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
  `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