Last updated on 2026-01-15 07:50:09 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3.0 | 7.18 | 256.25 | 263.43 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.3.0 | 4.67 | 150.44 | 155.11 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.3.0 | 13.00 | 322.25 | 335.25 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.3.0 | 12.00 | 196.96 | 208.96 | ERROR | |
| r-devel-windows-x86_64 | 1.3.0 | 8.00 | 225.00 | 233.00 | OK | |
| r-patched-linux-x86_64 | 1.3.0 | 6.68 | 234.38 | 241.06 | OK | |
| r-release-linux-x86_64 | 1.3.0 | 6.05 | 237.01 | 243.06 | OK | |
| r-release-macos-arm64 | 1.3.0 | OK | ||||
| r-release-macos-x86_64 | 1.3.0 | 5.00 | 274.00 | 279.00 | OK | |
| r-release-windows-x86_64 | 1.3.0 | 10.00 | 222.00 | 232.00 | OK | |
| r-oldrel-macos-arm64 | 1.3.0 | OK | ||||
| r-oldrel-macos-x86_64 | 1.3.0 | 5.00 | 251.00 | 256.00 | OK | |
| r-oldrel-windows-x86_64 | 1.3.0 | 12.00 | 300.00 | 312.00 | OK |
Version: 1.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [10s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat) # nolint: undesirable_function_linter
> library(admiralonco) # nolint: undesirable_function_linter
>
> test_check("admiralonco")
Saving _problems/test-check_crpr-31.R
Saving _problems/test-check_crpr-51.R
Saving _problems/test-check_crpr-62.R
Saving _problems/test-derive_param_bor-76.R
Saving _problems/test-derive_param_clinbenefit-54.R
Saving _problems/test-derive_param_confirmed_bor-64.R
`date_source()` was deprecated in admiral 1.2.0.
i Please use `event()` instead.
x This message will turn into a warning at the beginning of 2026.
i See admiral's deprecation guidance: https://pharmaverse.github.io/admiraldev/dev/articles/programming_strategy.html#deprecation
Saving _problems/test-derive_param_confirmed_resp-85.R
Saving _problems/test-derive_param_confirmed_resp-149.R
Saving _problems/test-derive_param_confirmed_resp-210.R
Saving _problems/test-derive_param_confirmed_resp-250.R
Saving _problems/test-derive_param_confirmed_resp-316.R
`date_source()` was deprecated in admiral 1.2.0.
i Please use `event()` instead.
x This message will turn into a warning at the beginning of 2026.
i See admiral's deprecation guidance: https://pharmaverse.github.io/admiraldev/dev/articles/programming_strategy.html#deprecation
Saving _problems/test-derive_param_response-75.R
Saving _problems/test-derive_param_response-117.R
Saving _problems/test-derive_param_response-162.R
`date_source()` was deprecated in admiral 1.2.0.
i Please use `event()` instead.
x This message will turn into a warning at the beginning of 2026.
i See admiral's deprecation guidance: https://pharmaverse.github.io/admiraldev/dev/articles/programming_strategy.html#deprecation
Saving _problems/test-filter_pd-49.R
`date_source()` was deprecated in admiral 1.2.0.
i Please use `event()` instead.
x This message will turn into a warning at the beginning of 2026.
i See admiral's deprecation guidance: https://pharmaverse.github.io/admiraldev/dev/articles/programming_strategy.html#deprecation
Saving _problems/test-filter_pd-104.R
`date_source()` was deprecated in admiral 1.2.0.
i Please use `event()` instead.
x This message will turn into a warning at the beginning of 2026.
i See admiral's deprecation guidance: https://pharmaverse.github.io/admiraldev/dev/articles/programming_strategy.html#deprecation
Saving _problems/test-filter_pd-154.R
`date_source()` was deprecated in admiral 1.2.0.
i Please use `event()` instead.
x This message will turn into a warning at the beginning of 2026.
i See admiral's deprecation guidance: https://pharmaverse.github.io/admiraldev/dev/articles/programming_strategy.html#deprecation
Saving _problems/test-filter_pd-202.R
`date_source()` was deprecated in admiral 1.2.0.
i Please use `event()` instead.
x This message will turn into a warning at the beginning of 2026.
i See admiral's deprecation guidance: https://pharmaverse.github.io/admiraldev/dev/articles/programming_strategy.html#deprecation
Saving _problems/test-filter_pd-247.R
[ FAIL 19 | WARN 0 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-check_crpr.R:20:3'): signal_crpr Test 1: warning is issued ─────
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-check_crpr.R:20:3
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. ├─admiralonco::signal_crpr(adrs, order = exprs(ADT))
8. │ └─admiral::filter_joined(...)
9. │ ├─... %>% remove_tmp_vars()
10. │ └─admiral:::get_joined_data(...)
11. │ └─data %>% ...
12. ├─admiraldev::remove_tmp_vars(.)
13. ├─dplyr::select(., colnames(dataset))
14. ├─dplyr::ungroup(.)
15. ├─dplyr::slice(., 1L)
16. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
17. └─admiral::derive_vars_merged(...)
18. └─base::tryCatch(...)
19. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
20. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
21. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-check_crpr.R:36:3'): signal_crpr Test 2: error with custom message ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-check_crpr.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. ├─admiralonco::signal_crpr(...)
8. │ └─admiral::filter_joined(...)
9. │ ├─... %>% remove_tmp_vars()
10. │ └─admiral:::get_joined_data(...)
11. │ └─data %>% ...
12. ├─admiraldev::remove_tmp_vars(.)
13. ├─dplyr::select(., colnames(dataset))
14. ├─dplyr::ungroup(.)
15. ├─dplyr::slice(., 1L)
16. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
17. └─admiral::derive_vars_merged(...)
18. └─base::tryCatch(...)
19. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
20. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
21. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-check_crpr.R:57:3'): get_crpr_dataset() Test 2: dataset if returned ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::suppress_warning(...) at test-check_crpr.R:57:3
2. │ └─base::withCallingHandlers(...)
3. ├─admiralonco::signal_crpr(adrs, order = exprs(ADT))
4. │ └─admiral::filter_joined(...)
5. │ ├─... %>% remove_tmp_vars()
6. │ └─admiral:::get_joined_data(...)
7. │ └─data %>% ...
8. ├─admiraldev::remove_tmp_vars(.)
9. ├─dplyr::select(., colnames(dataset))
10. ├─dplyr::ungroup(.)
11. ├─dplyr::slice(., 1L)
12. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
13. └─admiral::derive_vars_merged(...)
14. └─base::tryCatch(...)
15. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_bor.R:36:1'): (code run outside of `test_that()`) ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─... %>% ... at test-derive_param_bor.R:36:1
2. └─admiral::derive_vars_merged(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_clinbenefit.R:17:1'): (code run outside of `test_that()`) ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─... %>% ... at test-derive_param_clinbenefit.R:17:1
2. └─admiral::derive_vars_merged(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_confirmed_bor.R:18:1'): (code run outside of `test_that()`) ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─... %>% ... at test-derive_param_confirmed_bor.R:18:1
2. └─admiral::derive_vars_merged(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_confirmed_resp.R:69:3'): derive_param_confirmed_resp Test 1: default confirmed response ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::suppress_warning(...) at test-derive_param_confirmed_resp.R:69:3
2. │ └─base::withCallingHandlers(...)
3. ├─admiralonco::derive_param_confirmed_resp(...)
4. │ └─dataset %>% ...
5. ├─admiralonco::filter_pd(...)
6. │ └─... %>% select(-temp_date)
7. ├─dplyr::select(., -temp_date)
8. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
9. └─admiral::derive_vars_merged(...)
10. └─base::tryCatch(...)
11. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
12. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
13. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_confirmed_resp.R:131:3'): derive_param_confirmed_resp Test 2: accept SD ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::suppress_warning(...) at test-derive_param_confirmed_resp.R:131:3
2. │ └─base::withCallingHandlers(...)
3. ├─admiralonco::derive_param_confirmed_resp(...)
4. │ └─dataset %>% ...
5. ├─admiralonco::filter_pd(...)
6. │ └─... %>% select(-temp_date)
7. ├─dplyr::select(., -temp_date)
8. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
9. └─admiral::derive_vars_merged(...)
10. └─base::tryCatch(...)
11. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
12. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
13. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_confirmed_resp.R:196:3'): derive_param_confirmed_resp Test 3: error if invalid response values ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_param_confirmed_resp.R:196:3
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. ├─admiralonco::derive_param_confirmed_resp(...)
8. │ └─dataset %>% ...
9. ├─admiralonco::filter_pd(...)
10. │ └─... %>% select(-temp_date)
11. ├─dplyr::select(., -temp_date)
12. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
13. └─admiral::derive_vars_merged(...)
14. └─base::tryCatch(...)
15. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_confirmed_resp.R:237:3'): derive_param_confirmed_resp Test 4: No source_pd ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiralonco::derive_param_confirmed_resp(...) at test-derive_param_confirmed_resp.R:237:3
2. │ └─admiralonco::signal_crpr(source_data, order = exprs(ADT), subject_keys = subject_keys)
3. │ └─admiral::filter_joined(...)
4. │ ├─... %>% remove_tmp_vars()
5. │ └─admiral:::get_joined_data(...)
6. │ └─data %>% ...
7. ├─admiraldev::remove_tmp_vars(.)
8. ├─dplyr::select(., colnames(dataset))
9. ├─dplyr::ungroup(.)
10. ├─dplyr::slice(., 1L)
11. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
12. └─admiral::derive_vars_merged(...)
13. └─base::tryCatch(...)
14. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
15. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
16. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_confirmed_resp.R:300:3'): derive_param_confirmed_resp Test 5: Deprecation warning for aval_fun ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-derive_param_confirmed_resp.R:300:3
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. ├─admiralonco::derive_param_confirmed_resp(...)
8. │ └─admiralonco::signal_crpr(source_data, order = exprs(ADT), subject_keys = subject_keys)
9. │ └─admiral::filter_joined(...)
10. │ ├─... %>% remove_tmp_vars()
11. │ └─admiral:::get_joined_data(...)
12. │ └─data %>% ...
13. ├─admiraldev::remove_tmp_vars(.)
14. ├─dplyr::select(., colnames(dataset))
15. ├─dplyr::ungroup(.)
16. ├─dplyr::slice(., 1L)
17. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
18. └─admiral::derive_vars_merged(...)
19. └─base::tryCatch(...)
20. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
21. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
22. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_response.R:63:3'): derive_param_response Test 1: With source_pd ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─adrs %>% ... at test-derive_param_response.R:63:3
2. ├─admiralonco::derive_param_response(...)
3. │ └─dataset %>% ...
4. ├─admiralonco::filter_pd(...)
5. │ └─... %>% select(-temp_date)
6. ├─dplyr::select(., -temp_date)
7. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
8. └─admiral::derive_vars_merged(...)
9. └─base::tryCatch(...)
10. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
11. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
12. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_response.R:105:3'): derive_param_response Test 2: No source_pd ──
Error in `anti_join(select(dataset_ref, intersect(add_vars, ref_vars)), select(new_add_obs, !!!by_vars), by = map_chr(by_vars, as_name))`: could not find function "anti_join"
Backtrace:
▆
1. ├─adrs %>% ... at test-derive_param_response.R:105:3
2. ├─admiralonco::derive_param_response(...)
3. │ └─dataset %>% ...
4. └─admiral::derive_extreme_records(...)
── Error ('test-derive_param_response.R:147:3'): derive_param_response Test 3: deprecation warning for aval_fun ──
Error in `anti_join(select(dataset_ref, intersect(add_vars, ref_vars)), select(new_add_obs, !!!by_vars), by = map_chr(by_vars, as_name))`: could not find function "anti_join"
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-derive_param_response.R:147:3
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. ├─adrs %>% ...
8. ├─admiralonco::derive_param_response(...)
9. │ └─dataset %>% ...
10. └─admiral::derive_extreme_records(...)
── Error ('test-filter_pd.R:40:3'): filter_pd Test 1: first PD in separate BDS dataset ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiralonco::filter_pd(...) at test-filter_pd.R:40:3
2. │ └─... %>% select(-temp_date)
3. ├─dplyr::select(., -temp_date)
4. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
5. └─admiral::derive_vars_merged(...)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-filter_pd.R:96:3'): filter_pd Test 2: first PD in ADSL dataset ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiralonco::filter_pd(...) at test-filter_pd.R:96:3
2. │ └─... %>% select(-temp_date)
3. ├─dplyr::select(., -temp_date)
4. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
5. └─admiral::derive_vars_merged(...)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-filter_pd.R:145:3'): filter_pd Test 3: first PD in input dataset ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiralonco::filter_pd(...) at test-filter_pd.R:145:3
2. │ └─... %>% select(-temp_date)
3. ├─dplyr::select(., -temp_date)
4. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
5. └─admiral::derive_vars_merged(...)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-filter_pd.R:193:3'): filter_pd Test 4: first PD derived from input dataset ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiralonco::filter_pd(...) at test-filter_pd.R:193:3
2. │ └─... %>% select(-temp_date)
3. ├─dplyr::select(., -temp_date)
4. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
5. └─admiral::derive_vars_merged(...)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-filter_pd.R:229:3'): filter_pd Test 5: error if invalid source_datasets ──
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: `enumerate()` was deprecated in admiraldev 1.1.0 and is now defunct.
i This function was primarily used in error messaging, and can be replaced with 'cli' functionality: `cli::cli_abort('{.val {letters[1:3]}}')`
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-filter_pd.R:229:3
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. └─admiralonco::filter_pd(...)
8. ├─rlang::abort(...)
9. │ └─rlang::is_formula(message, scoped = TRUE, lhs = FALSE)
10. ├─base::paste0(...)
11. └─admiraldev::enumerate(source_names, quote_fun = squote)
12. └─lifecycle::deprecate_stop(...)
13. └─lifecycle:::deprecate_stop0(msg)
14. └─rlang::cnd_signal(...)
[ FAIL 19 | WARN 0 | SKIP 0 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [28s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat) # nolint: undesirable_function_linter
> library(admiralonco) # nolint: undesirable_function_linter
>
> test_check("admiralonco")
Saving _problems/test-check_crpr-31.R
Saving _problems/test-check_crpr-51.R
Saving _problems/test-check_crpr-62.R
Saving _problems/test-derive_param_bor-76.R
Saving _problems/test-derive_param_clinbenefit-54.R
Saving _problems/test-derive_param_confirmed_bor-64.R
`date_source()` was deprecated in admiral 1.2.0.
i Please use `event()` instead.
x This message will turn into a warning at the beginning of 2026.
i See admiral's deprecation guidance: https://pharmaverse.github.io/admiraldev/dev/articles/programming_strategy.html#deprecation
Saving _problems/test-derive_param_confirmed_resp-85.R
Saving _problems/test-derive_param_confirmed_resp-149.R
Saving _problems/test-derive_param_confirmed_resp-210.R
Saving _problems/test-derive_param_confirmed_resp-250.R
Saving _problems/test-derive_param_confirmed_resp-316.R
`date_source()` was deprecated in admiral 1.2.0.
i Please use `event()` instead.
x This message will turn into a warning at the beginning of 2026.
i See admiral's deprecation guidance: https://pharmaverse.github.io/admiraldev/dev/articles/programming_strategy.html#deprecation
Saving _problems/test-derive_param_response-75.R
Saving _problems/test-derive_param_response-117.R
Saving _problems/test-derive_param_response-162.R
`date_source()` was deprecated in admiral 1.2.0.
i Please use `event()` instead.
x This message will turn into a warning at the beginning of 2026.
i See admiral's deprecation guidance: https://pharmaverse.github.io/admiraldev/dev/articles/programming_strategy.html#deprecation
Saving _problems/test-filter_pd-49.R
`date_source()` was deprecated in admiral 1.2.0.
i Please use `event()` instead.
x This message will turn into a warning at the beginning of 2026.
i See admiral's deprecation guidance: https://pharmaverse.github.io/admiraldev/dev/articles/programming_strategy.html#deprecation
Saving _problems/test-filter_pd-104.R
`date_source()` was deprecated in admiral 1.2.0.
i Please use `event()` instead.
x This message will turn into a warning at the beginning of 2026.
i See admiral's deprecation guidance: https://pharmaverse.github.io/admiraldev/dev/articles/programming_strategy.html#deprecation
Saving _problems/test-filter_pd-154.R
`date_source()` was deprecated in admiral 1.2.0.
i Please use `event()` instead.
x This message will turn into a warning at the beginning of 2026.
i See admiral's deprecation guidance: https://pharmaverse.github.io/admiraldev/dev/articles/programming_strategy.html#deprecation
Saving _problems/test-filter_pd-202.R
`date_source()` was deprecated in admiral 1.2.0.
i Please use `event()` instead.
x This message will turn into a warning at the beginning of 2026.
i See admiral's deprecation guidance: https://pharmaverse.github.io/admiraldev/dev/articles/programming_strategy.html#deprecation
Saving _problems/test-filter_pd-247.R
[ FAIL 19 | WARN 0 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-check_crpr.R:20:3'): signal_crpr Test 1: warning is issued ─────
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-check_crpr.R:20:3
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. ├─admiralonco::signal_crpr(adrs, order = exprs(ADT))
8. │ └─admiral::filter_joined(...)
9. │ ├─... %>% remove_tmp_vars()
10. │ └─admiral:::get_joined_data(...)
11. │ └─data %>% ...
12. ├─admiraldev::remove_tmp_vars(.)
13. ├─dplyr::select(., colnames(dataset))
14. ├─dplyr::ungroup(.)
15. ├─dplyr::slice(., 1L)
16. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
17. └─admiral::derive_vars_merged(...)
18. └─base::tryCatch(...)
19. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
20. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
21. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-check_crpr.R:36:3'): signal_crpr Test 2: error with custom message ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-check_crpr.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. ├─admiralonco::signal_crpr(...)
8. │ └─admiral::filter_joined(...)
9. │ ├─... %>% remove_tmp_vars()
10. │ └─admiral:::get_joined_data(...)
11. │ └─data %>% ...
12. ├─admiraldev::remove_tmp_vars(.)
13. ├─dplyr::select(., colnames(dataset))
14. ├─dplyr::ungroup(.)
15. ├─dplyr::slice(., 1L)
16. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
17. └─admiral::derive_vars_merged(...)
18. └─base::tryCatch(...)
19. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
20. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
21. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-check_crpr.R:57:3'): get_crpr_dataset() Test 2: dataset if returned ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::suppress_warning(...) at test-check_crpr.R:57:3
2. │ └─base::withCallingHandlers(...)
3. ├─admiralonco::signal_crpr(adrs, order = exprs(ADT))
4. │ └─admiral::filter_joined(...)
5. │ ├─... %>% remove_tmp_vars()
6. │ └─admiral:::get_joined_data(...)
7. │ └─data %>% ...
8. ├─admiraldev::remove_tmp_vars(.)
9. ├─dplyr::select(., colnames(dataset))
10. ├─dplyr::ungroup(.)
11. ├─dplyr::slice(., 1L)
12. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
13. └─admiral::derive_vars_merged(...)
14. └─base::tryCatch(...)
15. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_bor.R:36:1'): (code run outside of `test_that()`) ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─... %>% ... at test-derive_param_bor.R:36:1
2. └─admiral::derive_vars_merged(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_clinbenefit.R:17:1'): (code run outside of `test_that()`) ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─... %>% ... at test-derive_param_clinbenefit.R:17:1
2. └─admiral::derive_vars_merged(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_confirmed_bor.R:18:1'): (code run outside of `test_that()`) ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─... %>% ... at test-derive_param_confirmed_bor.R:18:1
2. └─admiral::derive_vars_merged(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_confirmed_resp.R:69:3'): derive_param_confirmed_resp Test 1: default confirmed response ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::suppress_warning(...) at test-derive_param_confirmed_resp.R:69:3
2. │ └─base::withCallingHandlers(...)
3. ├─admiralonco::derive_param_confirmed_resp(...)
4. │ └─dataset %>% ...
5. ├─admiralonco::filter_pd(...)
6. │ └─... %>% select(-temp_date)
7. ├─dplyr::select(., -temp_date)
8. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
9. └─admiral::derive_vars_merged(...)
10. └─base::tryCatch(...)
11. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
12. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
13. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_confirmed_resp.R:131:3'): derive_param_confirmed_resp Test 2: accept SD ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::suppress_warning(...) at test-derive_param_confirmed_resp.R:131:3
2. │ └─base::withCallingHandlers(...)
3. ├─admiralonco::derive_param_confirmed_resp(...)
4. │ └─dataset %>% ...
5. ├─admiralonco::filter_pd(...)
6. │ └─... %>% select(-temp_date)
7. ├─dplyr::select(., -temp_date)
8. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
9. └─admiral::derive_vars_merged(...)
10. └─base::tryCatch(...)
11. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
12. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
13. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_confirmed_resp.R:196:3'): derive_param_confirmed_resp Test 3: error if invalid response values ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_param_confirmed_resp.R:196:3
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. ├─admiralonco::derive_param_confirmed_resp(...)
8. │ └─dataset %>% ...
9. ├─admiralonco::filter_pd(...)
10. │ └─... %>% select(-temp_date)
11. ├─dplyr::select(., -temp_date)
12. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
13. └─admiral::derive_vars_merged(...)
14. └─base::tryCatch(...)
15. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_confirmed_resp.R:237:3'): derive_param_confirmed_resp Test 4: No source_pd ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiralonco::derive_param_confirmed_resp(...) at test-derive_param_confirmed_resp.R:237:3
2. │ └─admiralonco::signal_crpr(source_data, order = exprs(ADT), subject_keys = subject_keys)
3. │ └─admiral::filter_joined(...)
4. │ ├─... %>% remove_tmp_vars()
5. │ └─admiral:::get_joined_data(...)
6. │ └─data %>% ...
7. ├─admiraldev::remove_tmp_vars(.)
8. ├─dplyr::select(., colnames(dataset))
9. ├─dplyr::ungroup(.)
10. ├─dplyr::slice(., 1L)
11. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
12. └─admiral::derive_vars_merged(...)
13. └─base::tryCatch(...)
14. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
15. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
16. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_confirmed_resp.R:300:3'): derive_param_confirmed_resp Test 5: Deprecation warning for aval_fun ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-derive_param_confirmed_resp.R:300:3
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. ├─admiralonco::derive_param_confirmed_resp(...)
8. │ └─admiralonco::signal_crpr(source_data, order = exprs(ADT), subject_keys = subject_keys)
9. │ └─admiral::filter_joined(...)
10. │ ├─... %>% remove_tmp_vars()
11. │ └─admiral:::get_joined_data(...)
12. │ └─data %>% ...
13. ├─admiraldev::remove_tmp_vars(.)
14. ├─dplyr::select(., colnames(dataset))
15. ├─dplyr::ungroup(.)
16. ├─dplyr::slice(., 1L)
17. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
18. └─admiral::derive_vars_merged(...)
19. └─base::tryCatch(...)
20. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
21. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
22. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_response.R:63:3'): derive_param_response Test 1: With source_pd ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─adrs %>% ... at test-derive_param_response.R:63:3
2. ├─admiralonco::derive_param_response(...)
3. │ └─dataset %>% ...
4. ├─admiralonco::filter_pd(...)
5. │ └─... %>% select(-temp_date)
6. ├─dplyr::select(., -temp_date)
7. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
8. └─admiral::derive_vars_merged(...)
9. └─base::tryCatch(...)
10. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
11. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
12. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_response.R:105:3'): derive_param_response Test 2: No source_pd ──
Error in `anti_join(select(dataset_ref, intersect(add_vars, ref_vars)), select(new_add_obs, !!!by_vars), by = map_chr(by_vars, as_name))`: could not find function "anti_join"
Backtrace:
▆
1. ├─adrs %>% ... at test-derive_param_response.R:105:3
2. ├─admiralonco::derive_param_response(...)
3. │ └─dataset %>% ...
4. └─admiral::derive_extreme_records(...)
── Error ('test-derive_param_response.R:147:3'): derive_param_response Test 3: deprecation warning for aval_fun ──
Error in `anti_join(select(dataset_ref, intersect(add_vars, ref_vars)), select(new_add_obs, !!!by_vars), by = map_chr(by_vars, as_name))`: could not find function "anti_join"
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-derive_param_response.R:147:3
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. ├─adrs %>% ...
8. ├─admiralonco::derive_param_response(...)
9. │ └─dataset %>% ...
10. └─admiral::derive_extreme_records(...)
── Error ('test-filter_pd.R:40:3'): filter_pd Test 1: first PD in separate BDS dataset ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiralonco::filter_pd(...) at test-filter_pd.R:40:3
2. │ └─... %>% select(-temp_date)
3. ├─dplyr::select(., -temp_date)
4. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
5. └─admiral::derive_vars_merged(...)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-filter_pd.R:96:3'): filter_pd Test 2: first PD in ADSL dataset ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiralonco::filter_pd(...) at test-filter_pd.R:96:3
2. │ └─... %>% select(-temp_date)
3. ├─dplyr::select(., -temp_date)
4. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
5. └─admiral::derive_vars_merged(...)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-filter_pd.R:145:3'): filter_pd Test 3: first PD in input dataset ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiralonco::filter_pd(...) at test-filter_pd.R:145:3
2. │ └─... %>% select(-temp_date)
3. ├─dplyr::select(., -temp_date)
4. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
5. └─admiral::derive_vars_merged(...)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-filter_pd.R:193:3'): filter_pd Test 4: first PD derived from input dataset ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiralonco::filter_pd(...) at test-filter_pd.R:193:3
2. │ └─... %>% select(-temp_date)
3. ├─dplyr::select(., -temp_date)
4. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
5. └─admiral::derive_vars_merged(...)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-filter_pd.R:229:3'): filter_pd Test 5: error if invalid source_datasets ──
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: `enumerate()` was deprecated in admiraldev 1.1.0 and is now defunct.
i This function was primarily used in error messaging, and can be replaced with 'cli' functionality: `cli::cli_abort('{.val {letters[1:3]}}')`
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-filter_pd.R:229:3
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. └─admiralonco::filter_pd(...)
8. ├─rlang::abort(...)
9. │ └─rlang::is_formula(message, scoped = TRUE, lhs = FALSE)
10. ├─base::paste0(...)
11. └─admiraldev::enumerate(source_names, quote_fun = squote)
12. └─lifecycle::deprecate_stop(...)
13. └─lifecycle:::deprecate_stop0(msg)
14. └─rlang::cnd_signal(...)
[ FAIL 19 | WARN 0 | SKIP 0 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [14s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat) # nolint: undesirable_function_linter
> library(admiralonco) # nolint: undesirable_function_linter
>
> test_check("admiralonco")
Saving _problems/test-check_crpr-31.R
Saving _problems/test-check_crpr-51.R
Saving _problems/test-check_crpr-62.R
Saving _problems/test-derive_param_bor-76.R
Saving _problems/test-derive_param_clinbenefit-54.R
Saving _problems/test-derive_param_confirmed_bor-64.R
`date_source()` was deprecated in admiral 1.2.0.
i Please use `event()` instead.
x This message will turn into a warning at the beginning of 2026.
i See admiral's deprecation guidance: https://pharmaverse.github.io/admiraldev/dev/articles/programming_strategy.html#deprecation
Saving _problems/test-derive_param_confirmed_resp-85.R
Saving _problems/test-derive_param_confirmed_resp-149.R
Saving _problems/test-derive_param_confirmed_resp-210.R
Saving _problems/test-derive_param_confirmed_resp-250.R
Saving _problems/test-derive_param_confirmed_resp-316.R
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i Please use `event()` instead.
x This message will turn into a warning at the beginning of 2026.
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Saving _problems/test-derive_param_response-75.R
Saving _problems/test-derive_param_response-117.R
Saving _problems/test-derive_param_response-162.R
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i Please use `event()` instead.
x This message will turn into a warning at the beginning of 2026.
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Saving _problems/test-filter_pd-49.R
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i Please use `event()` instead.
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i Please use `event()` instead.
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Saving _problems/test-filter_pd-202.R
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i Please use `event()` instead.
x This message will turn into a warning at the beginning of 2026.
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Saving _problems/test-filter_pd-247.R
[ FAIL 19 | WARN 0 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-check_crpr.R:20:3'): signal_crpr Test 1: warning is issued ─────
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-check_crpr.R:20:3
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. ├─admiralonco::signal_crpr(adrs, order = exprs(ADT))
8. │ └─admiral::filter_joined(...)
9. │ ├─... %>% remove_tmp_vars()
10. │ └─admiral:::get_joined_data(...)
11. │ └─data %>% ...
12. ├─admiraldev::remove_tmp_vars(.)
13. ├─dplyr::select(., colnames(dataset))
14. ├─dplyr::ungroup(.)
15. ├─dplyr::slice(., 1L)
16. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
17. └─admiral::derive_vars_merged(...)
18. └─base::tryCatch(...)
19. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
20. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
21. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-check_crpr.R:36:3'): signal_crpr Test 2: error with custom message ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-check_crpr.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. ├─admiralonco::signal_crpr(...)
8. │ └─admiral::filter_joined(...)
9. │ ├─... %>% remove_tmp_vars()
10. │ └─admiral:::get_joined_data(...)
11. │ └─data %>% ...
12. ├─admiraldev::remove_tmp_vars(.)
13. ├─dplyr::select(., colnames(dataset))
14. ├─dplyr::ungroup(.)
15. ├─dplyr::slice(., 1L)
16. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
17. └─admiral::derive_vars_merged(...)
18. └─base::tryCatch(...)
19. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
20. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
21. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-check_crpr.R:57:3'): get_crpr_dataset() Test 2: dataset if returned ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::suppress_warning(...) at test-check_crpr.R:57:3
2. │ └─base::withCallingHandlers(...)
3. ├─admiralonco::signal_crpr(adrs, order = exprs(ADT))
4. │ └─admiral::filter_joined(...)
5. │ ├─... %>% remove_tmp_vars()
6. │ └─admiral:::get_joined_data(...)
7. │ └─data %>% ...
8. ├─admiraldev::remove_tmp_vars(.)
9. ├─dplyr::select(., colnames(dataset))
10. ├─dplyr::ungroup(.)
11. ├─dplyr::slice(., 1L)
12. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
13. └─admiral::derive_vars_merged(...)
14. └─base::tryCatch(...)
15. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_bor.R:36:1'): (code run outside of `test_that()`) ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─... %>% ... at test-derive_param_bor.R:36:1
2. └─admiral::derive_vars_merged(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_clinbenefit.R:17:1'): (code run outside of `test_that()`) ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─... %>% ... at test-derive_param_clinbenefit.R:17:1
2. └─admiral::derive_vars_merged(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_confirmed_bor.R:18:1'): (code run outside of `test_that()`) ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─... %>% ... at test-derive_param_confirmed_bor.R:18:1
2. └─admiral::derive_vars_merged(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_confirmed_resp.R:69:3'): derive_param_confirmed_resp Test 1: default confirmed response ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::suppress_warning(...) at test-derive_param_confirmed_resp.R:69:3
2. │ └─base::withCallingHandlers(...)
3. ├─admiralonco::derive_param_confirmed_resp(...)
4. │ └─dataset %>% ...
5. ├─admiralonco::filter_pd(...)
6. │ └─... %>% select(-temp_date)
7. ├─dplyr::select(., -temp_date)
8. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
9. └─admiral::derive_vars_merged(...)
10. └─base::tryCatch(...)
11. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
12. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
13. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_confirmed_resp.R:131:3'): derive_param_confirmed_resp Test 2: accept SD ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::suppress_warning(...) at test-derive_param_confirmed_resp.R:131:3
2. │ └─base::withCallingHandlers(...)
3. ├─admiralonco::derive_param_confirmed_resp(...)
4. │ └─dataset %>% ...
5. ├─admiralonco::filter_pd(...)
6. │ └─... %>% select(-temp_date)
7. ├─dplyr::select(., -temp_date)
8. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
9. └─admiral::derive_vars_merged(...)
10. └─base::tryCatch(...)
11. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
12. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
13. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_confirmed_resp.R:196:3'): derive_param_confirmed_resp Test 3: error if invalid response values ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_param_confirmed_resp.R:196:3
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. ├─admiralonco::derive_param_confirmed_resp(...)
8. │ └─dataset %>% ...
9. ├─admiralonco::filter_pd(...)
10. │ └─... %>% select(-temp_date)
11. ├─dplyr::select(., -temp_date)
12. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
13. └─admiral::derive_vars_merged(...)
14. └─base::tryCatch(...)
15. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
16. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
17. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_confirmed_resp.R:237:3'): derive_param_confirmed_resp Test 4: No source_pd ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiralonco::derive_param_confirmed_resp(...) at test-derive_param_confirmed_resp.R:237:3
2. │ └─admiralonco::signal_crpr(source_data, order = exprs(ADT), subject_keys = subject_keys)
3. │ └─admiral::filter_joined(...)
4. │ ├─... %>% remove_tmp_vars()
5. │ └─admiral:::get_joined_data(...)
6. │ └─data %>% ...
7. ├─admiraldev::remove_tmp_vars(.)
8. ├─dplyr::select(., colnames(dataset))
9. ├─dplyr::ungroup(.)
10. ├─dplyr::slice(., 1L)
11. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
12. └─admiral::derive_vars_merged(...)
13. └─base::tryCatch(...)
14. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
15. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
16. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_confirmed_resp.R:300:3'): derive_param_confirmed_resp Test 5: Deprecation warning for aval_fun ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-derive_param_confirmed_resp.R:300:3
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. ├─admiralonco::derive_param_confirmed_resp(...)
8. │ └─admiralonco::signal_crpr(source_data, order = exprs(ADT), subject_keys = subject_keys)
9. │ └─admiral::filter_joined(...)
10. │ ├─... %>% remove_tmp_vars()
11. │ └─admiral:::get_joined_data(...)
12. │ └─data %>% ...
13. ├─admiraldev::remove_tmp_vars(.)
14. ├─dplyr::select(., colnames(dataset))
15. ├─dplyr::ungroup(.)
16. ├─dplyr::slice(., 1L)
17. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
18. └─admiral::derive_vars_merged(...)
19. └─base::tryCatch(...)
20. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
21. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
22. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_response.R:63:3'): derive_param_response Test 1: With source_pd ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─adrs %>% ... at test-derive_param_response.R:63:3
2. ├─admiralonco::derive_param_response(...)
3. │ └─dataset %>% ...
4. ├─admiralonco::filter_pd(...)
5. │ └─... %>% select(-temp_date)
6. ├─dplyr::select(., -temp_date)
7. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
8. └─admiral::derive_vars_merged(...)
9. └─base::tryCatch(...)
10. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
11. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
12. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_param_response.R:105:3'): derive_param_response Test 2: No source_pd ──
Error in `anti_join(select(dataset_ref, intersect(add_vars, ref_vars)), select(new_add_obs, !!!by_vars), by = map_chr(by_vars, as_name))`: could not find function "anti_join"
Backtrace:
▆
1. ├─adrs %>% ... at test-derive_param_response.R:105:3
2. ├─admiralonco::derive_param_response(...)
3. │ └─dataset %>% ...
4. └─admiral::derive_extreme_records(...)
── Error ('test-derive_param_response.R:147:3'): derive_param_response Test 3: deprecation warning for aval_fun ──
Error in `anti_join(select(dataset_ref, intersect(add_vars, ref_vars)), select(new_add_obs, !!!by_vars), by = map_chr(by_vars, as_name))`: could not find function "anti_join"
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-derive_param_response.R:147:3
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. ├─adrs %>% ...
8. ├─admiralonco::derive_param_response(...)
9. │ └─dataset %>% ...
10. └─admiral::derive_extreme_records(...)
── Error ('test-filter_pd.R:40:3'): filter_pd Test 1: first PD in separate BDS dataset ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiralonco::filter_pd(...) at test-filter_pd.R:40:3
2. │ └─... %>% select(-temp_date)
3. ├─dplyr::select(., -temp_date)
4. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
5. └─admiral::derive_vars_merged(...)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-filter_pd.R:96:3'): filter_pd Test 2: first PD in ADSL dataset ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiralonco::filter_pd(...) at test-filter_pd.R:96:3
2. │ └─... %>% select(-temp_date)
3. ├─dplyr::select(., -temp_date)
4. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
5. └─admiral::derive_vars_merged(...)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-filter_pd.R:145:3'): filter_pd Test 3: first PD in input dataset ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiralonco::filter_pd(...) at test-filter_pd.R:145:3
2. │ └─... %>% select(-temp_date)
3. ├─dplyr::select(., -temp_date)
4. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
5. └─admiral::derive_vars_merged(...)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-filter_pd.R:193:3'): filter_pd Test 4: first PD derived from input dataset ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiralonco::filter_pd(...) at test-filter_pd.R:193:3
2. │ └─... %>% select(-temp_date)
3. ├─dplyr::select(., -temp_date)
4. ├─dplyr::filter(., is.na(temp_date) | ADT <= temp_date)
5. └─admiral::derive_vars_merged(...)
6. └─base::tryCatch(...)
7. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
8. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
9. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-filter_pd.R:229:3'): filter_pd Test 5: error if invalid source_datasets ──
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: `enumerate()` was deprecated in admiraldev 1.1.0 and is now defunct.
i This function was primarily used in error messaging, and can be replaced with 'cli' functionality: `cli::cli_abort('{.val {letters[1:3]}}')`
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-filter_pd.R:229:3
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. └─admiralonco::filter_pd(...)
8. ├─rlang::abort(...)
9. │ └─rlang::is_formula(message, scoped = TRUE, lhs = FALSE)
10. ├─base::paste0(...)
11. └─admiraldev::enumerate(source_names, quote_fun = squote)
12. └─lifecycle::deprecate_stop(...)
13. └─lifecycle:::deprecate_stop0(msg)
14. └─rlang::cnd_signal(...)
[ FAIL 19 | WARN 0 | SKIP 0 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc