └─cards::as_card(...) 13. └─cards::check_ard_structure(...) 14. └─cards:::.message_or_error(...) 15. └─cli::cli_abort(msg, call = call, .envir = envir) 16. └─rlang::abort(...) ── Error ('test-ard_tabulate_abnormal.R:9:3'): ard_tabulate_abnormal() works ─── Error: `any_of()` must be used within a *selecting* function. i See for details. Backtrace: ▆ 1. ├─testthat::expect_message(...) at test-ard_tabulate_abnormal.R:9:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─testthat::expect_message(...) 8. │ └─testthat:::expect_condition_matching_(...) 9. │ └─testthat:::quasi_capture(...) 10. │ ├─testthat (local) .capture(...) 11. │ │ └─base::withCallingHandlers(...) 12. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 13. └─cardx::ard_tabulate_abnormal(...) 14. ├─cards::tidy_ard_row_order(...) 15. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 16. ├─cards::tidy_ard_column_order(...) 17. │ ├─dplyr::pull(...) 18. │ ├─dplyr::arrange(...) 19. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 20. │ └─dplyr::select(x, all_ard_groups()) 21. ├─cards::as_card(...) 22. │ └─cards:::check_class(x, cls = "data.frame") 23. ├─dplyr::mutate(...) 24. ├─dplyr::bind_rows(...) 25. │ └─rlang::list2(...) 26. └─base::lapply(...) 27. └─cardx (local) FUN(X[[i]], ...) 28. ├─dplyr::bind_cols(...) 29. │ └─rlang::list2(...) 30. ├─cards::ard_mvsummary(...) 31. ├─cards:::ard_mvsummary.data.frame(...) 32. └─tidyselect::any_of(by) 33. ├─vars %||% peek_vars(fn = "any_of") 34. └─tidyselect::peek_vars(fn = "any_of") 35. └─cli::cli_abort(...) 36. └─rlang::abort(...) ── Failure ('test-ard_tabulate_max.R:191:3'): ard_tabulate_max() works with pre-ordered factor variables ── Expected `res` to equal `dplyr::filter(res3, variable == "AESEV")`. Differences: `attr(actual, 'args')$variables`: "AESEV" `attr(expected, 'args')$variables`: "SEX" ── Error ('test-ard_tabulate_max.R:237:3'): ard_tabulate_max() works without any variables ── Error in `ard_tabulate_max(data = cards::ADAE, variables = starts_with("xxxx"), id = USUBJID, by = c(TRTA, AESEV))`: The following columns are not present: "variable", "stat_name", "stat_label", "stat", "fmt_fun", "warning", and "error". Backtrace: ▆ 1. └─cardx::ard_tabulate_max(...) 2. └─cards::as_card(dplyr::tibble()) 3. └─cards::check_ard_structure(...) 4. └─cards:::.message_or_error(...) 5. └─cli::cli_abort(msg, call = call, .envir = envir) 6. └─rlang::abort(...) ── Failure ('test-ard_tabulate.survey.design.R:12:3'): ard_tabulate.survey.design() works ── Expected `... <- NULL` not to throw any errors. Actually got a with message: The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-ard_tabulate.survey.design.R:12:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─cards::ard_tabulate(...) 8. └─cardx:::ard_tabulate.survey.design(svy_titanic, variables = c(Class, Age), by = Survived, denominator = "row") 9. ├─cards::tidy_ard_row_order(...) 10. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 11. ├─cards::tidy_ard_column_order(...) 12. │ ├─dplyr::pull(...) 13. │ ├─dplyr::arrange(...) 14. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 15. │ └─dplyr::select(x, all_ard_groups()) 16. ├─cards::as_card(...) 17. │ └─cards:::check_class(x, cls = "data.frame") 18. ├─dplyr::mutate(...) 19. └─cardx:::.restore_original_column_types(cards, data = data$variables) 20. └─cards::as_card(...) 21. └─cards::check_ard_structure(...) 22. └─cards:::.message_or_error(...) 23. └─cli::cli_abort(msg, call = call, .envir = envir) 24. └─rlang::abort(...) ── Error ('test-ard_tabulate.survey.design.R:22:3'): ard_tabulate.survey.design() works ── Error in `eval(code, test_env)`: object 'ard_svy_cat_row' not found Backtrace: ▆ 1. ├─testthat::expect_invisible(...) at test-ard_tabulate.survey.design.R:22:3 2. │ └─base::withVisible(call) 3. └─cards::check_ard_structure(ard_svy_cat_row, method = FALSE) ── Failure ('test-ard_tabulate.survey.design.R:475:3'): ard_tabulate.survey.design() works for unobserved factor levels ── Expected `... <- NULL` not to throw any errors. Actually got a with message: The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-ard_tabulate.survey.design.R:475:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─cards::ard_tabulate(...) 8. └─cardx:::ard_tabulate.survey.design(svy_titanic, variables = c(Class, Age), by = Survived, denominator = "row") 9. ├─cards::tidy_ard_row_order(...) 10. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 11. ├─cards::tidy_ard_column_order(...) 12. │ ├─dplyr::pull(...) 13. │ ├─dplyr::arrange(...) 14. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 15. │ └─dplyr::select(x, all_ard_groups()) 16. ├─cards::as_card(...) 17. │ └─cards:::check_class(x, cls = "data.frame") 18. ├─dplyr::mutate(...) 19. └─cardx:::.restore_original_column_types(cards, data = data$variables) 20. └─cards::as_card(...) 21. └─cards::check_ard_structure(...) 22. └─cards:::.message_or_error(...) 23. └─cli::cli_abort(msg, call = call, .envir = envir) 24. └─rlang::abort(...) ── Error ('test-ard_tabulate.survey.design.R:485:3'): ard_tabulate.survey.design() works for unobserved factor levels ── Error in `eval(code, test_env)`: object 'ard_svy_cat_row' not found Backtrace: ▆ 1. ├─testthat::expect_invisible(...) at test-ard_tabulate.survey.design.R:485:3 2. │ └─base::withVisible(call) 3. └─cards::check_ard_structure(ard_svy_cat_row, method = FALSE) ── Failure ('test-ard_tabulate.survey.design.R:771:3'): ard_tabulate.survey.design() works for unobserved logical levels ── Expected `... <- NULL` not to throw any errors. Actually got a with message: The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-ard_tabulate.survey.design.R:771:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─cards::ard_tabulate(...) 8. └─cardx:::ard_tabulate.survey.design(svy_titanic, variables = c(Class, Age), by = Survived, denominator = "row") 9. ├─cards::tidy_ard_row_order(...) 10. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 11. ├─cards::tidy_ard_column_order(...) 12. │ ├─dplyr::pull(...) 13. │ ├─dplyr::arrange(...) 14. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 15. │ └─dplyr::select(x, all_ard_groups()) 16. ├─cards::as_card(...) 17. │ └─cards:::check_class(x, cls = "data.frame") 18. ├─dplyr::mutate(...) 19. └─cardx:::.restore_original_column_types(cards, data = data$variables) 20. └─cards::as_card(...) 21. └─cards::check_ard_structure(...) 22. └─cards:::.message_or_error(...) 23. └─cli::cli_abort(msg, call = call, .envir = envir) 24. └─rlang::abort(...) ── Error ('test-ard_tabulate.survey.design.R:781:3'): ard_tabulate.survey.design() works for unobserved logical levels ── Error in `eval(code, test_env)`: object 'ard_svy_cat_row' not found Backtrace: ▆ 1. ├─testthat::expect_invisible(...) at test-ard_tabulate.survey.design.R:781:3 2. │ └─base::withVisible(call) 3. └─cards::check_ard_structure(ard_svy_cat_row, method = FALSE) ── Failure ('test-ard_tabulate.survey.design.R:1062:3'): ard_tabulate.survey.design() works with variables with only 1 level ── Expected `... <- NULL` not to throw any errors. Actually got a with message: The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-ard_tabulate.survey.design.R:1062:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─cards::ard_tabulate(...) 8. └─cardx:::ard_tabulate.survey.design(svy_titanic, variables = c(Class, Age), by = Survived, denominator = "row") 9. ├─cards::tidy_ard_row_order(...) 10. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 11. ├─cards::tidy_ard_column_order(...) 12. │ ├─dplyr::pull(...) 13. │ ├─dplyr::arrange(...) 14. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 15. │ └─dplyr::select(x, all_ard_groups()) 16. ├─cards::as_card(...) 17. │ └─cards:::check_class(x, cls = "data.frame") 18. ├─dplyr::mutate(...) 19. └─cardx:::.restore_original_column_types(cards, data = data$variables) 20. └─cards::as_card(...) 21. └─cards::check_ard_structure(...) 22. └─cards:::.message_or_error(...) 23. └─cli::cli_abort(msg, call = call, .envir = envir) 24. └─rlang::abort(...) ── Error ('test-ard_tabulate.survey.design.R:1072:3'): ard_tabulate.survey.design() works with variables with only 1 level ── Error in `eval(code, test_env)`: object 'ard_svy_cat_row' not found Backtrace: ▆ 1. ├─testthat::expect_invisible(...) at test-ard_tabulate.survey.design.R:1072:3 2. │ └─base::withVisible(call) 3. └─cards::check_ard_structure(ard_svy_cat_row, method = FALSE) ── Error ('test-ard_tabulate.survey.design.R:1226:3'): ard_tabulate.survey.design() works when using generic names ── Error in `ard_tabulate(svy_titanic, variables = c(Class, Age), by = Survived, denominator = "row")`: The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-ard_tabulate.survey.design.R:1226:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─dplyr::select(...) 5. ├─cards::ard_tabulate(...) 6. └─cardx:::ard_tabulate.survey.design(svy_titanic, variables = c(Class, Age), by = Survived, denominator = "row") 7. ├─cards::tidy_ard_row_order(...) 8. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 9. ├─cards::tidy_ard_column_order(...) 10. │ ├─dplyr::pull(...) 11. │ ├─dplyr::arrange(...) 12. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 13. │ └─dplyr::select(x, all_ard_groups()) 14. ├─cards::as_card(...) 15. │ └─cards:::check_class(x, cls = "data.frame") 16. ├─dplyr::mutate(...) 17. └─cardx:::.restore_original_column_types(cards, data = data$variables) 18. └─cards::as_card(...) 19. └─cards::check_ard_structure(...) 20. └─cards:::.message_or_error(...) 21. └─cli::cli_abort(msg, call = call, .envir = envir) 22. └─rlang::abort(...) ── Error ('test-ard_tabulate.survey.design.R:1297:3'): ard_tabulate.survey.design(statistic) properly excluded unweighted stats not selected ── Error in `ard_tabulate(svy_titanic, variables = Sex, statistic = ~c("N", "N_unweighted"))`: The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-ard_tabulate.survey.design.R:1297:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─dplyr::select(...) 5. ├─cards::ard_tabulate(...) 6. └─cardx:::ard_tabulate.survey.design(svy_titanic, variables = Sex, statistic = ~c("N", "N_unweighted")) 7. ├─cards::tidy_ard_row_order(...) 8. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 9. ├─cards::tidy_ard_column_order(...) 10. │ ├─dplyr::pull(...) 11. │ ├─dplyr::arrange(...) 12. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 13. │ └─dplyr::select(x, all_ard_groups()) 14. ├─cards::as_card(...) 15. │ └─cards:::check_class(x, cls = "data.frame") 16. ├─dplyr::mutate(...) 17. └─cardx:::.restore_original_column_types(cards, data = data$variables) 18. └─cards::as_card(...) 19. └─cards::check_ard_structure(...) 20. └─cards:::.message_or_error(...) 21. └─cli::cli_abort(msg, call = call, .envir = envir) 22. └─rlang::abort(...) ── Error ('test-ard_tabulate.survey.design.R:1317:3'): ard_tabulate follows ard structure ── Error in `cards::check_ard_structure(ard_tabulate(svy_titanic, variables = c(Class, Age), by = Survived, denominator = "row"), method = FALSE)`: The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-ard_tabulate.survey.design.R:1317:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. ├─cards::check_ard_structure(...) 10. ├─cards::ard_tabulate(...) 11. └─cardx:::ard_tabulate.survey.design(...) 12. ├─cards::tidy_ard_row_order(...) 13. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 14. ├─cards::tidy_ard_column_order(...) 15. │ ├─dplyr::pull(...) 16. │ ├─dplyr::arrange(...) 17. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 18. │ └─dplyr::select(x, all_ard_groups()) 19. ├─cards::as_card(...) 20. │ └─cards:::check_class(x, cls = "data.frame") 21. ├─dplyr::mutate(...) 22. └─cardx:::.restore_original_column_types(cards, data = data$variables) 23. └─cards::as_card(...) 24. └─cards::check_ard_structure(...) 25. └─cards:::.message_or_error(...) 26. └─cli::cli_abort(msg, call = call, .envir = envir) 27. └─rlang::abort(...) ── Error ('test-ard_tabulate.survey.design.R:1340:3'): ard_tabulate.survey.design() original types are retained ── Error in `ard_tabulate(svy_titanic, variables = c(Class, Age, Class.int, Class.dbl), by = Survived)`: The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-ard_tabulate.survey.design.R:1340:3 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. ├─cards::ard_tabulate(...) 10. └─cardx:::ard_tabulate.survey.design(...) 11. ├─cards::tidy_ard_row_order(...) 12. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 13. ├─cards::tidy_ard_column_order(...) 14. │ ├─dplyr::pull(...) 15. │ ├─dplyr::arrange(...) 16. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 17. │ └─dplyr::select(x, all_ard_groups()) 18. ├─cards::as_card(...) 19. │ └─cards:::check_class(x, cls = "data.frame") 20. ├─dplyr::mutate(...) 21. └─cardx:::.restore_original_column_types(cards, data = data$variables) 22. └─cards::as_card(...) 23. └─cards::check_ard_structure(...) 24. └─cards:::.message_or_error(...) 25. └─cli::cli_abort(msg, call = call, .envir = envir) 26. └─rlang::abort(...) ── Error ('test-ard_tabulate.survey.design.R:1375:3'): ard_tabulate.survey.design() works with all NA fct variables ── Error in `ard_tabulate(survey::svydesign(~1, data = dplyr::tibble(fct = factor(c(NA, NA), levels = c("no", "yes")), lgl = c(NA, NA)), weights = ~1), variables = fct)`: The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-ard_tabulate.survey.design.R:1375:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. ├─cards::ard_tabulate(...) 10. └─cardx:::ard_tabulate.survey.design(...) 11. ├─cards::tidy_ard_row_order(...) 12. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 13. ├─cards::tidy_ard_column_order(...) 14. │ ├─dplyr::pull(...) 15. │ ├─dplyr::arrange(...) 16. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 17. │ └─dplyr::select(x, all_ard_groups()) 18. ├─cards::as_card(...) 19. │ └─cards:::check_class(x, cls = "data.frame") 20. ├─dplyr::mutate(...) 21. └─cardx:::.restore_original_column_types(cards, data = data$variables) 22. └─cards::as_card(...) 23. └─cards::check_ard_structure(...) 24. └─cards:::.message_or_error(...) 25. └─cli::cli_abort(msg, call = call, .envir = envir) 26. └─rlang::abort(...) ── Failure ('test-ard_tabulate_value.survey.design.R:11:3'): ard_tabulate_value.survey.design() works ── Expected `... <- NULL` not to throw any errors. Actually got a with message: The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-ard_tabulate_value.survey.design.R:11:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─cards::ard_tabulate_value(...) 8. └─cardx:::ard_tabulate_value.survey.design(...) 9. ├─dplyr::mutate(...) 10. ├─dplyr::filter(...) 11. ├─cards::ard_tabulate(...) 12. └─cardx:::ard_tabulate.survey.design(...) 13. ├─cards::tidy_ard_row_order(...) 14. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 15. ├─cards::tidy_ard_column_order(...) 16. │ ├─dplyr::pull(...) 17. │ ├─dplyr::arrange(...) 18. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 19. │ └─dplyr::select(x, all_ard_groups()) 20. ├─cards::as_card(...) 21. │ └─cards:::check_class(x, cls = "data.frame") 22. ├─dplyr::mutate(...) 23. └─cardx:::.restore_original_column_types(cards, data = data$variables) 24. └─cards::as_card(...) 25. └─cards::check_ard_structure(...) 26. └─cards:::.message_or_error(...) 27. └─cli::cli_abort(msg, call = call, .envir = envir) 28. └─rlang::abort(...) ── Error ('test-ard_tabulate_value.survey.design.R:22:3'): ard_tabulate_value.survey.design() works ── Error in `eval(code, test_env)`: object 'ard_dichotomous_row' not found Backtrace: ▆ 1. ├─testthat::expect_invisible(...) at test-ard_tabulate_value.survey.design.R:22:3 2. │ └─base::withVisible(call) 3. └─cards::check_ard_structure(ard_dichotomous_row, method = FALSE) ── Failure ('test-ard_tabulate_value.survey.design.R:630:3'): ard_dichotomous.survey.design() works with various input types ── Expected `... <- NULL` not to throw any errors. Actually got a with message: The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-ard_tabulate_value.survey.design.R:630:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─cards::ard_tabulate_value(...) 8. └─cardx:::ard_tabulate_value.survey.design(...) 9. ├─dplyr::mutate(...) 10. ├─dplyr::filter(...) 11. ├─cards::ard_tabulate(...) 12. └─cardx:::ard_tabulate.survey.design(...) 13. ├─cards::tidy_ard_row_order(...) 14. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 15. ├─cards::tidy_ard_column_order(...) 16. │ ├─dplyr::pull(...) 17. │ ├─dplyr::arrange(...) 18. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 19. │ └─dplyr::select(x, all_ard_groups()) 20. ├─cards::as_card(...) 21. │ └─cards:::check_class(x, cls = "data.frame") 22. ├─dplyr::mutate(...) 23. └─cardx:::.restore_original_column_types(cards, data = data$variables) 24. └─cards::as_card(...) 25. └─cards::check_ard_structure(...) 26. └─cards:::.message_or_error(...) 27. └─cli::cli_abort(msg, call = call, .envir = envir) 28. └─rlang::abort(...) ── Error ('test-ard_tabulate_value.survey.design.R:641:3'): ard_dichotomous.survey.design() works with various input types ── Error in `eval(code, test_env)`: object 'ard_dichotomous_row' not found Backtrace: ▆ 1. ├─testthat::expect_invisible(...) at test-ard_tabulate_value.survey.design.R:641:3 2. │ └─base::withVisible(call) 3. └─cards::check_ard_structure(ard_dichotomous_row, method = FALSE) ── Error ('test-ard_tabulate_value.survey.design.R:790:3'): ard_tabulate_value.survey.design() follows ard structure ── Error in `cards::check_ard_structure(ard_tabulate_value(svy_dicho, by = vs, variables = c(cyl, am), value = list(cyl = 4), denominator = "row"), method = FALSE)`: The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-ard_tabulate_value.survey.design.R:790:3 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. ├─cards::check_ard_structure(...) 10. ├─cards::ard_tabulate_value(...) 11. └─cardx:::ard_tabulate_value.survey.design(...) 12. ├─dplyr::mutate(...) 13. ├─dplyr::filter(...) 14. ├─cards::ard_tabulate(...) 15. └─cardx:::ard_tabulate.survey.design(...) 16. ├─cards::tidy_ard_row_order(...) 17. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 18. ├─cards::tidy_ard_column_order(...) 19. │ ├─dplyr::pull(...) 20. │ ├─dplyr::arrange(...) 21. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 22. │ └─dplyr::select(x, all_ard_groups()) 23. ├─cards::as_card(...) 24. │ └─cards:::check_class(x, cls = "data.frame") 25. ├─dplyr::mutate(...) 26. └─cardx:::.restore_original_column_types(cards, data = data$variables) 27. └─cards::as_card(...) 28. └─cards::check_ard_structure(...) 29. └─cards:::.message_or_error(...) 30. └─cli::cli_abort(msg, call = call, .envir = envir) 31. └─rlang::abort(...) ── Error ('test-ard_total_n.survey.design.R:4:3'): ard_total_n.survey.design() works ── Error in `ard_total_n(survey::svydesign(~1, data = as.data.frame(Titanic), weights = ~Freq))`: The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─cards::ard_total_n(...) 2. └─cardx:::ard_total_n.survey.design(survey::svydesign(~1, data = as.data.frame(Titanic), weights = ~Freq)) 3. ├─dplyr::select(...) 4. ├─dplyr::mutate(...) 5. ├─cards::ard_tabulate_value(...) 6. └─cardx:::ard_tabulate_value.survey.design(...) 7. ├─dplyr::mutate(...) 8. ├─dplyr::filter(...) 9. ├─cards::ard_tabulate(...) 10. └─cardx:::ard_tabulate.survey.design(...) 11. ├─cards::tidy_ard_row_order(...) 12. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 13. ├─cards::tidy_ard_column_order(...) 14. │ ├─dplyr::pull(...) 15. │ ├─dplyr::arrange(...) 16. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 17. │ └─dplyr::select(x, all_ard_groups()) 18. ├─cards::as_card(...) 19. │ └─cards:::check_class(x, cls = "data.frame") 20. ├─dplyr::mutate(...) 21. └─cardx:::.restore_original_column_types(cards, data = data$variables) 22. └─cards::as_card(...) 23. └─cards::check_ard_structure(...) 24. └─cards:::.message_or_error(...) 25. └─cli::cli_abort(msg, call = call, .envir = envir) 26. └─rlang::abort(...) ── Error ('test-ard_total_n.survey.design.R:11:3'): ard_total_n.survey.design() follows ard structure ── Error in `cards::check_ard_structure(ard_total_n(survey::svydesign(~1, data = as.data.frame(Titanic), weights = ~Freq)), method = FALSE)`: The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-ard_total_n.survey.design.R:11:3 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. ├─cards::check_ard_structure(...) 10. ├─cards::ard_total_n(...) 11. └─cardx:::ard_total_n.survey.design(...) 12. ├─dplyr::select(...) 13. ├─dplyr::mutate(...) 14. ├─cards::ard_tabulate_value(...) 15. └─cardx:::ard_tabulate_value.survey.design(...) 16. ├─dplyr::mutate(...) 17. ├─dplyr::filter(...) 18. ├─cards::ard_tabulate(...) 19. └─cardx:::ard_tabulate.survey.design(...) 20. ├─cards::tidy_ard_row_order(...) 21. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 22. ├─cards::tidy_ard_column_order(...) 23. │ ├─dplyr::pull(...) 24. │ ├─dplyr::arrange(...) 25. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 26. │ └─dplyr::select(x, all_ard_groups()) 27. ├─cards::as_card(...) 28. │ └─cards:::check_class(x, cls = "data.frame") 29. ├─dplyr::mutate(...) 30. └─cardx:::.restore_original_column_types(cards, data = data$variables) 31. └─cards::as_card(...) 32. └─cards::check_ard_structure(...) 33. └─cards:::.message_or_error(...) 34. └─cli::cli_abort(msg, call = call, .envir = envir) 35. └─rlang::abort(...) ── Error ('test-ard_total_n.survey.design.R:29:3'): ard_total_n.survey.design() using `update()` ── Error in `ard_total_n(subset(survey::svydesign(id = ~1, weights = ~poids, data = database), !is.na(INDIV_GENDER)))`: The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-ard_total_n.survey.design.R:29:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. ├─cards::ard_total_n(...) 10. └─cardx:::ard_total_n.survey.design(...) 11. ├─dplyr::select(...) 12. ├─dplyr::mutate(...) 13. ├─cards::ard_tabulate_value(...) 14. └─cardx:::ard_tabulate_value.survey.design(...) 15. ├─dplyr::mutate(...) 16. ├─dplyr::filter(...) 17. ├─cards::ard_tabulate(...) 18. └─cardx:::ard_tabulate.survey.design(...) 19. ├─cards::tidy_ard_row_order(...) 20. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 21. ├─cards::tidy_ard_column_order(...) 22. │ ├─dplyr::pull(...) 23. │ ├─dplyr::arrange(...) 24. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 25. │ └─dplyr::select(x, all_ard_groups()) 26. ├─cards::as_card(...) 27. │ └─cards:::check_class(x, cls = "data.frame") 28. ├─dplyr::mutate(...) 29. └─cardx:::.restore_original_column_types(cards, data = data$variables) 30. └─cards::as_card(...) 31. └─cards::check_ard_structure(...) 32. └─cards:::.message_or_error(...) 33. └─cli::cli_abort(msg, call = call, .envir = envir) 34. └─rlang::abort(...) [ FAIL 52 | WARN 35 | SKIP 56 | PASS 315 ] Error: ! Test failures. Execution halted Package: gtsummary Check: examples New result: ERROR Running examples in ‘gtsummary-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: tbl_custom_summary > ### Title: Create a table of summary statistics using a custom summary > ### function > ### Aliases: tbl_custom_summary > > ### ** Examples > > # Example 1 ---------------------------------- > my_stats <- function(data, ...) { + marker_sum <- sum(data$marker, na.rm = TRUE) + mean_age <- mean(data$age, na.rm = TRUE) + dplyr::tibble( + marker_sum = marker_sum, + mean_age = mean_age + ) + } > > my_stats(trial) # A tibble: 1 × 2 marker_sum mean_age 1 174. 47.2 > > trial |> + tbl_custom_summary( + include = c("stage", "grade"), + by = "trt", + stat_fns = everything() ~ my_stats, + statistic = everything() ~ "A: {mean_age} - S: {marker_sum}", + digits = everything() ~ c(1, 0), + overall_row = TRUE, + overall_row_label = "All stages & grades" + ) |> + add_overall(last = TRUE) |> + modify_footnote_header( + footnote = "A: mean age - S: sum of marker", + columns = all_stat_cols() + ) |> + bold_labels()
Characteristic Drug A
N = 981		 Drug B
N = 1021		 Overall
N = 2001
All stages & grades A: 47.0 - S: 94 A: 47.4 - S: 80 A: 47.2 - S: 174
T Stage


    T1 A: 44.1 - S: 19 A: 49.5 - S: 15 A: 46.8 - S: 35
    T2 A: 50.2 - S: 29 A: 46.4 - S: 29 A: 48.1 - S: 59
    T3 A: 48.8 - S: 21 A: 50.0 - S: 18 A: 49.4 - S: 39
    T4 A: 45.3 - S: 24 A: 44.3 - S: 18 A: 44.8 - S: 42
Grade


    I A: 45.9 - S: 39 A: 46.4 - S: 31 A: 46.2 - S: 70
    II A: 44.6 - S: 24 A: 50.3 - S: 19 A: 47.5 - S: 43
    III A: 51.0 - S: 30 A: 45.7 - S: 30 A: 48.1 - S: 61
1 A: mean age - S: sum of marker
> > # Example 2 ---------------------------------- > # Use `data[[variable]]` to access the current variable > mean_ci <- function(data, variable, ...) { + test <- t.test(data[[variable]]) + dplyr::tibble( + mean = test$estimate, + conf.low = test$conf.int[1], + conf.high = test$conf.int[2] + ) + } > > trial |> + tbl_custom_summary( + include = c("marker", "ttdeath"), + by = "trt", + stat_fns = ~ mean_ci, + statistic = ~ "{mean} [{conf.low}; {conf.high}]" + ) |> + add_overall(last = TRUE) |> + modify_footnote_header( + footnote = "mean [95% CI]", + columns = all_stat_cols() + ) Error: ! `any_of()` must be used within a *selecting* function. ℹ See for details. Backtrace: ▆ 1. ├─gtsummary::modify_footnote_header(...) 2. ├─gtsummary::add_overall(...) 3. │ └─gtsummary:::check_class(x, "gtsummary") 4. └─gtsummary::tbl_custom_summary(...) 5. ├─dplyr::mutate(...) 6. ├─cards::ard_complex(...) 7. ├─cards:::ard_complex.data.frame(...) 8. │ ├─dplyr::mutate(ard_mvsummary(data = data, ...), context = "complex") 9. │ ├─cards::ard_mvsummary(data = data, ...) 10. │ └─cards:::ard_mvsummary.data.frame(data = data, ...) 11. └─tidyselect::any_of(by) 12. ├─vars %||% peek_vars(fn = "any_of") 13. └─tidyselect::peek_vars(fn = "any_of") 14. └─cli::cli_abort(...) 15. └─rlang::abort(...) Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed add_overall 5.038 0.052 5.103 Package: halfmoon Check: examples New result: ERROR Running examples in ‘halfmoon-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: add_ess_header > ### Title: Add ESS Table Header > ### Aliases: add_ess_header > > ### ** Examples > > ## Don't show: > if (rlang::is_installed(c("survey", "gtsummary", "cards", "cardx", "dplyr"))) withAutoprint({ # examplesIf + ## End(Don't show) + svy <- survey::svydesign(~1, data = nhefs_weights, weights = ~ w_ate) + + gtsummary::tbl_svysummary(svy, include = c(age, sex, smokeyrs)) |> + add_ess_header() + hdr <- paste0( + "**{level}** \n", + "N = {n_unweighted}; ESS = {format(n, digits = 1, nsmall = 1)}" + ) + gtsummary::tbl_svysummary(svy, by = qsmk, include = c(age, sex, smokeyrs)) |> + add_ess_header(header = hdr) + ## Don't show: + }) # examplesIf > svy <- survey::svydesign(~1, data = nhefs_weights, weights = ~w_ate) > add_ess_header(gtsummary::tbl_svysummary(svy, include = c(age, sex, smokeyrs))) Error in `gtsummary::tbl_svysummary()`: ! The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─base::withAutoprint(...) 2. │ └─base::source(...) 3. │ ├─base::withVisible(eval(ei, envir)) 4. │ └─base::eval(ei, envir) 5. │ └─base::eval(ei, envir) 6. ├─halfmoon::add_ess_header(...) 7. └─gtsummary::tbl_svysummary(svy, include = c(age, sex, smokeyrs)) 8. ├─cards::replace_null_statistic(...) 9. │ └─cards:::check_class(x, "card") 10. ├─cards::bind_ard(...) 11. │ └─dplyr::bind_rows(...) 12. │ └─rlang::list2(...) 13. ├─cardx::ard_total_n(data) 14. └─cardx:::ard_total_n.survey.design(data) 15. ├─dplyr::select(...) 16. ├─dplyr::mutate(...) 17. ├─cards::ard_tabulate_value(...) 18. └─cardx:::ard_tabulate_value.survey.design(...) 19. ├─dplyr::mutate(...) 20. ├─dplyr::filter(...) 21. ├─cards::ard_tabulate(...) 22. └─cardx:::ard_tabulate.survey.design(...) 23. ├─cards::tidy_ard_row_order(...) 24. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 25. ├─cards::tidy_ard_column_order(...) 26. │ ├─dplyr::pull(...) 27. │ ├─dplyr::arrange(...) 28. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 29. │ └─dplyr::select(x, all_ard_groups()) 30. ├─cards::as_card(...) 31. │ └─cards:::check_class(x, cls = "data.frame") 32. ├─dplyr::mutate(...) 33. └─cardx:::.restore_original_column_types(cards, data = data$variables) 34. └─cards::as_card(...) 35. └─cards::check_ard_structure(...) 36. └─cards:::.message_or_error(...) 37. └─cli::cli_abort(msg, call = call, .envir = envir) 38. └─rlang::abort(...) Execution halted Package: halfmoon Check: tests New result: ERROR Running ‘testthat.R’ [73s/73s] 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(halfmoon) > > test_check("halfmoon") Saving _problems/test-add_ess_header-8.R Ignoring unknown labels: * colour : "method" [ FAIL 1 | WARN 0 | SKIP 132 | PASS 1108 ] ══ Skipped tests (132) ═════════════════════════════════════════════════════════ • On CRAN (132): 'test-autoplot-methods.R:1:1', 'test-autoplot-methods.R:15:1', 'test-autoplot-methods.R:24:1', 'test-autoplot-methods.R:33:1', 'test-autoplot-methods.R:46:1', 'test-autoplot-methods.R:60:1', 'test-autoplot-methods.R:69:1', 'test-bal_model_auc.R:51:1', 'test-bal_model_roc_curve.R:42:1', 'test-bal_prognostic_score.R:48:1', 'test-bal_prognostic_score.R:172:1', 'test-bal_prognostic_score.R:187:1', 'test-bal_qq.R:43:1', 'test-bal_qq.R:60:1', 'test-bal_qq.R:86:1', 'test-check_balance.R:397:1', 'test-check_balance.R:724:1', 'test-check_balance.R:734:1', 'test-check_ess.R:105:1', 'test-check_model_auc.R:120:1', 'test-check_model_auc.R:200:1', 'test-check_model_auc.R:230:1', 'test-check_model_auc.R:310:1', 'test-compute_balance.R:128:1', 'test-compute_balance.R:265:1', 'test-compute_balance.R:383:1', 'test-compute_balance.R:489:1', 'test-compute_balance.R:507:1', 'test-compute_balance.R:642:3', 'test-compute_balance.R:686:3', 'test-compute_balance.R:727:3', 'test-compute_balance.R:751:3', 'test-compute_balance.R:777:3', 'test-compute_balance.R:820:3', 'test-compute_balance.R:1167:1', 'test-compute_balance.R:1233:1', 'test-compute_balance.R:1286:1', 'test-compute_balance.R:1364:3', 'test-compute_balance.R:1398:3', 'test-compute_balance.R:1428:3', 'test-compute_balance.R:1460:3', 'test-compute_balance_categorical.R:259:1', 'test-compute_balance_categorical.R:392:3', 'test-compute_balance_categorical.R:446:3', 'test-compute_balance_categorical.R:478:3', 'test-compute_balance_categorical.R:532:3', 'test-compute_balance_categorical.R:575:3', 'test-compute_balance_categorical.R:624:3', 'test-compute_balance_categorical.R:667:3', 'test-compute_balance_categorical.R:719:3', 'test-compute_balance_categorical.R:753:3', 'test-compute_balance_categorical.R:784:3', 'test-compute_balance_categorical.R:820:3', 'test-compute_qq.R:55:1', 'test-compute_qq.R:67:1', 'test-compute_qq.R:77:1', 'test-error-messages.R:1:1', 'test-error-messages.R:87:1', 'test-error-messages.R:111:1', 'test-geom_calibration.R:78:1', 'test-geom_calibration.R:424:1', 'test-geom_calibration.R:590:1', 'test-geom_calibration.R:663:1', 'test-geom_calibration.R:679:1', 'test-geom_calibration.R:693:1', 'test-geom_calibration.R:807:1', 'test-geom_calibration.R:830:1', 'test-geom_calibration.R:853:1', 'test-geom_calibration.R:876:1', 'test-geom_calibration.R:906:1', 'test-geom_calibration.R:928:1', 'test-geom_calibration.R:948:1', 'test-geom_calibration.R:1008:1', 'test-geom_calibration.R:1030:1', 'test-geom_calibration.R:1206:1', 'test-geom_calibration.R:1244:1', 'test-geom_ecdf.R:2:1', 'test-geom_mirrored_density.R:3:1', 'test-geom_mirrored_density.R:19:1', 'test-geom_mirrored_density.R:38:1', 'test-geom_mirrored_density.R:55:1', 'test-geom_mirrored_density.R:66:1', 'test-geom_mirrored_density.R:77:1', 'test-geom_mirrored_density.R:89:1', 'test-geom_mirrored_density.R:103:1', 'test-geom_mirrored_density.R:126:1', 'test-geom_mirrored_density.R:145:1', 'test-geom_mirrored_density.R:177:1', 'test-geom_mirrored_density.R:189:1', 'test-geom_mirrored_density.R:202:1', 'test-geom_mirrored_density.R:215:1', 'test-geom_mirrored_density.R:229:1', 'test-geom_mirrored_density.R:243:1', 'test-geom_mirrored_density.R:261:1', 'test-geom_mirrored_density.R:275:1', 'test-geom_mirrored_density.R:289:1', 'test-geom_mirrored_histogram.R:2:1', 'test-geom_mirrored_histogram.R:18:1', 'test-geom_mirrored_histogram.R:39:3', 'test-geom_qq2.R:122:1', 'test-geom_roc.R:57:1', 'test-geom_roc.R:130:1', 'test-plot_balance.R:129:1', 'test-plot_balance.R:253:1', 'test-plot_balance.R:378:1', 'test-plot_calibration.R:253:1', 'test-plot_ess.R:147:1', 'test-plot_mirror_distributions.R:3:1', 'test-plot_mirror_distributions.R:16:1', 'test-plot_mirror_distributions.R:29:1', 'test-plot_mirror_distributions.R:54:1', 'test-plot_mirror_distributions.R:68:1', 'test-plot_mirror_distributions.R:83:1', 'test-plot_mirror_distributions.R:108:1', 'test-plot_mirror_distributions.R:121:1', 'test-plot_mirror_distributions.R:134:1', 'test-plot_mirror_distributions.R:156:1', 'test-plot_mirror_distributions.R:193:1', 'test-plot_mirror_distributions.R:248:1', 'test-plot_mirror_distributions.R:283:1', 'test-plot_mirror_distributions.R:322:1', 'test-plot_mirror_distributions.R:346:1', 'test-plot_qq.R:56:1', 'test-plot_qq.R:68:1', 'test-plot_qq.R:80:1', 'test-plot_qq.R:111:1', 'test-plot_qq.R:124:1', 'test-plot_roc.R:59:1', 'test-plot_roc.R:176:1', 'test-plot_roc.R:217:1', 'test-plot_stratified_residuals.R:91:1', 'test-plot_stratified_residuals.R:215:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-add_ess_header.R:8:1'): (code run outside of `test_that()`) ──── Error in `tbl_svysummary(svy, include = c(age, sex, smokeyrs))`: The following columns are not present: "warning" and "error". Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-add_ess_header.R:8:1 2. │ └─base::withCallingHandlers(...) 3. └─gtsummary::tbl_svysummary(svy, include = c(age, sex, smokeyrs)) 4. ├─cards::replace_null_statistic(...) 5. │ └─cards:::check_class(x, "card") 6. ├─cards::bind_ard(...) 7. │ └─dplyr::bind_rows(...) 8. │ └─rlang::list2(...) 9. ├─cardx::ard_total_n(data) 10. └─cardx:::ard_total_n.survey.design(data) 11. ├─dplyr::select(...) 12. ├─dplyr::mutate(...) 13. ├─cards::ard_tabulate_value(...) 14. └─cardx:::ard_tabulate_value.survey.design(...) 15. ├─dplyr::mutate(...) 16. ├─dplyr::filter(...) 17. ├─cards::ard_tabulate(...) 18. └─cardx:::ard_tabulate.survey.design(...) 19. ├─cards::tidy_ard_row_order(...) 20. │ └─dplyr::select(x, all_ard_groups(c("names", "levels"))) 21. ├─cards::tidy_ard_column_order(...) 22. │ ├─dplyr::pull(...) 23. │ ├─dplyr::arrange(...) 24. │ ├─base::data.frame(colname = names(dplyr::select(x, all_ard_groups()))) 25. │ └─dplyr::select(x, all_ard_groups()) 26. ├─cards::as_card(...) 27. │ └─cards:::check_class(x, cls = "data.frame") 28. ├─dplyr::mutate(...) 29. └─cardx:::.restore_original_column_types(cards, data = data$variables) 30. └─cards::as_card(...) 31. └─cards::check_ard_structure(...) 32. └─cards:::.message_or_error(...) 33. └─cli::cli_abort(msg, call = call, .envir = envir) 34. └─rlang::abort(...) [ FAIL 1 | WARN 0 | SKIP 132 | PASS 1108 ] Error: ! Test failures. Execution halted