Last updated on 2026-05-05 15:52:06 CEST.
| Package | ERROR | OK |
|---|---|---|
| cards | 3 | 10 |
| cardx | 3 | 10 |
| dcurves | 13 | |
| ggsurvfit | 13 | |
| gtsummary | 3 | 10 |
| rstudio.prefs | 13 | |
| starter | 13 | |
| tidycmprsk | 13 | |
| updater | 13 |
Current CRAN status: ERROR: 3, OK: 10
Version: 0.7.1
Check: examples
Result: ERROR
Running examples in ‘cards-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ard_hierarchical
> ### Title: Hierarchical ARD Statistics
> ### Aliases: ard_hierarchical ard_hierarchical_count
> ### ard_hierarchical.data.frame ard_hierarchical_count.data.frame
>
> ### ** Examples
>
> ard_hierarchical(
+ data = ADAE |>
+ dplyr::slice_tail(n = 1L, by = c(USUBJID, TRTA, AESOC, AEDECOD)),
+ variables = c(AESOC, AEDECOD),
+ by = TRTA,
+ id = USUBJID,
+ denominator = ADSL
+ )
Error in as.data.frame.integer(x[[i]], optional = TRUE) :
row names contain missing values
Calls: ard_hierarchical ... data.frame -> as.data.frame -> as.data.frame.integer
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.7.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [252s/149s]
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(cards)
>
> test_check("cards")
Starting 2 test processes.
Saving _problems/test-ard_hierarchical-45.R
Saving _problems/test-ard_hierarchical-67.R
Saving _problems/test-ard_hierarchical-278.R
Saving _problems/test-ard_stack_hierarchical-73.R
Saving _problems/test-ard_stack_hierarchical-111.R
Saving _problems/test-ard_stack_hierarchical-182.R
Saving _problems/test-ard_stack_hierarchical-249.R
Saving _problems/test-ard_stack_hierarchical-263.R
Saving _problems/test-ard_stack_hierarchical-734.R
Saving _problems/test-ard_tabulate-151.R
Saving _problems/test-ard_tabulate-162.R
Saving _problems/test-ard_tabulate-471.R
Saving _problems/test-ard_tabulate-640.R
Saving _problems/test-ard_tabulate-769.R
Saving _problems/test-ard_tabulate-1315.R
> test-bind_ard.R: i 27 rows with duplicated statistic values have been removed.
> test-bind_ard.R: * See cards::bind_ard(.distinct) (`?cards::bind_ard()`) for details.
Saving _problems/test-shuffle_ard-366.R
Saving _problems/test-shuffle_ard-375.R
Saving _problems/test-shuffle_ard-633.R
[ FAIL 18 | WARN 0 | SKIP 109 | PASS 293 ]
══ Skipped tests (109) ═════════════════════════════════════════════════════════
• On CRAN (106): 'test-add_calculated_row.R:1:1',
'test-add_calculated_row.R:24:1', 'test-add_calculated_row.R:32:1',
'test-apply_fmt_fun.R:86:1', 'test-apply_fmt_fun.R:122:1',
'test-ard_formals.R:1:1', 'test-ard_attributes.R:3:1',
'test-ard_attributes.R:28:1', 'test-ard_identity.R:28:1',
'test-ard_missing.R:1:1', 'test-ard_missing.R:29:1',
'test-ard_mvsummary.R:85:1', 'test-ard_mvsummary.R:128:1',
'test-ard_pairwise.R:52:1', 'test-ard_pairwise.R:89:1',
'test-ard_pairwise.R:96:1', 'test-ard_hierarchical.R:2:1',
'test-ard_hierarchical.R:107:1', 'test-ard_hierarchical.R:117:1',
'test-ard_hierarchical.R:143:1', 'test-ard_hierarchical.R:253:1',
'test-ard_hierarchical.R:305:1', 'test-ard_hierarchical.R:328:1',
'test-ard_stack_hierarchical.R:76:1', 'test-ard_stack_hierarchical.R:335:1',
'test-ard_stack_hierarchical.R:349:1', 'test-ard_stack_hierarchical.R:497:1',
'test-ard_stack_hierarchical.R:575:1', 'test-ard_stack_hierarchical.R:586:1',
'test-ard_stack_hierarchical.R:599:1', 'test-ard_stack_hierarchical.R:667:1',
'test-ard_stack.R:221:1', 'test-ard_stack.R:239:1', 'test-ard_stack.R:267:1',
'test-ard_strata.R:1:1', 'test-ard_tabulate.R:1:1',
'test-ard_tabulate.R:67:1', 'test-ard_tabulate.R:101:1',
'test-ard_tabulate.R:245:1', 'test-ard_tabulate.R:563:1',
'test-ard_tabulate.R:699:1', 'test-ard_tabulate.R:772:1',
'test-ard_tabulate.R:1081:1', 'test-ard_tabulate.R:1130:1',
'test-ard_tabulate.R:1371:1', 'test-ard_tabulate_value.R:49:1',
'test-ard_tabulate_value.R:102:1', 'test-ard_total_n.R:1:1',
'test-as_card.R:1:1', 'test-as_card.R:21:1', 'test-as_nested_list.R:1:1',
'test-bind_ard.R:11:1', 'test-bind_ard.R:25:1', 'test-bind_ard.R:58:1',
'test-check_ard_structure.R:1:1', 'test-eval_capture_conditions.R:1:1',
'test-eval_capture_conditions.R:37:1', 'test-eval_capture_conditions.R:63:1',
'test-filter_ard_hierarchical.R:1:1', 'test-get_ard_statistics.R:1:1',
'test-mock.R:1:1', 'test-mock.R:12:1', 'test-mock.R:24:1',
'test-mock.R:34:1', 'test-mock.R:45:1', 'test-mock.R:56:1',
'test-mock.R:67:1', 'test-mock.R:77:1', 'test-mock.R:88:1',
'test-mock.R:97:1', 'test-mock.R:105:1', 'test-options.R:29:1',
'test-print.R:1:1', 'test-print_ard_conditions.R:1:1',
'test-print_ard_conditions.R:69:1', 'test-print_ard_conditions.R:99:1',
'test-print_ard_conditions.R:110:1', 'test-print_ard_conditions.R:137:1',
'test-process_selectors.R:51:1', 'test-process_selectors.R:63:1',
'test-rename_ard_columns.R:32:1', 'test-rename_ard_groups.R:1:1',
'test-rename_ard_groups.R:18:1', 'test-rename_ard_groups.R:27:1',
'test-round5.R:1:1', 'test-shuffle_ard.R:3:1', 'test-shuffle_ard.R:118:1',
'test-shuffle_ard.R:129:1', 'test-shuffle_ard.R:269:1',
'test-shuffle_ard.R:402:1', 'test-shuffle_ard.R:488:1',
'test-sort_ard_hierarchical.R:1:1', 'test-tidy_ard_row_order.R:1:1',
'test-tidy_as_ard.R:1:1', 'test-update_ard.R:1:1', 'test-update_ard.R:19:1',
'test-update_ard.R:28:1', 'test-update_ard.R:56:1', 'test-update_ard.R:64:1',
'test-ard_summary.R:1:1', 'test-ard_summary.R:34:1',
'test-ard_summary.R:84:1', 'test-ard_summary.R:104:1',
'test-ard_summary.R:228:1', 'test-ard_summary.R:249:1',
'test-ard_summary.R:419:1'
• Required package 'hms' is not installed (1): 'test-ard_tabulate.R:1111:3'
• package_version(paste(R.version$major, R.version$minor, sep = ".")) <=
package_version("4.5.0") is not TRUE (2): 'test-ard_strata.R:73:3',
'test-ard_tabulate_value.R:39:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-ard_hierarchical.R:36:3'): ard_hierarchical() works with by variable ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_hierarchical.R:36:3
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_hierarchical(...)
8. └─cards:::ard_hierarchical.data.frame(...)
9. ├─cards::ard_tabulate(...)
10. └─cards:::ard_tabulate.data.frame(...)
11. └─cards:::.calculate_tabulation_statistics(...)
12. └─cards:::.process_denominator(...)
13. ├─rlang::rep_named(...)
14. │ └─rlang::set_names(rep_len(x, length(names)), names)
15. ├─tidyr::drop_na(...)
16. └─cards:::.table_as_df(...)
17. ├─dplyr::as_tibble(...)
18. └─tibble:::as_tibble.table(...)
19. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
20. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
21. ├─base::eval(ex)
22. │ └─base::eval(ex)
23. └─base::data.frame(...)
24. ├─base::as.data.frame(x[[i]], optional = TRUE)
25. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_hierarchical.R:47:3'): ard_hierarchical() works with by variable ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'ard_heir_with_by' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_hierarchical.R:47:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─cards::get_ard_statistics(...)
5. │ └─dplyr::filter(x, ...)
6. └─dplyr::filter(...)
── Error ('test-ard_hierarchical.R:265:3'): ard_hierarchical() and ard_hierarchical_count() with grouped data works ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_hierarchical.R:265:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─cards::ard_hierarchical(...)
5. └─cards:::ard_hierarchical.data.frame(...)
6. ├─cards::ard_tabulate(...)
7. └─cards:::ard_tabulate.data.frame(...)
8. └─cards:::.calculate_tabulation_statistics(...)
9. └─cards:::.process_denominator(...)
10. ├─rlang::rep_named(...)
11. │ └─rlang::set_names(rep_len(x, length(names)), names)
12. ├─tidyr::drop_na(...)
13. └─cards:::.table_as_df(...)
14. ├─dplyr::as_tibble(...)
15. └─tibble:::as_tibble.table(...)
16. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
17. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
18. ├─base::eval(ex)
19. │ └─base::eval(ex)
20. └─base::data.frame(...)
21. ├─base::as.data.frame(x[[i]], optional = TRUE)
22. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_stack_hierarchical.R:64:3'): ard_stack_hierarchical(variables) messaging removed obs ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. └─cards::ard_stack_hierarchical(...)
2. └─cards:::internal_stack_hierarchical(...)
3. ├─base::append(...)
4. └─cards:::.run_hierarchical_fun(...)
5. ├─cards::ard_hierarchical(...)
6. └─cards:::ard_hierarchical.data.frame(...)
7. ├─cards::ard_tabulate(...)
8. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─rlang::rep_named(...)
12. │ └─rlang::set_names(rep_len(x, length(names)), names)
13. ├─tidyr::drop_na(...)
14. └─cards:::.table_as_df(...)
15. ├─dplyr::as_tibble(...)
16. └─tibble:::as_tibble.table(...)
17. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
18. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
19. ├─base::eval(ex)
20. │ └─base::eval(ex)
21. └─base::data.frame(...)
22. ├─base::as.data.frame(x[[i]], optional = TRUE)
23. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_stack_hierarchical.R:102:3'): ard_stack_hierarchical(by) ───
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-ard_stack_hierarchical.R:102:3
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_stack_hierarchical(...)
10. └─cards:::internal_stack_hierarchical(...)
11. ├─base::append(...)
12. └─cards:::.run_hierarchical_fun(...)
13. ├─cards::ard_hierarchical(...)
14. └─cards:::ard_hierarchical.data.frame(...)
15. ├─cards::ard_tabulate(...)
16. └─cards:::ard_tabulate.data.frame(...)
17. └─cards:::.calculate_tabulation_statistics(...)
18. └─cards:::.process_denominator(...)
19. ├─rlang::rep_named(...)
20. │ └─rlang::set_names(rep_len(x, length(names)), names)
21. ├─tidyr::drop_na(...)
22. └─cards:::.table_as_df(...)
23. ├─dplyr::as_tibble(...)
24. └─tibble:::as_tibble.table(...)
25. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
26. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
27. ├─base::eval(ex)
28. │ └─base::eval(ex)
29. └─base::data.frame(...)
30. ├─base::as.data.frame(x[[i]], optional = TRUE)
31. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_stack_hierarchical.R:173:3'): ard_stack_hierarchical(by) messaging ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. └─cards::ard_stack_hierarchical(...)
2. └─cards:::internal_stack_hierarchical(...)
3. ├─base::append(...)
4. └─cards:::.run_hierarchical_fun(...)
5. ├─cards::ard_hierarchical(...)
6. └─cards:::ard_hierarchical.data.frame(...)
7. ├─cards::ard_tabulate(...)
8. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─rlang::rep_named(...)
12. │ └─rlang::set_names(rep_len(x, length(names)), names)
13. ├─tidyr::drop_na(...)
14. └─cards:::.table_as_df(...)
15. ├─dplyr::as_tibble(...)
16. └─tibble:::as_tibble.table(...)
17. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
18. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
19. ├─base::eval(ex)
20. │ └─base::eval(ex)
21. └─base::data.frame(...)
22. ├─base::as.data.frame(x[[i]], optional = TRUE)
23. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_stack_hierarchical.R:232:3'): ard_stack_hierarchical(denominator) messaging ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_stack_hierarchical.R:232:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─cards::ard_stack_hierarchical(...)
5. └─cards:::internal_stack_hierarchical(...)
6. ├─base::append(...)
7. └─cards:::.run_hierarchical_fun(...)
8. ├─cards::ard_hierarchical(...)
9. └─cards:::ard_hierarchical.data.frame(...)
10. ├─cards::ard_tabulate(...)
11. └─cards:::ard_tabulate.data.frame(...)
12. └─cards:::.calculate_tabulation_statistics(...)
13. └─cards:::.process_denominator(...)
14. ├─rlang::rep_named(...)
15. │ └─rlang::set_names(rep_len(x, length(names)), names)
16. ├─tidyr::drop_na(...)
17. └─cards:::.table_as_df(...)
18. ├─dplyr::as_tibble(...)
19. └─tibble:::as_tibble.table(...)
20. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
21. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
22. ├─base::eval(ex)
23. │ └─base::eval(ex)
24. └─base::data.frame(...)
25. ├─base::as.data.frame(x[[i]], optional = TRUE)
26. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_stack_hierarchical.R:254:3'): ard_stack_hierarchical(by) with columns not in `denominator` ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_message(...) at test-ard_stack_hierarchical.R:254:3
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_stack_hierarchical(...)
8. └─cards:::internal_stack_hierarchical(...)
9. ├─base::append(...)
10. └─cards:::.run_hierarchical_fun(...)
11. ├─cards::ard_hierarchical(...)
12. └─cards:::ard_hierarchical.data.frame(...)
13. ├─cards::ard_tabulate(...)
14. └─cards:::ard_tabulate.data.frame(...)
15. └─cards:::.calculate_tabulation_statistics(...)
16. └─cards:::.process_denominator(...)
17. ├─rlang::rep_named(...)
18. │ └─rlang::set_names(rep_len(x, length(names)), names)
19. ├─tidyr::drop_na(...)
20. └─cards:::.table_as_df(...)
21. ├─dplyr::as_tibble(...)
22. └─tibble:::as_tibble.table(...)
23. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
24. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
25. ├─base::eval(ex)
26. │ └─base::eval(ex)
27. └─base::data.frame(...)
28. ├─base::as.data.frame(x[[i]], optional = TRUE)
29. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_stack_hierarchical.R:724:3'): ard_stack_hierarchical() by_stats argument ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-ard_stack_hierarchical.R:724:3
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_stack_hierarchical(...)
10. └─cards:::internal_stack_hierarchical(...)
11. ├─base::append(...)
12. └─cards:::.run_hierarchical_fun(...)
13. ├─cards::ard_hierarchical(...)
14. └─cards:::ard_hierarchical.data.frame(...)
15. ├─cards::ard_tabulate(...)
16. └─cards:::ard_tabulate.data.frame(...)
17. └─cards:::.calculate_tabulation_statistics(...)
18. └─cards:::.process_denominator(...)
19. ├─rlang::rep_named(...)
20. │ └─rlang::set_names(rep_len(x, length(names)), names)
21. ├─tidyr::drop_na(...)
22. └─cards:::.table_as_df(...)
23. ├─dplyr::as_tibble(...)
24. └─tibble:::as_tibble.table(...)
25. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
26. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
27. ├─base::eval(ex)
28. │ └─base::eval(ex)
29. └─base::data.frame(...)
30. ├─base::as.data.frame(x[[i]], optional = TRUE)
31. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Failure ('test-ard_tabulate.R:141:3'): ard_tabulate() with strata and by arguments ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_tabulate.R:141:3
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. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─rlang::rep_named(...)
12. │ └─rlang::set_names(rep_len(x, length(names)), names)
13. ├─tidyr::drop_na(...)
14. └─cards:::.table_as_df(...)
15. ├─dplyr::as_tibble(...)
16. └─tibble:::as_tibble.table(...)
17. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
18. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
19. ├─base::eval(ex)
20. │ └─base::eval(ex)
21. └─base::data.frame(...)
22. ├─base::as.data.frame(x[[i]], optional = TRUE)
23. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate.R:154:3'): ard_tabulate() with strata and by arguments ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'card_ae_strata' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_tabulate.R:154:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(...)
5. └─dplyr::filter(...)
── Error ('test-ard_tabulate.R:461:3'): ard_tabulate(denominator='row') works ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_tabulate.R:461:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unlist(...)
5. ├─dplyr::pull(...)
6. ├─cards::ard_tabulate(...)
7. └─cards:::ard_tabulate.data.frame(...)
8. └─cards:::.calculate_tabulation_statistics(...)
9. └─cards:::.process_denominator(...)
10. ├─stats::setNames(...)
11. └─base::lapply(...)
12. └─cards (local) FUN(X[[i]], ...)
13. ├─dplyr::summarise(...)
14. ├─tidyr::drop_na(...)
15. └─cards:::.table_as_df(...)
16. ├─dplyr::as_tibble(...)
17. └─tibble:::as_tibble.table(...)
18. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
19. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
20. ├─base::eval(ex)
21. │ └─base::eval(ex)
22. └─base::data.frame(...)
23. ├─base::as.data.frame(x[[i]], optional = TRUE)
24. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate.R:627:3'): ard_tabulate(denominator=<data frame without counts>) works ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_tabulate.R:627:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unique(...)
5. ├─base::unlist(...)
6. ├─dplyr::pull(...)
7. ├─cards::ard_tabulate(...)
8. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─rlang::rep_named(...)
12. │ └─rlang::set_names(rep_len(x, length(names)), names)
13. ├─tidyr::drop_na(...)
14. └─cards:::.table_as_df(...)
15. ├─dplyr::as_tibble(...)
16. └─tibble:::as_tibble.table(...)
17. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
18. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
19. ├─base::eval(ex)
20. │ └─base::eval(ex)
21. └─base::data.frame(...)
22. ├─base::as.data.frame(x[[i]], optional = TRUE)
23. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate.R:751:3'): ard_tabulate(strata) returns results in proper order ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_tabulate.R:751:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unique(...)
5. ├─base::unlist(...)
6. ├─dplyr::select(...)
7. ├─cards::ard_tabulate(...)
8. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─rlang::rep_named(...)
12. │ └─rlang::set_names(rep_len(x, length(names)), names)
13. ├─tidyr::drop_na(...)
14. └─cards:::.table_as_df(...)
15. ├─dplyr::as_tibble(...)
16. └─tibble:::as_tibble.table(...)
17. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
18. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
19. ├─base::eval(ex)
20. │ └─base::eval(ex)
21. └─base::data.frame(...)
22. ├─base::as.data.frame(x[[i]], optional = TRUE)
23. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate.R:1307:3'): ard_tabulate(denominator='row') with cumulative counts ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-ard_tabulate.R:1307:3
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. └─cards:::ard_tabulate.data.frame(...)
11. └─cards:::.calculate_tabulation_statistics(...)
12. └─cards:::.process_denominator(...)
13. ├─stats::setNames(...)
14. └─base::lapply(...)
15. └─cards (local) FUN(X[[i]], ...)
16. ├─dplyr::summarise(...)
17. ├─tidyr::drop_na(...)
18. └─cards:::.table_as_df(...)
19. ├─dplyr::as_tibble(...)
20. └─tibble:::as_tibble.table(...)
21. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
22. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
23. ├─base::eval(ex)
24. │ └─base::eval(ex)
25. └─base::data.frame(...)
26. ├─base::as.data.frame(x[[i]], optional = TRUE)
27. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Failure ('test-shuffle_ard.R:349:3'): shuffle_ard() fills grouping columns with `Overall <var>` or `Any <var>` ──
Expected `expect_warning(...)` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
── Error ('test-shuffle_ard.R:368:3'): shuffle_ard() fills grouping columns with `Overall <var>` or `Any <var>` ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'shuffled_ard' not found
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-shuffle_ard.R:368:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─dplyr::pull(...)
5. └─dplyr::filter(shuffled_ard, variable == "..ard_total_n..")
── Error ('test-shuffle_ard.R:624:3'): shuffle_ard() preserves the attributes of a `card` object ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. └─cards::ard_stack_hierarchical(...) at test-shuffle_ard.R:624:3
2. └─cards:::internal_stack_hierarchical(...)
3. ├─base::append(...)
4. └─cards:::.run_hierarchical_fun(...)
5. ├─cards::ard_hierarchical(...)
6. └─cards:::ard_hierarchical.data.frame(...)
7. ├─cards::ard_tabulate(...)
8. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─rlang::rep_named(...)
12. │ └─rlang::set_names(rep_len(x, length(names)), names)
13. ├─tidyr::drop_na(...)
14. └─cards:::.table_as_df(...)
15. ├─dplyr::as_tibble(...)
16. └─tibble:::as_tibble.table(...)
17. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
18. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
19. ├─base::eval(ex)
20. │ └─base::eval(ex)
21. └─base::data.frame(...)
22. ├─base::as.data.frame(x[[i]], optional = TRUE)
23. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
[ FAIL 18 | WARN 0 | SKIP 109 | PASS 293 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.7.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [157s/97s]
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(cards)
>
> test_check("cards")
Starting 2 test processes.
Saving _problems/test-ard_hierarchical-45.R
Saving _problems/test-ard_hierarchical-67.R
Saving _problems/test-ard_hierarchical-278.R
Saving _problems/test-ard_stack_hierarchical-73.R
Saving _problems/test-ard_stack_hierarchical-111.R
Saving _problems/test-ard_stack_hierarchical-182.R
Saving _problems/test-ard_stack_hierarchical-249.R
Saving _problems/test-ard_stack_hierarchical-263.R
Saving _problems/test-ard_stack_hierarchical-734.R
Saving _problems/test-ard_tabulate-151.R
Saving _problems/test-ard_tabulate-162.R
Saving _problems/test-ard_tabulate-471.R
Saving _problems/test-ard_tabulate-640.R
Saving _problems/test-ard_tabulate-769.R
Saving _problems/test-ard_tabulate-1315.R
> test-bind_ard.R: i 27 rows with duplicated statistic values have been removed.
> test-bind_ard.R: * See cards::bind_ard(.distinct) (`?cards::bind_ard()`) for details.
Saving _problems/test-shuffle_ard-366.R
Saving _problems/test-shuffle_ard-375.R
Saving _problems/test-shuffle_ard-633.R
[ FAIL 18 | WARN 0 | SKIP 109 | PASS 293 ]
══ Skipped tests (109) ═════════════════════════════════════════════════════════
• On CRAN (106): 'test-add_calculated_row.R:1:1',
'test-add_calculated_row.R:24:1', 'test-add_calculated_row.R:32:1',
'test-apply_fmt_fun.R:86:1', 'test-apply_fmt_fun.R:122:1',
'test-ard_formals.R:1:1', 'test-ard_attributes.R:3:1',
'test-ard_attributes.R:28:1', 'test-ard_identity.R:28:1',
'test-ard_missing.R:1:1', 'test-ard_missing.R:29:1',
'test-ard_mvsummary.R:85:1', 'test-ard_mvsummary.R:128:1',
'test-ard_pairwise.R:52:1', 'test-ard_pairwise.R:89:1',
'test-ard_pairwise.R:96:1', 'test-ard_hierarchical.R:2:1',
'test-ard_hierarchical.R:107:1', 'test-ard_hierarchical.R:117:1',
'test-ard_hierarchical.R:143:1', 'test-ard_hierarchical.R:253:1',
'test-ard_hierarchical.R:305:1', 'test-ard_hierarchical.R:328:1',
'test-ard_stack_hierarchical.R:76:1', 'test-ard_stack_hierarchical.R:335:1',
'test-ard_stack_hierarchical.R:349:1', 'test-ard_stack_hierarchical.R:497:1',
'test-ard_stack_hierarchical.R:575:1', 'test-ard_stack_hierarchical.R:586:1',
'test-ard_stack_hierarchical.R:599:1', 'test-ard_stack_hierarchical.R:667:1',
'test-ard_stack.R:221:1', 'test-ard_stack.R:239:1', 'test-ard_stack.R:267:1',
'test-ard_strata.R:1:1', 'test-ard_tabulate.R:1:1',
'test-ard_tabulate.R:67:1', 'test-ard_tabulate.R:101:1',
'test-ard_tabulate.R:245:1', 'test-ard_tabulate.R:563:1',
'test-ard_tabulate.R:699:1', 'test-ard_tabulate.R:772:1',
'test-ard_tabulate.R:1081:1', 'test-ard_tabulate.R:1130:1',
'test-ard_tabulate.R:1371:1', 'test-ard_tabulate_value.R:49:1',
'test-ard_tabulate_value.R:102:1', 'test-ard_total_n.R:1:1',
'test-as_card.R:1:1', 'test-as_card.R:21:1', 'test-as_nested_list.R:1:1',
'test-bind_ard.R:11:1', 'test-bind_ard.R:25:1', 'test-bind_ard.R:58:1',
'test-check_ard_structure.R:1:1', 'test-eval_capture_conditions.R:1:1',
'test-eval_capture_conditions.R:37:1', 'test-eval_capture_conditions.R:63:1',
'test-filter_ard_hierarchical.R:1:1', 'test-get_ard_statistics.R:1:1',
'test-mock.R:1:1', 'test-mock.R:12:1', 'test-mock.R:24:1',
'test-mock.R:34:1', 'test-mock.R:45:1', 'test-mock.R:56:1',
'test-mock.R:67:1', 'test-mock.R:77:1', 'test-mock.R:88:1',
'test-mock.R:97:1', 'test-mock.R:105:1', 'test-options.R:29:1',
'test-print.R:1:1', 'test-print_ard_conditions.R:1:1',
'test-print_ard_conditions.R:69:1', 'test-print_ard_conditions.R:99:1',
'test-print_ard_conditions.R:110:1', 'test-print_ard_conditions.R:137:1',
'test-process_selectors.R:51:1', 'test-process_selectors.R:63:1',
'test-rename_ard_columns.R:32:1', 'test-rename_ard_groups.R:1:1',
'test-rename_ard_groups.R:18:1', 'test-rename_ard_groups.R:27:1',
'test-round5.R:1:1', 'test-shuffle_ard.R:3:1', 'test-shuffle_ard.R:118:1',
'test-shuffle_ard.R:129:1', 'test-shuffle_ard.R:269:1',
'test-shuffle_ard.R:402:1', 'test-shuffle_ard.R:488:1',
'test-sort_ard_hierarchical.R:1:1', 'test-tidy_ard_row_order.R:1:1',
'test-tidy_as_ard.R:1:1', 'test-update_ard.R:1:1', 'test-update_ard.R:19:1',
'test-update_ard.R:28:1', 'test-update_ard.R:56:1', 'test-update_ard.R:64:1',
'test-ard_summary.R:1:1', 'test-ard_summary.R:34:1',
'test-ard_summary.R:84:1', 'test-ard_summary.R:104:1',
'test-ard_summary.R:228:1', 'test-ard_summary.R:249:1',
'test-ard_summary.R:419:1'
• Required package 'hms' is not installed (1): 'test-ard_tabulate.R:1111:3'
• package_version(paste(R.version$major, R.version$minor, sep = ".")) <=
package_version("4.5.0") is not TRUE (2): 'test-ard_strata.R:73:3',
'test-ard_tabulate_value.R:39:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-ard_hierarchical.R:36:3'): ard_hierarchical() works with by variable ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_hierarchical.R:36:3
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_hierarchical(...)
8. └─cards:::ard_hierarchical.data.frame(...)
9. ├─cards::ard_tabulate(...)
10. └─cards:::ard_tabulate.data.frame(...)
11. └─cards:::.calculate_tabulation_statistics(...)
12. └─cards:::.process_denominator(...)
13. ├─rlang::rep_named(...)
14. │ └─rlang::set_names(rep_len(x, length(names)), names)
15. ├─tidyr::drop_na(...)
16. └─cards:::.table_as_df(...)
17. ├─dplyr::as_tibble(...)
18. └─tibble:::as_tibble.table(...)
19. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
20. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
21. ├─base::eval(ex)
22. │ └─base::eval(ex)
23. └─base::data.frame(...)
24. ├─base::as.data.frame(x[[i]], optional = TRUE)
25. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_hierarchical.R:47:3'): ard_hierarchical() works with by variable ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'ard_heir_with_by' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_hierarchical.R:47:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─cards::get_ard_statistics(...)
5. │ └─dplyr::filter(x, ...)
6. └─dplyr::filter(...)
── Error ('test-ard_hierarchical.R:265:3'): ard_hierarchical() and ard_hierarchical_count() with grouped data works ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_hierarchical.R:265:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─cards::ard_hierarchical(...)
5. └─cards:::ard_hierarchical.data.frame(...)
6. ├─cards::ard_tabulate(...)
7. └─cards:::ard_tabulate.data.frame(...)
8. └─cards:::.calculate_tabulation_statistics(...)
9. └─cards:::.process_denominator(...)
10. ├─rlang::rep_named(...)
11. │ └─rlang::set_names(rep_len(x, length(names)), names)
12. ├─tidyr::drop_na(...)
13. └─cards:::.table_as_df(...)
14. ├─dplyr::as_tibble(...)
15. └─tibble:::as_tibble.table(...)
16. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
17. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
18. ├─base::eval(ex)
19. │ └─base::eval(ex)
20. └─base::data.frame(...)
21. ├─base::as.data.frame(x[[i]], optional = TRUE)
22. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_stack_hierarchical.R:64:3'): ard_stack_hierarchical(variables) messaging removed obs ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. └─cards::ard_stack_hierarchical(...)
2. └─cards:::internal_stack_hierarchical(...)
3. ├─base::append(...)
4. └─cards:::.run_hierarchical_fun(...)
5. ├─cards::ard_hierarchical(...)
6. └─cards:::ard_hierarchical.data.frame(...)
7. ├─cards::ard_tabulate(...)
8. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─rlang::rep_named(...)
12. │ └─rlang::set_names(rep_len(x, length(names)), names)
13. ├─tidyr::drop_na(...)
14. └─cards:::.table_as_df(...)
15. ├─dplyr::as_tibble(...)
16. └─tibble:::as_tibble.table(...)
17. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
18. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
19. ├─base::eval(ex)
20. │ └─base::eval(ex)
21. └─base::data.frame(...)
22. ├─base::as.data.frame(x[[i]], optional = TRUE)
23. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_stack_hierarchical.R:102:3'): ard_stack_hierarchical(by) ───
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-ard_stack_hierarchical.R:102:3
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_stack_hierarchical(...)
10. └─cards:::internal_stack_hierarchical(...)
11. ├─base::append(...)
12. └─cards:::.run_hierarchical_fun(...)
13. ├─cards::ard_hierarchical(...)
14. └─cards:::ard_hierarchical.data.frame(...)
15. ├─cards::ard_tabulate(...)
16. └─cards:::ard_tabulate.data.frame(...)
17. └─cards:::.calculate_tabulation_statistics(...)
18. └─cards:::.process_denominator(...)
19. ├─rlang::rep_named(...)
20. │ └─rlang::set_names(rep_len(x, length(names)), names)
21. ├─tidyr::drop_na(...)
22. └─cards:::.table_as_df(...)
23. ├─dplyr::as_tibble(...)
24. └─tibble:::as_tibble.table(...)
25. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
26. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
27. ├─base::eval(ex)
28. │ └─base::eval(ex)
29. └─base::data.frame(...)
30. ├─base::as.data.frame(x[[i]], optional = TRUE)
31. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_stack_hierarchical.R:173:3'): ard_stack_hierarchical(by) messaging ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. └─cards::ard_stack_hierarchical(...)
2. └─cards:::internal_stack_hierarchical(...)
3. ├─base::append(...)
4. └─cards:::.run_hierarchical_fun(...)
5. ├─cards::ard_hierarchical(...)
6. └─cards:::ard_hierarchical.data.frame(...)
7. ├─cards::ard_tabulate(...)
8. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─rlang::rep_named(...)
12. │ └─rlang::set_names(rep_len(x, length(names)), names)
13. ├─tidyr::drop_na(...)
14. └─cards:::.table_as_df(...)
15. ├─dplyr::as_tibble(...)
16. └─tibble:::as_tibble.table(...)
17. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
18. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
19. ├─base::eval(ex)
20. │ └─base::eval(ex)
21. └─base::data.frame(...)
22. ├─base::as.data.frame(x[[i]], optional = TRUE)
23. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_stack_hierarchical.R:232:3'): ard_stack_hierarchical(denominator) messaging ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_stack_hierarchical.R:232:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─cards::ard_stack_hierarchical(...)
5. └─cards:::internal_stack_hierarchical(...)
6. ├─base::append(...)
7. └─cards:::.run_hierarchical_fun(...)
8. ├─cards::ard_hierarchical(...)
9. └─cards:::ard_hierarchical.data.frame(...)
10. ├─cards::ard_tabulate(...)
11. └─cards:::ard_tabulate.data.frame(...)
12. └─cards:::.calculate_tabulation_statistics(...)
13. └─cards:::.process_denominator(...)
14. ├─rlang::rep_named(...)
15. │ └─rlang::set_names(rep_len(x, length(names)), names)
16. ├─tidyr::drop_na(...)
17. └─cards:::.table_as_df(...)
18. ├─dplyr::as_tibble(...)
19. └─tibble:::as_tibble.table(...)
20. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
21. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
22. ├─base::eval(ex)
23. │ └─base::eval(ex)
24. └─base::data.frame(...)
25. ├─base::as.data.frame(x[[i]], optional = TRUE)
26. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_stack_hierarchical.R:254:3'): ard_stack_hierarchical(by) with columns not in `denominator` ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_message(...) at test-ard_stack_hierarchical.R:254:3
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_stack_hierarchical(...)
8. └─cards:::internal_stack_hierarchical(...)
9. ├─base::append(...)
10. └─cards:::.run_hierarchical_fun(...)
11. ├─cards::ard_hierarchical(...)
12. └─cards:::ard_hierarchical.data.frame(...)
13. ├─cards::ard_tabulate(...)
14. └─cards:::ard_tabulate.data.frame(...)
15. └─cards:::.calculate_tabulation_statistics(...)
16. └─cards:::.process_denominator(...)
17. ├─rlang::rep_named(...)
18. │ └─rlang::set_names(rep_len(x, length(names)), names)
19. ├─tidyr::drop_na(...)
20. └─cards:::.table_as_df(...)
21. ├─dplyr::as_tibble(...)
22. └─tibble:::as_tibble.table(...)
23. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
24. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
25. ├─base::eval(ex)
26. │ └─base::eval(ex)
27. └─base::data.frame(...)
28. ├─base::as.data.frame(x[[i]], optional = TRUE)
29. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_stack_hierarchical.R:724:3'): ard_stack_hierarchical() by_stats argument ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-ard_stack_hierarchical.R:724:3
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_stack_hierarchical(...)
10. └─cards:::internal_stack_hierarchical(...)
11. ├─base::append(...)
12. └─cards:::.run_hierarchical_fun(...)
13. ├─cards::ard_hierarchical(...)
14. └─cards:::ard_hierarchical.data.frame(...)
15. ├─cards::ard_tabulate(...)
16. └─cards:::ard_tabulate.data.frame(...)
17. └─cards:::.calculate_tabulation_statistics(...)
18. └─cards:::.process_denominator(...)
19. ├─rlang::rep_named(...)
20. │ └─rlang::set_names(rep_len(x, length(names)), names)
21. ├─tidyr::drop_na(...)
22. └─cards:::.table_as_df(...)
23. ├─dplyr::as_tibble(...)
24. └─tibble:::as_tibble.table(...)
25. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
26. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
27. ├─base::eval(ex)
28. │ └─base::eval(ex)
29. └─base::data.frame(...)
30. ├─base::as.data.frame(x[[i]], optional = TRUE)
31. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Failure ('test-ard_tabulate.R:141:3'): ard_tabulate() with strata and by arguments ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_tabulate.R:141:3
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. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─rlang::rep_named(...)
12. │ └─rlang::set_names(rep_len(x, length(names)), names)
13. ├─tidyr::drop_na(...)
14. └─cards:::.table_as_df(...)
15. ├─dplyr::as_tibble(...)
16. └─tibble:::as_tibble.table(...)
17. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
18. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
19. ├─base::eval(ex)
20. │ └─base::eval(ex)
21. └─base::data.frame(...)
22. ├─base::as.data.frame(x[[i]], optional = TRUE)
23. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate.R:154:3'): ard_tabulate() with strata and by arguments ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'card_ae_strata' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_tabulate.R:154:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(...)
5. └─dplyr::filter(...)
── Error ('test-ard_tabulate.R:461:3'): ard_tabulate(denominator='row') works ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_tabulate.R:461:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unlist(...)
5. ├─dplyr::pull(...)
6. ├─cards::ard_tabulate(...)
7. └─cards:::ard_tabulate.data.frame(...)
8. └─cards:::.calculate_tabulation_statistics(...)
9. └─cards:::.process_denominator(...)
10. ├─stats::setNames(...)
11. └─base::lapply(...)
12. └─cards (local) FUN(X[[i]], ...)
13. ├─dplyr::summarise(...)
14. ├─tidyr::drop_na(...)
15. └─cards:::.table_as_df(...)
16. ├─dplyr::as_tibble(...)
17. └─tibble:::as_tibble.table(...)
18. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
19. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
20. ├─base::eval(ex)
21. │ └─base::eval(ex)
22. └─base::data.frame(...)
23. ├─base::as.data.frame(x[[i]], optional = TRUE)
24. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate.R:627:3'): ard_tabulate(denominator=<data frame without counts>) works ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_tabulate.R:627:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unique(...)
5. ├─base::unlist(...)
6. ├─dplyr::pull(...)
7. ├─cards::ard_tabulate(...)
8. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─rlang::rep_named(...)
12. │ └─rlang::set_names(rep_len(x, length(names)), names)
13. ├─tidyr::drop_na(...)
14. └─cards:::.table_as_df(...)
15. ├─dplyr::as_tibble(...)
16. └─tibble:::as_tibble.table(...)
17. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
18. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
19. ├─base::eval(ex)
20. │ └─base::eval(ex)
21. └─base::data.frame(...)
22. ├─base::as.data.frame(x[[i]], optional = TRUE)
23. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate.R:751:3'): ard_tabulate(strata) returns results in proper order ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_tabulate.R:751:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unique(...)
5. ├─base::unlist(...)
6. ├─dplyr::select(...)
7. ├─cards::ard_tabulate(...)
8. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─rlang::rep_named(...)
12. │ └─rlang::set_names(rep_len(x, length(names)), names)
13. ├─tidyr::drop_na(...)
14. └─cards:::.table_as_df(...)
15. ├─dplyr::as_tibble(...)
16. └─tibble:::as_tibble.table(...)
17. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
18. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
19. ├─base::eval(ex)
20. │ └─base::eval(ex)
21. └─base::data.frame(...)
22. ├─base::as.data.frame(x[[i]], optional = TRUE)
23. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate.R:1307:3'): ard_tabulate(denominator='row') with cumulative counts ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-ard_tabulate.R:1307:3
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. └─cards:::ard_tabulate.data.frame(...)
11. └─cards:::.calculate_tabulation_statistics(...)
12. └─cards:::.process_denominator(...)
13. ├─stats::setNames(...)
14. └─base::lapply(...)
15. └─cards (local) FUN(X[[i]], ...)
16. ├─dplyr::summarise(...)
17. ├─tidyr::drop_na(...)
18. └─cards:::.table_as_df(...)
19. ├─dplyr::as_tibble(...)
20. └─tibble:::as_tibble.table(...)
21. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
22. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
23. ├─base::eval(ex)
24. │ └─base::eval(ex)
25. └─base::data.frame(...)
26. ├─base::as.data.frame(x[[i]], optional = TRUE)
27. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Failure ('test-shuffle_ard.R:349:3'): shuffle_ard() fills grouping columns with `Overall <var>` or `Any <var>` ──
Expected `expect_warning(...)` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
── Error ('test-shuffle_ard.R:368:3'): shuffle_ard() fills grouping columns with `Overall <var>` or `Any <var>` ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'shuffled_ard' not found
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-shuffle_ard.R:368:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─dplyr::pull(...)
5. └─dplyr::filter(shuffled_ard, variable == "..ard_total_n..")
── Error ('test-shuffle_ard.R:624:3'): shuffle_ard() preserves the attributes of a `card` object ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. └─cards::ard_stack_hierarchical(...) at test-shuffle_ard.R:624:3
2. └─cards:::internal_stack_hierarchical(...)
3. ├─base::append(...)
4. └─cards:::.run_hierarchical_fun(...)
5. ├─cards::ard_hierarchical(...)
6. └─cards:::ard_hierarchical.data.frame(...)
7. ├─cards::ard_tabulate(...)
8. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─rlang::rep_named(...)
12. │ └─rlang::set_names(rep_len(x, length(names)), names)
13. ├─tidyr::drop_na(...)
14. └─cards:::.table_as_df(...)
15. ├─dplyr::as_tibble(...)
16. └─tibble:::as_tibble.table(...)
17. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
18. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
19. ├─base::eval(ex)
20. │ └─base::eval(ex)
21. └─base::data.frame(...)
22. ├─base::as.data.frame(x[[i]], optional = TRUE)
23. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
[ FAIL 18 | WARN 0 | SKIP 109 | PASS 293 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.7.1
Check: examples
Result: ERROR
Running examples in 'cards-Ex.R' failed
The error most likely occurred in:
> ### Name: ard_hierarchical
> ### Title: Hierarchical ARD Statistics
> ### Aliases: ard_hierarchical ard_hierarchical_count
> ### ard_hierarchical.data.frame ard_hierarchical_count.data.frame
>
> ### ** Examples
>
> ard_hierarchical(
+ data = ADAE |>
+ dplyr::slice_tail(n = 1L, by = c(USUBJID, TRTA, AESOC, AEDECOD)),
+ variables = c(AESOC, AEDECOD),
+ by = TRTA,
+ id = USUBJID,
+ denominator = ADSL
+ )
Error in as.data.frame.integer(x[[i]], optional = TRUE) :
row names contain missing values
Calls: ard_hierarchical ... data.frame -> as.data.frame -> as.data.frame.integer
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.7.1
Check: tests
Result: ERROR
Running 'testthat.R' [110s]
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(cards)
>
> test_check("cards")
Starting 2 test processes.
Saving _problems/test-ard_hierarchical-45.R
Saving _problems/test-ard_hierarchical-67.R
Saving _problems/test-ard_hierarchical-278.R
Saving _problems/test-ard_stack_hierarchical-73.R
Saving _problems/test-ard_stack_hierarchical-111.R
Saving _problems/test-ard_stack_hierarchical-182.R
Saving _problems/test-ard_stack_hierarchical-249.R
Saving _problems/test-ard_stack_hierarchical-263.R
Saving _problems/test-ard_stack_hierarchical-734.R
Saving _problems/test-ard_tabulate-151.R
Saving _problems/test-ard_tabulate-162.R
Saving _problems/test-ard_tabulate-471.R
Saving _problems/test-ard_tabulate-640.R
Saving _problems/test-ard_tabulate-769.R
Saving _problems/test-ard_tabulate-1315.R
> test-bind_ard.R: i 27 rows with duplicated statistic values have been removed.
> test-bind_ard.R: * See cards::bind_ard(.distinct) (`?cards::bind_ard()`) for details.
Saving _problems/test-shuffle_ard-366.R
Saving _problems/test-shuffle_ard-375.R
Saving _problems/test-shuffle_ard-633.R
[ FAIL 18 | WARN 0 | SKIP 109 | PASS 293 ]
══ Skipped tests (109) ═════════════════════════════════════════════════════════
• On CRAN (106): 'test-add_calculated_row.R:1:1',
'test-add_calculated_row.R:24:1', 'test-add_calculated_row.R:32:1',
'test-apply_fmt_fun.R:86:1', 'test-apply_fmt_fun.R:122:1',
'test-ard_formals.R:1:1', 'test-ard_attributes.R:3:1',
'test-ard_attributes.R:28:1', 'test-ard_identity.R:28:1',
'test-ard_missing.R:1:1', 'test-ard_missing.R:29:1',
'test-ard_mvsummary.R:85:1', 'test-ard_mvsummary.R:128:1',
'test-ard_pairwise.R:52:1', 'test-ard_pairwise.R:89:1',
'test-ard_pairwise.R:96:1', 'test-ard_hierarchical.R:2:1',
'test-ard_hierarchical.R:107:1', 'test-ard_hierarchical.R:117:1',
'test-ard_hierarchical.R:143:1', 'test-ard_hierarchical.R:253:1',
'test-ard_hierarchical.R:305:1', 'test-ard_hierarchical.R:328:1',
'test-ard_stack.R:221:1', 'test-ard_stack.R:239:1', 'test-ard_stack.R:267:1',
'test-ard_stack_hierarchical.R:76:1', 'test-ard_stack_hierarchical.R:335:1',
'test-ard_stack_hierarchical.R:349:1', 'test-ard_stack_hierarchical.R:497:1',
'test-ard_stack_hierarchical.R:575:1', 'test-ard_stack_hierarchical.R:586:1',
'test-ard_stack_hierarchical.R:599:1', 'test-ard_stack_hierarchical.R:667:1',
'test-ard_strata.R:1:1', 'test-ard_tabulate.R:1:1',
'test-ard_tabulate.R:67:1', 'test-ard_tabulate.R:101:1',
'test-ard_tabulate.R:245:1', 'test-ard_tabulate.R:563:1',
'test-ard_tabulate.R:699:1', 'test-ard_tabulate.R:772:1',
'test-ard_tabulate.R:1081:1', 'test-ard_tabulate.R:1130:1',
'test-ard_tabulate.R:1371:1', 'test-ard_tabulate_value.R:49:1',
'test-ard_tabulate_value.R:102:1', 'test-ard_total_n.R:1:1',
'test-as_card.R:1:1', 'test-as_card.R:21:1', 'test-as_nested_list.R:1:1',
'test-bind_ard.R:11:1', 'test-bind_ard.R:25:1', 'test-bind_ard.R:58:1',
'test-check_ard_structure.R:1:1', 'test-eval_capture_conditions.R:1:1',
'test-eval_capture_conditions.R:37:1', 'test-eval_capture_conditions.R:63:1',
'test-filter_ard_hierarchical.R:1:1', 'test-get_ard_statistics.R:1:1',
'test-mock.R:1:1', 'test-mock.R:12:1', 'test-mock.R:24:1',
'test-mock.R:34:1', 'test-mock.R:45:1', 'test-mock.R:56:1',
'test-mock.R:67:1', 'test-mock.R:77:1', 'test-mock.R:88:1',
'test-mock.R:97:1', 'test-mock.R:105:1', 'test-options.R:29:1',
'test-print.R:1:1', 'test-print_ard_conditions.R:1:1',
'test-print_ard_conditions.R:69:1', 'test-print_ard_conditions.R:99:1',
'test-print_ard_conditions.R:110:1', 'test-print_ard_conditions.R:137:1',
'test-process_selectors.R:51:1', 'test-process_selectors.R:63:1',
'test-rename_ard_columns.R:32:1', 'test-rename_ard_groups.R:1:1',
'test-rename_ard_groups.R:18:1', 'test-rename_ard_groups.R:27:1',
'test-round5.R:1:1', 'test-shuffle_ard.R:3:1', 'test-shuffle_ard.R:118:1',
'test-shuffle_ard.R:129:1', 'test-shuffle_ard.R:269:1',
'test-shuffle_ard.R:402:1', 'test-shuffle_ard.R:488:1',
'test-sort_ard_hierarchical.R:1:1', 'test-tidy_ard_row_order.R:1:1',
'test-tidy_as_ard.R:1:1', 'test-update_ard.R:1:1', 'test-update_ard.R:19:1',
'test-update_ard.R:28:1', 'test-update_ard.R:56:1', 'test-update_ard.R:64:1',
'test-ard_summary.R:1:1', 'test-ard_summary.R:34:1',
'test-ard_summary.R:84:1', 'test-ard_summary.R:104:1',
'test-ard_summary.R:228:1', 'test-ard_summary.R:249:1',
'test-ard_summary.R:419:1'
• Required package 'hms' is not installed (1): 'test-ard_tabulate.R:1111:3'
• package_version(paste(R.version$major, R.version$minor, sep = ".")) <=
package_version("4.5.0") is not TRUE (2): 'test-ard_strata.R:73:3',
'test-ard_tabulate_value.R:39:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-ard_hierarchical.R:36:3'): ard_hierarchical() works with by variable ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_hierarchical.R:36:3
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_hierarchical(...)
8. └─cards:::ard_hierarchical.data.frame(...)
9. ├─cards::ard_tabulate(...)
10. └─cards:::ard_tabulate.data.frame(...)
11. └─cards:::.calculate_tabulation_statistics(...)
12. └─cards:::.process_denominator(...)
13. ├─rlang::rep_named(...)
14. │ └─rlang::set_names(rep_len(x, length(names)), names)
15. ├─tidyr::drop_na(...)
16. └─cards:::.table_as_df(...)
17. ├─dplyr::as_tibble(...)
18. └─tibble:::as_tibble.table(...)
19. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
20. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
21. ├─base::eval(ex)
22. │ └─base::eval(ex)
23. └─base::data.frame(...)
24. ├─base::as.data.frame(x[[i]], optional = TRUE)
25. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_hierarchical.R:47:3'): ard_hierarchical() works with by variable ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'ard_heir_with_by' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_hierarchical.R:47:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─cards::get_ard_statistics(...)
5. │ └─dplyr::filter(x, ...)
6. └─dplyr::filter(...)
── Error ('test-ard_hierarchical.R:265:3'): ard_hierarchical() and ard_hierarchical_count() with grouped data works ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_hierarchical.R:265:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─cards::ard_hierarchical(...)
5. └─cards:::ard_hierarchical.data.frame(...)
6. ├─cards::ard_tabulate(...)
7. └─cards:::ard_tabulate.data.frame(...)
8. └─cards:::.calculate_tabulation_statistics(...)
9. └─cards:::.process_denominator(...)
10. ├─rlang::rep_named(...)
11. │ └─rlang::set_names(rep_len(x, length(names)), names)
12. ├─tidyr::drop_na(...)
13. └─cards:::.table_as_df(...)
14. ├─dplyr::as_tibble(...)
15. └─tibble:::as_tibble.table(...)
16. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
17. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
18. ├─base::eval(ex)
19. │ └─base::eval(ex)
20. └─base::data.frame(...)
21. ├─base::as.data.frame(x[[i]], optional = TRUE)
22. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_stack_hierarchical.R:64:3'): ard_stack_hierarchical(variables) messaging removed obs ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. └─cards::ard_stack_hierarchical(...)
2. └─cards:::internal_stack_hierarchical(...)
3. ├─base::append(...)
4. └─cards:::.run_hierarchical_fun(...)
5. ├─cards::ard_hierarchical(...)
6. └─cards:::ard_hierarchical.data.frame(...)
7. ├─cards::ard_tabulate(...)
8. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─rlang::rep_named(...)
12. │ └─rlang::set_names(rep_len(x, length(names)), names)
13. ├─tidyr::drop_na(...)
14. └─cards:::.table_as_df(...)
15. ├─dplyr::as_tibble(...)
16. └─tibble:::as_tibble.table(...)
17. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
18. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
19. ├─base::eval(ex)
20. │ └─base::eval(ex)
21. └─base::data.frame(...)
22. ├─base::as.data.frame(x[[i]], optional = TRUE)
23. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_stack_hierarchical.R:102:3'): ard_stack_hierarchical(by) ───
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-ard_stack_hierarchical.R:102:3
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_stack_hierarchical(...)
10. └─cards:::internal_stack_hierarchical(...)
11. ├─base::append(...)
12. └─cards:::.run_hierarchical_fun(...)
13. ├─cards::ard_hierarchical(...)
14. └─cards:::ard_hierarchical.data.frame(...)
15. ├─cards::ard_tabulate(...)
16. └─cards:::ard_tabulate.data.frame(...)
17. └─cards:::.calculate_tabulation_statistics(...)
18. └─cards:::.process_denominator(...)
19. ├─rlang::rep_named(...)
20. │ └─rlang::set_names(rep_len(x, length(names)), names)
21. ├─tidyr::drop_na(...)
22. └─cards:::.table_as_df(...)
23. ├─dplyr::as_tibble(...)
24. └─tibble:::as_tibble.table(...)
25. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
26. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
27. ├─base::eval(ex)
28. │ └─base::eval(ex)
29. └─base::data.frame(...)
30. ├─base::as.data.frame(x[[i]], optional = TRUE)
31. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_stack_hierarchical.R:173:3'): ard_stack_hierarchical(by) messaging ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. └─cards::ard_stack_hierarchical(...)
2. └─cards:::internal_stack_hierarchical(...)
3. ├─base::append(...)
4. └─cards:::.run_hierarchical_fun(...)
5. ├─cards::ard_hierarchical(...)
6. └─cards:::ard_hierarchical.data.frame(...)
7. ├─cards::ard_tabulate(...)
8. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─rlang::rep_named(...)
12. │ └─rlang::set_names(rep_len(x, length(names)), names)
13. ├─tidyr::drop_na(...)
14. └─cards:::.table_as_df(...)
15. ├─dplyr::as_tibble(...)
16. └─tibble:::as_tibble.table(...)
17. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
18. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
19. ├─base::eval(ex)
20. │ └─base::eval(ex)
21. └─base::data.frame(...)
22. ├─base::as.data.frame(x[[i]], optional = TRUE)
23. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_stack_hierarchical.R:232:3'): ard_stack_hierarchical(denominator) messaging ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_stack_hierarchical.R:232:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─cards::ard_stack_hierarchical(...)
5. └─cards:::internal_stack_hierarchical(...)
6. ├─base::append(...)
7. └─cards:::.run_hierarchical_fun(...)
8. ├─cards::ard_hierarchical(...)
9. └─cards:::ard_hierarchical.data.frame(...)
10. ├─cards::ard_tabulate(...)
11. └─cards:::ard_tabulate.data.frame(...)
12. └─cards:::.calculate_tabulation_statistics(...)
13. └─cards:::.process_denominator(...)
14. ├─rlang::rep_named(...)
15. │ └─rlang::set_names(rep_len(x, length(names)), names)
16. ├─tidyr::drop_na(...)
17. └─cards:::.table_as_df(...)
18. ├─dplyr::as_tibble(...)
19. └─tibble:::as_tibble.table(...)
20. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
21. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
22. ├─base::eval(ex)
23. │ └─base::eval(ex)
24. └─base::data.frame(...)
25. ├─base::as.data.frame(x[[i]], optional = TRUE)
26. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_stack_hierarchical.R:254:3'): ard_stack_hierarchical(by) with columns not in `denominator` ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_message(...) at test-ard_stack_hierarchical.R:254:3
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_stack_hierarchical(...)
8. └─cards:::internal_stack_hierarchical(...)
9. ├─base::append(...)
10. └─cards:::.run_hierarchical_fun(...)
11. ├─cards::ard_hierarchical(...)
12. └─cards:::ard_hierarchical.data.frame(...)
13. ├─cards::ard_tabulate(...)
14. └─cards:::ard_tabulate.data.frame(...)
15. └─cards:::.calculate_tabulation_statistics(...)
16. └─cards:::.process_denominator(...)
17. ├─rlang::rep_named(...)
18. │ └─rlang::set_names(rep_len(x, length(names)), names)
19. ├─tidyr::drop_na(...)
20. └─cards:::.table_as_df(...)
21. ├─dplyr::as_tibble(...)
22. └─tibble:::as_tibble.table(...)
23. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
24. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
25. ├─base::eval(ex)
26. │ └─base::eval(ex)
27. └─base::data.frame(...)
28. ├─base::as.data.frame(x[[i]], optional = TRUE)
29. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_stack_hierarchical.R:724:3'): ard_stack_hierarchical() by_stats argument ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-ard_stack_hierarchical.R:724:3
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_stack_hierarchical(...)
10. └─cards:::internal_stack_hierarchical(...)
11. ├─base::append(...)
12. └─cards:::.run_hierarchical_fun(...)
13. ├─cards::ard_hierarchical(...)
14. └─cards:::ard_hierarchical.data.frame(...)
15. ├─cards::ard_tabulate(...)
16. └─cards:::ard_tabulate.data.frame(...)
17. └─cards:::.calculate_tabulation_statistics(...)
18. └─cards:::.process_denominator(...)
19. ├─rlang::rep_named(...)
20. │ └─rlang::set_names(rep_len(x, length(names)), names)
21. ├─tidyr::drop_na(...)
22. └─cards:::.table_as_df(...)
23. ├─dplyr::as_tibble(...)
24. └─tibble:::as_tibble.table(...)
25. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
26. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
27. ├─base::eval(ex)
28. │ └─base::eval(ex)
29. └─base::data.frame(...)
30. ├─base::as.data.frame(x[[i]], optional = TRUE)
31. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Failure ('test-ard_tabulate.R:141:3'): ard_tabulate() with strata and by arguments ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_tabulate.R:141:3
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. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─rlang::rep_named(...)
12. │ └─rlang::set_names(rep_len(x, length(names)), names)
13. ├─tidyr::drop_na(...)
14. └─cards:::.table_as_df(...)
15. ├─dplyr::as_tibble(...)
16. └─tibble:::as_tibble.table(...)
17. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
18. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
19. ├─base::eval(ex)
20. │ └─base::eval(ex)
21. └─base::data.frame(...)
22. ├─base::as.data.frame(x[[i]], optional = TRUE)
23. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate.R:154:3'): ard_tabulate() with strata and by arguments ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'card_ae_strata' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_tabulate.R:154:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(...)
5. └─dplyr::filter(...)
── Error ('test-ard_tabulate.R:461:3'): ard_tabulate(denominator='row') works ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_tabulate.R:461:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unlist(...)
5. ├─dplyr::pull(...)
6. ├─cards::ard_tabulate(...)
7. └─cards:::ard_tabulate.data.frame(...)
8. └─cards:::.calculate_tabulation_statistics(...)
9. └─cards:::.process_denominator(...)
10. ├─stats::setNames(...)
11. └─base::lapply(...)
12. └─cards (local) FUN(X[[i]], ...)
13. ├─dplyr::summarise(...)
14. ├─tidyr::drop_na(...)
15. └─cards:::.table_as_df(...)
16. ├─dplyr::as_tibble(...)
17. └─tibble:::as_tibble.table(...)
18. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
19. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
20. ├─base::eval(ex)
21. │ └─base::eval(ex)
22. └─base::data.frame(...)
23. ├─base::as.data.frame(x[[i]], optional = TRUE)
24. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate.R:627:3'): ard_tabulate(denominator=<data frame without counts>) works ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_tabulate.R:627:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unique(...)
5. ├─base::unlist(...)
6. ├─dplyr::pull(...)
7. ├─cards::ard_tabulate(...)
8. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─rlang::rep_named(...)
12. │ └─rlang::set_names(rep_len(x, length(names)), names)
13. ├─tidyr::drop_na(...)
14. └─cards:::.table_as_df(...)
15. ├─dplyr::as_tibble(...)
16. └─tibble:::as_tibble.table(...)
17. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
18. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
19. ├─base::eval(ex)
20. │ └─base::eval(ex)
21. └─base::data.frame(...)
22. ├─base::as.data.frame(x[[i]], optional = TRUE)
23. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate.R:751:3'): ard_tabulate(strata) returns results in proper order ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_tabulate.R:751:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unique(...)
5. ├─base::unlist(...)
6. ├─dplyr::select(...)
7. ├─cards::ard_tabulate(...)
8. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─rlang::rep_named(...)
12. │ └─rlang::set_names(rep_len(x, length(names)), names)
13. ├─tidyr::drop_na(...)
14. └─cards:::.table_as_df(...)
15. ├─dplyr::as_tibble(...)
16. └─tibble:::as_tibble.table(...)
17. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
18. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
19. ├─base::eval(ex)
20. │ └─base::eval(ex)
21. └─base::data.frame(...)
22. ├─base::as.data.frame(x[[i]], optional = TRUE)
23. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate.R:1307:3'): ard_tabulate(denominator='row') with cumulative counts ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-ard_tabulate.R:1307:3
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. └─cards:::ard_tabulate.data.frame(...)
11. └─cards:::.calculate_tabulation_statistics(...)
12. └─cards:::.process_denominator(...)
13. ├─stats::setNames(...)
14. └─base::lapply(...)
15. └─cards (local) FUN(X[[i]], ...)
16. ├─dplyr::summarise(...)
17. ├─tidyr::drop_na(...)
18. └─cards:::.table_as_df(...)
19. ├─dplyr::as_tibble(...)
20. └─tibble:::as_tibble.table(...)
21. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
22. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
23. ├─base::eval(ex)
24. │ └─base::eval(ex)
25. └─base::data.frame(...)
26. ├─base::as.data.frame(x[[i]], optional = TRUE)
27. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Failure ('test-shuffle_ard.R:349:3'): shuffle_ard() fills grouping columns with `Overall <var>` or `Any <var>` ──
Expected `expect_warning(...)` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
── Error ('test-shuffle_ard.R:368:3'): shuffle_ard() fills grouping columns with `Overall <var>` or `Any <var>` ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'shuffled_ard' not found
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-shuffle_ard.R:368:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─dplyr::pull(...)
5. └─dplyr::filter(shuffled_ard, variable == "..ard_total_n..")
── Error ('test-shuffle_ard.R:624:3'): shuffle_ard() preserves the attributes of a `card` object ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. └─cards::ard_stack_hierarchical(...) at test-shuffle_ard.R:624:3
2. └─cards:::internal_stack_hierarchical(...)
3. ├─base::append(...)
4. └─cards:::.run_hierarchical_fun(...)
5. ├─cards::ard_hierarchical(...)
6. └─cards:::ard_hierarchical.data.frame(...)
7. ├─cards::ard_tabulate(...)
8. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─rlang::rep_named(...)
12. │ └─rlang::set_names(rep_len(x, length(names)), names)
13. ├─tidyr::drop_na(...)
14. └─cards:::.table_as_df(...)
15. ├─dplyr::as_tibble(...)
16. └─tibble:::as_tibble.table(...)
17. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
18. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
19. ├─base::eval(ex)
20. │ └─base::eval(ex)
21. └─base::data.frame(...)
22. ├─base::as.data.frame(x[[i]], optional = TRUE)
23. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
[ FAIL 18 | WARN 0 | SKIP 109 | PASS 293 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64
Current CRAN status: ERROR: 3, OK: 10
Version: 0.3.2
Check: examples
Result: ERROR
Running examples in ‘cardx-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ard_tabulate_max
> ### Title: ARD to Calculate Categorical Occurrence Rates by Maximum Level
> ### Per Unique ID
> ### Aliases: ard_tabulate_max
>
> ### ** Examples
>
> # Occurrence Rates by Max Level (Highest Severity) --------------------------
> ard_tabulate_max(
+ cards::ADAE,
+ variables = c(AESER, AESEV),
+ id = USUBJID,
+ by = TRTA,
+ denominator = cards::ADSL
+ )
Error in as.data.frame.integer(x[[i]], optional = TRUE) :
row names contain missing values
Calls: ard_tabulate_max ... data.frame -> as.data.frame -> as.data.frame.integer
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.3.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [335s/210s]
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.
> test-ard_categorical_ci.data.frame.R: 5 missing observations in the "am" column have been removed.
> test-ard_effectsize_cohens_d.R: For paired samples, 'repeated_measures_d()' provides more options.
> test-ard_effectsize_hedges_g.R: For paired samples, 'repeated_measures_d()' provides more options.
> test-ard_stats_oneway_test.R: Multiple parameters; naming those columns num.df and den.df.
> test-ard_summary.survey.design.R: Expecting a row with `stat_name = 'method'`, but it is not present.
> test-ard_summary.survey.design.R: Expecting a row with `stat_name = 'method'`, but it is not present.
Saving _problems/test-ard_tabulate.survey.design-241.R
Saving _problems/test-ard_tabulate.survey.design-275.R
Saving _problems/test-ard_tabulate.survey.design-693.R
Saving _problems/test-ard_tabulate.survey.design-990.R
Saving _problems/test-ard_tabulate.survey.design-1111.R
> test-ard_tabulate_max.R: `AESEV`: "MILD" < "MODERATE" < "SEVERE"
Saving _problems/test-ard_tabulate_max-42.R
Saving _problems/test-ard_tabulate_max-112.R
Saving _problems/test-ard_tabulate_max-134.R
Saving _problems/test-ard_tabulate_value.survey.design-582.R
[ FAIL 9 | WARN 0 | SKIP 62 | PASS 593 ]
══ Skipped tests (62) ══════════════════════════════════════════════════════════
• On CRAN (62): '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_emmeans.R:3:1', 'test-ard_emmeans_emmeans.R:93:1',
'test-ard_incidence_rate.R:7:1', 'test-ard_incidence_rate.R:43:1',
'test-ard_incidence_rate.R:66:1', 'test-ard_emmeans_contrast.R:3:1',
'test-ard_emmeans_contrast.R:100:1', '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.survey.design.R:421:1',
'test-ard_tabulate.survey.design.R:1176:1',
'test-ard_tabulate.survey.design.R:1410:1',
'test-ard_tabulate_abnormal.R:5:1', 'test-ard_tabulate_abnormal.R:41:1',
'test-ard_tabulate_max.R:60:1', 'test-ard_tabulate_max.R:75:1',
'test-ard_tabulate_max.R:210:1', 'test-ard_tabulate_max.R:236:1',
'test-ard_tabulate_max.R:258:1',
'test-ard_tabulate_value.survey.design.R:736:1',
'test-ard_total_n.survey.design.R:3:1', 'test-construction_helpers.R:3:1',
'test-construction_helpers.R:103:1', 'test-proportion_ci.R:3:1',
'test-proportion_ci.R:122:1', 'test-ard_summary.survey.design.R:3:1',
'test-ard_summary.survey.design.R:318:1',
'test-ard_summary.survey.design.R:334:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-ard_tabulate.survey.design.R:233:3'): ard_tabulate.survey.design() works ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_tabulate.survey.design.R:233:3
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(svy_titanic, variables = c(Class, Age), denominator = "row")
8. └─cardx:::ard_tabulate.survey.design(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr::select(...)
11. ├─dplyr::mutate(...)
12. ├─cards::ard_tabulate(...)
13. └─cards:::ard_tabulate.data.frame(...)
14. └─cards:::.calculate_tabulation_statistics(...)
15. └─cards:::.process_denominator(...)
16. ├─stats::setNames(...)
17. └─base::lapply(...)
18. └─cards (local) FUN(X[[i]], ...)
19. ├─dplyr::summarise(...)
20. ├─tidyr::drop_na(...)
21. └─cards:::.table_as_df(...)
22. ├─dplyr::as_tibble(...)
23. └─tibble:::as_tibble.table(...)
24. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
25. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
26. ├─base::eval(ex)
27. │ └─base::eval(ex)
28. └─base::data.frame(...)
29. ├─base::as.data.frame(x[[i]], optional = TRUE)
30. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate.survey.design.R:271:3'): ard_tabulate.survey.design() works ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_tabulate.survey.design.R:271:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unlist(...)
5. ├─cards::get_ard_statistics(...)
6. │ └─dplyr::filter(x, ...)
7. ├─cards::ard_tabulate(...)
8. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─stats::setNames(...)
12. └─base::lapply(...)
13. └─cards (local) FUN(X[[i]], ...)
14. ├─dplyr::summarise(...)
15. ├─tidyr::drop_na(...)
16. └─cards:::.table_as_df(...)
17. ├─dplyr::as_tibble(...)
18. └─tibble:::as_tibble.table(...)
19. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
20. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
21. ├─base::eval(ex)
22. │ └─base::eval(ex)
23. └─base::data.frame(...)
24. ├─base::as.data.frame(x[[i]], optional = TRUE)
25. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Failure ('test-ard_tabulate.survey.design.R:685:3'): ard_tabulate.survey.design() works for unobserved factor levels ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_tabulate.survey.design.R:685:3
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(svy_titanic, variables = c(Class, Age), denominator = "row")
8. └─cardx:::ard_tabulate.survey.design(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr::select(...)
11. ├─dplyr::mutate(...)
12. ├─cards::ard_tabulate(...)
13. └─cards:::ard_tabulate.data.frame(...)
14. └─cards:::.calculate_tabulation_statistics(...)
15. └─cards:::.process_denominator(...)
16. ├─stats::setNames(...)
17. └─base::lapply(...)
18. └─cards (local) FUN(X[[i]], ...)
19. ├─dplyr::summarise(...)
20. ├─tidyr::drop_na(...)
21. └─cards:::.table_as_df(...)
22. ├─dplyr::as_tibble(...)
23. └─tibble:::as_tibble.table(...)
24. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
25. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
26. ├─base::eval(ex)
27. │ └─base::eval(ex)
28. └─base::data.frame(...)
29. ├─base::as.data.frame(x[[i]], optional = TRUE)
30. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Failure ('test-ard_tabulate.survey.design.R:982:3'): ard_tabulate.survey.design() works for unobserved logical levels ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_tabulate.survey.design.R:982:3
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(svy_titanic, variables = c(Class, Age), denominator = "row")
8. └─cardx:::ard_tabulate.survey.design(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr::select(...)
11. ├─dplyr::mutate(...)
12. ├─cards::ard_tabulate(...)
13. └─cards:::ard_tabulate.data.frame(...)
14. └─cards:::.calculate_tabulation_statistics(...)
15. └─cards:::.process_denominator(...)
16. ├─stats::setNames(...)
17. └─base::lapply(...)
18. └─cards (local) FUN(X[[i]], ...)
19. ├─dplyr::summarise(...)
20. ├─tidyr::drop_na(...)
21. └─cards:::.table_as_df(...)
22. ├─dplyr::as_tibble(...)
23. └─tibble:::as_tibble.table(...)
24. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
25. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
26. ├─base::eval(ex)
27. │ └─base::eval(ex)
28. └─base::data.frame(...)
29. ├─base::as.data.frame(x[[i]], optional = TRUE)
30. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Failure ('test-ard_tabulate.survey.design.R:1103:3'): ard_tabulate.survey.design() works with variables with only 1 level ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_tabulate.survey.design.R:1103:3
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(svy_titanic, variables = c(Class, Age), denominator = "row")
8. └─cardx:::ard_tabulate.survey.design(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr::select(...)
11. ├─dplyr::mutate(...)
12. ├─cards::ard_tabulate(...)
13. └─cards:::ard_tabulate.data.frame(...)
14. └─cards:::.calculate_tabulation_statistics(...)
15. └─cards:::.process_denominator(...)
16. ├─stats::setNames(...)
17. └─base::lapply(...)
18. └─cards (local) FUN(X[[i]], ...)
19. ├─dplyr::summarise(...)
20. ├─tidyr::drop_na(...)
21. └─cards:::.table_as_df(...)
22. ├─dplyr::as_tibble(...)
23. └─tibble:::as_tibble.table(...)
24. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
25. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
26. ├─base::eval(ex)
27. │ └─base::eval(ex)
28. └─base::data.frame(...)
29. ├─base::as.data.frame(x[[i]], optional = TRUE)
30. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate_max.R:34:3'): ard_tabulate_max() works with default settings ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─base::print(...)
2. └─cardx::ard_tabulate_max(...)
3. └─base::lapply(...)
4. └─cardx (local) FUN(X[[i]], ...)
5. ├─cards::ard_categorical(...)
6. └─cards:::ard_categorical.data.frame(...)
7. ├─dplyr::mutate(ard_tabulate(data = data, ...), context = "categorical")
8. ├─cards::ard_tabulate(data = data, ...)
9. └─cards:::ard_tabulate.data.frame(data = data, ...)
10. └─cards:::.calculate_tabulation_statistics(...)
11. └─cards:::.process_denominator(...)
12. ├─rlang::rep_named(...)
13. │ └─rlang::set_names(rep_len(x, length(names)), names)
14. ├─tidyr::drop_na(...)
15. └─cards:::.table_as_df(...)
16. ├─dplyr::as_tibble(...)
17. └─tibble:::as_tibble.table(...)
18. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
19. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
20. ├─base::eval(ex)
21. │ └─base::eval(ex)
22. └─base::data.frame(...)
23. ├─base::as.data.frame(x[[i]], optional = TRUE)
24. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate_max.R:103:3'): ard_tabulate_max(quiet) works ──────
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-ard_tabulate_max.R:103:3
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_tabulate_max(...)
10. └─base::lapply(...)
11. └─cardx (local) FUN(X[[i]], ...)
12. ├─cards::ard_categorical(...)
13. └─cards:::ard_categorical.data.frame(...)
14. ├─dplyr::mutate(ard_tabulate(data = data, ...), context = "categorical")
15. ├─cards::ard_tabulate(data = data, ...)
16. └─cards:::ard_tabulate.data.frame(data = data, ...)
17. └─cards:::.calculate_tabulation_statistics(...)
18. └─cards:::.process_denominator(...)
19. ├─rlang::rep_named(...)
20. │ └─rlang::set_names(rep_len(x, length(names)), names)
21. ├─tidyr::drop_na(...)
22. └─cards:::.table_as_df(...)
23. ├─dplyr::as_tibble(...)
24. └─tibble:::as_tibble.table(...)
25. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
26. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
27. ├─base::eval(ex)
28. │ └─base::eval(ex)
29. └─base::data.frame(...)
30. ├─base::as.data.frame(x[[i]], optional = TRUE)
31. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate_max.R:125:3'): ard_tabulate_max() works with pre-ordered factor variables ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_message(...) at test-ard_tabulate_max.R:125:3
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. └─cardx::ard_tabulate_max(...)
8. └─base::lapply(...)
9. └─cardx (local) FUN(X[[i]], ...)
10. ├─cards::ard_categorical(...)
11. └─cards:::ard_categorical.data.frame(...)
12. ├─dplyr::mutate(ard_tabulate(data = data, ...), context = "categorical")
13. ├─cards::ard_tabulate(data = data, ...)
14. └─cards:::ard_tabulate.data.frame(data = data, ...)
15. └─cards:::.calculate_tabulation_statistics(...)
16. └─cards:::.process_denominator(...)
17. ├─rlang::rep_named(...)
18. │ └─rlang::set_names(rep_len(x, length(names)), names)
19. ├─tidyr::drop_na(...)
20. └─cards:::.table_as_df(...)
21. ├─dplyr::as_tibble(...)
22. └─tibble:::as_tibble.table(...)
23. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
24. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
25. ├─base::eval(ex)
26. │ └─base::eval(ex)
27. └─base::data.frame(...)
28. ├─base::as.data.frame(x[[i]], optional = TRUE)
29. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Failure ('test-ard_tabulate_value.survey.design.R:573:3'): ard_tabulate_value.survey.design() works ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_tabulate_value.survey.design.R:573:3
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. ├─dplyr::mutate(...)
14. ├─dplyr::select(...)
15. ├─dplyr::mutate(...)
16. ├─cards::ard_tabulate(...)
17. └─cards:::ard_tabulate.data.frame(...)
18. └─cards:::.calculate_tabulation_statistics(...)
19. └─cards:::.process_denominator(...)
20. ├─stats::setNames(...)
21. └─base::lapply(...)
22. └─cards (local) FUN(X[[i]], ...)
23. ├─dplyr::summarise(...)
24. ├─tidyr::drop_na(...)
25. └─cards:::.table_as_df(...)
26. ├─dplyr::as_tibble(...)
27. └─tibble:::as_tibble.table(...)
28. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
29. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
30. ├─base::eval(ex)
31. │ └─base::eval(ex)
32. └─base::data.frame(...)
33. ├─base::as.data.frame(x[[i]], optional = TRUE)
34. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
[ FAIL 9 | WARN 0 | SKIP 62 | PASS 593 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.3.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [225s/140s]
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.
> test-ard_categorical_ci.data.frame.R: 5 missing observations in the "am" column have been removed.
> test-ard_effectsize_cohens_d.R: For paired samples, 'repeated_measures_d()' provides more options.
> test-ard_effectsize_hedges_g.R: For paired samples, 'repeated_measures_d()' provides more options.
> test-ard_stats_oneway_test.R: Multiple parameters; naming those columns num.df and den.df.
> test-ard_summary.survey.design.R: Expecting a row with `stat_name = 'method'`, but it is not present.
> test-ard_summary.survey.design.R: Expecting a row with `stat_name = 'method'`, but it is not present.
Saving _problems/test-ard_tabulate.survey.design-241.R
Saving _problems/test-ard_tabulate.survey.design-275.R
Saving _problems/test-ard_tabulate.survey.design-693.R
Saving _problems/test-ard_tabulate.survey.design-990.R
Saving _problems/test-ard_tabulate.survey.design-1111.R
> test-ard_tabulate_max.R: `AESEV`: "MILD" < "MODERATE" < "SEVERE"
Saving _problems/test-ard_tabulate_max-42.R
Saving _problems/test-ard_tabulate_max-112.R
Saving _problems/test-ard_tabulate_max-134.R
Saving _problems/test-ard_tabulate_value.survey.design-582.R
[ FAIL 9 | WARN 0 | SKIP 62 | PASS 593 ]
══ Skipped tests (62) ══════════════════════════════════════════════════════════
• On CRAN (62): 'test-ard_attributes.survey.design.R:3:1',
'test-ard_aod_wald_test.R:3:1', 'test-ard_car_anova.R:3:1',
'test-ard_car_anova.R:15:1', 'test-ard_car_vif.R:3:1',
'test-ard_car_vif.R:28:1', '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:7:1', 'test-ard_incidence_rate.R:43:1',
'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_oneway_test.R:3:1',
'test-ard_stats_mood_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.survey.design.R:421:1',
'test-ard_tabulate.survey.design.R:1176:1',
'test-ard_tabulate.survey.design.R:1410:1',
'test-ard_tabulate_abnormal.R:5:1', 'test-ard_tabulate_abnormal.R:41:1',
'test-ard_tabulate_max.R:60:1', 'test-ard_tabulate_max.R:75:1',
'test-ard_tabulate_max.R:210:1', 'test-ard_tabulate_max.R:236:1',
'test-ard_tabulate_max.R:258:1',
'test-ard_tabulate_value.survey.design.R:736:1',
'test-ard_total_n.survey.design.R:3:1', 'test-construction_helpers.R:3:1',
'test-construction_helpers.R:103:1', 'test-proportion_ci.R:3:1',
'test-proportion_ci.R:122:1', 'test-ard_summary.survey.design.R:3:1',
'test-ard_summary.survey.design.R:318:1',
'test-ard_summary.survey.design.R:334:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-ard_tabulate.survey.design.R:233:3'): ard_tabulate.survey.design() works ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_tabulate.survey.design.R:233:3
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(svy_titanic, variables = c(Class, Age), denominator = "row")
8. └─cardx:::ard_tabulate.survey.design(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr::select(...)
11. ├─dplyr::mutate(...)
12. ├─cards::ard_tabulate(...)
13. └─cards:::ard_tabulate.data.frame(...)
14. └─cards:::.calculate_tabulation_statistics(...)
15. └─cards:::.process_denominator(...)
16. ├─stats::setNames(...)
17. └─base::lapply(...)
18. └─cards (local) FUN(X[[i]], ...)
19. ├─dplyr::summarise(...)
20. ├─tidyr::drop_na(...)
21. └─cards:::.table_as_df(...)
22. ├─dplyr::as_tibble(...)
23. └─tibble:::as_tibble.table(...)
24. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
25. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
26. ├─base::eval(ex)
27. │ └─base::eval(ex)
28. └─base::data.frame(...)
29. ├─base::as.data.frame(x[[i]], optional = TRUE)
30. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate.survey.design.R:271:3'): ard_tabulate.survey.design() works ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_tabulate.survey.design.R:271:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unlist(...)
5. ├─cards::get_ard_statistics(...)
6. │ └─dplyr::filter(x, ...)
7. ├─cards::ard_tabulate(...)
8. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─stats::setNames(...)
12. └─base::lapply(...)
13. └─cards (local) FUN(X[[i]], ...)
14. ├─dplyr::summarise(...)
15. ├─tidyr::drop_na(...)
16. └─cards:::.table_as_df(...)
17. ├─dplyr::as_tibble(...)
18. └─tibble:::as_tibble.table(...)
19. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
20. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
21. ├─base::eval(ex)
22. │ └─base::eval(ex)
23. └─base::data.frame(...)
24. ├─base::as.data.frame(x[[i]], optional = TRUE)
25. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Failure ('test-ard_tabulate.survey.design.R:685:3'): ard_tabulate.survey.design() works for unobserved factor levels ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_tabulate.survey.design.R:685:3
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(svy_titanic, variables = c(Class, Age), denominator = "row")
8. └─cardx:::ard_tabulate.survey.design(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr::select(...)
11. ├─dplyr::mutate(...)
12. ├─cards::ard_tabulate(...)
13. └─cards:::ard_tabulate.data.frame(...)
14. └─cards:::.calculate_tabulation_statistics(...)
15. └─cards:::.process_denominator(...)
16. ├─stats::setNames(...)
17. └─base::lapply(...)
18. └─cards (local) FUN(X[[i]], ...)
19. ├─dplyr::summarise(...)
20. ├─tidyr::drop_na(...)
21. └─cards:::.table_as_df(...)
22. ├─dplyr::as_tibble(...)
23. └─tibble:::as_tibble.table(...)
24. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
25. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
26. ├─base::eval(ex)
27. │ └─base::eval(ex)
28. └─base::data.frame(...)
29. ├─base::as.data.frame(x[[i]], optional = TRUE)
30. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Failure ('test-ard_tabulate.survey.design.R:982:3'): ard_tabulate.survey.design() works for unobserved logical levels ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_tabulate.survey.design.R:982:3
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(svy_titanic, variables = c(Class, Age), denominator = "row")
8. └─cardx:::ard_tabulate.survey.design(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr::select(...)
11. ├─dplyr::mutate(...)
12. ├─cards::ard_tabulate(...)
13. └─cards:::ard_tabulate.data.frame(...)
14. └─cards:::.calculate_tabulation_statistics(...)
15. └─cards:::.process_denominator(...)
16. ├─stats::setNames(...)
17. └─base::lapply(...)
18. └─cards (local) FUN(X[[i]], ...)
19. ├─dplyr::summarise(...)
20. ├─tidyr::drop_na(...)
21. └─cards:::.table_as_df(...)
22. ├─dplyr::as_tibble(...)
23. └─tibble:::as_tibble.table(...)
24. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
25. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
26. ├─base::eval(ex)
27. │ └─base::eval(ex)
28. └─base::data.frame(...)
29. ├─base::as.data.frame(x[[i]], optional = TRUE)
30. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Failure ('test-ard_tabulate.survey.design.R:1103:3'): ard_tabulate.survey.design() works with variables with only 1 level ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_tabulate.survey.design.R:1103:3
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(svy_titanic, variables = c(Class, Age), denominator = "row")
8. └─cardx:::ard_tabulate.survey.design(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr::select(...)
11. ├─dplyr::mutate(...)
12. ├─cards::ard_tabulate(...)
13. └─cards:::ard_tabulate.data.frame(...)
14. └─cards:::.calculate_tabulation_statistics(...)
15. └─cards:::.process_denominator(...)
16. ├─stats::setNames(...)
17. └─base::lapply(...)
18. └─cards (local) FUN(X[[i]], ...)
19. ├─dplyr::summarise(...)
20. ├─tidyr::drop_na(...)
21. └─cards:::.table_as_df(...)
22. ├─dplyr::as_tibble(...)
23. └─tibble:::as_tibble.table(...)
24. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
25. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
26. ├─base::eval(ex)
27. │ └─base::eval(ex)
28. └─base::data.frame(...)
29. ├─base::as.data.frame(x[[i]], optional = TRUE)
30. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate_max.R:34:3'): ard_tabulate_max() works with default settings ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─base::print(...)
2. └─cardx::ard_tabulate_max(...)
3. └─base::lapply(...)
4. └─cardx (local) FUN(X[[i]], ...)
5. ├─cards::ard_categorical(...)
6. └─cards:::ard_categorical.data.frame(...)
7. ├─dplyr::mutate(ard_tabulate(data = data, ...), context = "categorical")
8. ├─cards::ard_tabulate(data = data, ...)
9. └─cards:::ard_tabulate.data.frame(data = data, ...)
10. └─cards:::.calculate_tabulation_statistics(...)
11. └─cards:::.process_denominator(...)
12. ├─rlang::rep_named(...)
13. │ └─rlang::set_names(rep_len(x, length(names)), names)
14. ├─tidyr::drop_na(...)
15. └─cards:::.table_as_df(...)
16. ├─dplyr::as_tibble(...)
17. └─tibble:::as_tibble.table(...)
18. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
19. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
20. ├─base::eval(ex)
21. │ └─base::eval(ex)
22. └─base::data.frame(...)
23. ├─base::as.data.frame(x[[i]], optional = TRUE)
24. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate_max.R:103:3'): ard_tabulate_max(quiet) works ──────
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-ard_tabulate_max.R:103:3
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_tabulate_max(...)
10. └─base::lapply(...)
11. └─cardx (local) FUN(X[[i]], ...)
12. ├─cards::ard_categorical(...)
13. └─cards:::ard_categorical.data.frame(...)
14. ├─dplyr::mutate(ard_tabulate(data = data, ...), context = "categorical")
15. ├─cards::ard_tabulate(data = data, ...)
16. └─cards:::ard_tabulate.data.frame(data = data, ...)
17. └─cards:::.calculate_tabulation_statistics(...)
18. └─cards:::.process_denominator(...)
19. ├─rlang::rep_named(...)
20. │ └─rlang::set_names(rep_len(x, length(names)), names)
21. ├─tidyr::drop_na(...)
22. └─cards:::.table_as_df(...)
23. ├─dplyr::as_tibble(...)
24. └─tibble:::as_tibble.table(...)
25. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
26. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
27. ├─base::eval(ex)
28. │ └─base::eval(ex)
29. └─base::data.frame(...)
30. ├─base::as.data.frame(x[[i]], optional = TRUE)
31. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate_max.R:125:3'): ard_tabulate_max() works with pre-ordered factor variables ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_message(...) at test-ard_tabulate_max.R:125:3
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. └─cardx::ard_tabulate_max(...)
8. └─base::lapply(...)
9. └─cardx (local) FUN(X[[i]], ...)
10. ├─cards::ard_categorical(...)
11. └─cards:::ard_categorical.data.frame(...)
12. ├─dplyr::mutate(ard_tabulate(data = data, ...), context = "categorical")
13. ├─cards::ard_tabulate(data = data, ...)
14. └─cards:::ard_tabulate.data.frame(data = data, ...)
15. └─cards:::.calculate_tabulation_statistics(...)
16. └─cards:::.process_denominator(...)
17. ├─rlang::rep_named(...)
18. │ └─rlang::set_names(rep_len(x, length(names)), names)
19. ├─tidyr::drop_na(...)
20. └─cards:::.table_as_df(...)
21. ├─dplyr::as_tibble(...)
22. └─tibble:::as_tibble.table(...)
23. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
24. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
25. ├─base::eval(ex)
26. │ └─base::eval(ex)
27. └─base::data.frame(...)
28. ├─base::as.data.frame(x[[i]], optional = TRUE)
29. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Failure ('test-ard_tabulate_value.survey.design.R:573:3'): ard_tabulate_value.survey.design() works ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_tabulate_value.survey.design.R:573:3
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. ├─dplyr::mutate(...)
14. ├─dplyr::select(...)
15. ├─dplyr::mutate(...)
16. ├─cards::ard_tabulate(...)
17. └─cards:::ard_tabulate.data.frame(...)
18. └─cards:::.calculate_tabulation_statistics(...)
19. └─cards:::.process_denominator(...)
20. ├─stats::setNames(...)
21. └─base::lapply(...)
22. └─cards (local) FUN(X[[i]], ...)
23. ├─dplyr::summarise(...)
24. ├─tidyr::drop_na(...)
25. └─cards:::.table_as_df(...)
26. ├─dplyr::as_tibble(...)
27. └─tibble:::as_tibble.table(...)
28. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
29. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
30. ├─base::eval(ex)
31. │ └─base::eval(ex)
32. └─base::data.frame(...)
33. ├─base::as.data.frame(x[[i]], optional = TRUE)
34. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
[ FAIL 9 | WARN 0 | SKIP 62 | PASS 593 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.2
Check: examples
Result: ERROR
Running examples in 'cardx-Ex.R' failed
The error most likely occurred in:
> ### Name: ard_tabulate_max
> ### Title: ARD to Calculate Categorical Occurrence Rates by Maximum Level
> ### Per Unique ID
> ### Aliases: ard_tabulate_max
>
> ### ** Examples
>
> # Occurrence Rates by Max Level (Highest Severity) --------------------------
> ard_tabulate_max(
+ cards::ADAE,
+ variables = c(AESER, AESEV),
+ id = USUBJID,
+ by = TRTA,
+ denominator = cards::ADSL
+ )
Error in as.data.frame.integer(x[[i]], optional = TRUE) :
row names contain missing values
Calls: ard_tabulate_max ... data.frame -> as.data.frame -> as.data.frame.integer
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.3.2
Check: tests
Result: ERROR
Running 'testthat.R' [143s]
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.
> test-ard_categorical_ci.data.frame.R: 5 missing observations in the "am" column have been removed.
> test-ard_effectsize_cohens_d.R: For paired samples, 'repeated_measures_d()' provides more options.
> test-ard_effectsize_hedges_g.R: For paired samples, 'repeated_measures_d()' provides more options.
> test-ard_stats_oneway_test.R: Multiple parameters; naming those columns num.df and den.df.
> test-ard_summary.survey.design.R: Expecting a row with `stat_name = 'method'`, but it is not present.
> test-ard_summary.survey.design.R: Expecting a row with `stat_name = 'method'`, but it is not present.
Saving _problems/test-ard_tabulate.survey.design-241.R
Saving _problems/test-ard_tabulate.survey.design-275.R
Saving _problems/test-ard_tabulate.survey.design-693.R
Saving _problems/test-ard_tabulate.survey.design-990.R
Saving _problems/test-ard_tabulate.survey.design-1111.R
> test-ard_tabulate_max.R: `AESEV`: "MILD" < "MODERATE" < "SEVERE"
Saving _problems/test-ard_tabulate_max-42.R
Saving _problems/test-ard_tabulate_max-112.R
Saving _problems/test-ard_tabulate_max-134.R
Saving _problems/test-ard_tabulate_value.survey.design-582.R
[ FAIL 9 | WARN 0 | SKIP 62 | PASS 593 ]
══ Skipped tests (62) ══════════════════════════════════════════════════════════
• On CRAN (62): '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_hedges_g.R:3:1', 'test-ard_effectsize_cohens_d.R:3:1',
'test-ard_emmeans_contrast.R:3:1', 'test-ard_emmeans_contrast.R:100:1',
'test-ard_incidence_rate.R:7:1', 'test-ard_incidence_rate.R:43:1',
'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_stats_aov.R:3:1', 'test-ard_regression.R:3:1',
'test-ard_regression.R:40:1', '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.survey.design.R:421:1',
'test-ard_tabulate.survey.design.R:1176:1',
'test-ard_tabulate.survey.design.R:1410:1',
'test-ard_tabulate_abnormal.R:5:1', 'test-ard_tabulate_abnormal.R:41:1',
'test-ard_tabulate_max.R:60:1', 'test-ard_tabulate_max.R:75:1',
'test-ard_tabulate_max.R:210:1', 'test-ard_tabulate_max.R:236:1',
'test-ard_tabulate_max.R:258:1',
'test-ard_tabulate_value.survey.design.R:736:1',
'test-ard_total_n.survey.design.R:3:1', 'test-construction_helpers.R:3:1',
'test-construction_helpers.R:103:1', 'test-proportion_ci.R:3:1',
'test-proportion_ci.R:122:1', 'test-ard_summary.survey.design.R:3:1',
'test-ard_summary.survey.design.R:318:1',
'test-ard_summary.survey.design.R:334:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-ard_tabulate.survey.design.R:233:3'): ard_tabulate.survey.design() works ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_tabulate.survey.design.R:233:3
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(svy_titanic, variables = c(Class, Age), denominator = "row")
8. └─cardx:::ard_tabulate.survey.design(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr::select(...)
11. ├─dplyr::mutate(...)
12. ├─cards::ard_tabulate(...)
13. └─cards:::ard_tabulate.data.frame(...)
14. └─cards:::.calculate_tabulation_statistics(...)
15. └─cards:::.process_denominator(...)
16. ├─stats::setNames(...)
17. └─base::lapply(...)
18. └─cards (local) FUN(X[[i]], ...)
19. ├─dplyr::summarise(...)
20. ├─tidyr::drop_na(...)
21. └─cards:::.table_as_df(...)
22. ├─dplyr::as_tibble(...)
23. └─tibble:::as_tibble.table(...)
24. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
25. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
26. ├─base::eval(ex)
27. │ └─base::eval(ex)
28. └─base::data.frame(...)
29. ├─base::as.data.frame(x[[i]], optional = TRUE)
30. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate.survey.design.R:271:3'): ard_tabulate.survey.design() works ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-ard_tabulate.survey.design.R:271:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::unlist(...)
5. ├─cards::get_ard_statistics(...)
6. │ └─dplyr::filter(x, ...)
7. ├─cards::ard_tabulate(...)
8. └─cards:::ard_tabulate.data.frame(...)
9. └─cards:::.calculate_tabulation_statistics(...)
10. └─cards:::.process_denominator(...)
11. ├─stats::setNames(...)
12. └─base::lapply(...)
13. └─cards (local) FUN(X[[i]], ...)
14. ├─dplyr::summarise(...)
15. ├─tidyr::drop_na(...)
16. └─cards:::.table_as_df(...)
17. ├─dplyr::as_tibble(...)
18. └─tibble:::as_tibble.table(...)
19. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
20. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
21. ├─base::eval(ex)
22. │ └─base::eval(ex)
23. └─base::data.frame(...)
24. ├─base::as.data.frame(x[[i]], optional = TRUE)
25. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Failure ('test-ard_tabulate.survey.design.R:685:3'): ard_tabulate.survey.design() works for unobserved factor levels ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_tabulate.survey.design.R:685:3
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(svy_titanic, variables = c(Class, Age), denominator = "row")
8. └─cardx:::ard_tabulate.survey.design(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr::select(...)
11. ├─dplyr::mutate(...)
12. ├─cards::ard_tabulate(...)
13. └─cards:::ard_tabulate.data.frame(...)
14. └─cards:::.calculate_tabulation_statistics(...)
15. └─cards:::.process_denominator(...)
16. ├─stats::setNames(...)
17. └─base::lapply(...)
18. └─cards (local) FUN(X[[i]], ...)
19. ├─dplyr::summarise(...)
20. ├─tidyr::drop_na(...)
21. └─cards:::.table_as_df(...)
22. ├─dplyr::as_tibble(...)
23. └─tibble:::as_tibble.table(...)
24. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
25. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
26. ├─base::eval(ex)
27. │ └─base::eval(ex)
28. └─base::data.frame(...)
29. ├─base::as.data.frame(x[[i]], optional = TRUE)
30. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Failure ('test-ard_tabulate.survey.design.R:982:3'): ard_tabulate.survey.design() works for unobserved logical levels ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_tabulate.survey.design.R:982:3
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(svy_titanic, variables = c(Class, Age), denominator = "row")
8. └─cardx:::ard_tabulate.survey.design(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr::select(...)
11. ├─dplyr::mutate(...)
12. ├─cards::ard_tabulate(...)
13. └─cards:::ard_tabulate.data.frame(...)
14. └─cards:::.calculate_tabulation_statistics(...)
15. └─cards:::.process_denominator(...)
16. ├─stats::setNames(...)
17. └─base::lapply(...)
18. └─cards (local) FUN(X[[i]], ...)
19. ├─dplyr::summarise(...)
20. ├─tidyr::drop_na(...)
21. └─cards:::.table_as_df(...)
22. ├─dplyr::as_tibble(...)
23. └─tibble:::as_tibble.table(...)
24. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
25. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
26. ├─base::eval(ex)
27. │ └─base::eval(ex)
28. └─base::data.frame(...)
29. ├─base::as.data.frame(x[[i]], optional = TRUE)
30. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Failure ('test-ard_tabulate.survey.design.R:1103:3'): ard_tabulate.survey.design() works with variables with only 1 level ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_tabulate.survey.design.R:1103:3
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(svy_titanic, variables = c(Class, Age), denominator = "row")
8. └─cardx:::ard_tabulate.survey.design(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr::select(...)
11. ├─dplyr::mutate(...)
12. ├─cards::ard_tabulate(...)
13. └─cards:::ard_tabulate.data.frame(...)
14. └─cards:::.calculate_tabulation_statistics(...)
15. └─cards:::.process_denominator(...)
16. ├─stats::setNames(...)
17. └─base::lapply(...)
18. └─cards (local) FUN(X[[i]], ...)
19. ├─dplyr::summarise(...)
20. ├─tidyr::drop_na(...)
21. └─cards:::.table_as_df(...)
22. ├─dplyr::as_tibble(...)
23. └─tibble:::as_tibble.table(...)
24. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
25. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
26. ├─base::eval(ex)
27. │ └─base::eval(ex)
28. └─base::data.frame(...)
29. ├─base::as.data.frame(x[[i]], optional = TRUE)
30. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate_max.R:34:3'): ard_tabulate_max() works with default settings ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─base::print(...)
2. └─cardx::ard_tabulate_max(...)
3. └─base::lapply(...)
4. └─cardx (local) FUN(X[[i]], ...)
5. ├─cards::ard_categorical(...)
6. └─cards:::ard_categorical.data.frame(...)
7. ├─dplyr::mutate(ard_tabulate(data = data, ...), context = "categorical")
8. ├─cards::ard_tabulate(data = data, ...)
9. └─cards:::ard_tabulate.data.frame(data = data, ...)
10. └─cards:::.calculate_tabulation_statistics(...)
11. └─cards:::.process_denominator(...)
12. ├─rlang::rep_named(...)
13. │ └─rlang::set_names(rep_len(x, length(names)), names)
14. ├─tidyr::drop_na(...)
15. └─cards:::.table_as_df(...)
16. ├─dplyr::as_tibble(...)
17. └─tibble:::as_tibble.table(...)
18. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
19. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
20. ├─base::eval(ex)
21. │ └─base::eval(ex)
22. └─base::data.frame(...)
23. ├─base::as.data.frame(x[[i]], optional = TRUE)
24. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate_max.R:103:3'): ard_tabulate_max(quiet) works ──────
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-ard_tabulate_max.R:103:3
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_tabulate_max(...)
10. └─base::lapply(...)
11. └─cardx (local) FUN(X[[i]], ...)
12. ├─cards::ard_categorical(...)
13. └─cards:::ard_categorical.data.frame(...)
14. ├─dplyr::mutate(ard_tabulate(data = data, ...), context = "categorical")
15. ├─cards::ard_tabulate(data = data, ...)
16. └─cards:::ard_tabulate.data.frame(data = data, ...)
17. └─cards:::.calculate_tabulation_statistics(...)
18. └─cards:::.process_denominator(...)
19. ├─rlang::rep_named(...)
20. │ └─rlang::set_names(rep_len(x, length(names)), names)
21. ├─tidyr::drop_na(...)
22. └─cards:::.table_as_df(...)
23. ├─dplyr::as_tibble(...)
24. └─tibble:::as_tibble.table(...)
25. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
26. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
27. ├─base::eval(ex)
28. │ └─base::eval(ex)
29. └─base::data.frame(...)
30. ├─base::as.data.frame(x[[i]], optional = TRUE)
31. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Error ('test-ard_tabulate_max.R:125:3'): ard_tabulate_max() works with pre-ordered factor variables ──
Error in `as.data.frame.integer(x[[i]], optional = TRUE)`: row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_message(...) at test-ard_tabulate_max.R:125:3
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. └─cardx::ard_tabulate_max(...)
8. └─base::lapply(...)
9. └─cardx (local) FUN(X[[i]], ...)
10. ├─cards::ard_categorical(...)
11. └─cards:::ard_categorical.data.frame(...)
12. ├─dplyr::mutate(ard_tabulate(data = data, ...), context = "categorical")
13. ├─cards::ard_tabulate(data = data, ...)
14. └─cards:::ard_tabulate.data.frame(data = data, ...)
15. └─cards:::.calculate_tabulation_statistics(...)
16. └─cards:::.process_denominator(...)
17. ├─rlang::rep_named(...)
18. │ └─rlang::set_names(rep_len(x, length(names)), names)
19. ├─tidyr::drop_na(...)
20. └─cards:::.table_as_df(...)
21. ├─dplyr::as_tibble(...)
22. └─tibble:::as_tibble.table(...)
23. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
24. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
25. ├─base::eval(ex)
26. │ └─base::eval(ex)
27. └─base::data.frame(...)
28. ├─base::as.data.frame(x[[i]], optional = TRUE)
29. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
── Failure ('test-ard_tabulate_value.survey.design.R:573:3'): ard_tabulate_value.survey.design() works ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
row names contain missing values
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-ard_tabulate_value.survey.design.R:573:3
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. ├─dplyr::mutate(...)
14. ├─dplyr::select(...)
15. ├─dplyr::mutate(...)
16. ├─cards::ard_tabulate(...)
17. └─cards:::ard_tabulate.data.frame(...)
18. └─cards:::.calculate_tabulation_statistics(...)
19. └─cards:::.process_denominator(...)
20. ├─stats::setNames(...)
21. └─base::lapply(...)
22. └─cards (local) FUN(X[[i]], ...)
23. ├─dplyr::summarise(...)
24. ├─tidyr::drop_na(...)
25. └─cards:::.table_as_df(...)
26. ├─dplyr::as_tibble(...)
27. └─tibble:::as_tibble.table(...)
28. ├─base::as.data.frame(x, stringsAsFactors = FALSE)
29. └─base::as.data.frame.table(x, stringsAsFactors = FALSE)
30. ├─base::eval(ex)
31. │ └─base::eval(ex)
32. └─base::data.frame(...)
33. ├─base::as.data.frame(x[[i]], optional = TRUE)
34. └─base::as.data.frame.integer(x[[i]], optional = TRUE)
[ FAIL 9 | WARN 0 | SKIP 62 | PASS 593 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 3, OK: 10
Version: 2.5.0
Check: examples
Result: ERROR
Running examples in ‘gtsummary-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_overall
> ### Title: Add overall column
> ### Aliases: add_overall add_overall.tbl_summary add_overall.tbl_continuous
> ### add_overall.tbl_svysummary add_overall.tbl_custom_summary
> ### add_overall.tbl_hierarchical add_overall.tbl_hierarchical_count
>
> ### ** Examples
>
> # Example 1 ----------------------------------
> trial |>
+ tbl_summary(include = c(age, grade), by = trt) |>
+ add_overall()
<div id="ydgabwknrs" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
<style>#ydgabwknrs table {
font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji';
-webkit-font-smoothing: antialiased;
-moz-osx-font-smoothing: grayscale;
}
#ydgabwknrs thead, #ydgabwknrs tbody, #ydgabwknrs tfoot, #ydgabwknrs tr, #ydgabwknrs td, #ydgabwknrs th {
border-style: none;
}
#ydgabwknrs p {
margin: 0;
padding: 0;
}
#ydgabwknrs .gt_table {
display: table;
border-collapse: collapse;
line-height: normal;
margin-left: auto;
margin-right: auto;
color: #333333;
font-size: 16px;
font-weight: normal;
font-style: normal;
background-color: #FFFFFF;
width: auto;
border-top-style: solid;
border-top-width: 2px;
border-top-color: #A8A8A8;
border-right-style: none;
border-right-width: 2px;
border-right-color: #D3D3D3;
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #A8A8A8;
border-left-style: none;
border-left-width: 2px;
border-left-color: #D3D3D3;
}
#ydgabwknrs .gt_caption {
padding-top: 4px;
padding-bottom: 4px;
}
#ydgabwknrs .gt_title {
color: #333333;
font-size: 125%;
font-weight: initial;
padding-top: 4px;
padding-bottom: 4px;
padding-left: 5px;
padding-right: 5px;
border-bottom-color: #FFFFFF;
border-bottom-width: 0;
}
#ydgabwknrs .gt_subtitle {
color: #333333;
font-size: 85%;
font-weight: initial;
padding-top: 3px;
padding-bottom: 5px;
padding-left: 5px;
padding-right: 5px;
border-top-color: #FFFFFF;
border-top-width: 0;
}
#ydgabwknrs .gt_heading {
background-color: #FFFFFF;
text-align: center;
border-bottom-color: #FFFFFF;
border-left-style: none;
border-left-width: 1px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 1px;
border-right-color: #D3D3D3;
}
#ydgabwknrs .gt_bottom_border {
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
}
#ydgabwknrs .gt_col_headings {
border-top-style: solid;
border-top-width: 2px;
border-top-color: #D3D3D3;
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
border-left-style: none;
border-left-width: 1px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 1px;
border-right-color: #D3D3D3;
}
#ydgabwknrs .gt_col_heading {
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
font-weight: normal;
text-transform: inherit;
border-left-style: none;
border-left-width: 1px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 1px;
border-right-color: #D3D3D3;
vertical-align: bottom;
padding-top: 5px;
padding-bottom: 6px;
padding-left: 5px;
padding-right: 5px;
overflow-x: hidden;
}
#ydgabwknrs .gt_column_spanner_outer {
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
font-weight: normal;
text-transform: inherit;
padding-top: 0;
padding-bottom: 0;
padding-left: 4px;
padding-right: 4px;
}
#ydgabwknrs .gt_column_spanner_outer:first-child {
padding-left: 0;
}
#ydgabwknrs .gt_column_spanner_outer:last-child {
padding-right: 0;
}
#ydgabwknrs .gt_column_spanner {
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
vertical-align: bottom;
padding-top: 5px;
padding-bottom: 5px;
overflow-x: hidden;
display: inline-block;
width: 100%;
}
#ydgabwknrs .gt_spanner_row {
border-bottom-style: hidden;
}
#ydgabwknrs .gt_group_heading {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
font-weight: initial;
text-transform: inherit;
border-top-style: solid;
border-top-width: 2px;
border-top-color: #D3D3D3;
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
border-left-style: none;
border-left-width: 1px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 1px;
border-right-color: #D3D3D3;
vertical-align: middle;
text-align: left;
}
#ydgabwknrs .gt_empty_group_heading {
padding: 0.5px;
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
font-weight: initial;
border-top-style: solid;
border-top-width: 2px;
border-top-color: #D3D3D3;
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
vertical-align: middle;
}
#ydgabwknrs .gt_from_md > :first-child {
margin-top: 0;
}
#ydgabwknrs .gt_from_md > :last-child {
margin-bottom: 0;
}
#ydgabwknrs .gt_row {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
margin: 10px;
border-top-style: solid;
border-top-width: 1px;
border-top-color: #D3D3D3;
border-left-style: none;
border-left-width: 1px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 1px;
border-right-color: #D3D3D3;
vertical-align: middle;
overflow-x: hidden;
}
#ydgabwknrs .gt_stub {
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
font-weight: initial;
text-transform: inherit;
border-right-style: solid;
border-right-width: 2px;
border-right-color: #D3D3D3;
padding-left: 5px;
padding-right: 5px;
}
#ydgabwknrs .gt_stub_row_group {
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
font-weight: initial;
text-transform: inherit;
border-right-style: solid;
border-right-width: 2px;
border-right-color: #D3D3D3;
padding-left: 5px;
padding-right: 5px;
vertical-align: top;
}
#ydgabwknrs .gt_row_group_first td {
border-top-width: 2px;
}
#ydgabwknrs .gt_row_group_first th {
border-top-width: 2px;
}
#ydgabwknrs .gt_summary_row {
color: #333333;
background-color: #FFFFFF;
text-transform: inherit;
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
}
#ydgabwknrs .gt_first_summary_row {
border-top-style: solid;
border-top-color: #D3D3D3;
}
#ydgabwknrs .gt_first_summary_row.thick {
border-top-width: 2px;
}
#ydgabwknrs .gt_last_summary_row {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
}
#ydgabwknrs .gt_grand_summary_row {
color: #333333;
background-color: #FFFFFF;
text-transform: inherit;
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
}
#ydgabwknrs .gt_first_grand_summary_row {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
border-top-style: double;
border-top-width: 6px;
border-top-color: #D3D3D3;
}
#ydgabwknrs .gt_last_grand_summary_row_top {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
border-bottom-style: double;
border-bottom-width: 6px;
border-bottom-color: #D3D3D3;
}
#ydgabwknrs .gt_striped {
background-color: rgba(128, 128, 128, 0.05);
}
#ydgabwknrs .gt_table_body {
border-top-style: solid;
border-top-width: 2px;
border-top-color: #D3D3D3;
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
}
#ydgabwknrs .gt_footnotes {
color: #333333;
background-color: #FFFFFF;
border-bottom-style: none;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
border-left-style: none;
border-left-width: 2px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 2px;
border-right-color: #D3D3D3;
}
#ydgabwknrs .gt_footnote {
margin: 0px;
font-size: 90%;
padding-top: 4px;
padding-bottom: 4px;
padding-left: 5px;
padding-right: 5px;
}
#ydgabwknrs .gt_sourcenotes {
color: #333333;
background-color: #FFFFFF;
border-bottom-style: none;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
border-left-style: none;
border-left-width: 2px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 2px;
border-right-color: #D3D3D3;
}
#ydgabwknrs .gt_sourcenote {
font-size: 90%;
padding-top: 4px;
padding-bottom: 4px;
padding-left: 5px;
padding-right: 5px;
}
#ydgabwknrs .gt_left {
text-align: left;
}
#ydgabwknrs .gt_center {
text-align: center;
}
#ydgabwknrs .gt_right {
text-align: right;
font-variant-numeric: tabular-nums;
}
#ydgabwknrs .gt_font_normal {
font-weight: normal;
}
#ydgabwknrs .gt_font_bold {
font-weight: bold;
}
#ydgabwknrs .gt_font_italic {
font-style: italic;
}
#ydgabwknrs .gt_super {
font-size: 65%;
}
#ydgabwknrs .gt_footnote_marks {
font-size: 75%;
vertical-align: 0.4em;
position: initial;
}
#ydgabwknrs .gt_asterisk {
font-size: 100%;
vertical-align: 0;
}
#ydgabwknrs .gt_indent_1 {
text-indent: 5px;
}
#ydgabwknrs .gt_indent_2 {
text-indent: 10px;
}
#ydgabwknrs .gt_indent_3 {
text-indent: 15px;
}
#ydgabwknrs .gt_indent_4 {
text-indent: 20px;
}
#ydgabwknrs .gt_indent_5 {
text-indent: 25px;
}
#ydgabwknrs .katex-display {
display: inline-flex !important;
margin-bottom: 0.75em !important;
}
#ydgabwknrs div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after {
height: 0px !important;
}
</style>
<table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
<thead>
<tr class="gt_col_headings">
<th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="label"><span class='gt_from_md'><strong>Characteristic</strong></span></th>
<th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col" id="stat_0"><span class='gt_from_md'><strong>Overall</strong><br />
N = 200</span><span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;line-height:0;"><sup>1</sup></span></th>
<th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col" id="stat_1"><span class='gt_from_md'><strong>Drug A</strong><br />
N = 98</span><span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;line-height:0;"><sup>1</sup></span></th>
<th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col" id="stat_2"><span class='gt_from_md'><strong>Drug B</strong><br />
N = 102</span><span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;line-height:0;"><sup>1</sup></span></th>
</tr>
</thead>
<tbody class="gt_table_body">
<tr><td headers="label" class="gt_row gt_left">Age</td>
<td headers="stat_0" class="gt_row gt_center">47 (38, 57)</td>
<td headers="stat_1" class="gt_row gt_center">46 (37, 60)</td>
<td headers="stat_2" class="gt_row gt_center">48 (39, 56)</td></tr>
<tr><td headers="label" class="gt_row gt_left"> Unknown</td>
<td headers="stat_0" class="gt_row gt_center">11</td>
<td headers="stat_1" class="gt_row gt_center">7</td>
<td headers="stat_2" class="gt_row gt_center">4</td></tr>
<tr><td headers="label" class="gt_row gt_left">Grade</td>
<td headers="stat_0" class="gt_row gt_center"><br /></td>
<td headers="stat_1" class="gt_row gt_center"><br /></td>
<td headers="stat_2" class="gt_row gt_center"><br /></td></tr>
<tr><td headers="label" class="gt_row gt_left"> I</td>
<td headers="stat_0" class="gt_row gt_center">68 (34%)</td>
<td headers="stat_1" class="gt_row gt_center">35 (36%)</td>
<td headers="stat_2" class="gt_row gt_center">33 (32%)</td></tr>
<tr><td headers="label" class="gt_row gt_left"> II</td>
<td headers="stat_0" class="gt_row gt_center">68 (34%)</td>
<td headers="stat_1" class="gt_row gt_center">32 (33%)</td>
<td headers="stat_2" class="gt_row gt_center">36 (35%)</td></tr>
<tr><td headers="label" class="gt_row gt_left"> III</td>
<td headers="stat_0" class="gt_row gt_center">64 (32%)</td>
<td headers="stat_1" class="gt_row gt_center">31 (32%)</td>
<td headers="stat_2" class="gt_row gt_center">33 (32%)</td></tr>
</tbody>
<tfoot>
<tr class="gt_footnotes">
<td class="gt_footnote" colspan="4"><span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;line-height:0;"><sup>1</sup></span> <span class='gt_from_md'>Median (Q1, Q3); n (%)</span></td>
</tr>
</tfoot>
</table>
</div>
>
> # Example 2 ----------------------------------
> trial |>
+ tbl_summary(
+ include = grade,
+ by = trt,
+ percent = "row",
+ statistic = ~"{p}%",
+ digits = ~1
+ ) |>
+ add_overall(
+ last = TRUE,
+ statistic = ~"{p}% (n={n})",
+ digits = ~ c(1, 0)
+ )
Error in as.data.frame.integer(x[[i]], optional = TRUE) :
row names contain missing values
Calls: add_overall ... data.frame -> as.data.frame -> as.data.frame.integer
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 2.5.0
Check: examples
Result: ERROR
Running examples in 'gtsummary-Ex.R' failed
The error most likely occurred in:
> ### Name: add_overall
> ### Title: Add overall column
> ### Aliases: add_overall add_overall.tbl_summary add_overall.tbl_continuous
> ### add_overall.tbl_svysummary add_overall.tbl_custom_summary
> ### add_overall.tbl_hierarchical add_overall.tbl_hierarchical_count
>
> ### ** Examples
>
> # Example 1 ----------------------------------
> trial |>
+ tbl_summary(include = c(age, grade), by = trt) |>
+ add_overall()
<div id="ydgabwknrs" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
<style>#ydgabwknrs table {
font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji';
-webkit-font-smoothing: antialiased;
-moz-osx-font-smoothing: grayscale;
}
#ydgabwknrs thead, #ydgabwknrs tbody, #ydgabwknrs tfoot, #ydgabwknrs tr, #ydgabwknrs td, #ydgabwknrs th {
border-style: none;
}
#ydgabwknrs p {
margin: 0;
padding: 0;
}
#ydgabwknrs .gt_table {
display: table;
border-collapse: collapse;
line-height: normal;
margin-left: auto;
margin-right: auto;
color: #333333;
font-size: 16px;
font-weight: normal;
font-style: normal;
background-color: #FFFFFF;
width: auto;
border-top-style: solid;
border-top-width: 2px;
border-top-color: #A8A8A8;
border-right-style: none;
border-right-width: 2px;
border-right-color: #D3D3D3;
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #A8A8A8;
border-left-style: none;
border-left-width: 2px;
border-left-color: #D3D3D3;
}
#ydgabwknrs .gt_caption {
padding-top: 4px;
padding-bottom: 4px;
}
#ydgabwknrs .gt_title {
color: #333333;
font-size: 125%;
font-weight: initial;
padding-top: 4px;
padding-bottom: 4px;
padding-left: 5px;
padding-right: 5px;
border-bottom-color: #FFFFFF;
border-bottom-width: 0;
}
#ydgabwknrs .gt_subtitle {
color: #333333;
font-size: 85%;
font-weight: initial;
padding-top: 3px;
padding-bottom: 5px;
padding-left: 5px;
padding-right: 5px;
border-top-color: #FFFFFF;
border-top-width: 0;
}
#ydgabwknrs .gt_heading {
background-color: #FFFFFF;
text-align: center;
border-bottom-color: #FFFFFF;
border-left-style: none;
border-left-width: 1px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 1px;
border-right-color: #D3D3D3;
}
#ydgabwknrs .gt_bottom_border {
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
}
#ydgabwknrs .gt_col_headings {
border-top-style: solid;
border-top-width: 2px;
border-top-color: #D3D3D3;
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
border-left-style: none;
border-left-width: 1px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 1px;
border-right-color: #D3D3D3;
}
#ydgabwknrs .gt_col_heading {
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
font-weight: normal;
text-transform: inherit;
border-left-style: none;
border-left-width: 1px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 1px;
border-right-color: #D3D3D3;
vertical-align: bottom;
padding-top: 5px;
padding-bottom: 6px;
padding-left: 5px;
padding-right: 5px;
overflow-x: hidden;
}
#ydgabwknrs .gt_column_spanner_outer {
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
font-weight: normal;
text-transform: inherit;
padding-top: 0;
padding-bottom: 0;
padding-left: 4px;
padding-right: 4px;
}
#ydgabwknrs .gt_column_spanner_outer:first-child {
padding-left: 0;
}
#ydgabwknrs .gt_column_spanner_outer:last-child {
padding-right: 0;
}
#ydgabwknrs .gt_column_spanner {
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
vertical-align: bottom;
padding-top: 5px;
padding-bottom: 5px;
overflow-x: hidden;
display: inline-block;
width: 100%;
}
#ydgabwknrs .gt_spanner_row {
border-bottom-style: hidden;
}
#ydgabwknrs .gt_group_heading {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
font-weight: initial;
text-transform: inherit;
border-top-style: solid;
border-top-width: 2px;
border-top-color: #D3D3D3;
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
border-left-style: none;
border-left-width: 1px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 1px;
border-right-color: #D3D3D3;
vertical-align: middle;
text-align: left;
}
#ydgabwknrs .gt_empty_group_heading {
padding: 0.5px;
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
font-weight: initial;
border-top-style: solid;
border-top-width: 2px;
border-top-color: #D3D3D3;
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
vertical-align: middle;
}
#ydgabwknrs .gt_from_md > :first-child {
margin-top: 0;
}
#ydgabwknrs .gt_from_md > :last-child {
margin-bottom: 0;
}
#ydgabwknrs .gt_row {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
margin: 10px;
border-top-style: solid;
border-top-width: 1px;
border-top-color: #D3D3D3;
border-left-style: none;
border-left-width: 1px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 1px;
border-right-color: #D3D3D3;
vertical-align: middle;
overflow-x: hidden;
}
#ydgabwknrs .gt_stub {
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
font-weight: initial;
text-transform: inherit;
border-right-style: solid;
border-right-width: 2px;
border-right-color: #D3D3D3;
padding-left: 5px;
padding-right: 5px;
}
#ydgabwknrs .gt_stub_row_group {
color: #333333;
background-color: #FFFFFF;
font-size: 100%;
font-weight: initial;
text-transform: inherit;
border-right-style: solid;
border-right-width: 2px;
border-right-color: #D3D3D3;
padding-left: 5px;
padding-right: 5px;
vertical-align: top;
}
#ydgabwknrs .gt_row_group_first td {
border-top-width: 2px;
}
#ydgabwknrs .gt_row_group_first th {
border-top-width: 2px;
}
#ydgabwknrs .gt_summary_row {
color: #333333;
background-color: #FFFFFF;
text-transform: inherit;
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
}
#ydgabwknrs .gt_first_summary_row {
border-top-style: solid;
border-top-color: #D3D3D3;
}
#ydgabwknrs .gt_first_summary_row.thick {
border-top-width: 2px;
}
#ydgabwknrs .gt_last_summary_row {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
}
#ydgabwknrs .gt_grand_summary_row {
color: #333333;
background-color: #FFFFFF;
text-transform: inherit;
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
}
#ydgabwknrs .gt_first_grand_summary_row {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
border-top-style: double;
border-top-width: 6px;
border-top-color: #D3D3D3;
}
#ydgabwknrs .gt_last_grand_summary_row_top {
padding-top: 8px;
padding-bottom: 8px;
padding-left: 5px;
padding-right: 5px;
border-bottom-style: double;
border-bottom-width: 6px;
border-bottom-color: #D3D3D3;
}
#ydgabwknrs .gt_striped {
background-color: rgba(128, 128, 128, 0.05);
}
#ydgabwknrs .gt_table_body {
border-top-style: solid;
border-top-width: 2px;
border-top-color: #D3D3D3;
border-bottom-style: solid;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
}
#ydgabwknrs .gt_footnotes {
color: #333333;
background-color: #FFFFFF;
border-bottom-style: none;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
border-left-style: none;
border-left-width: 2px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 2px;
border-right-color: #D3D3D3;
}
#ydgabwknrs .gt_footnote {
margin: 0px;
font-size: 90%;
padding-top: 4px;
padding-bottom: 4px;
padding-left: 5px;
padding-right: 5px;
}
#ydgabwknrs .gt_sourcenotes {
color: #333333;
background-color: #FFFFFF;
border-bottom-style: none;
border-bottom-width: 2px;
border-bottom-color: #D3D3D3;
border-left-style: none;
border-left-width: 2px;
border-left-color: #D3D3D3;
border-right-style: none;
border-right-width: 2px;
border-right-color: #D3D3D3;
}
#ydgabwknrs .gt_sourcenote {
font-size: 90%;
padding-top: 4px;
padding-bottom: 4px;
padding-left: 5px;
padding-right: 5px;
}
#ydgabwknrs .gt_left {
text-align: left;
}
#ydgabwknrs .gt_center {
text-align: center;
}
#ydgabwknrs .gt_right {
text-align: right;
font-variant-numeric: tabular-nums;
}
#ydgabwknrs .gt_font_normal {
font-weight: normal;
}
#ydgabwknrs .gt_font_bold {
font-weight: bold;
}
#ydgabwknrs .gt_font_italic {
font-style: italic;
}
#ydgabwknrs .gt_super {
font-size: 65%;
}
#ydgabwknrs .gt_footnote_marks {
font-size: 75%;
vertical-align: 0.4em;
position: initial;
}
#ydgabwknrs .gt_asterisk {
font-size: 100%;
vertical-align: 0;
}
#ydgabwknrs .gt_indent_1 {
text-indent: 5px;
}
#ydgabwknrs .gt_indent_2 {
text-indent: 10px;
}
#ydgabwknrs .gt_indent_3 {
text-indent: 15px;
}
#ydgabwknrs .gt_indent_4 {
text-indent: 20px;
}
#ydgabwknrs .gt_indent_5 {
text-indent: 25px;
}
#ydgabwknrs .katex-display {
display: inline-flex !important;
margin-bottom: 0.75em !important;
}
#ydgabwknrs div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after {
height: 0px !important;
}
</style>
<table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
<thead>
<tr class="gt_col_headings">
<th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="label"><span class='gt_from_md'><strong>Characteristic</strong></span></th>
<th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col" id="stat_0"><span class='gt_from_md'><strong>Overall</strong><br />
N = 200</span><span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;line-height:0;"><sup>1</sup></span></th>
<th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col" id="stat_1"><span class='gt_from_md'><strong>Drug A</strong><br />
N = 98</span><span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;line-height:0;"><sup>1</sup></span></th>
<th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col" id="stat_2"><span class='gt_from_md'><strong>Drug B</strong><br />
N = 102</span><span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;line-height:0;"><sup>1</sup></span></th>
</tr>
</thead>
<tbody class="gt_table_body">
<tr><td headers="label" class="gt_row gt_left">Age</td>
<td headers="stat_0" class="gt_row gt_center">47 (38, 57)</td>
<td headers="stat_1" class="gt_row gt_center">46 (37, 60)</td>
<td headers="stat_2" class="gt_row gt_center">48 (39, 56)</td></tr>
<tr><td headers="label" class="gt_row gt_left"> Unknown</td>
<td headers="stat_0" class="gt_row gt_center">11</td>
<td headers="stat_1" class="gt_row gt_center">7</td>
<td headers="stat_2" class="gt_row gt_center">4</td></tr>
<tr><td headers="label" class="gt_row gt_left">Grade</td>
<td headers="stat_0" class="gt_row gt_center"><br /></td>
<td headers="stat_1" class="gt_row gt_center"><br /></td>
<td headers="stat_2" class="gt_row gt_center"><br /></td></tr>
<tr><td headers="label" class="gt_row gt_left"> I</td>
<td headers="stat_0" class="gt_row gt_center">68 (34%)</td>
<td headers="stat_1" class="gt_row gt_center">35 (36%)</td>
<td headers="stat_2" class="gt_row gt_center">33 (32%)</td></tr>
<tr><td headers="label" class="gt_row gt_left"> II</td>
<td headers="stat_0" class="gt_row gt_center">68 (34%)</td>
<td headers="stat_1" class="gt_row gt_center">32 (33%)</td>
<td headers="stat_2" class="gt_row gt_center">36 (35%)</td></tr>
<tr><td headers="label" class="gt_row gt_left"> III</td>
<td headers="stat_0" class="gt_row gt_center">64 (32%)</td>
<td headers="stat_1" class="gt_row gt_center">31 (32%)</td>
<td headers="stat_2" class="gt_row gt_center">33 (32%)</td></tr>
</tbody>
<tfoot>
<tr class="gt_footnotes">
<td class="gt_footnote" colspan="4"><span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;line-height:0;"><sup>1</sup></span> <span class='gt_from_md'>Median (Q1, Q3); n (%)</span></td>
</tr>
</tfoot>
</table>
</div>
>
> # Example 2 ----------------------------------
> trial |>
+ tbl_summary(
+ include = grade,
+ by = trt,
+ percent = "row",
+ statistic = ~"{p}%",
+ digits = ~1
+ ) |>
+ add_overall(
+ last = TRUE,
+ statistic = ~"{p}% (n={n})",
+ digits = ~ c(1, 0)
+ )
Error in as.data.frame.integer(x[[i]], optional = TRUE) :
row names contain missing values
Calls: add_overall ... data.frame -> as.data.frame -> as.data.frame.integer
Execution halted
Flavor: r-devel-windows-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13