* using log directory 'd:/Rcompile/CRANpkg/local/4.7/cardx.Rcheck' * using R Under development (unstable) (2026-05-01 r89993 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * current time: 2026-05-03 10:33:38 UTC * checking for file 'cardx/DESCRIPTION' ... OK * this is package 'cardx' version '0.3.2' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'cardx' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s] OK * checking whether the package can be loaded with stated dependencies ... [1s] OK * checking whether the package can be unloaded cleanly ... [1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s] OK * checking whether the namespace can be unloaded cleanly ... [1s] OK * checking loading without being on the library search path ... [1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [9s] OK * checking Rd files ... [1s] OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... [29s] 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 * checking for unstated dependencies in 'tests' ... OK * checking tests ... [143s] 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 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 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 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 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 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 * checking PDF version of manual ... [23s] OK * checking HTML version of manual ... [17s] OK * DONE Status: 2 ERRORs