Last updated on 2025-12-19 17:49:56 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.0.4 | 5.14 | 63.57 | 68.71 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 0.0.4 | 3.60 | 44.71 | 48.31 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.0.4 | 10.00 | 95.80 | 105.80 | NOTE | |
| r-devel-linux-x86_64-fedora-gcc | 0.0.4 | 9.00 | 96.69 | 105.69 | ERROR | |
| r-devel-windows-x86_64 | 0.0.4 | 7.00 | 75.00 | 82.00 | NOTE | |
| r-patched-linux-x86_64 | 0.0.4 | 5.76 | 56.44 | 62.20 | NOTE | |
| r-release-linux-x86_64 | 0.0.4 | 5.37 | 56.02 | 61.39 | NOTE | |
| r-release-macos-arm64 | 0.0.4 | NOTE | ||||
| r-release-macos-x86_64 | 0.0.4 | 4.00 | 60.00 | 64.00 | NOTE | |
| r-release-windows-x86_64 | 0.0.4 | 7.00 | 72.00 | 79.00 | NOTE | |
| r-oldrel-macos-arm64 | 0.0.4 | OK | ||||
| r-oldrel-macos-x86_64 | 0.0.4 | 4.00 | 99.00 | 103.00 | OK | |
| r-oldrel-windows-x86_64 | 0.0.4 | 11.00 | 90.00 | 101.00 | OK |
Version: 0.0.4
Check: DESCRIPTION meta-information
Result: NOTE
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘da.Rd’ ‘da_object_oriented_functions.R’
‘higher_level_disprop_analysis.R’ ‘lower_level_disprop_analysis.R’
‘print.da.Rd’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-windows-x86_64
Version: 0.0.4
Check: tests
Result: ERROR
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> Sys.setenv("OMP_THREAD_LIMIT" = 2)
>
> library(testthat)
> library(pvda)
>
> test_check("pvda")
Saving _problems/test-disprop_analysis-47.R
Saving _problems/test-disprop_analysis-70.R
Saving _problems/test-disprop_analysis-90.R
Saving _problems/test-disprop_analysis-109.R
Saving _problems/test-disprop_analysis-128.R
Saving _problems/test-disprop_analysis-175.R
Saving _problems/test-disprop_analysis-185.R
Saving _problems/test-disprop_analysis-231.R
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 4 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-disprop_analysis.R:43:3'): 5-10. Function add_expected_count works ──
Error in ``[.data.table`(unique(copy(`_DT1`))[, `:=`(n_tot = uniqueN(report_id))], , `:=`(n_drug = uniqueN(report_id)), by = .(drug))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─pvda::add_expected_counts(...) at test-disprop_analysis.R:43:3
2. │ ├─dplyr::desc(x = as.data.frame(count_dt)$obs)
3. │ │ └─vctrs::obj_check_vector(x)
4. │ ├─base::as.data.frame(count_dt)
5. │ └─dtplyr:::as.data.frame.dtplyr_step(count_dt)
6. │ ├─base::as.data.frame(dt_eval(x))
7. │ └─dtplyr:::dt_eval(x)
8. │ └─rlang::eval_tidy(quo)
9. ├─data.table::setcolorder(...)
10. │ └─data.table:::check_duplicate_names(x)
11. │ └─base::anyDuplicated(nm <- names(x))
12. ├─data.table::setnames(...)
13. │ └─base::is.data.frame(x)
14. ├─...[]
15. └─data.table:::`[.data.table`(...)
── Error ('test-disprop_analysis.R:66:3'): 11. The whole disproportionality function chain runs without NA output except in PRR and ROR ──
Error in ``[.data.table`(unique(copy(`_DT2`))[, `:=`(n_tot = uniqueN(report_id))], , `:=`(n_drug = uniqueN(report_id)), by = .(drug))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─dplyr::select(...) at test-disprop_analysis.R:66:3
2. ├─dplyr::select(...)
3. ├─purrr::pluck(pvda::da(pvda::drug_event_df), "da_df")
4. │ └─purrr:::pluck_raw(.x, list2(...), .default = .default)
5. ├─pvda::da(pvda::drug_event_df)
6. │ ├─pvda:::round_and_sort_by_lower_da_limit(...)
7. │ │ ├─dplyr::summarise(...)
8. │ │ └─dplyr::group_by(df, !!df_syms$drug, !!df_syms$event)
9. │ ├─pvda::add_disproportionality(...)
10. │ └─pvda::add_expected_counts(...)
11. │ ├─dplyr::desc(x = as.data.frame(count_dt)$obs)
12. │ │ └─vctrs::obj_check_vector(x)
13. │ ├─base::as.data.frame(count_dt)
14. │ └─dtplyr:::as.data.frame.dtplyr_step(count_dt)
15. │ ├─base::as.data.frame(dt_eval(x))
16. │ └─dtplyr:::dt_eval(x)
17. │ └─rlang::eval_tidy(quo)
18. ├─data.table::setcolorder(...)
19. │ └─data.table:::check_duplicate_names(x)
20. │ └─base::anyDuplicated(nm <- names(x))
21. ├─data.table::setnames(...)
22. │ └─base::is.data.frame(x)
23. ├─...[]
24. └─data.table:::`[.data.table`(...)
── Error ('test-disprop_analysis.R:80:3'): 12. The grouping functionality runs ──
<purrr_error_indexed/rlang_error/error/condition>
Error in `purrr::map(split(df, f = df[[df_colnames$group_by]]), grouped_da, df_colnames = df_colnames, df_syms = df_syms, expected_count_estimators = expected_count_estimators, da_estimators = da_estimators, conf_lvl = conf_lvl, rule_of_N = rule_of_N, number_of_digits = number_of_digits)`: i In index: 1.
i With name: 0.
Caused by error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─purrr::pluck(...) at test-disprop_analysis.R:80:3
2. │ └─purrr:::pluck_raw(.x, list2(...), .default = .default)
3. ├─pvda::da(...)
4. │ ├─pvda:::round_and_sort_by_lower_da_limit(...)
5. │ │ ├─dplyr::summarise(...)
6. │ │ └─dplyr::group_by(df, !!df_syms$drug, !!df_syms$event)
7. │ ├─dplyr::select(...)
8. │ ├─purrr::list_rbind(...)
9. │ │ └─purrr:::check_list_of_data_frames(x)
10. │ │ └─vctrs::obj_check_list(x, call = error_call)
11. │ └─purrr::map(...)
12. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
13. │ ├─purrr:::with_indexed_errors(...)
14. │ │ └─base::withCallingHandlers(...)
15. │ ├─purrr:::call_with_cleanup(...)
16. │ └─pvda (local) .f(.x[[i]], ...)
17. │ ├─dplyr::bind_cols(...)
18. │ │ └─rlang::list2(...)
19. │ ├─pvda::add_disproportionality(...)
20. │ └─pvda::add_expected_counts(...)
21. │ ├─dplyr::desc(x = as.data.frame(count_dt)$obs)
22. │ │ └─vctrs::obj_check_vector(x)
23. │ ├─base::as.data.frame(count_dt)
24. │ └─dtplyr:::as.data.frame.dtplyr_step(count_dt)
25. │ ├─base::as.data.frame(dt_eval(x))
26. │ └─dtplyr:::dt_eval(x)
27. │ └─rlang::eval_tidy(quo)
28. ├─data.table::setcolorder(...)
29. │ └─data.table:::check_duplicate_names(x)
30. │ └─base::anyDuplicated(nm <- names(x))
31. ├─data.table::setnames(...)
32. │ └─base::is.data.frame(x)
33. ├─...[]
34. ├─data.table:::`[.data.table`(...)
35. └─base::.handleSimpleError(...)
36. └─purrr (local) h(simpleError(msg, call))
37. └─cli::cli_abort(...)
38. └─rlang::abort(...)
── Error ('test-disprop_analysis.R:102:3'): 13. Custom column names can be passed through the df_colnames list ──
Error in ``[.data.table`(unique(copy(`_DT4`))[, `:=`(n_tot = uniqueN(RepId))], , `:=`(n_drug = uniqueN(RepId)), by = .(Drug))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─purrr::pluck(...) at test-disprop_analysis.R:102:3
2. │ └─purrr:::pluck_raw(.x, list2(...), .default = .default)
3. ├─pvda::da(...)
4. │ ├─pvda:::round_and_sort_by_lower_da_limit(...)
5. │ │ ├─dplyr::summarise(...)
6. │ │ └─dplyr::group_by(df, !!df_syms$drug, !!df_syms$event)
7. │ ├─pvda::add_disproportionality(...)
8. │ └─pvda::add_expected_counts(...)
9. │ ├─dplyr::desc(x = as.data.frame(count_dt)$obs)
10. │ │ └─vctrs::obj_check_vector(x)
11. │ ├─base::as.data.frame(count_dt)
12. │ └─dtplyr:::as.data.frame.dtplyr_step(count_dt)
13. │ ├─base::as.data.frame(dt_eval(x))
14. │ └─dtplyr:::dt_eval(x)
15. │ └─rlang::eval_tidy(quo)
16. ├─data.table::setcolorder(...)
17. │ └─data.table:::check_duplicate_names(x)
18. │ └─base::anyDuplicated(nm <- names(x))
19. ├─data.table::setnames(...)
20. │ └─base::is.data.frame(x)
21. ├─...[]
22. └─data.table:::`[.data.table`(...)
── Error ('test-disprop_analysis.R:118:3'): 14. Sorting works as expected ──────
<purrr_error_indexed/rlang_error/error/condition>
Error in `purrr::map(split(df, f = df[[df_colnames$group_by]]), grouped_da, df_colnames = df_colnames, df_syms = df_syms, expected_count_estimators = expected_count_estimators, da_estimators = da_estimators, conf_lvl = conf_lvl, rule_of_N = rule_of_N, number_of_digits = number_of_digits)`: i In index: 1.
i With name: 0.
Caused by error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─purrr::pluck(...) at test-disprop_analysis.R:118:3
2. │ └─purrr:::pluck_raw(.x, list2(...), .default = .default)
3. ├─pvda::da(...)
4. │ ├─pvda:::round_and_sort_by_lower_da_limit(...)
5. │ │ ├─dplyr::summarise(...)
6. │ │ └─dplyr::group_by(df, !!df_syms$drug, !!df_syms$event)
7. │ ├─dplyr::select(...)
8. │ ├─purrr::list_rbind(...)
9. │ │ └─purrr:::check_list_of_data_frames(x)
10. │ │ └─vctrs::obj_check_list(x, call = error_call)
11. │ └─purrr::map(...)
12. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
13. │ ├─purrr:::with_indexed_errors(...)
14. │ │ └─base::withCallingHandlers(...)
15. │ ├─purrr:::call_with_cleanup(...)
16. │ └─pvda (local) .f(.x[[i]], ...)
17. │ ├─dplyr::bind_cols(...)
18. │ │ └─rlang::list2(...)
19. │ ├─pvda::add_disproportionality(...)
20. │ └─pvda::add_expected_counts(...)
21. │ ├─dplyr::desc(x = as.data.frame(count_dt)$obs)
22. │ │ └─vctrs::obj_check_vector(x)
23. │ ├─base::as.data.frame(count_dt)
24. │ └─dtplyr:::as.data.frame.dtplyr_step(count_dt)
25. │ ├─base::as.data.frame(dt_eval(x))
26. │ └─dtplyr:::dt_eval(x)
27. │ └─rlang::eval_tidy(quo)
28. ├─data.table::setcolorder(...)
29. │ └─data.table:::check_duplicate_names(x)
30. │ └─base::anyDuplicated(nm <- names(x))
31. ├─data.table::setnames(...)
32. │ └─base::is.data.frame(x)
33. ├─...[]
34. ├─data.table:::`[.data.table`(...)
35. └─base::.handleSimpleError(...)
36. └─purrr (local) h(simpleError(msg, call))
37. └─cli::cli_abort(...)
38. └─rlang::abort(...)
── Error ('test-disprop_analysis.R:160:3'): 15. Summary table contains a prr2.5 by default ──
Error in ``[.data.table`(unique(copy(`_DT6`))[, `:=`(n_tot = uniqueN(report_id))], , `:=`(n_drug = uniqueN(report_id)), by = .(drug))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressMessages(invisible(capture.output(summary_output <- summary.da(pvda::da(pvda::drug_event_df))))) at test-disprop_analysis.R:160:3
2. │ └─base::withCallingHandlers(...)
3. ├─utils::capture.output(summary_output <- summary.da(pvda::da(pvda::drug_event_df)))
4. │ └─base::withVisible(...elt(i))
5. ├─pvda:::summary.da(pvda::da(pvda::drug_event_df))
6. ├─pvda::da(pvda::drug_event_df)
7. │ ├─pvda:::round_and_sort_by_lower_da_limit(...)
8. │ │ ├─dplyr::summarise(...)
9. │ │ └─dplyr::group_by(df, !!df_syms$drug, !!df_syms$event)
10. │ ├─pvda::add_disproportionality(...)
11. │ └─pvda::add_expected_counts(...)
12. │ ├─dplyr::desc(x = as.data.frame(count_dt)$obs)
13. │ │ └─vctrs::obj_check_vector(x)
14. │ ├─base::as.data.frame(count_dt)
15. │ └─dtplyr:::as.data.frame.dtplyr_step(count_dt)
16. │ ├─base::as.data.frame(dt_eval(x))
17. │ └─dtplyr:::dt_eval(x)
18. │ └─rlang::eval_tidy(quo)
19. ├─data.table::setcolorder(...)
20. │ └─data.table:::check_duplicate_names(x)
21. │ └─base::anyDuplicated(nm <- names(x))
22. ├─data.table::setnames(...)
23. │ └─base::is.data.frame(x)
24. ├─...[]
25. └─data.table:::`[.data.table`(...)
── Error ('test-disprop_analysis.R:168:3'): 16. print function runs and has the same number of characters in first row as it has before ──
Error in ``[.data.table`(unique(copy(`_DT7`))[, `:=`(n_tot = uniqueN(report_id))], , `:=`(n_drug = uniqueN(report_id)), by = .(drug))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressMessages(invisible(printed <- capture.output(print(pvda::da(pvda::drug_event_df))))) at test-disprop_analysis.R:168:3
2. │ └─base::withCallingHandlers(...)
3. ├─utils::capture.output(print(pvda::da(pvda::drug_event_df)))
4. │ └─base::withVisible(...elt(i))
5. ├─base::print(pvda::da(pvda::drug_event_df))
6. ├─pvda::da(pvda::drug_event_df)
7. │ ├─pvda:::round_and_sort_by_lower_da_limit(...)
8. │ │ ├─dplyr::summarise(...)
9. │ │ └─dplyr::group_by(df, !!df_syms$drug, !!df_syms$event)
10. │ ├─pvda::add_disproportionality(...)
11. │ └─pvda::add_expected_counts(...)
12. │ ├─dplyr::desc(x = as.data.frame(count_dt)$obs)
13. │ │ └─vctrs::obj_check_vector(x)
14. │ ├─base::as.data.frame(count_dt)
15. │ └─dtplyr:::as.data.frame.dtplyr_step(count_dt)
16. │ ├─base::as.data.frame(dt_eval(x))
17. │ └─dtplyr:::dt_eval(x)
18. │ └─rlang::eval_tidy(quo)
19. ├─data.table::setcolorder(...)
20. │ └─data.table:::check_duplicate_names(x)
21. │ └─base::anyDuplicated(nm <- names(x))
22. ├─data.table::setnames(...)
23. │ └─base::is.data.frame(x)
24. ├─...[]
25. └─data.table:::`[.data.table`(...)
── Error ('test-disprop_analysis.R:173:3'): 17. Grouped output from summary function works. ──
<purrr_error_indexed/rlang_error/error/condition>
Error in `purrr::map(split(df, f = df[[df_colnames$group_by]]), grouped_da, df_colnames = df_colnames, df_syms = df_syms, expected_count_estimators = expected_count_estimators, da_estimators = da_estimators, conf_lvl = conf_lvl, rule_of_N = rule_of_N, number_of_digits = number_of_digits)`: i In index: 1.
i With name: 0.
Caused by error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─base::summary(...) at test-disprop_analysis.R:173:3
2. ├─pvda::da(pvda::drug_event_df, df_colnames = list(group_by = "group"))
3. │ ├─pvda:::round_and_sort_by_lower_da_limit(...)
4. │ │ ├─dplyr::summarise(...)
5. │ │ └─dplyr::group_by(df, !!df_syms$drug, !!df_syms$event)
6. │ ├─dplyr::select(...)
7. │ ├─purrr::list_rbind(...)
8. │ │ └─purrr:::check_list_of_data_frames(x)
9. │ │ └─vctrs::obj_check_list(x, call = error_call)
10. │ └─purrr::map(...)
11. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
12. │ ├─purrr:::with_indexed_errors(...)
13. │ │ └─base::withCallingHandlers(...)
14. │ ├─purrr:::call_with_cleanup(...)
15. │ └─pvda (local) .f(.x[[i]], ...)
16. │ ├─dplyr::bind_cols(...)
17. │ │ └─rlang::list2(...)
18. │ ├─pvda::add_disproportionality(...)
19. │ └─pvda::add_expected_counts(...)
20. │ ├─dplyr::desc(x = as.data.frame(count_dt)$obs)
21. │ │ └─vctrs::obj_check_vector(x)
22. │ ├─base::as.data.frame(count_dt)
23. │ └─dtplyr:::as.data.frame.dtplyr_step(count_dt)
24. │ ├─base::as.data.frame(dt_eval(x))
25. │ └─dtplyr:::dt_eval(x)
26. │ └─rlang::eval_tidy(quo)
27. ├─data.table::setcolorder(...)
28. │ └─data.table:::check_duplicate_names(x)
29. │ └─base::anyDuplicated(nm <- names(x))
30. ├─data.table::setnames(...)
31. │ └─base::is.data.frame(x)
32. ├─...[]
33. ├─data.table:::`[.data.table`(...)
34. └─base::.handleSimpleError(...)
35. └─purrr (local) h(simpleError(msg, call))
36. └─cli::cli_abort(...)
37. └─rlang::abort(...)
── Error ('test-disprop_analysis.R:181:3'): 18. It's possible to name the group_by something else than 'group' ──
<purrr_error_indexed/rlang_error/error/condition>
Error in `purrr::map(split(df, f = df[[df_colnames$group_by]]), grouped_da, df_colnames = df_colnames, df_syms = df_syms, expected_count_estimators = expected_count_estimators, da_estimators = da_estimators, conf_lvl = conf_lvl, rule_of_N = rule_of_N, number_of_digits = number_of_digits)`: i In index: 1.
i With name: 0.
Caused by error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─base::summary(...) at test-disprop_analysis.R:181:3
2. ├─pvda::da(...)
3. │ ├─pvda:::round_and_sort_by_lower_da_limit(...)
4. │ │ ├─dplyr::summarise(...)
5. │ │ └─dplyr::group_by(df, !!df_syms$drug, !!df_syms$event)
6. │ ├─dplyr::select(...)
7. │ ├─purrr::list_rbind(...)
8. │ │ └─purrr:::check_list_of_data_frames(x)
9. │ │ └─vctrs::obj_check_list(x, call = error_call)
10. │ └─purrr::map(...)
11. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
12. │ ├─purrr:::with_indexed_errors(...)
13. │ │ └─base::withCallingHandlers(...)
14. │ ├─purrr:::call_with_cleanup(...)
15. │ └─pvda (local) .f(.x[[i]], ...)
16. │ ├─dplyr::bind_cols(...)
17. │ │ └─rlang::list2(...)
18. │ ├─pvda::add_disproportionality(...)
19. │ └─pvda::add_expected_counts(...)
20. │ ├─dplyr::desc(x = as.data.frame(count_dt)$obs)
21. │ │ └─vctrs::obj_check_vector(x)
22. │ ├─base::as.data.frame(count_dt)
23. │ └─dtplyr:::as.data.frame.dtplyr_step(count_dt)
24. │ ├─base::as.data.frame(dt_eval(x))
25. │ └─dtplyr:::dt_eval(x)
26. │ └─rlang::eval_tidy(quo)
27. ├─data.table::setcolorder(...)
28. │ └─data.table:::check_duplicate_names(x)
29. │ └─base::anyDuplicated(nm <- names(x))
30. ├─data.table::setnames(...)
31. │ └─base::is.data.frame(x)
32. ├─...[]
33. ├─data.table:::`[.data.table`(...)
34. └─base::.handleSimpleError(...)
35. └─purrr (local) h(simpleError(msg, call))
36. └─cli::cli_abort(...)
37. └─rlang::abort(...)
── Error ('test-disprop_analysis.R:231:3'): 19. The IC values match manually calculated IC-values ──
Error in ``[.data.table`(unique(copy(`_DT10`))[, `:=`(n_tot = uniqueN(report_id))], , `:=`(n_drug = uniqueN(report_id)), by = .(drug))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─pvda::da(pvda::drug_event_df) at test-disprop_analysis.R:231:3
2. │ ├─pvda:::round_and_sort_by_lower_da_limit(...)
3. │ │ ├─dplyr::summarise(...)
4. │ │ └─dplyr::group_by(df, !!df_syms$drug, !!df_syms$event)
5. │ ├─pvda::add_disproportionality(...)
6. │ └─pvda::add_expected_counts(...)
7. │ ├─dplyr::desc(x = as.data.frame(count_dt)$obs)
8. │ │ └─vctrs::obj_check_vector(x)
9. │ ├─base::as.data.frame(count_dt)
10. │ └─dtplyr:::as.data.frame.dtplyr_step(count_dt)
11. │ ├─base::as.data.frame(dt_eval(x))
12. │ └─dtplyr:::dt_eval(x)
13. │ └─rlang::eval_tidy(quo)
14. ├─data.table::setcolorder(...)
15. │ └─data.table:::check_duplicate_names(x)
16. │ └─base::anyDuplicated(nm <- names(x))
17. ├─data.table::setnames(...)
18. │ └─base::is.data.frame(x)
19. ├─...[]
20. └─data.table:::`[.data.table`(...)
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 4 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.0.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Disproportionality_analysis.Rmd’ using rmarkdown
Quitting from Disproportionality_analysis.Rmd:46-52 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. ├─pvda::da(drug_event_df)
2. │ ├─pvda:::round_and_sort_by_lower_da_limit(...)
3. │ │ ├─dplyr::summarise(...)
4. │ │ └─dplyr::group_by(df, !!df_syms$drug, !!df_syms$event)
5. │ ├─pvda::add_disproportionality(...)
6. │ └─pvda::add_expected_counts(...)
7. │ ├─dplyr::desc(x = as.data.frame(count_dt)$obs)
8. │ │ └─vctrs::obj_check_vector(x)
9. │ ├─base::as.data.frame(count_dt)
10. │ └─dtplyr:::as.data.frame.dtplyr_step(count_dt)
11. │ ├─base::as.data.frame(dt_eval(x))
12. │ └─dtplyr:::dt_eval(x)
13. │ └─rlang::eval_tidy(quo)
14. ├─data.table::setcolorder(...)
15. │ └─data.table:::check_duplicate_names(x)
16. │ └─base::anyDuplicated(nm <- names(x))
17. ├─data.table::setnames(...)
18. │ └─base::is.data.frame(x)
19. ├─...[]
20. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Disproportionality_analysis.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘Disproportionality_analysis.Rmd’
SUMMARY: processing the following file failed:
‘Disproportionality_analysis.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.0.4
Check: DESCRIPTION meta-information
Result: NOTE
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘da_object_oriented_functions.R’ ‘higher_level_disprop_analysis.R’
‘lower_level_disprop_analysis.R’
Flavor: r-release-macos-x86_64