Last updated on 2026-01-14 17:49:57 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3.1 | 17.60 | 575.99 | 593.59 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.3.1 | 12.05 | 375.47 | 387.52 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.3.1 | 29.00 | 605.48 | 634.48 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.3.1 | 27.00 | 409.55 | 436.55 | ERROR | |
| r-devel-windows-x86_64 | 1.3.1 | 23.00 | 548.00 | 571.00 | OK | |
| r-patched-linux-x86_64 | 1.3.1 | 22.26 | 531.08 | 553.34 | OK | |
| r-release-linux-x86_64 | 1.3.1 | 15.46 | 529.79 | 545.25 | OK | |
| r-release-macos-arm64 | 1.3.1 | OK | ||||
| r-release-macos-x86_64 | 1.3.1 | 11.00 | 478.00 | 489.00 | OK | |
| r-release-windows-x86_64 | 1.3.1 | 21.00 | 517.00 | 538.00 | OK | |
| r-oldrel-macos-arm64 | 1.3.1 | OK | ||||
| r-oldrel-macos-x86_64 | 1.3.1 | 12.00 | 466.00 | 478.00 | OK | |
| r-oldrel-windows-x86_64 | 1.3.1 | 31.00 | 702.00 | 733.00 | OK |
Version: 1.3.1
Check: relative paths in package URLs
Result: NOTE
Found the following (possibly) invalid URL:
URL: ../reference/#computation-functions-for-vectors
From: inst/doc/generic.html
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.3.1
Check: R code for possible problems
Result: NOTE
create_single_dose_dataset: no visible global function definition for
‘anti_join’
create_single_dose_dataset: no visible global function definition for
‘left_join’
derive_expected_records: no visible global function definition for
‘anti_join’
derive_extreme_records: no visible global function definition for
‘anti_join’
derive_locf_records: no visible global function definition for
‘anti_join’
derive_param_computed: no visible global function definition for
‘inner_join’
derive_param_tte: no visible global function definition for
‘inner_join’
derive_param_wbc_abs: no visible global function definition for
‘left_join’
derive_summary_records: no visible global function definition for
‘anti_join’
derive_vars_merged: no visible global function definition for
‘left_join’
derive_vars_transposed: no visible global function definition for
‘left_join’
filter_not_exist: no visible global function definition for ‘anti_join’
get_hori_data: no visible global function definition for ‘left_join’
get_joined_data: no visible global function definition for ‘inner_join’
get_joined_sub_data: no visible global function definition for
‘left_join’
get_vars_query: no visible global function definition for ‘inner_join’
Undefined global functions or variables:
anti_join inner_join left_join
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.3.1
Check: examples
Result: ERROR
Running examples in ‘admiral-Ex.R’ failed
The error most likely occurred in:
> ### Name: derive_expected_records
> ### Title: Derive Expected Records
> ### Aliases: derive_expected_records
> ### Keywords: der_prm_bds_findings
>
> ### ** Examples
>
> library(tibble)
>
> adqs <- tribble(
+ ~USUBJID, ~PARAMCD, ~AVISITN, ~AVISIT, ~AVAL,
+ "1", "a", 1, "WEEK 1", 10,
+ "1", "b", 1, "WEEK 1", 11,
+ "2", "a", 2, "WEEK 2", 12,
+ "2", "b", 2, "WEEK 2", 14
+ )
>
> # Example 1. visit variables are parameter independent
> parm_visit_ref <- tribble(
+ ~AVISITN, ~AVISIT,
+ 1, "WEEK 1",
+ 2, "WEEK 2"
+ )
>
> derive_expected_records(
+ dataset = adqs,
+ dataset_ref = parm_visit_ref,
+ by_vars = exprs(USUBJID, PARAMCD),
+ set_values_to = exprs(DTYPE = "DERIVED")
+ )
Error in anti_join(., dataset %>% select(all_of(exp_obs_vars)), by = c(exp_obs_vars)) :
could not find function "anti_join"
Calls: derive_expected_records -> %>%
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.3.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [274s/333s]
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
>
> library(testthat) # nolint: undesirable_function_linter
> library(admiral) # nolint: undesirable_function_linter
>
> test_check("admiral", stop_on_warning = TRUE)
Saving _problems/test-call_derivation-74.R
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The default value of `ignore_seconds_flag` will change to "TRUE" in admiral 1.4.0.
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[ FAIL 175 | WARN 0 | SKIP 112 | PASS 663 ]
══ Skipped tests (112) ═════════════════════════════════════════════════════════
• On CRAN (112): 'test-admiral_options.R:8:1', 'test-call_derivation.R:211:1',
'test-call_user_fun.R:1:1', 'test-compute_age_years.R:34:1',
'test-compute_scale.R:108:1', 'test-compute_scale.R:121:1',
'test-consolidate_metadata.R:64:1', 'test-create_query_data.R:253:1',
'test-create_query_data.R:314:1', 'test-create_query_data.R:334:1',
'test-create_query_data.R:352:1', 'test-create_query_data.R:379:1',
'test-create_query_data.R:390:1', 'test-create_query_data.R:403:1',
'test-create_query_data.R:416:1', 'test-create_query_data.R:427:1',
'test-create_query_data.R:439:1', 'test-create_query_data.R:450:1',
'test-create_query_data.R:461:1', 'test-create_query_data.R:472:1',
'test-create_query_data.R:484:1', 'test-create_query_data.R:497:1',
'test-create_query_data.R:510:1', 'test-create_query_data.R:518:1',
'test-create_single_dose_dataset.R:211:1',
'test-create_single_dose_dataset.R:227:1',
'test-create_single_dose_dataset.R:251:1',
'test-create_single_dose_dataset.R:270:1',
'test-derive_extreme_event.R:605:1', 'test-derive_joined.R:254:1',
'test-derive_merged.R:145:1', 'test-derive_merged.R:280:1',
'test-derive_merged.R:295:1', 'test-derive_merged.R:311:1',
'test-derive_merged.R:324:1', 'test-derive_merged.R:338:1',
'test-derive_merged.R:645:1', 'test-derive_merged.R:671:1',
'test-derive_param_bmi.R:99:1', 'test-derive_param_bsa.R:290:1',
'test-derive_param_computed.R:464:1', 'test-derive_param_computed.R:530:1',
'test-derive_param_computed.R:539:1',
'test-derive_param_extreme_record.R:3:1', 'test-derive_param_map.R:133:1',
'test-derive_param_qtc.R:102:1', 'test-derive_param_rr.R:43:1',
'test-derive_param_tte.R:413:1', 'test-derive_param_tte.R:474:1',
'test-derive_param_tte.R:535:1', 'test-derive_param_tte.R:594:1',
'test-derive_param_tte.R:891:1', 'test-derive_param_tte.R:1121:1',
'test-derive_var_base.R:116:1', 'test-derive_var_dthcaus.R:615:1',
'test-derive_var_extreme_date.R:321:1',
'test-derive_var_merged_ef_msrc.R:105:1', 'test-derive_var_ontrtfl.R:408:1',
'test-derive_var_trtemfl.R:153:1', 'test-derive_var_trtemfl.R:164:1',
'test-derive_var_trtemfl.R:175:1', 'test-derive_var_trtemfl.R:186:1',
'test-derive_var_trtemfl.R:209:1', 'test-derive_vars_aage.R:67:1',
'test-derive_vars_aage.R:76:1', 'test-derive_vars_aage.R:139:1',
'test-derive_vars_atc.R:52:1', 'test-derive_vars_cat.R:72:1',
'test-derive_vars_cat.R:323:1', 'test-derive_vars_cat.R:335:1',
'test-derive_vars_crit_flag.R:68:1', 'test-derive_vars_crit_flag.R:87:1',
'test-derive_vars_dt.R:180:1', 'test-derive_vars_dt.R:196:1',
'test-derive_vars_dt.R:212:1', 'test-derive_vars_dt.R:236:1',
'test-derive_vars_dt.R:552:1', 'test-derive_vars_dt.R:597:1',
'test-derive_vars_dt.R:617:1', 'test-derive_vars_dt_dtm_utils.R:474:1',
'test-derive_vars_dtm.R:242:1', 'test-derive_vars_dtm.R:257:1',
'test-derive_vars_dtm.R:273:1', 'test-derive_vars_dtm.R:284:1',
'test-derive_vars_dtm.R:432:1', 'test-derive_vars_dtm.R:618:1',
'test-derive_vars_dtm.R:714:1', 'test-derive_vars_dtm.R:763:1',
'test-derive_vars_dtm.R:784:1', 'test-derive_vars_dtm.R:864:1',
'test-derive_vars_dy.R:242:1', 'test-derive_vars_joined_summary.R:79:1',
'test-derive_vars_query.R:159:1', 'test-derive_vars_query.R:231:1',
'test-derive_vars_query.R:256:1', 'test-derive_vars_transposed.R:80:1',
'test-dt_level.R:41:1', 'test-dt_level.R:48:1', 'test-duplicates.R:43:1',
'test-get_summary_records.R:2:1', 'test-period_dataset.R:115:1',
'test-period_dataset.R:138:1', 'test-period_dataset.R:161:1',
'test-period_dataset.R:305:1', 'test-period_dataset.R:332:1',
'test-roxygen2.R:19:1', 'test-slice_derivation.R:235:1',
'test-transform_range.R:27:1', 'test-transform_range.R:39:1',
'test-user_helpers.R:15:1', 'test-user_helpers.R:38:1',
'test-user_utils.R:249:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-call_derivation.R:73:3'): call_derivation Test 2: Test that call_derivation generates expected imputation ──
Error in `left_join(., admiral_adsl, by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% left_join(admiral_adsl, by = "USUBJID") at test-call_derivation.R:73:3
── Error ('test-call_derivation.R:109:3'): call_derivation Test 3: Test that Error is thrown if ... has no arguments ──
Error in `left_join(., admiral_adsl, by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% left_join(admiral_adsl, by = "USUBJID") at test-call_derivation.R:109:3
── Error ('test-call_derivation.R:128:3'): call_derivation Test 4: Error is thrown if ... arguments are not properly named ──
Error in `left_join(., admiral_adsl, by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% left_join(admiral_adsl, by = "USUBJID") at test-call_derivation.R:128:3
── Error ('test-call_derivation.R:149:3'): call_derivation Test 5: Error is thrown if params is empty ──
Error in `left_join(., admiral_adsl, by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% left_join(admiral_adsl, by = "USUBJID") at test-call_derivation.R:149:3
── Error ('test-call_derivation.R:170:3'): call_derivation Test 6: Error is thrown if passed params are not properly named ──
Error in `left_join(., admiral_adsl, by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% left_join(admiral_adsl, by = "USUBJID") at test-call_derivation.R:170:3
── Error ('test-call_derivation.R:191:3'): call_derivation Test 7: Error is thrown if `...` arguments are not properly named ──
Error in `left_join(., admiral_adsl, by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% left_join(admiral_adsl, by = "USUBJID") at test-call_derivation.R:191:3
── Error ('test-call_derivation.R:221:3'): call_derivation Test 9: Test new environment when variable_env != fixed_env ──
Error in `left_join(., admiral_adsl, by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% left_join(admiral_adsl, by = "USUBJID") at test-call_derivation.R:221:3
── Error ('test-create_single_dose_dataset.R:25:3'): create_single_dose_dataset Test 1: Works as expected for Q*/EVERY * cases ──
Error in `anti_join(., lookup, by = as.character(dose_freq))`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-create_single_dose_dataset.R:25:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::create_single_dose_dataset(input)
4. │ └─... %>% unique()
5. └─base::unique(.)
── Error ('test-create_single_dose_dataset.R:97:3'): create_single_dose_dataset Test 2: Works as expected for # TIMES PER cases ──
Error in `anti_join(., lookup, by = as.character(dose_freq))`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-create_single_dose_dataset.R:97:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::create_single_dose_dataset(...)
4. │ └─... %>% unique()
5. └─base::unique(.)
── Error ('test-create_single_dose_dataset.R:134:3'): create_single_dose_dataset Test 3: Works for different treatments ──
Error in `anti_join(., lookup, by = as.character(dose_freq))`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-create_single_dose_dataset.R:134:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::create_single_dose_dataset(...)
4. │ └─... %>% unique()
5. └─base::unique(.)
── Error ('test-create_single_dose_dataset.R:181:3'): create_single_dose_dataset Test 4: Custom lookup works ──
Error in `anti_join(., lookup, by = as.character(dose_freq))`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-create_single_dose_dataset.R:181:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::create_single_dose_dataset(...)
4. │ └─... %>% unique()
5. └─base::unique(.)
── Error ('test-create_single_dose_dataset.R:320:3'): create_single_dose_dataset Test 10: Works as expected for BID cases ──
Error in `anti_join(., lookup, by = as.character(dose_freq))`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-create_single_dose_dataset.R:320:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::create_single_dose_dataset(...)
4. │ └─... %>% unique()
5. └─base::unique(.)
── Error ('test-create_single_dose_dataset.R:380:3'): create_single_dose_dataset Test 11: Works as expected for cases with nominal time ──
Error in `anti_join(., lookup, by = as.character(dose_freq))`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-create_single_dose_dataset.R:380:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::create_single_dose_dataset(...)
4. │ └─... %>% unique()
5. └─base::unique(.)
── Error ('test-create_single_dose_dataset.R:417:3'): create_single_dose_dataset Test 12: Error if lookup_column contains duplicates ──
Error in `anti_join(., lookup, by = as.character(dose_freq))`: could not find function "anti_join"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-create_single_dose_dataset.R:417:3
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. ├─admiral::create_single_dose_dataset(...)
8. │ └─... %>% unique()
9. └─base::unique(.)
── Error ('test-derive_expected_records.R:31:3'): derive_expected_records Test 1: missing values in `by_vars` ──
Error in `anti_join(., dataset %>% select(all_of(exp_obs_vars)), by = c(exp_obs_vars))`: could not find function "anti_join"
Backtrace:
▆
1. └─admiral::derive_expected_records(...) at test-derive_expected_records.R:31:3
2. └─exp_obsv %>% mutate(!!!set_values_to) %>% ...
── Error ('test-derive_expected_records.R:72:3'): derive_expected_records Test 2: `by_vars` = NULL ──
Error in `anti_join(., dataset %>% select(all_of(exp_obs_vars)), by = c(exp_obs_vars))`: could not find function "anti_join"
Backtrace:
▆
1. └─admiral::derive_expected_records(...) at test-derive_expected_records.R:72:3
2. └─exp_obsv %>% mutate(!!!set_values_to) %>% ...
── Error ('test-derive_expected_records.R:115:3'): derive_expected_records Test 3: visit variables are parameter independent ──
Error in `anti_join(., dataset %>% select(all_of(exp_obs_vars)), by = c(exp_obs_vars))`: could not find function "anti_join"
Backtrace:
▆
1. └─admiral::derive_expected_records(...) at test-derive_expected_records.R:115:3
2. └─exp_obsv %>% mutate(!!!set_values_to) %>% ...
── Error ('test-derive_expected_records.R:158:3'): derive_expected_records Test 4: visit variables are parameter dependent ──
Error in `anti_join(., dataset %>% select(all_of(exp_obs_vars)), by = c(exp_obs_vars))`: could not find function "anti_join"
Backtrace:
▆
1. └─admiral::derive_expected_records(...) at test-derive_expected_records.R:158:3
2. └─exp_obsv %>% mutate(!!!set_values_to) %>% ...
── Error ('test-derive_extreme_event.R:154:3'): derive_extreme_event Test 3: `source_datasets` works ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─... %>% ... at test-derive_extreme_event.R:154:3
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_extreme_event.R:364:3'): derive_extreme_event Test 5: event_joined() is handled correctly ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─... %>% ... at test-derive_extreme_event.R:364:3
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_extreme_event.R:530:3'): derive_extreme_event Test 6: no tmp_event_nr_var ──
<purrr_error_indexed/rlang_error/error/condition>
Error in `map2(events, event_index, function(event, index) { if (is.null(event$dataset_name)) { data_source <- dataset } else { data_source <- source_datasets[[event$dataset_name]] } if (!is.null(tmp_event_nr_var)) { data_source <- mutate(data_source, `:=`(!!tmp_event_nr_var, index)) } if (is.null(event$order)) { event_order <- order } else { event_order <- event$order } if (inherits(event, "event")) { data_events <- data_source %>% group_by(!!!by_vars) %>% filter_if(event$condition) %>% ungroup() if (!is.null(event$mode)) { if (check_type != "none") { signal_duplicate_records(dataset = data_events, by_vars = append(by_vars, event_order), msg = paste("Check duplicates: ", event$dataset_name, "dataset contains duplicate records with respect to", "{.var {replace_values_by_names(by_vars)}}"), cnd_type = check_type) } data_events <- filter_extreme(data_events, by_vars = by_vars, order = event_order, mode = event$mode, check_type = "none") } } else { if (check_type != "none") { signal_duplicate_records(dataset = data_source, by_vars = append(by_vars, event_order), msg = paste("Check duplicates: ", event$dataset_name, "dataset contains duplicate records with respect to", "{.var {replace_values_by_names(by_vars)}}"), cnd_type = check_type) } data_events <- filter_joined(data_source, dataset_add = data_source, by_vars = by_vars, join_vars = event$join_vars, join_type = event$join_type, first_cond_lower = !!event$first_cond_lower, first_cond_upper = !!event$first_cond_upper, order = event_order, check_type = "none", filter_join = !!event$condition) } if (is.null(event$keep_source_vars)) { event_keep_source_vars <- keep_source_vars } else { event_keep_source_vars <- event$keep_source_vars } data_events %>% process_set_values_to(set_values_to = event$set_values_to) %>% select(!!!event_keep_source_vars, !!tmp_event_nr_var, !!!by_vars, names(event$set_values_to)) })`: i In index: 1.
Caused by error in `left_join()`:
! could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_extreme_event(...) at test-derive_extreme_event.R:530:3
2. │ └─purrr::map2(...)
3. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
4. │ ├─purrr:::with_indexed_errors(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ ├─purrr:::call_with_cleanup(...)
7. │ └─admiral (local) .f(.x[[i]], .y[[i]], ...)
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)
22. └─base::.handleSimpleError(...)
23. └─purrr (local) h(simpleError(msg, call))
24. └─cli::cli_abort(...)
25. └─rlang::abort(...)
── Error ('test-derive_extreme_records.R:73:3'): derive_extreme_records Test 2: derive first PD date ──
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. └─admiral::derive_extreme_records(...) at test-derive_extreme_records.R:73:3
── Error ('test-derive_extreme_records.R:121:3'): derive_extreme_records Test 3: derive death date parameter ──
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. └─admiral::derive_extreme_records(...) at test-derive_extreme_records.R:121:3
── Error ('test-derive_extreme_records.R:191:3'): derive_extreme_records Test 4: latest evaluable tumor assessment date parameter ──
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. └─admiral::derive_extreme_records(...) at test-derive_extreme_records.R:191:3
── Error ('test-derive_extreme_records.R:266:3'): derive_extreme_records Test 5: latest evaluable tumor assessment date parameter without overwriting existing result ──
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. └─admiral::derive_extreme_records(...) at test-derive_extreme_records.R:266:3
── Error ('test-derive_extreme_records.R:407:3'): derive_extreme_records Test 9: order vars from dataset_add ──
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. └─admiral::derive_extreme_records(...) at test-derive_extreme_records.R:407:3
── Error ('test-derive_joined.R:21:3'): derive_vars_joined Test 1: no by_vars, no order, no new_vars ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:21:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
5. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:49:3'): derive_vars_joined Test 2: new_vars with rename ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:49:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
5. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:87:3'): derive_vars_joined Test 3: by_vars with rename ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:87:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
5. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:122:3'): derive_vars_joined Test 4: order with expression ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:122:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
5. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:164:3'): derive_vars_joined Test 5: join_vars with expression ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:164:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
5. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:202:3'): derive_vars_joined Test 6: no join_vars, no filter_join ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:202:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
5. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:234:3'): derive_vars_joined Test 7: new_vars expressions using variables from both datasets ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:234:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
5. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:297:3'): derive_vars_joined Test 9: fixing a bug from issue 1966 ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_joined(...) at test-derive_joined.R:297:3
2. └─admiral:::get_joined_data(...)
3. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:321:3'): derive_vars_joined Test 10: order vars are selected properly in function body ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_joined(...) at test-derive_joined.R:321:3
2. └─admiral:::get_joined_data(...)
3. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:365:3'): derive_vars_joined Test 11: Ensure exist_flag, true/false value arguments work ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:365:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
5. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:399:3'): derive_vars_joined Test 12: by_vars with rename, no new_vars ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:399:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
5. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:434:3'): derive_vars_joined Test 13: with save_memory and no by_vars ──
<purrr_error_indexed/rlang_error/error/condition>
Error in `map2(data_list, data_add_list, function(x, y) { get_joined_sub_data(x, y, by_vars = by_vars_left, tmp_obs_nr_var = tmp_obs_nr_var, tmp_obs_nr_left = tmp_obs_nr_left, join_type = join_type, first_cond_upper = first_cond_upper, first_cond_lower = first_cond_lower, filter_join = filter_join) })`: i In index: 1.
Caused by error in `left_join()`:
! could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:434:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_vars_joined(...)
4. │ └─admiral:::get_joined_data(...)
5. │ └─purrr::map2(...)
6. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
7. │ ├─purrr:::with_indexed_errors(...)
8. │ │ └─base::withCallingHandlers(...)
9. │ ├─purrr:::call_with_cleanup(...)
10. │ └─admiral (local) .f(.x[[i]], .y[[i]], ...)
11. │ └─admiral:::get_joined_sub_data(...)
12. └─base::.handleSimpleError(...)
13. └─purrr (local) h(simpleError(msg, call))
14. └─cli::cli_abort(...)
15. └─rlang::abort(...)
── Error ('test-derive_joined.R:466:3'): derive_vars_joined Test 14: save_memory with by_vars ──
Error in `inner_join(data_nest, data_add_nest, by = vars2chr(by_vars_left))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:466:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
── Error ('test-derive_joined.R:498:3'): derive_vars_joined Test 15: filter_add is not ignored when join_type != 'all' ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:498:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_vars_joined(...)
4. │ └─admiral:::get_joined_data(...)
5. │ └─data %>% ...
6. └─admiral::derive_vars_merged(...)
7. └─base::tryCatch(...)
8. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_joined.R:549:3'): derive_vars_joined Test 16: warning if `order` is not unique ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_vars_joined(...)
2. │ └─admiral:::get_joined_data(...)
3. │ └─data %>% ...
4. └─admiral::derive_vars_merged(...)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_joined.R:581:3'): derive_vars_joined Test 17: order with unnamed expression ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:581:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_vars_joined(...)
4. │ └─admiral:::get_joined_data(...)
5. │ └─data %>% ...
6. └─admiral::derive_vars_merged(...)
7. └─base::tryCatch(...)
8. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_joined.R:627:3'): get_joined_data Test 18: `first_cond_lower` works ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:627:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral:::get_joined_data(...)
4. │ └─data %>% ...
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-derive_locf_records.R:31:3'): derive_locf_records Test 1: visits are missing ──
Error in `anti_join(., advs_unique_original, by = exp_obs_by_vars)`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiral::derive_locf_records(...) at test-derive_locf_records.R:31:3
2. │ └─... %>% mutate(!!tmp_new_records := "new")
3. └─dplyr::mutate(., `:=`(!!tmp_new_records, "new"))
── Error ('test-derive_locf_records.R:78:3'): derive_locf_records Test 2: some visits have missing AVAL ──
Error in `anti_join(., advs_unique_original, by = exp_obs_by_vars)`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiral::derive_locf_records(...) at test-derive_locf_records.R:78:3
2. │ └─... %>% mutate(!!tmp_new_records := "new")
3. └─dplyr::mutate(., `:=`(!!tmp_new_records, "new"))
── Error ('test-derive_locf_records.R:136:3'): derive_locf_records Test 3: visits are missing - and DTYPE already exits ──
Error in `anti_join(., advs_unique_original, by = exp_obs_by_vars)`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiral::derive_locf_records(...) at test-derive_locf_records.R:136:3
2. │ └─... %>% mutate(!!tmp_new_records := "new")
3. └─dplyr::mutate(., `:=`(!!tmp_new_records, "new"))
── Error ('test-derive_locf_records.R:181:3'): derive_locf_records Test 4: visit variables are parameter independent ──
Error in `anti_join(., advs_unique_original, by = exp_obs_by_vars)`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiral::derive_locf_records(...) at test-derive_locf_records.R:181:3
2. │ └─... %>% mutate(!!tmp_new_records := "new")
3. └─dplyr::mutate(., `:=`(!!tmp_new_records, "new"))
── Error ('test-derive_locf_records.R:234:3'): derive_locf_records Test 5: visit variables are parameter dependent ──
Error in `anti_join(., advs_unique_original, by = exp_obs_by_vars)`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiral::derive_locf_records(...) at test-derive_locf_records.R:234:3
2. │ └─... %>% mutate(!!tmp_new_records := "new")
3. └─dplyr::mutate(., `:=`(!!tmp_new_records, "new"))
── Error ('test-derive_locf_records.R:287:3'): derive_locf_records Test 6: analysis visits are assigned based on time windows ──
Error in `anti_join(., advs_unique_original, by = exp_obs_by_vars)`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiral::derive_locf_records(...) at test-derive_locf_records.R:287:3
2. │ └─... %>% mutate(!!tmp_new_records := "new")
3. └─dplyr::mutate(., `:=`(!!tmp_new_records, "new"))
── Error ('test-derive_locf_records.R:343:3'): derive_locf_records Test 7: imputation = update ──
Error in `anti_join(., dataset, by = exp_obs_by_vars)`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiral::derive_locf_records(...) at test-derive_locf_records.R:343:3
2. │ └─... %>% mutate(!!tmp_new_records := "new")
3. └─dplyr::mutate(., `:=`(!!tmp_new_records, "new"))
── Error ('test-derive_locf_records.R:399:3'): derive_locf_records Test 8: imputation = update_add ──
Error in `anti_join(., dataset, by = exp_obs_by_vars)`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiral::derive_locf_records(...) at test-derive_locf_records.R:399:3
2. │ └─... %>% mutate(!!tmp_new_records := "new")
3. └─dplyr::mutate(., `:=`(!!tmp_new_records, "new"))
── Error ('test-derive_locf_records.R:455:3'): derive_locf_records Test 9: fill variables other than analysis_var for imputed
records ──
Error in `anti_join(., dataset, by = exp_obs_by_vars)`: could not find function "anti_join"
Backtrace:
▆
1. ├─dplyr::arrange(...) at test-derive_locf_records.R:455:3
2. ├─admiral::derive_locf_records(...)
3. │ └─... %>% mutate(!!tmp_new_records := "new")
4. └─dplyr::mutate(., `:=`(!!tmp_new_records, "new"))
── Error ('test-derive_merged.R:67:3'): derive_vars_merged Test 1: merge all variables ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...) at test-derive_merged.R:67:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:83:3'): derive_vars_merged Test 2: merge selected variables ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...) at test-derive_merged.R:83:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:100:3'): derive_vars_merged Test 3: merge last value and flag matched by groups ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...) at test-derive_merged.R:100:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:122:3'): derive_vars_merged Test 4: merge last value and flag matched by groups ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...) at test-derive_merged.R:122:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:157:3'): derive_vars_merged Test 6: by_vars with rename ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...) at test-derive_merged.R:157:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:175:3'): derive_vars_merged Test 7: expressions for new_vars and missing_values ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...) at test-derive_merged.R:175:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:199:3'): derive_vars_merged Test 8: Use of missing_values and exist_flags ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...) at test-derive_merged.R:199:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:248:3'): derive_vars_merged Test 9: use new variables in filter_add and order ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...) at test-derive_merged.R:248:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:267:3'): derive_vars_merged Test 10: warning if not unique w.r.t the by variables and the order ──
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_merged.R:267:3
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. └─admiral::derive_vars_merged(...)
8. └─base::tryCatch(...)
9. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
10. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:355:3'): derive_var_merged_exist_flag Test 16: merge existence flag ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_merged_exist_flag(...) at test-derive_merged.R:355:3
2. │ ├─... %>% ...
3. │ └─admiral::derive_vars_merged(...)
4. │ └─base::tryCatch(...)
5. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
8. └─dplyr::mutate(...)
── Error ('test-derive_merged.R:373:3'): derive_var_merged_exist_flag Test 17: by_vars with rename ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_merged_exist_flag(...) at test-derive_merged.R:373:3
2. │ ├─... %>% ...
3. │ └─admiral::derive_vars_merged(...)
4. │ └─base::tryCatch(...)
5. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
8. └─dplyr::mutate(...)
── Error ('test-derive_merged.R:405:3'): derive_vars_merged_lookup Test 18: merge lookup table ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged_lookup(...)
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_merged.R:443:3'): derive_vars_merged_lookup Test 19: all by_vars have records in the lookup table ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_message(...) at test-derive_merged.R:443:3
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. └─admiral::derive_vars_merged_lookup(...)
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_merged.R:478:3'): derive_vars_merged_lookup Test 20: by_vars with rename ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged_lookup(...)
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_merged.R:513:3'): get_not_mapped Test 21: not all by_vars have records in the lookup table ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged_lookup(...)
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_merged.R:554:3'): derive_var_merged_summary Test 22: dataset == dataset_add, no filter ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_merged.R:554:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_var_merged_summary(...)
4. ├─base::tryCatch(...)
5. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
8. ├─base::withCallingHandlers(...)
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_merged.R:585:3'): derive_var_merged_summary Test 23: dataset != dataset_add, filter ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_merged.R:585:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_var_merged_summary(...)
4. ├─base::tryCatch(...)
5. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
8. ├─base::withCallingHandlers(...)
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_merged.R:614:3'): derive_var_merged_summary Test 24: by_vars with rename ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_merged.R:614:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_var_merged_summary(...)
4. ├─base::tryCatch(...)
5. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
8. ├─base::withCallingHandlers(...)
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_merged.R:628:3'): derive_var_merged_summary Test 25: merge relationship as 'many-to-one' ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...) at test-derive_merged.R:628:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:659:3'): derive_var_merged_summary Test 27: merge sel vars 'one-to-one' ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...)
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:704:3'): derive_vars_merged_lookup Test 29: test get_not_mapped with unmapped records ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged_lookup(...) at test-derive_merged.R:704:3
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_bmi.R:178:3'): derive_param_bmi Test 10: Derive BMI where height is measured only once ──
Error in `inner_join(hori_data, hori_const_data, by = vars2chr(constant_by_vars))`: could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_param_computed(...) at test-derive_param_bmi.R:178:3
── Error ('test-derive_param_bsa.R:586:3'): derive_param_bsa Test 35: Derive BSA where height is measured only once ──
Error in `inner_join(hori_data, hori_const_data, by = vars2chr(constant_by_vars))`: could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_param_computed(...) at test-derive_param_bsa.R:586:3
── Error ('test-derive_param_computed.R:16:3'): derive_param_computed Test 1: new observations are derived correctly ──
Error in `inner_join(input %>% filter(PARAMCD == "DIABP") %>% select(USUBJID, VISIT, AVAL), input %>% filter(PARAMCD == "SYSBP") %>% select(USUBJID, VISIT, AVAL), by = c("USUBJID", "VISIT"), suffix = c(".DIABP", ".SYSBP"))`: could not find function "inner_join"
Backtrace:
▆
1. ├─... %>% select(-AVAL.DIABP, -AVAL.SYSBP) at test-derive_param_computed.R:16:3
2. ├─dplyr::select(., -AVAL.DIABP, -AVAL.SYSBP)
3. └─dplyr::mutate(...)
── Error ('test-derive_param_computed.R:63:3'): derive_param_computed Test 2: new observations with constant parameters ──
Error in `inner_join(input %>% filter(PARAMCD == "HEIGHT") %>% select(USUBJID, AVAL), input %>% filter(PARAMCD == "WEIGHT") %>% select(USUBJID, VISIT, AVAL), by = c("USUBJID"), suffix = c(".HEIGHT", ".WEIGHT"))`: could not find function "inner_join"
Backtrace:
▆
1. ├─... %>% select(-AVAL.HEIGHT, -AVAL.WEIGHT) at test-derive_param_computed.R:63:3
2. ├─dplyr::select(., -AVAL.HEIGHT, -AVAL.WEIGHT)
3. └─dplyr::mutate(...)
── Error ('test-derive_param_computed.R:198:3'): derive_param_computed Test 5: `dataset_add`, creating new parameters ──
Error in `left_join(hori_data, pivoted_data, by = vars2chr(by_vars))`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_param_computed.R:198:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_param_computed(...)
4. └─admiral:::get_hori_data(...)
── Error ('test-derive_param_computed.R:240:3'): derive_param_computed Test 6: no input dataset ──
Error in `left_join(hori_data, pivoted_data, by = vars2chr(by_vars))`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_param_computed.R:240:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_param_computed(...)
4. └─admiral:::get_hori_data(...)
── Error ('test-derive_param_computed.R:285:3'): derive_param_computed Test 7: expression in constant_parameters ──
Error in `inner_join(vs %>% filter(VSTESTCD == "HGHT") %>% select(USUBJID, AVAL = VSSTRESN), input %>% filter(PARAMCD == "WEIGHT") %>% select(USUBJID, VISIT, AVAL), by = c("USUBJID"), suffix = c(".HEIGHT", ".WEIGHT"))`: could not find function "inner_join"
Backtrace:
▆
1. ├─... %>% select(-AVAL.HEIGHT, -AVAL.WEIGHT) at test-derive_param_computed.R:285:3
2. ├─dplyr::select(., -AVAL.HEIGHT, -AVAL.WEIGHT)
3. └─dplyr::mutate(...)
── Error ('test-derive_param_computed.R:381:3'): derive_param_computed Test 9: compute multiple variables, keep_nas ──
Error in `left_join(hori_data, pivoted_data, by = vars2chr(by_vars))`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_param_computed(...) at test-derive_param_computed.R:381:3
2. └─admiral:::get_hori_data(...)
── Error ('test-derive_param_computed.R:442:3'): derive_param_computed Test 10: specify variables for keep_nas ──
Error in `left_join(hori_data, pivoted_data, by = vars2chr(by_vars))`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_param_computed(...) at test-derive_param_computed.R:442:3
2. └─admiral:::get_hori_data(...)
── Error ('test-derive_param_computed.R:514:3'): derive_param_computed Test 12: inform if no new records due to NAs ──
Error in `left_join(hori_data, pivoted_data, by = vars2chr(by_vars))`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_param_computed(...)
2. └─admiral:::get_hori_data(...)
── Error ('test-derive_param_doseint.R:24:3'): new observations are derived correctly when zero_doses is NULL ──
Error in `inner_join(input %>% filter(PARAMCD == "TNDOSE" & !is.na(AVAL)) %>% select(USUBJID, VISIT, AVAL), input %>% filter(PARAMCD == "TSNDOSE" & !is.na(AVAL)) %>% select(USUBJID, VISIT, AVAL), by = c("USUBJID", "VISIT"), suffix = c(".TNDOSE", ".TSNDOSE"))`: could not find function "inner_join"
Backtrace:
▆
1. ├─... %>% select(-AVAL.TSNDOSE, -AVAL.TNDOSE) at test-derive_param_doseint.R:24:3
2. ├─dplyr::select(., -AVAL.TSNDOSE, -AVAL.TNDOSE)
3. └─dplyr::mutate(., AVAL = AVAL.TNDOSE/AVAL.TSNDOSE * 100, PARAMCD = "TNDOSINT")
── Error ('test-derive_param_doseint.R:70:3'): new observations are derived correctly when zero_doses is Y ──
Error in `inner_join(input %>% filter(PARAMCD == "TNDOSE" & !is.na(AVAL)) %>% select(USUBJID, VISIT, AVAL), input %>% filter(PARAMCD == "TSNDOSE" & !is.na(AVAL)) %>% select(USUBJID, VISIT, AVAL), by = c("USUBJID", "VISIT"), suffix = c(".TNDOSE", ".TSNDOSE"))`: could not find function "inner_join"
Backtrace:
▆
1. ├─... %>% select(-AVAL.TSNDOSE, -AVAL.TNDOSE) at test-derive_param_doseint.R:70:3
2. ├─dplyr::select(., -AVAL.TSNDOSE, -AVAL.TNDOSE)
3. └─dplyr::mutate(...)
── Error ('test-derive_param_exist_flag.R:34:3'): derive_param_merged_exist_flag Test 1: derive parameter indicating PD ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_param_exist_flag(...) at test-derive_param_exist_flag.R:34:3
2. │ └─admiral::derive_var_merged_exist_flag(...)
3. │ ├─... %>% ...
4. │ └─admiral::derive_vars_merged(...)
5. │ └─base::tryCatch(...)
6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
9. └─dplyr::mutate(...)
── Error ('test-derive_param_framingham.R:20:3'): derive_param_framingham Test 1: New observations are derived correctly ──
Error in `left_join(., select(filter(input, PARAMCD == "CHOLHDL"), USUBJID, VISIT, AVAL), by = c("USUBJID", "VISIT"))`: could not find function "left_join"
Backtrace:
▆
1. ├─... %>% select(-AVAL_CHOLHDL, -AVAL_CHOL, -AVAL_SYSBP) at test-derive_param_framingham.R:20:3
2. ├─dplyr::select(., -AVAL_CHOLHDL, -AVAL_CHOL, -AVAL_SYSBP)
3. ├─dplyr::mutate(...)
4. └─dplyr::rename(., AVAL_CHOLHDL = AVAL)
── Error ('test-derive_param_tte.R:33:3'): derive_param_tte Test 1: new observations with analysis date are derived correctly ──
Error in `left_join(., select(adsl, USUBJID, STARTDT = TRTSDT, STARTDTF = TRTSDTF), by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% ... at test-derive_param_tte.R:33:3
── Error ('test-derive_param_tte.R:134:3'): derive_param_tte Test 2: new parameter with analysis datetime is derived correctly ──
Error in `left_join(., select(adsl, USUBJID, STARTDTM = TRTSDTM, STARTDTF = TRTSDTF, STARTTMF = TRTSTMF), by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% ... at test-derive_param_tte.R:134:3
── Error ('test-derive_param_tte.R:245:3'): derive_param_tte Test 3: no records for subjects not in ADSL, multiple events/cens ──
Error in `left_join(., select(adsl, USUBJID, STARTDT = RSPDT), by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% ... at test-derive_param_tte.R:245:3
── Error ('test-derive_param_tte.R:377:3'): derive_param_tte Test 5: by_vars parameter works correctly ──
Error in `left_join(., select(adsl, USUBJID, STARTDT = TRTSDT), by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% ... at test-derive_param_tte.R:377:3
── Error ('test-derive_param_tte.R:696:3'): derive_param_tte Test 10: error is issued if parameter code already exists ──
Error in `left_join(., select(adsl, USUBJID, STARTDT = TRTSDT), by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% ... at test-derive_param_tte.R:696:3
── Error ('test-derive_param_tte.R:764:3'): derive_param_tte Test 11: ensuring ADT is not NA because of missing start_date ──
Error in `inner_join(., adsl, by = vars2chr(subject_keys))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiral::derive_param_tte(...) at test-derive_param_tte.R:764:3
2. │ └─... %>% remove_tmp_vars()
3. ├─admiraldev::remove_tmp_vars(.)
4. ├─dplyr::mutate(...)
5. └─admiraldev::process_set_values_to(., set_values_to)
6. └─admiraldev::assert_data_frame(dataset)
7. └─admiraldev::assert_s3_class(...)
── Error ('test-derive_param_tte.R:837:3'): derive_param_tte Test 12: test dataset and dynamic byvars populated ──
Error in `inner_join(., adsl, by = vars2chr(subject_keys))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiral::derive_param_tte(...) at test-derive_param_tte.R:837:3
2. │ └─... %>% remove_tmp_vars()
3. ├─admiraldev::remove_tmp_vars(.)
4. ├─dplyr::mutate(...)
5. └─admiraldev::process_set_values_to(., set_values_to)
6. └─admiraldev::assert_data_frame(dataset)
7. └─admiraldev::assert_s3_class(...)
── Error ('test-derive_param_tte.R:981:3'): derive_param_tte Test 14: detects duplicates in input datasets via pipeline functions ──
Error in `inner_join(., adsl, by = vars2chr(subject_keys))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiral::derive_param_tte(...)
2. │ └─... %>% remove_tmp_vars()
3. ├─admiraldev::remove_tmp_vars(.)
4. ├─dplyr::mutate(...)
5. └─admiraldev::process_set_values_to(., set_values_to)
6. └─admiraldev::assert_data_frame(dataset)
7. └─admiraldev::assert_s3_class(...)
── Error ('test-derive_param_tte.R:1017:3'): derive_param_tte Test 15: using order for resolving ties ──
Error in `inner_join(., adsl, by = vars2chr(subject_keys))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiral::derive_param_tte(...) at test-derive_param_tte.R:1017:3
2. │ └─... %>% remove_tmp_vars()
3. ├─admiraldev::remove_tmp_vars(.)
4. ├─dplyr::mutate(...)
5. └─admiraldev::process_set_values_to(., set_values_to)
6. └─admiraldev::assert_data_frame(dataset)
7. └─admiraldev::assert_s3_class(...)
── Error ('test-derive_param_tte.R:1095:3'): derive_param_tte Test 16: produces consistent results regardless of input sort order ──
Error in `inner_join(., adsl, by = vars2chr(subject_keys))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiral::derive_param_tte(...) at test-derive_param_tte.R:1095:3
2. │ └─... %>% remove_tmp_vars()
3. ├─admiraldev::remove_tmp_vars(.)
4. ├─dplyr::mutate(...)
5. └─admiraldev::process_set_values_to(., set_values_to)
6. └─admiraldev::assert_data_frame(dataset)
7. └─admiraldev::assert_s3_class(...)
── Error ('test-derive_param_wbc_abs.R:19:3'): Test 1: Test adding absolute records for each by group ──
Error in `left_join(., dataset_abs, by = by_vars_str)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-derive_param_wbc_abs.R:19:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─admiral::derive_param_wbc_abs(...)
5. │ └─... %>% filter(is.na(temp_flag))
6. └─dplyr::filter(., is.na(temp_flag))
── Error ('test-derive_param_wbc_abs.R:54:3'): Test 2: Test when only one of WBC/differential is present ──
Error in `left_join(., dataset_abs, by = by_vars_str)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-derive_param_wbc_abs.R:54:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─admiral::derive_param_wbc_abs(...)
5. │ └─... %>% filter(is.na(temp_flag))
6. └─dplyr::filter(., is.na(temp_flag))
── Error ('test-derive_param_wbc_abs.R:90:3'): Test 3: Test when absolute record already present in source dataset 1 ──
Error in `left_join(., dataset_abs, by = by_vars_str)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_message(...) at test-derive_param_wbc_abs.R:90:3
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. ├─testthat::expect_equal(...)
8. │ └─testthat::quasi_label(enquo(object), label)
9. │ └─rlang::eval_bare(expr, quo_get_env(quo))
10. ├─admiral::derive_param_wbc_abs(...)
11. │ └─... %>% filter(is.na(temp_flag))
12. └─dplyr::filter(., is.na(temp_flag))
── Error ('test-derive_param_wbc_abs.R:131:3'): Test 4: Test when absolute record already present in source dataset 2 ──
Error in `left_join(., dataset_abs, by = by_vars_str)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-derive_param_wbc_abs.R:131:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─admiral::derive_param_wbc_abs(...)
5. │ └─... %>% filter(is.na(temp_flag))
6. └─dplyr::filter(., is.na(temp_flag))
── Error ('test-derive_param_wbc_abs.R:170:3'): Test 5: Test percent differential type ──
Error in `left_join(., dataset_abs, by = by_vars_str)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-derive_param_wbc_abs.R:170:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─admiral::derive_param_wbc_abs(...)
5. │ └─... %>% filter(is.na(temp_flag))
6. └─dplyr::filter(., is.na(temp_flag))
── Error ('test-derive_summary_records.R:178:3'): derive_summary_records Test 6: test missing values with dataset_ref ──
Error in `anti_join(select(dataset_ref, !!!by_vars), select(summary_records, !!!by_vars), by = map_chr(by_vars, as_name))`: could not find function "anti_join"
Backtrace:
▆
1. ├─input %>% ... at test-derive_summary_records.R:178:3
2. └─admiral::derive_summary_records(...)
── Error ('test-derive_var_base.R:33:3'): derive_var_base Test 1: `target` is set to `source` where `ABLFL == 'Y'` ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_base(...) at test-derive_var_base.R:33:3
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_var_base.R:67:3'): derive_var_base Test 2: `target` is set to `NA` if a baseline record is missing ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_base(...) at test-derive_var_base.R:67:3
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_var_base.R:101:3'): derive_var_base Test 3: only the `target` variable is added to the input dataset ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_base(...) at test-derive_var_base.R:101:3
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_var_dthcaus.R:32:3'): derive_var_dthcaus Test 1: deprecation message if function is called ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_dthcaus(...)
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_var_dthcaus.R:129:3'): derive_var_dthcaus Test 3: DTHCAUS is added from AE and DS ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_dthcaus(...) at test-derive_var_dthcaus.R:129:3
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_var_dthcaus.R:193:3'): derive_var_dthcaus Test 4: `dthcaus` handles symbols and string literals correctly ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_dthcaus(...) at test-derive_var_dthcaus.R:193:3
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_var_dthcaus.R:264:3'): derive_var_dthcaus Test 5: traceability variables are added from AE and DS ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_dthcaus(...) at test-derive_var_dthcaus.R:264:3
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_var_dthcaus.R:336:3'): derive_var_dthcaus Test 6: DTHCAUS/traceabiity are added from 2 input datasets ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_dthcaus(...) at test-derive_var_dthcaus.R:336:3
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_var_dthcaus.R:407:3'): derive_var_dthcaus Test 7: DTHCAUS is added from AE and DS if filter is not specified ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_dthcaus(...) at test-derive_var_dthcaus.R:407:3
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_var_dthcaus.R:487:3'): derive_var_dthcaus Test 9: `dataset` is sorted using the `order` parameter ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_dthcaus(...) at test-derive_var_dthcaus.R:487:3
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_var_dthcaus.R:545:3'): derive_var_dthcaus Test 10: multiple observations from different sources ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─adsl %>% ... at test-derive_var_dthcaus.R:545:3
2. └─admiral::derive_var_dthcaus(...)
3. └─admiral::derive_vars_merged(...)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_var_dthcaus.R:604:3'): derive_var_dthcaus Test 11: multiple observations with same date ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─adsl %>% ... at test-derive_var_dthcaus.R:604:3
2. └─admiral::derive_var_dthcaus(...)
3. └─admiral::derive_vars_merged(...)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_var_extreme_date.R:28:3'): derive_var_extreme_dt Test 1: deprecation message if function is called ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_extreme_dt(...)
2. │ ├─... %>% mutate(!!new_var := date(!!new_var))
3. │ └─admiral::derive_var_extreme_dtm(...)
4. │ └─admiral::derive_vars_merged(...)
5. │ └─base::tryCatch(...)
6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
9. └─dplyr::mutate(., `:=`(!!new_var, date(!!new_var)))
── Error ('test-derive_var_extreme_date.R:90:3'): derive_var_extreme_dt Test 2: LSTALVDT is derived ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_extreme_dt(...) at test-derive_var_extreme_date.R:90:3
2. │ ├─... %>% mutate(!!new_var := date(!!new_var))
3. │ └─admiral::derive_var_extreme_dtm(...)
4. │ └─admiral::derive_vars_merged(...)
5. │ └─base::tryCatch(...)
6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
9. └─dplyr::mutate(., `:=`(!!new_var, date(!!new_var)))
── Error ('test-derive_var_extreme_date.R:126:3'): derive_var_extreme_dt Test 3: LSTALVDT is derived for Date class as well ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_extreme_dt(...) at test-derive_var_extreme_date.R:126:3
2. │ ├─... %>% mutate(!!new_var := date(!!new_var))
3. │ └─admiral::derive_var_extreme_dtm(...)
4. │ └─admiral::derive_vars_merged(...)
5. │ └─base::tryCatch(...)
6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
9. └─dplyr::mutate(., `:=`(!!new_var, date(!!new_var)))
── Error ('test-derive_var_extreme_date.R:153:3'): derive_var_extreme_dt Test 4: `NA` dates are excluded ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_extreme_dt(...) at test-derive_var_extreme_date.R:153:3
2. │ ├─... %>% mutate(!!new_var := date(!!new_var))
3. │ └─admiral::derive_var_extreme_dtm(...)
4. │ └─admiral::derive_vars_merged(...)
5. │ └─base::tryCatch(...)
6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
9. └─dplyr::mutate(., `:=`(!!new_var, date(!!new_var)))
── Error ('test-derive_var_extreme_date.R:171:3'): derive_var_extreme_dtm Test 5: Message sent to users ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_extreme_dtm(...)
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_var_extreme_date.R:278:3'): derive_var_extreme_dtm Test 6: `LSTALVDTM` and traceability variables are derived ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_extreme_dtm(...) at test-derive_var_extreme_date.R:278:3
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_var_joined_exist_flag.R:24:3'): derive_var_joined_exist_flag Test 1: filter without first_cond ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_joined_exist_flag(...) at test-derive_var_joined_exist_flag.R:24:3
2. │ └─admiral::filter_joined(...)
3. │ ├─... %>% remove_tmp_vars()
4. │ └─admiral:::get_joined_data(...)
5. │ └─data %>% ...
6. ├─admiraldev::remove_tmp_vars(.)
7. ├─dplyr::select(., colnames(dataset))
8. ├─dplyr::ungroup(.)
9. ├─dplyr::slice(., 1L)
10. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
11. └─admiral::derive_vars_merged(...)
12. └─base::tryCatch(...)
13. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_var_joined_exist_flag.R:80:3'): derive_var_joined_exist_flag Test 2: filter with first_cond ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_joined_exist_flag(...) at test-derive_var_joined_exist_flag.R:80:3
2. │ └─admiral::filter_joined(...)
3. │ ├─... %>% remove_tmp_vars()
4. │ └─admiral:::get_joined_data(...)
5. │ └─data %>% ...
6. ├─admiraldev::remove_tmp_vars(.)
7. ├─dplyr::select(., colnames(dataset))
8. ├─dplyr::ungroup(.)
9. ├─dplyr::slice(., 1L)
10. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
11. └─admiral::derive_vars_merged(...)
12. └─base::tryCatch(...)
13. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_var_joined_exist_flag.R:122:3'): derive_var_joined_exist_flag Test 3: filter with first_cond and summary function ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_joined_exist_flag(...) at test-derive_var_joined_exist_flag.R:122:3
2. │ └─admiral::filter_joined(...)
3. │ ├─... %>% remove_tmp_vars()
4. │ └─admiral:::get_joined_data(...)
5. │ └─data %>% ...
6. ├─admiraldev::remove_tmp_vars(.)
7. ├─dplyr::select(., colnames(dataset))
8. ├─dplyr::ungroup(.)
9. ├─dplyr::slice(., 1L)
10. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
11. └─admiral::derive_vars_merged(...)
12. └─base::tryCatch(...)
13. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_var_joined_exist_flag.R:181:3'): derive_var_joined_exist_flag Test 4: join_type = 'all' ──
Error in `inner_join(data_nest, data_add_nest, by = vars2chr(by_vars_left))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiral::derive_var_joined_exist_flag(...) at test-derive_var_joined_exist_flag.R:181:3
2. │ └─admiral::filter_joined(...)
3. │ ├─... %>% remove_tmp_vars()
4. │ └─admiral:::get_joined_data(...)
5. ├─admiraldev::remove_tmp_vars(.)
6. ├─dplyr::select(., colnames(dataset))
7. ├─dplyr::ungroup(.)
8. ├─dplyr::slice(., 1L)
9. └─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
── Error ('test-derive_var_joined_exist_flag.R:225:3'): derive_var_joined_exist_flag Test 5: join_type = 'before' ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_joined_exist_flag(...) at test-derive_var_joined_exist_flag.R:225:3
2. │ └─admiral::filter_joined(...)
3. │ ├─... %>% remove_tmp_vars()
4. │ └─admiral:::get_joined_data(...)
5. │ └─data %>% ...
6. ├─admiraldev::remove_tmp_vars(.)
7. ├─dplyr::select(., colnames(dataset))
8. ├─dplyr::ungroup(.)
9. ├─dplyr::slice(., 1L)
10. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
11. └─admiral::derive_vars_merged(...)
12. └─base::tryCatch(...)
13. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_var_joined_exist_flag.R:271:3'): derive_var_joined_exist_flag Test 6: tmp_obs_nr_var argument works ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_var_joined_exist_flag.R:271:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_var_joined_exist_flag(...)
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_var_joined_exist_flag.R:312:3'): derive_var_joined_exist_flag Test 7: no warning if multiple records match ──
Error in `inner_join(data_nest, data_add_nest, by = vars2chr(by_vars_left))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_var_joined_exist_flag.R:312:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_var_joined_exist_flag(...)
4. │ └─admiral::filter_joined(...)
5. │ ├─... %>% remove_tmp_vars()
6. │ └─admiral:::get_joined_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)
── Error ('test-derive_var_merged_ef_msrc.R:27:3'): derive_var_merged_ef_msrc Test 1: wihtout by_vars ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_merged_ef_msrc(...) at test-derive_var_merged_ef_msrc.R:27:3
2. │ └─admiral::derive_var_merged_exist_flag(...)
3. │ ├─... %>% ...
4. │ └─admiral::derive_vars_merged(...)
5. │ └─base::tryCatch(...)
6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
9. └─dplyr::mutate(...)
── Error ('test-derive_var_merged_ef_msrc.R:74:3'): derive_var_merged_ef_msrc Test 2: with by_vars ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_merged_ef_msrc(...) at test-derive_var_merged_ef_msrc.R:74:3
2. │ └─admiral::derive_var_merged_exist_flag(...)
3. │ ├─... %>% ...
4. │ └─admiral::derive_vars_merged(...)
5. │ └─base::tryCatch(...)
6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
9. └─dplyr::mutate(...)
── Error ('test-derive_var_relative_flag.R:23:3'): derive_var_relative_flag Test 1: flag observations up to first PD ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_var_relative_flag.R:23:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_var_relative_flag(...)
4. └─admiral::filter_relative(...)
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-derive_var_relative_flag.R:55:3'): derive_var_relative_flag Test 2: Flag AEs after COVID AE ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_var_relative_flag.R:55:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_var_relative_flag(...)
4. └─admiral::filter_relative(...)
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-derive_var_trtemfl.R:103:3'): derive_var_trtemfl Test 3: with end_window and worsening within grouping variable ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_var_trtemfl.R:103:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_var_trtemfl(...)
4. │ └─... %>% ...
5. ├─dplyr::mutate(...)
6. └─admiral::derive_vars_merged(...)
7. └─base::tryCatch(...)
8. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_var_trtemfl.R:137:3'): derive_var_trtemfl Test 5: considering trt end time ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_var_trtemfl.R:137:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_var_trtemfl(...)
4. │ └─... %>% ...
5. ├─dplyr::mutate(...)
6. └─admiral::derive_vars_merged(...)
7. └─base::tryCatch(...)
8. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_var_trtemfl.R:198:3'): derive_var_trtemfl Test 10: error if `intensity` without `initial_intensity` ──
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_var_trtemfl.R:198:3
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. ├─admiral::derive_var_trtemfl(...)
8. │ └─... %>% ...
9. ├─dplyr::mutate(...)
10. └─admiral::derive_vars_merged(...)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_vars_atc.R:42:3'): derive_vars_atc Test 1: ATC variables are merged properly ──
Error in `left_join(dataset, dataset_transposed, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_atc(dataset = cm, dataset_facm = facm, id_vars = exprs(FAGRPID)) at test-derive_vars_atc.R:42:3
2. ├─base::tryCatch(...)
3. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
6. └─admiral::derive_vars_transposed(...)
7. └─base::tryCatch(...)
8. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. ├─base (local) tryCatchOne(...)
10. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
11. └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
12. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
13. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_vars_computed.R:33:3'): derive_vars_computed Test 1: new variable is derived correctly ──
Error in `inner_join(hori_data, hori_const_data, by = vars2chr(constant_by_vars))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_vars_computed.R:33:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_computed(...)
4. └─admiral::derive_param_computed(...)
── Error ('test-derive_vars_extreme_event.R:12:3'): derive_vars_extreme_event Test 1: derive_vars_extreme_event ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_extreme_event(...) at test-derive_vars_extreme_event.R:12:3
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_vars_joined_summary.R:23:3'): derive_vars_joined_summary Test 1: summing up values up to current record ──
Error in `inner_join(data_nest, data_add_nest, by = vars2chr(by_vars_left))`: could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_vars_joined_summary(...) at test-derive_vars_joined_summary.R:23:3
2. └─admiral:::get_joined_data(...)
── Error ('test-derive_vars_joined_summary.R:60:3'): derive_vars_joined_summary Test 2: missing_values works ──
Error in `inner_join(data_nest, data_add_nest, by = vars2chr(by_vars_left))`: could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_vars_joined_summary(...) at test-derive_vars_joined_summary.R:60:3
2. └─admiral:::get_joined_data(...)
── Error ('test-derive_vars_query.R:33:3'): derive_vars_query Test 1: Derive CQ and SMQ variables with two term levels ──
Error in `value[[3L]](cond)`: Error in derive_vars_query call of get_vars_query: Error in inner_join(., queries_wide, by = c("SRCVAR", "TERM_NAME_ID")): could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_vars_query(adae, queries) at test-derive_vars_query.R:33:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test-derive_vars_query.R:62:3'): derive_vars_query Test 2: Derive when no unique key excluding `SRCVAR` columns ──
Error in `value[[3L]](cond)`: Error in derive_vars_query call of get_vars_query: Error in inner_join(., queries_wide, by = c("SRCVAR", "TERM_NAME_ID")): could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_vars_query(my_ae, dataset_queries = query) at test-derive_vars_query.R:62:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test-derive_vars_query.R:91:3'): derive_vars_query Test 3: Derive when an adverse event is in multiple baskets ──
Error in `value[[3L]](cond)`: Error in derive_vars_query call of get_vars_query: Error in inner_join(., queries_wide, by = c("SRCVAR", "TERM_NAME_ID")): could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_vars_query(my_ae, dataset_queries = query) at test-derive_vars_query.R:91:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test-derive_vars_query.R:113:3'): derive_vars_query Test 4: Derive when no GRPID or SCOPE column ──
Error in `value[[3L]](cond)`: Error in derive_vars_query call of get_vars_query: Error in inner_join(., queries_wide, by = c("SRCVAR", "TERM_NAME_ID")): could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_vars_query(my_ae, dataset_queries = query) at test-derive_vars_query.R:113:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test-derive_vars_query.R:141:3'): derive_vars_query Test 5: Derive decides between TERMCHAR and TERMNUM based on type ──
Error in `value[[3L]](cond)`: Error in derive_vars_query call of get_vars_query: Error in inner_join(., queries_wide, by = c("SRCVAR", "TERM_NAME_ID")): could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_vars_query(my_ae, dataset_queries = query) at test-derive_vars_query.R:141:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test-derive_vars_query.R:192:3'): derive_vars_query Test 7: character SRCVAR and just TERMCHAR is provided ──
Error in `value[[3L]](cond)`: Error in derive_vars_query call of get_vars_query: Error in inner_join(., queries_wide, by = c("SRCVAR", "TERM_NAME_ID")): could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_vars_query(my_ae, dataset_queries = query) at test-derive_vars_query.R:192:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test-derive_vars_query.R:218:3'): derive_vars_query Test 8: numeric SRCVAR and just TERMNUM is provided ──
Error in `value[[3L]](cond)`: Error in derive_vars_query call of get_vars_query: Error in inner_join(., queries_wide, by = c("SRCVAR", "TERM_NAME_ID")): could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_vars_query(my_ae, dataset_queries = query) at test-derive_vars_query.R:218:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test-derive_vars_transposed.R:23:3'): derive_vars_transposed Test 1: the merge dataset is transposed and merged correctly ──
Error in `left_join(dataset, dataset_transposed, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_transposed(...) at test-derive_vars_transposed.R:23:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. ├─base (local) tryCatchOne(...)
5. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
6. └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_vars_transposed.R:52:3'): derive_vars_transposed Test 2: filtering the merge dataset works ──
Error in `left_join(dataset, dataset_transposed, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_transposed(...) at test-derive_vars_transposed.R:52:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. ├─base (local) tryCatchOne(...)
5. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
6. └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_vars_transposed.R:66:3'): derive_vars_transposed Test 3: filter merge dataset 'many-to-one' ──
Error in `left_join(dataset, dataset_transposed, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_transposed(...)
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. ├─base (local) tryCatchOne(...)
5. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
6. └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-event.R:38:3'): event Test 1: Cover event$order ────────────────
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_extreme_event(...) at test-event.R:38:3
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-filter_exist.R:56:3'): filter_not_exist Test 2: filter_not_exist() works as expected ──
Error in `anti_join(., dataset_add %>% filter_if(filter_add), by = vars2chr(by_vars))`: could not find function "anti_join"
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-filter_exist.R:56:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─admiral::filter_not_exist(...)
5. └─dataset %>% ...
── Error ('test-filter_joined.R:22:3'): filter_joined Test 1: filter without first_cond_upper ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::filter_joined(...) at test-filter_joined.R:22:3
2. │ ├─... %>% remove_tmp_vars()
3. │ └─admiral:::get_joined_data(...)
4. │ └─data %>% ...
5. ├─admiraldev::remove_tmp_vars(.)
6. ├─dplyr::select(., colnames(dataset))
7. ├─dplyr::ungroup(.)
8. ├─dplyr::slice(., 1L)
9. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
10. └─admiral::derive_vars_merged(...)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-filter_joined.R:49:3'): filter_joined Test 2: filter with first_cond ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::filter_joined(...) at test-filter_joined.R:49:3
2. │ ├─... %>% remove_tmp_vars()
3. │ └─admiral:::get_joined_data(...)
4. │ └─data %>% ...
5. ├─admiraldev::remove_tmp_vars(.)
6. ├─dplyr::select(., colnames(dataset))
7. ├─dplyr::ungroup(.)
8. ├─dplyr::slice(., 1L)
9. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
10. └─admiral::derive_vars_merged(...)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-filter_joined.R:76:3'): filter_joined Test 3: filter with first_cond and summary function ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::filter_joined(...) at test-filter_joined.R:76:3
2. │ ├─... %>% remove_tmp_vars()
3. │ └─admiral:::get_joined_data(...)
4. │ └─data %>% ...
5. ├─admiraldev::remove_tmp_vars(.)
6. ├─dplyr::select(., colnames(dataset))
7. ├─dplyr::ungroup(.)
8. ├─dplyr::slice(., 1L)
9. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
10. └─admiral::derive_vars_merged(...)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-filter_joined.R:117:3'): filter_joined Test 4: join_type = 'all' ──
Error in `inner_join(data_nest, data_add_nest, by = vars2chr(by_vars_left))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiral::filter_joined(...) at test-filter_joined.R:117:3
2. │ ├─... %>% remove_tmp_vars()
3. │ └─admiral:::get_joined_data(...)
4. ├─admiraldev::remove_tmp_vars(.)
5. ├─dplyr::select(., colnames(dataset))
6. ├─dplyr::ungroup(.)
7. ├─dplyr::slice(., 1L)
8. └─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
── Error ('test-filter_relative.R:22:3'): filter_relative Test 1: mode = first, selection = before, inclusive = TRUE ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::filter_relative(...) at test-filter_relative.R:22:3
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-filter_relative.R:55:3'): filter_relative Test 2: mode = first, selection = before, inclusive = FALSE ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::filter_relative(...) at test-filter_relative.R:55:3
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-filter_relative.R:81:3'): filter_relative Test 3: mode = first, selection = after, inclusive = TRUE ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::filter_relative(...) at test-filter_relative.R:81:3
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-filter_relative.R:111:3'): filter_relative Test 4: mode = first, selection = after, inclusive = FALSE ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::filter_relative(...) at test-filter_relative.R:111:3
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-filter_relative.R:144:3'): filter_relative Test 1: mode = last, selection = before, inclusive = TRUE ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::filter_relative(...) at test-filter_relative.R:144:3
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-filter_relative.R:178:3'): filter_relative Test 2: mode = last, selection = before, inclusive = FALSE ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::filter_relative(...) at test-filter_relative.R:178:3
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-filter_relative.R:208:3'): filter_relative Test 7: mode = last, selection = after, inclusive = TRUE ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::filter_relative(...) at test-filter_relative.R:208:3
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-filter_relative.R:240:3'): filter_relative Test 8: mode = last, selection = after, inclusive = FALSE ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::filter_relative(...) at test-filter_relative.R:240:3
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-period_dataset.R:29:3'): create_period_dataset Test 1: periods ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-period_dataset.R:29:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::create_period_dataset(...)
4. └─admiral::derive_vars_merged(...)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-period_dataset.R:65:3'): create_period_dataset Test 2: phases ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-period_dataset.R:65:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::create_period_dataset(...)
4. └─admiral::derive_vars_merged(...)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-period_dataset.R:104:3'): create_period_dataset Test 3: subperiods ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-period_dataset.R:104:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::create_period_dataset(...)
4. └─admiral::derive_vars_merged(...)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-period_dataset.R:213:3'): derive_vars_period Test 7: periods ───
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-period_dataset.R:213:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_vars_period(...)
4. │ ├─... %>% rename(all_of(rename_arg))
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)
10. └─dplyr::rename(., all_of(rename_arg))
── Error ('test-period_dataset.R:252:3'): derive_vars_period Test 8: phases ────
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-period_dataset.R:252:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_vars_period(...)
4. │ ├─... %>% rename(all_of(rename_arg))
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)
10. └─dplyr::rename(., all_of(rename_arg))
── Error ('test-period_dataset.R:294:3'): derive_vars_period Test 9: subperiods ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-period_dataset.R:294:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_vars_period(...)
4. │ ├─... %>% rename(all_of(rename_arg))
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)
10. └─dplyr::rename(., all_of(rename_arg))
── Error ('test-period_dataset.R:386:3'): create_period_dataset Test 12: DT and DTM columns exist, pulls only one unique col ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-period_dataset.R:386:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::create_period_dataset(...)
4. └─admiral::derive_vars_merged(...)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-period_dataset.R:426:3'): derive_vars_period Test 13: periods ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-period_dataset.R:426:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_vars_period(...)
4. │ ├─... %>% rename(all_of(rename_arg))
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)
10. └─dplyr::rename(., all_of(rename_arg))
── Error ('test-period_dataset.R:467:3'): derive_vars_period Test 14: periods variable derived when only one variable needed ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-period_dataset.R:467:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_vars_period(adsl, dataset_ref = period_ref, new_vars = exprs(APxxSDT = APERSDT))
4. │ ├─... %>% rename(all_of(rename_arg))
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)
10. └─dplyr::rename(., all_of(rename_arg))
── Error ('test-restrict_derivation.R:15:3'): restrict_derivation Test 1: restrict derivation with parameters ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::restrict_derivation(...) at test-restrict_derivation.R:15:3
2. └─base::eval(call, envir = list(data_derive = data_derive), enclos = parent.frame())
3. └─base::eval(call, envir = list(data_derive = data_derive), enclos = parent.frame())
4. └─admiral::derive_var_base(data_derive, by_vars = exprs(USUBJID))
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-slice_derivation.R:169:5'): slice_derivation Test 5: calling it in a function ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-slice_derivation.R:187:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral (local) my_merge(dataset = select(expected, -MVAL), my_b_data = b_data)
4. │ └─admiral::slice_derivation(...) at test-slice_derivation.R:169:5
5. │ └─rlang::eval_tidy(call, env = eval_env)
6. └─admiral (local) `<fn>`(...)
7. └─base::tryCatch(...)
8. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
[ FAIL 175 | WARN 0 | SKIP 112 | PASS 663 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.3.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘adsl.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘adsl.Rmd’
--- re-building ‘bds_exposure.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘bds_exposure.Rmd’
--- re-building ‘bds_finding.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘bds_finding.Rmd’
--- re-building ‘bds_tte.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘bds_tte.Rmd’
--- re-building ‘concepts_conventions.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘concepts_conventions.Rmd’
--- re-building ‘generic.Rmd’ using rmarkdown
Quitting from generic.Rmd:203-227 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `left_join()`:
! could not find function "left_join"
---
Backtrace:
▆
1. └─admiral::derive_vars_merged(...)
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'generic.Rmd' failed with diagnostics:
could not find function "left_join"
--- failed re-building ‘generic.Rmd’
--- re-building ‘higher_order.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘higher_order.Rmd’
--- re-building ‘hys_law.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘hys_law.Rmd’
--- re-building ‘imputation.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘imputation.Rmd’
--- re-building ‘lab_grading.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘lab_grading.Rmd’
--- re-building ‘occds.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘occds.Rmd’
--- re-building ‘pk_adnca.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘pk_adnca.Rmd’
--- re-building ‘queries_dataset.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘queries_dataset.Rmd’
--- re-building ‘questionnaires.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘questionnaires.Rmd’
--- re-building ‘visits_periods.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘visits_periods.Rmd’
SUMMARY: processing the following file failed:
‘generic.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.3.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [158s/159s]
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
>
> library(testthat) # nolint: undesirable_function_linter
> library(admiral) # nolint: undesirable_function_linter
>
> test_check("admiral", stop_on_warning = TRUE)
Saving _problems/test-call_derivation-74.R
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Saving _problems/test-derive_vars_atc-46.R
Saving _problems/test-derive_vars_computed-46.R
The default value of `ignore_seconds_flag` will change to "TRUE" in admiral 1.4.0.
Saving _problems/test-derive_vars_extreme_event-31.R
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Saving _problems/test-period_dataset-475.R
Saving _problems/test-restrict_derivation-20.R
Saving _problems/test-slice_derivation-184.R
[ FAIL 175 | WARN 0 | SKIP 112 | PASS 663 ]
══ Skipped tests (112) ═════════════════════════════════════════════════════════
• On CRAN (112): 'test-admiral_options.R:8:1', 'test-call_derivation.R:211:1',
'test-call_user_fun.R:1:1', 'test-compute_age_years.R:34:1',
'test-compute_scale.R:108:1', 'test-compute_scale.R:121:1',
'test-consolidate_metadata.R:64:1', 'test-create_query_data.R:253:1',
'test-create_query_data.R:314:1', 'test-create_query_data.R:334:1',
'test-create_query_data.R:352:1', 'test-create_query_data.R:379:1',
'test-create_query_data.R:390:1', 'test-create_query_data.R:403:1',
'test-create_query_data.R:416:1', 'test-create_query_data.R:427:1',
'test-create_query_data.R:439:1', 'test-create_query_data.R:450:1',
'test-create_query_data.R:461:1', 'test-create_query_data.R:472:1',
'test-create_query_data.R:484:1', 'test-create_query_data.R:497:1',
'test-create_query_data.R:510:1', 'test-create_query_data.R:518:1',
'test-create_single_dose_dataset.R:211:1',
'test-create_single_dose_dataset.R:227:1',
'test-create_single_dose_dataset.R:251:1',
'test-create_single_dose_dataset.R:270:1',
'test-derive_extreme_event.R:605:1', 'test-derive_joined.R:254:1',
'test-derive_merged.R:145:1', 'test-derive_merged.R:280:1',
'test-derive_merged.R:295:1', 'test-derive_merged.R:311:1',
'test-derive_merged.R:324:1', 'test-derive_merged.R:338:1',
'test-derive_merged.R:645:1', 'test-derive_merged.R:671:1',
'test-derive_param_bmi.R:99:1', 'test-derive_param_bsa.R:290:1',
'test-derive_param_computed.R:464:1', 'test-derive_param_computed.R:530:1',
'test-derive_param_computed.R:539:1',
'test-derive_param_extreme_record.R:3:1', 'test-derive_param_map.R:133:1',
'test-derive_param_qtc.R:102:1', 'test-derive_param_rr.R:43:1',
'test-derive_param_tte.R:413:1', 'test-derive_param_tte.R:474:1',
'test-derive_param_tte.R:535:1', 'test-derive_param_tte.R:594:1',
'test-derive_param_tte.R:891:1', 'test-derive_param_tte.R:1121:1',
'test-derive_var_base.R:116:1', 'test-derive_var_dthcaus.R:615:1',
'test-derive_var_extreme_date.R:321:1',
'test-derive_var_merged_ef_msrc.R:105:1', 'test-derive_var_ontrtfl.R:408:1',
'test-derive_var_trtemfl.R:153:1', 'test-derive_var_trtemfl.R:164:1',
'test-derive_var_trtemfl.R:175:1', 'test-derive_var_trtemfl.R:186:1',
'test-derive_var_trtemfl.R:209:1', 'test-derive_vars_aage.R:67:1',
'test-derive_vars_aage.R:76:1', 'test-derive_vars_aage.R:139:1',
'test-derive_vars_atc.R:52:1', 'test-derive_vars_cat.R:72:1',
'test-derive_vars_cat.R:323:1', 'test-derive_vars_cat.R:335:1',
'test-derive_vars_crit_flag.R:68:1', 'test-derive_vars_crit_flag.R:87:1',
'test-derive_vars_dt.R:180:1', 'test-derive_vars_dt.R:196:1',
'test-derive_vars_dt.R:212:1', 'test-derive_vars_dt.R:236:1',
'test-derive_vars_dt.R:552:1', 'test-derive_vars_dt.R:597:1',
'test-derive_vars_dt.R:617:1', 'test-derive_vars_dt_dtm_utils.R:474:1',
'test-derive_vars_dtm.R:242:1', 'test-derive_vars_dtm.R:257:1',
'test-derive_vars_dtm.R:273:1', 'test-derive_vars_dtm.R:284:1',
'test-derive_vars_dtm.R:432:1', 'test-derive_vars_dtm.R:618:1',
'test-derive_vars_dtm.R:714:1', 'test-derive_vars_dtm.R:763:1',
'test-derive_vars_dtm.R:784:1', 'test-derive_vars_dtm.R:864:1',
'test-derive_vars_dy.R:242:1', 'test-derive_vars_joined_summary.R:79:1',
'test-derive_vars_query.R:159:1', 'test-derive_vars_query.R:231:1',
'test-derive_vars_query.R:256:1', 'test-derive_vars_transposed.R:80:1',
'test-dt_level.R:41:1', 'test-dt_level.R:48:1', 'test-duplicates.R:43:1',
'test-get_summary_records.R:2:1', 'test-period_dataset.R:115:1',
'test-period_dataset.R:138:1', 'test-period_dataset.R:161:1',
'test-period_dataset.R:305:1', 'test-period_dataset.R:332:1',
'test-roxygen2.R:19:1', 'test-slice_derivation.R:235:1',
'test-transform_range.R:27:1', 'test-transform_range.R:39:1',
'test-user_helpers.R:15:1', 'test-user_helpers.R:38:1',
'test-user_utils.R:249:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-call_derivation.R:73:3'): call_derivation Test 2: Test that call_derivation generates expected imputation ──
Error in `left_join(., admiral_adsl, by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% left_join(admiral_adsl, by = "USUBJID") at test-call_derivation.R:73:3
── Error ('test-call_derivation.R:109:3'): call_derivation Test 3: Test that Error is thrown if ... has no arguments ──
Error in `left_join(., admiral_adsl, by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% left_join(admiral_adsl, by = "USUBJID") at test-call_derivation.R:109:3
── Error ('test-call_derivation.R:128:3'): call_derivation Test 4: Error is thrown if ... arguments are not properly named ──
Error in `left_join(., admiral_adsl, by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% left_join(admiral_adsl, by = "USUBJID") at test-call_derivation.R:128:3
── Error ('test-call_derivation.R:149:3'): call_derivation Test 5: Error is thrown if params is empty ──
Error in `left_join(., admiral_adsl, by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% left_join(admiral_adsl, by = "USUBJID") at test-call_derivation.R:149:3
── Error ('test-call_derivation.R:170:3'): call_derivation Test 6: Error is thrown if passed params are not properly named ──
Error in `left_join(., admiral_adsl, by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% left_join(admiral_adsl, by = "USUBJID") at test-call_derivation.R:170:3
── Error ('test-call_derivation.R:191:3'): call_derivation Test 7: Error is thrown if `...` arguments are not properly named ──
Error in `left_join(., admiral_adsl, by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% left_join(admiral_adsl, by = "USUBJID") at test-call_derivation.R:191:3
── Error ('test-call_derivation.R:221:3'): call_derivation Test 9: Test new environment when variable_env != fixed_env ──
Error in `left_join(., admiral_adsl, by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% left_join(admiral_adsl, by = "USUBJID") at test-call_derivation.R:221:3
── Error ('test-create_single_dose_dataset.R:25:3'): create_single_dose_dataset Test 1: Works as expected for Q*/EVERY * cases ──
Error in `anti_join(., lookup, by = as.character(dose_freq))`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-create_single_dose_dataset.R:25:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::create_single_dose_dataset(input)
4. │ └─... %>% unique()
5. └─base::unique(.)
── Error ('test-create_single_dose_dataset.R:97:3'): create_single_dose_dataset Test 2: Works as expected for # TIMES PER cases ──
Error in `anti_join(., lookup, by = as.character(dose_freq))`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-create_single_dose_dataset.R:97:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::create_single_dose_dataset(...)
4. │ └─... %>% unique()
5. └─base::unique(.)
── Error ('test-create_single_dose_dataset.R:134:3'): create_single_dose_dataset Test 3: Works for different treatments ──
Error in `anti_join(., lookup, by = as.character(dose_freq))`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-create_single_dose_dataset.R:134:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::create_single_dose_dataset(...)
4. │ └─... %>% unique()
5. └─base::unique(.)
── Error ('test-create_single_dose_dataset.R:181:3'): create_single_dose_dataset Test 4: Custom lookup works ──
Error in `anti_join(., lookup, by = as.character(dose_freq))`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-create_single_dose_dataset.R:181:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::create_single_dose_dataset(...)
4. │ └─... %>% unique()
5. └─base::unique(.)
── Error ('test-create_single_dose_dataset.R:320:3'): create_single_dose_dataset Test 10: Works as expected for BID cases ──
Error in `anti_join(., lookup, by = as.character(dose_freq))`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-create_single_dose_dataset.R:320:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::create_single_dose_dataset(...)
4. │ └─... %>% unique()
5. └─base::unique(.)
── Error ('test-create_single_dose_dataset.R:380:3'): create_single_dose_dataset Test 11: Works as expected for cases with nominal time ──
Error in `anti_join(., lookup, by = as.character(dose_freq))`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-create_single_dose_dataset.R:380:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::create_single_dose_dataset(...)
4. │ └─... %>% unique()
5. └─base::unique(.)
── Error ('test-create_single_dose_dataset.R:417:3'): create_single_dose_dataset Test 12: Error if lookup_column contains duplicates ──
Error in `anti_join(., lookup, by = as.character(dose_freq))`: could not find function "anti_join"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-create_single_dose_dataset.R:417:3
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. ├─admiral::create_single_dose_dataset(...)
8. │ └─... %>% unique()
9. └─base::unique(.)
── Error ('test-derive_expected_records.R:31:3'): derive_expected_records Test 1: missing values in `by_vars` ──
Error in `anti_join(., dataset %>% select(all_of(exp_obs_vars)), by = c(exp_obs_vars))`: could not find function "anti_join"
Backtrace:
▆
1. └─admiral::derive_expected_records(...) at test-derive_expected_records.R:31:3
2. └─exp_obsv %>% mutate(!!!set_values_to) %>% ...
── Error ('test-derive_expected_records.R:72:3'): derive_expected_records Test 2: `by_vars` = NULL ──
Error in `anti_join(., dataset %>% select(all_of(exp_obs_vars)), by = c(exp_obs_vars))`: could not find function "anti_join"
Backtrace:
▆
1. └─admiral::derive_expected_records(...) at test-derive_expected_records.R:72:3
2. └─exp_obsv %>% mutate(!!!set_values_to) %>% ...
── Error ('test-derive_expected_records.R:115:3'): derive_expected_records Test 3: visit variables are parameter independent ──
Error in `anti_join(., dataset %>% select(all_of(exp_obs_vars)), by = c(exp_obs_vars))`: could not find function "anti_join"
Backtrace:
▆
1. └─admiral::derive_expected_records(...) at test-derive_expected_records.R:115:3
2. └─exp_obsv %>% mutate(!!!set_values_to) %>% ...
── Error ('test-derive_expected_records.R:158:3'): derive_expected_records Test 4: visit variables are parameter dependent ──
Error in `anti_join(., dataset %>% select(all_of(exp_obs_vars)), by = c(exp_obs_vars))`: could not find function "anti_join"
Backtrace:
▆
1. └─admiral::derive_expected_records(...) at test-derive_expected_records.R:158:3
2. └─exp_obsv %>% mutate(!!!set_values_to) %>% ...
── Error ('test-derive_extreme_event.R:154:3'): derive_extreme_event Test 3: `source_datasets` works ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─... %>% ... at test-derive_extreme_event.R:154:3
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_extreme_event.R:364:3'): derive_extreme_event Test 5: event_joined() is handled correctly ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─... %>% ... at test-derive_extreme_event.R:364:3
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_extreme_event.R:530:3'): derive_extreme_event Test 6: no tmp_event_nr_var ──
<purrr_error_indexed/rlang_error/error/condition>
Error in `map2(events, event_index, function(event, index) { if (is.null(event$dataset_name)) { data_source <- dataset } else { data_source <- source_datasets[[event$dataset_name]] } if (!is.null(tmp_event_nr_var)) { data_source <- mutate(data_source, `:=`(!!tmp_event_nr_var, index)) } if (is.null(event$order)) { event_order <- order } else { event_order <- event$order } if (inherits(event, "event")) { data_events <- data_source %>% group_by(!!!by_vars) %>% filter_if(event$condition) %>% ungroup() if (!is.null(event$mode)) { if (check_type != "none") { signal_duplicate_records(dataset = data_events, by_vars = append(by_vars, event_order), msg = paste("Check duplicates: ", event$dataset_name, "dataset contains duplicate records with respect to", "{.var {replace_values_by_names(by_vars)}}"), cnd_type = check_type) } data_events <- filter_extreme(data_events, by_vars = by_vars, order = event_order, mode = event$mode, check_type = "none") } } else { if (check_type != "none") { signal_duplicate_records(dataset = data_source, by_vars = append(by_vars, event_order), msg = paste("Check duplicates: ", event$dataset_name, "dataset contains duplicate records with respect to", "{.var {replace_values_by_names(by_vars)}}"), cnd_type = check_type) } data_events <- filter_joined(data_source, dataset_add = data_source, by_vars = by_vars, join_vars = event$join_vars, join_type = event$join_type, first_cond_lower = !!event$first_cond_lower, first_cond_upper = !!event$first_cond_upper, order = event_order, check_type = "none", filter_join = !!event$condition) } if (is.null(event$keep_source_vars)) { event_keep_source_vars <- keep_source_vars } else { event_keep_source_vars <- event$keep_source_vars } data_events %>% process_set_values_to(set_values_to = event$set_values_to) %>% select(!!!event_keep_source_vars, !!tmp_event_nr_var, !!!by_vars, names(event$set_values_to)) })`: i In index: 1.
Caused by error in `left_join()`:
! could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_extreme_event(...) at test-derive_extreme_event.R:530:3
2. │ └─purrr::map2(...)
3. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
4. │ ├─purrr:::with_indexed_errors(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ ├─purrr:::call_with_cleanup(...)
7. │ └─admiral (local) .f(.x[[i]], .y[[i]], ...)
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)
22. └─base::.handleSimpleError(...)
23. └─purrr (local) h(simpleError(msg, call))
24. └─cli::cli_abort(...)
25. └─rlang::abort(...)
── Error ('test-derive_extreme_records.R:73:3'): derive_extreme_records Test 2: derive first PD date ──
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. └─admiral::derive_extreme_records(...) at test-derive_extreme_records.R:73:3
── Error ('test-derive_extreme_records.R:121:3'): derive_extreme_records Test 3: derive death date parameter ──
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. └─admiral::derive_extreme_records(...) at test-derive_extreme_records.R:121:3
── Error ('test-derive_extreme_records.R:191:3'): derive_extreme_records Test 4: latest evaluable tumor assessment date parameter ──
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. └─admiral::derive_extreme_records(...) at test-derive_extreme_records.R:191:3
── Error ('test-derive_extreme_records.R:266:3'): derive_extreme_records Test 5: latest evaluable tumor assessment date parameter without overwriting existing result ──
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. └─admiral::derive_extreme_records(...) at test-derive_extreme_records.R:266:3
── Error ('test-derive_extreme_records.R:407:3'): derive_extreme_records Test 9: order vars from dataset_add ──
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. └─admiral::derive_extreme_records(...) at test-derive_extreme_records.R:407:3
── Error ('test-derive_joined.R:21:3'): derive_vars_joined Test 1: no by_vars, no order, no new_vars ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:21:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
5. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:49:3'): derive_vars_joined Test 2: new_vars with rename ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:49:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
5. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:87:3'): derive_vars_joined Test 3: by_vars with rename ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:87:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
5. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:122:3'): derive_vars_joined Test 4: order with expression ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:122:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
5. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:164:3'): derive_vars_joined Test 5: join_vars with expression ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:164:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
5. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:202:3'): derive_vars_joined Test 6: no join_vars, no filter_join ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:202:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
5. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:234:3'): derive_vars_joined Test 7: new_vars expressions using variables from both datasets ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:234:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
5. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:297:3'): derive_vars_joined Test 9: fixing a bug from issue 1966 ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_joined(...) at test-derive_joined.R:297:3
2. └─admiral:::get_joined_data(...)
3. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:321:3'): derive_vars_joined Test 10: order vars are selected properly in function body ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_joined(...) at test-derive_joined.R:321:3
2. └─admiral:::get_joined_data(...)
3. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:365:3'): derive_vars_joined Test 11: Ensure exist_flag, true/false value arguments work ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:365:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
5. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:399:3'): derive_vars_joined Test 12: by_vars with rename, no new_vars ──
Error in `left_join(dataset, dataset_add, by = vars2chr(by_vars), suffix = c("", ".join"), relationship = "many-to-many")`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:399:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
5. └─admiral:::get_joined_sub_data(...)
── Error ('test-derive_joined.R:434:3'): derive_vars_joined Test 13: with save_memory and no by_vars ──
<purrr_error_indexed/rlang_error/error/condition>
Error in `map2(data_list, data_add_list, function(x, y) { get_joined_sub_data(x, y, by_vars = by_vars_left, tmp_obs_nr_var = tmp_obs_nr_var, tmp_obs_nr_left = tmp_obs_nr_left, join_type = join_type, first_cond_upper = first_cond_upper, first_cond_lower = first_cond_lower, filter_join = filter_join) })`: i In index: 1.
Caused by error in `left_join()`:
! could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:434:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_vars_joined(...)
4. │ └─admiral:::get_joined_data(...)
5. │ └─purrr::map2(...)
6. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
7. │ ├─purrr:::with_indexed_errors(...)
8. │ │ └─base::withCallingHandlers(...)
9. │ ├─purrr:::call_with_cleanup(...)
10. │ └─admiral (local) .f(.x[[i]], .y[[i]], ...)
11. │ └─admiral:::get_joined_sub_data(...)
12. └─base::.handleSimpleError(...)
13. └─purrr (local) h(simpleError(msg, call))
14. └─cli::cli_abort(...)
15. └─rlang::abort(...)
── Error ('test-derive_joined.R:466:3'): derive_vars_joined Test 14: save_memory with by_vars ──
Error in `inner_join(data_nest, data_add_nest, by = vars2chr(by_vars_left))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:466:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_joined(...)
4. └─admiral:::get_joined_data(...)
── Error ('test-derive_joined.R:498:3'): derive_vars_joined Test 15: filter_add is not ignored when join_type != 'all' ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:498:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_vars_joined(...)
4. │ └─admiral:::get_joined_data(...)
5. │ └─data %>% ...
6. └─admiral::derive_vars_merged(...)
7. └─base::tryCatch(...)
8. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_joined.R:549:3'): derive_vars_joined Test 16: warning if `order` is not unique ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_vars_joined(...)
2. │ └─admiral:::get_joined_data(...)
3. │ └─data %>% ...
4. └─admiral::derive_vars_merged(...)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_joined.R:581:3'): derive_vars_joined Test 17: order with unnamed expression ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:581:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_vars_joined(...)
4. │ └─admiral:::get_joined_data(...)
5. │ └─data %>% ...
6. └─admiral::derive_vars_merged(...)
7. └─base::tryCatch(...)
8. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_joined.R:627:3'): get_joined_data Test 18: `first_cond_lower` works ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_joined.R:627:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral:::get_joined_data(...)
4. │ └─data %>% ...
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-derive_locf_records.R:31:3'): derive_locf_records Test 1: visits are missing ──
Error in `anti_join(., advs_unique_original, by = exp_obs_by_vars)`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiral::derive_locf_records(...) at test-derive_locf_records.R:31:3
2. │ └─... %>% mutate(!!tmp_new_records := "new")
3. └─dplyr::mutate(., `:=`(!!tmp_new_records, "new"))
── Error ('test-derive_locf_records.R:78:3'): derive_locf_records Test 2: some visits have missing AVAL ──
Error in `anti_join(., advs_unique_original, by = exp_obs_by_vars)`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiral::derive_locf_records(...) at test-derive_locf_records.R:78:3
2. │ └─... %>% mutate(!!tmp_new_records := "new")
3. └─dplyr::mutate(., `:=`(!!tmp_new_records, "new"))
── Error ('test-derive_locf_records.R:136:3'): derive_locf_records Test 3: visits are missing - and DTYPE already exits ──
Error in `anti_join(., advs_unique_original, by = exp_obs_by_vars)`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiral::derive_locf_records(...) at test-derive_locf_records.R:136:3
2. │ └─... %>% mutate(!!tmp_new_records := "new")
3. └─dplyr::mutate(., `:=`(!!tmp_new_records, "new"))
── Error ('test-derive_locf_records.R:181:3'): derive_locf_records Test 4: visit variables are parameter independent ──
Error in `anti_join(., advs_unique_original, by = exp_obs_by_vars)`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiral::derive_locf_records(...) at test-derive_locf_records.R:181:3
2. │ └─... %>% mutate(!!tmp_new_records := "new")
3. └─dplyr::mutate(., `:=`(!!tmp_new_records, "new"))
── Error ('test-derive_locf_records.R:234:3'): derive_locf_records Test 5: visit variables are parameter dependent ──
Error in `anti_join(., advs_unique_original, by = exp_obs_by_vars)`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiral::derive_locf_records(...) at test-derive_locf_records.R:234:3
2. │ └─... %>% mutate(!!tmp_new_records := "new")
3. └─dplyr::mutate(., `:=`(!!tmp_new_records, "new"))
── Error ('test-derive_locf_records.R:287:3'): derive_locf_records Test 6: analysis visits are assigned based on time windows ──
Error in `anti_join(., advs_unique_original, by = exp_obs_by_vars)`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiral::derive_locf_records(...) at test-derive_locf_records.R:287:3
2. │ └─... %>% mutate(!!tmp_new_records := "new")
3. └─dplyr::mutate(., `:=`(!!tmp_new_records, "new"))
── Error ('test-derive_locf_records.R:343:3'): derive_locf_records Test 7: imputation = update ──
Error in `anti_join(., dataset, by = exp_obs_by_vars)`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiral::derive_locf_records(...) at test-derive_locf_records.R:343:3
2. │ └─... %>% mutate(!!tmp_new_records := "new")
3. └─dplyr::mutate(., `:=`(!!tmp_new_records, "new"))
── Error ('test-derive_locf_records.R:399:3'): derive_locf_records Test 8: imputation = update_add ──
Error in `anti_join(., dataset, by = exp_obs_by_vars)`: could not find function "anti_join"
Backtrace:
▆
1. ├─admiral::derive_locf_records(...) at test-derive_locf_records.R:399:3
2. │ └─... %>% mutate(!!tmp_new_records := "new")
3. └─dplyr::mutate(., `:=`(!!tmp_new_records, "new"))
── Error ('test-derive_locf_records.R:455:3'): derive_locf_records Test 9: fill variables other than analysis_var for imputed
records ──
Error in `anti_join(., dataset, by = exp_obs_by_vars)`: could not find function "anti_join"
Backtrace:
▆
1. ├─dplyr::arrange(...) at test-derive_locf_records.R:455:3
2. ├─admiral::derive_locf_records(...)
3. │ └─... %>% mutate(!!tmp_new_records := "new")
4. └─dplyr::mutate(., `:=`(!!tmp_new_records, "new"))
── Error ('test-derive_merged.R:67:3'): derive_vars_merged Test 1: merge all variables ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...) at test-derive_merged.R:67:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:83:3'): derive_vars_merged Test 2: merge selected variables ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...) at test-derive_merged.R:83:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:100:3'): derive_vars_merged Test 3: merge last value and flag matched by groups ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...) at test-derive_merged.R:100:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:122:3'): derive_vars_merged Test 4: merge last value and flag matched by groups ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...) at test-derive_merged.R:122:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:157:3'): derive_vars_merged Test 6: by_vars with rename ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...) at test-derive_merged.R:157:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:175:3'): derive_vars_merged Test 7: expressions for new_vars and missing_values ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...) at test-derive_merged.R:175:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:199:3'): derive_vars_merged Test 8: Use of missing_values and exist_flags ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...) at test-derive_merged.R:199:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:248:3'): derive_vars_merged Test 9: use new variables in filter_add and order ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...) at test-derive_merged.R:248:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:267:3'): derive_vars_merged Test 10: warning if not unique w.r.t the by variables and the order ──
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_merged.R:267:3
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. └─admiral::derive_vars_merged(...)
8. └─base::tryCatch(...)
9. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
10. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:355:3'): derive_var_merged_exist_flag Test 16: merge existence flag ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_merged_exist_flag(...) at test-derive_merged.R:355:3
2. │ ├─... %>% ...
3. │ └─admiral::derive_vars_merged(...)
4. │ └─base::tryCatch(...)
5. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
8. └─dplyr::mutate(...)
── Error ('test-derive_merged.R:373:3'): derive_var_merged_exist_flag Test 17: by_vars with rename ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_merged_exist_flag(...) at test-derive_merged.R:373:3
2. │ ├─... %>% ...
3. │ └─admiral::derive_vars_merged(...)
4. │ └─base::tryCatch(...)
5. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
8. └─dplyr::mutate(...)
── Error ('test-derive_merged.R:405:3'): derive_vars_merged_lookup Test 18: merge lookup table ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged_lookup(...)
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_merged.R:443:3'): derive_vars_merged_lookup Test 19: all by_vars have records in the lookup table ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_message(...) at test-derive_merged.R:443:3
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. └─admiral::derive_vars_merged_lookup(...)
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_merged.R:478:3'): derive_vars_merged_lookup Test 20: by_vars with rename ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged_lookup(...)
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_merged.R:513:3'): get_not_mapped Test 21: not all by_vars have records in the lookup table ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged_lookup(...)
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_merged.R:554:3'): derive_var_merged_summary Test 22: dataset == dataset_add, no filter ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_merged.R:554:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_var_merged_summary(...)
4. ├─base::tryCatch(...)
5. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
8. ├─base::withCallingHandlers(...)
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_merged.R:585:3'): derive_var_merged_summary Test 23: dataset != dataset_add, filter ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_merged.R:585:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_var_merged_summary(...)
4. ├─base::tryCatch(...)
5. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
8. ├─base::withCallingHandlers(...)
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_merged.R:614:3'): derive_var_merged_summary Test 24: by_vars with rename ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_merged.R:614:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_var_merged_summary(...)
4. ├─base::tryCatch(...)
5. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
8. ├─base::withCallingHandlers(...)
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_merged.R:628:3'): derive_var_merged_summary Test 25: merge relationship as 'many-to-one' ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...) at test-derive_merged.R:628:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:659:3'): derive_var_merged_summary Test 27: merge sel vars 'one-to-one' ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged(...)
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_merged.R:704:3'): derive_vars_merged_lookup Test 29: test get_not_mapped with unmapped records ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_merged_lookup(...) at test-derive_merged.R:704:3
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_bmi.R:178:3'): derive_param_bmi Test 10: Derive BMI where height is measured only once ──
Error in `inner_join(hori_data, hori_const_data, by = vars2chr(constant_by_vars))`: could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_param_computed(...) at test-derive_param_bmi.R:178:3
── Error ('test-derive_param_bsa.R:586:3'): derive_param_bsa Test 35: Derive BSA where height is measured only once ──
Error in `inner_join(hori_data, hori_const_data, by = vars2chr(constant_by_vars))`: could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_param_computed(...) at test-derive_param_bsa.R:586:3
── Error ('test-derive_param_computed.R:16:3'): derive_param_computed Test 1: new observations are derived correctly ──
Error in `inner_join(input %>% filter(PARAMCD == "DIABP") %>% select(USUBJID, VISIT, AVAL), input %>% filter(PARAMCD == "SYSBP") %>% select(USUBJID, VISIT, AVAL), by = c("USUBJID", "VISIT"), suffix = c(".DIABP", ".SYSBP"))`: could not find function "inner_join"
Backtrace:
▆
1. ├─... %>% select(-AVAL.DIABP, -AVAL.SYSBP) at test-derive_param_computed.R:16:3
2. ├─dplyr::select(., -AVAL.DIABP, -AVAL.SYSBP)
3. └─dplyr::mutate(...)
── Error ('test-derive_param_computed.R:63:3'): derive_param_computed Test 2: new observations with constant parameters ──
Error in `inner_join(input %>% filter(PARAMCD == "HEIGHT") %>% select(USUBJID, AVAL), input %>% filter(PARAMCD == "WEIGHT") %>% select(USUBJID, VISIT, AVAL), by = c("USUBJID"), suffix = c(".HEIGHT", ".WEIGHT"))`: could not find function "inner_join"
Backtrace:
▆
1. ├─... %>% select(-AVAL.HEIGHT, -AVAL.WEIGHT) at test-derive_param_computed.R:63:3
2. ├─dplyr::select(., -AVAL.HEIGHT, -AVAL.WEIGHT)
3. └─dplyr::mutate(...)
── Error ('test-derive_param_computed.R:198:3'): derive_param_computed Test 5: `dataset_add`, creating new parameters ──
Error in `left_join(hori_data, pivoted_data, by = vars2chr(by_vars))`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_param_computed.R:198:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_param_computed(...)
4. └─admiral:::get_hori_data(...)
── Error ('test-derive_param_computed.R:240:3'): derive_param_computed Test 6: no input dataset ──
Error in `left_join(hori_data, pivoted_data, by = vars2chr(by_vars))`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_param_computed.R:240:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_param_computed(...)
4. └─admiral:::get_hori_data(...)
── Error ('test-derive_param_computed.R:285:3'): derive_param_computed Test 7: expression in constant_parameters ──
Error in `inner_join(vs %>% filter(VSTESTCD == "HGHT") %>% select(USUBJID, AVAL = VSSTRESN), input %>% filter(PARAMCD == "WEIGHT") %>% select(USUBJID, VISIT, AVAL), by = c("USUBJID"), suffix = c(".HEIGHT", ".WEIGHT"))`: could not find function "inner_join"
Backtrace:
▆
1. ├─... %>% select(-AVAL.HEIGHT, -AVAL.WEIGHT) at test-derive_param_computed.R:285:3
2. ├─dplyr::select(., -AVAL.HEIGHT, -AVAL.WEIGHT)
3. └─dplyr::mutate(...)
── Error ('test-derive_param_computed.R:381:3'): derive_param_computed Test 9: compute multiple variables, keep_nas ──
Error in `left_join(hori_data, pivoted_data, by = vars2chr(by_vars))`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_param_computed(...) at test-derive_param_computed.R:381:3
2. └─admiral:::get_hori_data(...)
── Error ('test-derive_param_computed.R:442:3'): derive_param_computed Test 10: specify variables for keep_nas ──
Error in `left_join(hori_data, pivoted_data, by = vars2chr(by_vars))`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_param_computed(...) at test-derive_param_computed.R:442:3
2. └─admiral:::get_hori_data(...)
── Error ('test-derive_param_computed.R:514:3'): derive_param_computed Test 12: inform if no new records due to NAs ──
Error in `left_join(hori_data, pivoted_data, by = vars2chr(by_vars))`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_param_computed(...)
2. └─admiral:::get_hori_data(...)
── Error ('test-derive_param_doseint.R:24:3'): new observations are derived correctly when zero_doses is NULL ──
Error in `inner_join(input %>% filter(PARAMCD == "TNDOSE" & !is.na(AVAL)) %>% select(USUBJID, VISIT, AVAL), input %>% filter(PARAMCD == "TSNDOSE" & !is.na(AVAL)) %>% select(USUBJID, VISIT, AVAL), by = c("USUBJID", "VISIT"), suffix = c(".TNDOSE", ".TSNDOSE"))`: could not find function "inner_join"
Backtrace:
▆
1. ├─... %>% select(-AVAL.TSNDOSE, -AVAL.TNDOSE) at test-derive_param_doseint.R:24:3
2. ├─dplyr::select(., -AVAL.TSNDOSE, -AVAL.TNDOSE)
3. └─dplyr::mutate(., AVAL = AVAL.TNDOSE/AVAL.TSNDOSE * 100, PARAMCD = "TNDOSINT")
── Error ('test-derive_param_doseint.R:70:3'): new observations are derived correctly when zero_doses is Y ──
Error in `inner_join(input %>% filter(PARAMCD == "TNDOSE" & !is.na(AVAL)) %>% select(USUBJID, VISIT, AVAL), input %>% filter(PARAMCD == "TSNDOSE" & !is.na(AVAL)) %>% select(USUBJID, VISIT, AVAL), by = c("USUBJID", "VISIT"), suffix = c(".TNDOSE", ".TSNDOSE"))`: could not find function "inner_join"
Backtrace:
▆
1. ├─... %>% select(-AVAL.TSNDOSE, -AVAL.TNDOSE) at test-derive_param_doseint.R:70:3
2. ├─dplyr::select(., -AVAL.TSNDOSE, -AVAL.TNDOSE)
3. └─dplyr::mutate(...)
── Error ('test-derive_param_exist_flag.R:34:3'): derive_param_merged_exist_flag Test 1: derive parameter indicating PD ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_param_exist_flag(...) at test-derive_param_exist_flag.R:34:3
2. │ └─admiral::derive_var_merged_exist_flag(...)
3. │ ├─... %>% ...
4. │ └─admiral::derive_vars_merged(...)
5. │ └─base::tryCatch(...)
6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
9. └─dplyr::mutate(...)
── Error ('test-derive_param_framingham.R:20:3'): derive_param_framingham Test 1: New observations are derived correctly ──
Error in `left_join(., select(filter(input, PARAMCD == "CHOLHDL"), USUBJID, VISIT, AVAL), by = c("USUBJID", "VISIT"))`: could not find function "left_join"
Backtrace:
▆
1. ├─... %>% select(-AVAL_CHOLHDL, -AVAL_CHOL, -AVAL_SYSBP) at test-derive_param_framingham.R:20:3
2. ├─dplyr::select(., -AVAL_CHOLHDL, -AVAL_CHOL, -AVAL_SYSBP)
3. ├─dplyr::mutate(...)
4. └─dplyr::rename(., AVAL_CHOLHDL = AVAL)
── Error ('test-derive_param_tte.R:33:3'): derive_param_tte Test 1: new observations with analysis date are derived correctly ──
Error in `left_join(., select(adsl, USUBJID, STARTDT = TRTSDT, STARTDTF = TRTSDTF), by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% ... at test-derive_param_tte.R:33:3
── Error ('test-derive_param_tte.R:134:3'): derive_param_tte Test 2: new parameter with analysis datetime is derived correctly ──
Error in `left_join(., select(adsl, USUBJID, STARTDTM = TRTSDTM, STARTDTF = TRTSDTF, STARTTMF = TRTSTMF), by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% ... at test-derive_param_tte.R:134:3
── Error ('test-derive_param_tte.R:245:3'): derive_param_tte Test 3: no records for subjects not in ADSL, multiple events/cens ──
Error in `left_join(., select(adsl, USUBJID, STARTDT = RSPDT), by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% ... at test-derive_param_tte.R:245:3
── Error ('test-derive_param_tte.R:377:3'): derive_param_tte Test 5: by_vars parameter works correctly ──
Error in `left_join(., select(adsl, USUBJID, STARTDT = TRTSDT), by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% ... at test-derive_param_tte.R:377:3
── Error ('test-derive_param_tte.R:696:3'): derive_param_tte Test 10: error is issued if parameter code already exists ──
Error in `left_join(., select(adsl, USUBJID, STARTDT = TRTSDT), by = "USUBJID")`: could not find function "left_join"
Backtrace:
▆
1. └─... %>% ... at test-derive_param_tte.R:696:3
── Error ('test-derive_param_tte.R:764:3'): derive_param_tte Test 11: ensuring ADT is not NA because of missing start_date ──
Error in `inner_join(., adsl, by = vars2chr(subject_keys))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiral::derive_param_tte(...) at test-derive_param_tte.R:764:3
2. │ └─... %>% remove_tmp_vars()
3. ├─admiraldev::remove_tmp_vars(.)
4. ├─dplyr::mutate(...)
5. └─admiraldev::process_set_values_to(., set_values_to)
6. └─admiraldev::assert_data_frame(dataset)
7. └─admiraldev::assert_s3_class(...)
── Error ('test-derive_param_tte.R:837:3'): derive_param_tte Test 12: test dataset and dynamic byvars populated ──
Error in `inner_join(., adsl, by = vars2chr(subject_keys))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiral::derive_param_tte(...) at test-derive_param_tte.R:837:3
2. │ └─... %>% remove_tmp_vars()
3. ├─admiraldev::remove_tmp_vars(.)
4. ├─dplyr::mutate(...)
5. └─admiraldev::process_set_values_to(., set_values_to)
6. └─admiraldev::assert_data_frame(dataset)
7. └─admiraldev::assert_s3_class(...)
── Error ('test-derive_param_tte.R:981:3'): derive_param_tte Test 14: detects duplicates in input datasets via pipeline functions ──
Error in `inner_join(., adsl, by = vars2chr(subject_keys))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiral::derive_param_tte(...)
2. │ └─... %>% remove_tmp_vars()
3. ├─admiraldev::remove_tmp_vars(.)
4. ├─dplyr::mutate(...)
5. └─admiraldev::process_set_values_to(., set_values_to)
6. └─admiraldev::assert_data_frame(dataset)
7. └─admiraldev::assert_s3_class(...)
── Error ('test-derive_param_tte.R:1017:3'): derive_param_tte Test 15: using order for resolving ties ──
Error in `inner_join(., adsl, by = vars2chr(subject_keys))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiral::derive_param_tte(...) at test-derive_param_tte.R:1017:3
2. │ └─... %>% remove_tmp_vars()
3. ├─admiraldev::remove_tmp_vars(.)
4. ├─dplyr::mutate(...)
5. └─admiraldev::process_set_values_to(., set_values_to)
6. └─admiraldev::assert_data_frame(dataset)
7. └─admiraldev::assert_s3_class(...)
── Error ('test-derive_param_tte.R:1095:3'): derive_param_tte Test 16: produces consistent results regardless of input sort order ──
Error in `inner_join(., adsl, by = vars2chr(subject_keys))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiral::derive_param_tte(...) at test-derive_param_tte.R:1095:3
2. │ └─... %>% remove_tmp_vars()
3. ├─admiraldev::remove_tmp_vars(.)
4. ├─dplyr::mutate(...)
5. └─admiraldev::process_set_values_to(., set_values_to)
6. └─admiraldev::assert_data_frame(dataset)
7. └─admiraldev::assert_s3_class(...)
── Error ('test-derive_param_wbc_abs.R:19:3'): Test 1: Test adding absolute records for each by group ──
Error in `left_join(., dataset_abs, by = by_vars_str)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-derive_param_wbc_abs.R:19:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─admiral::derive_param_wbc_abs(...)
5. │ └─... %>% filter(is.na(temp_flag))
6. └─dplyr::filter(., is.na(temp_flag))
── Error ('test-derive_param_wbc_abs.R:54:3'): Test 2: Test when only one of WBC/differential is present ──
Error in `left_join(., dataset_abs, by = by_vars_str)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-derive_param_wbc_abs.R:54:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─admiral::derive_param_wbc_abs(...)
5. │ └─... %>% filter(is.na(temp_flag))
6. └─dplyr::filter(., is.na(temp_flag))
── Error ('test-derive_param_wbc_abs.R:90:3'): Test 3: Test when absolute record already present in source dataset 1 ──
Error in `left_join(., dataset_abs, by = by_vars_str)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_message(...) at test-derive_param_wbc_abs.R:90:3
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. ├─testthat::expect_equal(...)
8. │ └─testthat::quasi_label(enquo(object), label)
9. │ └─rlang::eval_bare(expr, quo_get_env(quo))
10. ├─admiral::derive_param_wbc_abs(...)
11. │ └─... %>% filter(is.na(temp_flag))
12. └─dplyr::filter(., is.na(temp_flag))
── Error ('test-derive_param_wbc_abs.R:131:3'): Test 4: Test when absolute record already present in source dataset 2 ──
Error in `left_join(., dataset_abs, by = by_vars_str)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-derive_param_wbc_abs.R:131:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─admiral::derive_param_wbc_abs(...)
5. │ └─... %>% filter(is.na(temp_flag))
6. └─dplyr::filter(., is.na(temp_flag))
── Error ('test-derive_param_wbc_abs.R:170:3'): Test 5: Test percent differential type ──
Error in `left_join(., dataset_abs, by = by_vars_str)`: could not find function "left_join"
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-derive_param_wbc_abs.R:170:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─admiral::derive_param_wbc_abs(...)
5. │ └─... %>% filter(is.na(temp_flag))
6. └─dplyr::filter(., is.na(temp_flag))
── Error ('test-derive_summary_records.R:178:3'): derive_summary_records Test 6: test missing values with dataset_ref ──
Error in `anti_join(select(dataset_ref, !!!by_vars), select(summary_records, !!!by_vars), by = map_chr(by_vars, as_name))`: could not find function "anti_join"
Backtrace:
▆
1. ├─input %>% ... at test-derive_summary_records.R:178:3
2. └─admiral::derive_summary_records(...)
── Error ('test-derive_var_base.R:33:3'): derive_var_base Test 1: `target` is set to `source` where `ABLFL == 'Y'` ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_base(...) at test-derive_var_base.R:33:3
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_var_base.R:67:3'): derive_var_base Test 2: `target` is set to `NA` if a baseline record is missing ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_base(...) at test-derive_var_base.R:67:3
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_var_base.R:101:3'): derive_var_base Test 3: only the `target` variable is added to the input dataset ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_base(...) at test-derive_var_base.R:101:3
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_var_dthcaus.R:32:3'): derive_var_dthcaus Test 1: deprecation message if function is called ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_dthcaus(...)
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_var_dthcaus.R:129:3'): derive_var_dthcaus Test 3: DTHCAUS is added from AE and DS ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_dthcaus(...) at test-derive_var_dthcaus.R:129:3
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_var_dthcaus.R:193:3'): derive_var_dthcaus Test 4: `dthcaus` handles symbols and string literals correctly ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_dthcaus(...) at test-derive_var_dthcaus.R:193:3
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_var_dthcaus.R:264:3'): derive_var_dthcaus Test 5: traceability variables are added from AE and DS ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_dthcaus(...) at test-derive_var_dthcaus.R:264:3
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_var_dthcaus.R:336:3'): derive_var_dthcaus Test 6: DTHCAUS/traceabiity are added from 2 input datasets ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_dthcaus(...) at test-derive_var_dthcaus.R:336:3
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_var_dthcaus.R:407:3'): derive_var_dthcaus Test 7: DTHCAUS is added from AE and DS if filter is not specified ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_dthcaus(...) at test-derive_var_dthcaus.R:407:3
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_var_dthcaus.R:487:3'): derive_var_dthcaus Test 9: `dataset` is sorted using the `order` parameter ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_dthcaus(...) at test-derive_var_dthcaus.R:487:3
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_var_dthcaus.R:545:3'): derive_var_dthcaus Test 10: multiple observations from different sources ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─adsl %>% ... at test-derive_var_dthcaus.R:545:3
2. └─admiral::derive_var_dthcaus(...)
3. └─admiral::derive_vars_merged(...)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_var_dthcaus.R:604:3'): derive_var_dthcaus Test 11: multiple observations with same date ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─adsl %>% ... at test-derive_var_dthcaus.R:604:3
2. └─admiral::derive_var_dthcaus(...)
3. └─admiral::derive_vars_merged(...)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_var_extreme_date.R:28:3'): derive_var_extreme_dt Test 1: deprecation message if function is called ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_extreme_dt(...)
2. │ ├─... %>% mutate(!!new_var := date(!!new_var))
3. │ └─admiral::derive_var_extreme_dtm(...)
4. │ └─admiral::derive_vars_merged(...)
5. │ └─base::tryCatch(...)
6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
9. └─dplyr::mutate(., `:=`(!!new_var, date(!!new_var)))
── Error ('test-derive_var_extreme_date.R:90:3'): derive_var_extreme_dt Test 2: LSTALVDT is derived ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_extreme_dt(...) at test-derive_var_extreme_date.R:90:3
2. │ ├─... %>% mutate(!!new_var := date(!!new_var))
3. │ └─admiral::derive_var_extreme_dtm(...)
4. │ └─admiral::derive_vars_merged(...)
5. │ └─base::tryCatch(...)
6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
9. └─dplyr::mutate(., `:=`(!!new_var, date(!!new_var)))
── Error ('test-derive_var_extreme_date.R:126:3'): derive_var_extreme_dt Test 3: LSTALVDT is derived for Date class as well ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_extreme_dt(...) at test-derive_var_extreme_date.R:126:3
2. │ ├─... %>% mutate(!!new_var := date(!!new_var))
3. │ └─admiral::derive_var_extreme_dtm(...)
4. │ └─admiral::derive_vars_merged(...)
5. │ └─base::tryCatch(...)
6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
9. └─dplyr::mutate(., `:=`(!!new_var, date(!!new_var)))
── Error ('test-derive_var_extreme_date.R:153:3'): derive_var_extreme_dt Test 4: `NA` dates are excluded ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_extreme_dt(...) at test-derive_var_extreme_date.R:153:3
2. │ ├─... %>% mutate(!!new_var := date(!!new_var))
3. │ └─admiral::derive_var_extreme_dtm(...)
4. │ └─admiral::derive_vars_merged(...)
5. │ └─base::tryCatch(...)
6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
9. └─dplyr::mutate(., `:=`(!!new_var, date(!!new_var)))
── Error ('test-derive_var_extreme_date.R:171:3'): derive_var_extreme_dtm Test 5: Message sent to users ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_extreme_dtm(...)
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_var_extreme_date.R:278:3'): derive_var_extreme_dtm Test 6: `LSTALVDTM` and traceability variables are derived ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_var_extreme_dtm(...) at test-derive_var_extreme_date.R:278:3
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_var_joined_exist_flag.R:24:3'): derive_var_joined_exist_flag Test 1: filter without first_cond ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_joined_exist_flag(...) at test-derive_var_joined_exist_flag.R:24:3
2. │ └─admiral::filter_joined(...)
3. │ ├─... %>% remove_tmp_vars()
4. │ └─admiral:::get_joined_data(...)
5. │ └─data %>% ...
6. ├─admiraldev::remove_tmp_vars(.)
7. ├─dplyr::select(., colnames(dataset))
8. ├─dplyr::ungroup(.)
9. ├─dplyr::slice(., 1L)
10. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
11. └─admiral::derive_vars_merged(...)
12. └─base::tryCatch(...)
13. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_var_joined_exist_flag.R:80:3'): derive_var_joined_exist_flag Test 2: filter with first_cond ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_joined_exist_flag(...) at test-derive_var_joined_exist_flag.R:80:3
2. │ └─admiral::filter_joined(...)
3. │ ├─... %>% remove_tmp_vars()
4. │ └─admiral:::get_joined_data(...)
5. │ └─data %>% ...
6. ├─admiraldev::remove_tmp_vars(.)
7. ├─dplyr::select(., colnames(dataset))
8. ├─dplyr::ungroup(.)
9. ├─dplyr::slice(., 1L)
10. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
11. └─admiral::derive_vars_merged(...)
12. └─base::tryCatch(...)
13. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_var_joined_exist_flag.R:122:3'): derive_var_joined_exist_flag Test 3: filter with first_cond and summary function ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_joined_exist_flag(...) at test-derive_var_joined_exist_flag.R:122:3
2. │ └─admiral::filter_joined(...)
3. │ ├─... %>% remove_tmp_vars()
4. │ └─admiral:::get_joined_data(...)
5. │ └─data %>% ...
6. ├─admiraldev::remove_tmp_vars(.)
7. ├─dplyr::select(., colnames(dataset))
8. ├─dplyr::ungroup(.)
9. ├─dplyr::slice(., 1L)
10. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
11. └─admiral::derive_vars_merged(...)
12. └─base::tryCatch(...)
13. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_var_joined_exist_flag.R:181:3'): derive_var_joined_exist_flag Test 4: join_type = 'all' ──
Error in `inner_join(data_nest, data_add_nest, by = vars2chr(by_vars_left))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiral::derive_var_joined_exist_flag(...) at test-derive_var_joined_exist_flag.R:181:3
2. │ └─admiral::filter_joined(...)
3. │ ├─... %>% remove_tmp_vars()
4. │ └─admiral:::get_joined_data(...)
5. ├─admiraldev::remove_tmp_vars(.)
6. ├─dplyr::select(., colnames(dataset))
7. ├─dplyr::ungroup(.)
8. ├─dplyr::slice(., 1L)
9. └─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
── Error ('test-derive_var_joined_exist_flag.R:225:3'): derive_var_joined_exist_flag Test 5: join_type = 'before' ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_joined_exist_flag(...) at test-derive_var_joined_exist_flag.R:225:3
2. │ └─admiral::filter_joined(...)
3. │ ├─... %>% remove_tmp_vars()
4. │ └─admiral:::get_joined_data(...)
5. │ └─data %>% ...
6. ├─admiraldev::remove_tmp_vars(.)
7. ├─dplyr::select(., colnames(dataset))
8. ├─dplyr::ungroup(.)
9. ├─dplyr::slice(., 1L)
10. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
11. └─admiral::derive_vars_merged(...)
12. └─base::tryCatch(...)
13. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_var_joined_exist_flag.R:271:3'): derive_var_joined_exist_flag Test 6: tmp_obs_nr_var argument works ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_var_joined_exist_flag.R:271:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_var_joined_exist_flag(...)
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_var_joined_exist_flag.R:312:3'): derive_var_joined_exist_flag Test 7: no warning if multiple records match ──
Error in `inner_join(data_nest, data_add_nest, by = vars2chr(by_vars_left))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_var_joined_exist_flag.R:312:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_var_joined_exist_flag(...)
4. │ └─admiral::filter_joined(...)
5. │ ├─... %>% remove_tmp_vars()
6. │ └─admiral:::get_joined_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)
── Error ('test-derive_var_merged_ef_msrc.R:27:3'): derive_var_merged_ef_msrc Test 1: wihtout by_vars ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_merged_ef_msrc(...) at test-derive_var_merged_ef_msrc.R:27:3
2. │ └─admiral::derive_var_merged_exist_flag(...)
3. │ ├─... %>% ...
4. │ └─admiral::derive_vars_merged(...)
5. │ └─base::tryCatch(...)
6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
9. └─dplyr::mutate(...)
── Error ('test-derive_var_merged_ef_msrc.R:74:3'): derive_var_merged_ef_msrc Test 2: with by_vars ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::derive_var_merged_ef_msrc(...) at test-derive_var_merged_ef_msrc.R:74:3
2. │ └─admiral::derive_var_merged_exist_flag(...)
3. │ ├─... %>% ...
4. │ └─admiral::derive_vars_merged(...)
5. │ └─base::tryCatch(...)
6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
9. └─dplyr::mutate(...)
── Error ('test-derive_var_relative_flag.R:23:3'): derive_var_relative_flag Test 1: flag observations up to first PD ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_var_relative_flag.R:23:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_var_relative_flag(...)
4. └─admiral::filter_relative(...)
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-derive_var_relative_flag.R:55:3'): derive_var_relative_flag Test 2: Flag AEs after COVID AE ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_var_relative_flag.R:55:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_var_relative_flag(...)
4. └─admiral::filter_relative(...)
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-derive_var_trtemfl.R:103:3'): derive_var_trtemfl Test 3: with end_window and worsening within grouping variable ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_var_trtemfl.R:103:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_var_trtemfl(...)
4. │ └─... %>% ...
5. ├─dplyr::mutate(...)
6. └─admiral::derive_vars_merged(...)
7. └─base::tryCatch(...)
8. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_var_trtemfl.R:137:3'): derive_var_trtemfl Test 5: considering trt end time ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_var_trtemfl.R:137:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_var_trtemfl(...)
4. │ └─... %>% ...
5. ├─dplyr::mutate(...)
6. └─admiral::derive_vars_merged(...)
7. └─base::tryCatch(...)
8. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_var_trtemfl.R:198:3'): derive_var_trtemfl Test 10: error if `intensity` without `initial_intensity` ──
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_var_trtemfl.R:198:3
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. ├─admiral::derive_var_trtemfl(...)
8. │ └─... %>% ...
9. ├─dplyr::mutate(...)
10. └─admiral::derive_vars_merged(...)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_vars_atc.R:42:3'): derive_vars_atc Test 1: ATC variables are merged properly ──
Error in `left_join(dataset, dataset_transposed, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_atc(dataset = cm, dataset_facm = facm, id_vars = exprs(FAGRPID)) at test-derive_vars_atc.R:42:3
2. ├─base::tryCatch(...)
3. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
6. └─admiral::derive_vars_transposed(...)
7. └─base::tryCatch(...)
8. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. ├─base (local) tryCatchOne(...)
10. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
11. └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
12. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
13. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_vars_computed.R:33:3'): derive_vars_computed Test 1: new variable is derived correctly ──
Error in `inner_join(hori_data, hori_const_data, by = vars2chr(constant_by_vars))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-derive_vars_computed.R:33:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::derive_vars_computed(...)
4. └─admiral::derive_param_computed(...)
── Error ('test-derive_vars_extreme_event.R:12:3'): derive_vars_extreme_event Test 1: derive_vars_extreme_event ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_extreme_event(...) at test-derive_vars_extreme_event.R:12:3
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_vars_joined_summary.R:23:3'): derive_vars_joined_summary Test 1: summing up values up to current record ──
Error in `inner_join(data_nest, data_add_nest, by = vars2chr(by_vars_left))`: could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_vars_joined_summary(...) at test-derive_vars_joined_summary.R:23:3
2. └─admiral:::get_joined_data(...)
── Error ('test-derive_vars_joined_summary.R:60:3'): derive_vars_joined_summary Test 2: missing_values works ──
Error in `inner_join(data_nest, data_add_nest, by = vars2chr(by_vars_left))`: could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_vars_joined_summary(...) at test-derive_vars_joined_summary.R:60:3
2. └─admiral:::get_joined_data(...)
── Error ('test-derive_vars_query.R:33:3'): derive_vars_query Test 1: Derive CQ and SMQ variables with two term levels ──
Error in `value[[3L]](cond)`: Error in derive_vars_query call of get_vars_query: Error in inner_join(., queries_wide, by = c("SRCVAR", "TERM_NAME_ID")): could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_vars_query(adae, queries) at test-derive_vars_query.R:33:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test-derive_vars_query.R:62:3'): derive_vars_query Test 2: Derive when no unique key excluding `SRCVAR` columns ──
Error in `value[[3L]](cond)`: Error in derive_vars_query call of get_vars_query: Error in inner_join(., queries_wide, by = c("SRCVAR", "TERM_NAME_ID")): could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_vars_query(my_ae, dataset_queries = query) at test-derive_vars_query.R:62:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test-derive_vars_query.R:91:3'): derive_vars_query Test 3: Derive when an adverse event is in multiple baskets ──
Error in `value[[3L]](cond)`: Error in derive_vars_query call of get_vars_query: Error in inner_join(., queries_wide, by = c("SRCVAR", "TERM_NAME_ID")): could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_vars_query(my_ae, dataset_queries = query) at test-derive_vars_query.R:91:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test-derive_vars_query.R:113:3'): derive_vars_query Test 4: Derive when no GRPID or SCOPE column ──
Error in `value[[3L]](cond)`: Error in derive_vars_query call of get_vars_query: Error in inner_join(., queries_wide, by = c("SRCVAR", "TERM_NAME_ID")): could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_vars_query(my_ae, dataset_queries = query) at test-derive_vars_query.R:113:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test-derive_vars_query.R:141:3'): derive_vars_query Test 5: Derive decides between TERMCHAR and TERMNUM based on type ──
Error in `value[[3L]](cond)`: Error in derive_vars_query call of get_vars_query: Error in inner_join(., queries_wide, by = c("SRCVAR", "TERM_NAME_ID")): could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_vars_query(my_ae, dataset_queries = query) at test-derive_vars_query.R:141:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test-derive_vars_query.R:192:3'): derive_vars_query Test 7: character SRCVAR and just TERMCHAR is provided ──
Error in `value[[3L]](cond)`: Error in derive_vars_query call of get_vars_query: Error in inner_join(., queries_wide, by = c("SRCVAR", "TERM_NAME_ID")): could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_vars_query(my_ae, dataset_queries = query) at test-derive_vars_query.R:192:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test-derive_vars_query.R:218:3'): derive_vars_query Test 8: numeric SRCVAR and just TERMNUM is provided ──
Error in `value[[3L]](cond)`: Error in derive_vars_query call of get_vars_query: Error in inner_join(., queries_wide, by = c("SRCVAR", "TERM_NAME_ID")): could not find function "inner_join"
Backtrace:
▆
1. └─admiral::derive_vars_query(my_ae, dataset_queries = query) at test-derive_vars_query.R:218:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test-derive_vars_transposed.R:23:3'): derive_vars_transposed Test 1: the merge dataset is transposed and merged correctly ──
Error in `left_join(dataset, dataset_transposed, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_transposed(...) at test-derive_vars_transposed.R:23:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. ├─base (local) tryCatchOne(...)
5. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
6. └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_vars_transposed.R:52:3'): derive_vars_transposed Test 2: filtering the merge dataset works ──
Error in `left_join(dataset, dataset_transposed, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_transposed(...) at test-derive_vars_transposed.R:52:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. ├─base (local) tryCatchOne(...)
5. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
6. └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-derive_vars_transposed.R:66:3'): derive_vars_transposed Test 3: filter merge dataset 'many-to-one' ──
Error in `left_join(dataset, dataset_transposed, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_transposed(...)
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. ├─base (local) tryCatchOne(...)
5. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
6. └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-event.R:38:3'): event Test 1: Cover event$order ────────────────
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::derive_vars_extreme_event(...) at test-event.R:38:3
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-filter_exist.R:56:3'): filter_not_exist Test 2: filter_not_exist() works as expected ──
Error in `anti_join(., dataset_add %>% filter_if(filter_add), by = vars2chr(by_vars))`: could not find function "anti_join"
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-filter_exist.R:56:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─admiral::filter_not_exist(...)
5. └─dataset %>% ...
── Error ('test-filter_joined.R:22:3'): filter_joined Test 1: filter without first_cond_upper ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::filter_joined(...) at test-filter_joined.R:22:3
2. │ ├─... %>% remove_tmp_vars()
3. │ └─admiral:::get_joined_data(...)
4. │ └─data %>% ...
5. ├─admiraldev::remove_tmp_vars(.)
6. ├─dplyr::select(., colnames(dataset))
7. ├─dplyr::ungroup(.)
8. ├─dplyr::slice(., 1L)
9. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
10. └─admiral::derive_vars_merged(...)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-filter_joined.R:49:3'): filter_joined Test 2: filter with first_cond ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::filter_joined(...) at test-filter_joined.R:49:3
2. │ ├─... %>% remove_tmp_vars()
3. │ └─admiral:::get_joined_data(...)
4. │ └─data %>% ...
5. ├─admiraldev::remove_tmp_vars(.)
6. ├─dplyr::select(., colnames(dataset))
7. ├─dplyr::ungroup(.)
8. ├─dplyr::slice(., 1L)
9. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
10. └─admiral::derive_vars_merged(...)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-filter_joined.R:76:3'): filter_joined Test 3: filter with first_cond and summary function ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiral::filter_joined(...) at test-filter_joined.R:76:3
2. │ ├─... %>% remove_tmp_vars()
3. │ └─admiral:::get_joined_data(...)
4. │ └─data %>% ...
5. ├─admiraldev::remove_tmp_vars(.)
6. ├─dplyr::select(., colnames(dataset))
7. ├─dplyr::ungroup(.)
8. ├─dplyr::slice(., 1L)
9. ├─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
10. └─admiral::derive_vars_merged(...)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-filter_joined.R:117:3'): filter_joined Test 4: join_type = 'all' ──
Error in `inner_join(data_nest, data_add_nest, by = vars2chr(by_vars_left))`: could not find function "inner_join"
Backtrace:
▆
1. ├─admiral::filter_joined(...) at test-filter_joined.R:117:3
2. │ ├─... %>% remove_tmp_vars()
3. │ └─admiral:::get_joined_data(...)
4. ├─admiraldev::remove_tmp_vars(.)
5. ├─dplyr::select(., colnames(dataset))
6. ├─dplyr::ungroup(.)
7. ├─dplyr::slice(., 1L)
8. └─dplyr::group_by(., !!!by_vars, !!tmp_obs_nr_unique)
── Error ('test-filter_relative.R:22:3'): filter_relative Test 1: mode = first, selection = before, inclusive = TRUE ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::filter_relative(...) at test-filter_relative.R:22:3
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-filter_relative.R:55:3'): filter_relative Test 2: mode = first, selection = before, inclusive = FALSE ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::filter_relative(...) at test-filter_relative.R:55:3
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-filter_relative.R:81:3'): filter_relative Test 3: mode = first, selection = after, inclusive = TRUE ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::filter_relative(...) at test-filter_relative.R:81:3
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-filter_relative.R:111:3'): filter_relative Test 4: mode = first, selection = after, inclusive = FALSE ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::filter_relative(...) at test-filter_relative.R:111:3
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-filter_relative.R:144:3'): filter_relative Test 1: mode = last, selection = before, inclusive = TRUE ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::filter_relative(...) at test-filter_relative.R:144:3
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-filter_relative.R:178:3'): filter_relative Test 2: mode = last, selection = before, inclusive = FALSE ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::filter_relative(...) at test-filter_relative.R:178:3
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-filter_relative.R:208:3'): filter_relative Test 7: mode = last, selection = after, inclusive = TRUE ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::filter_relative(...) at test-filter_relative.R:208:3
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-filter_relative.R:240:3'): filter_relative Test 8: mode = last, selection = after, inclusive = FALSE ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::filter_relative(...) at test-filter_relative.R:240:3
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-period_dataset.R:29:3'): create_period_dataset Test 1: periods ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-period_dataset.R:29:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::create_period_dataset(...)
4. └─admiral::derive_vars_merged(...)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-period_dataset.R:65:3'): create_period_dataset Test 2: phases ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-period_dataset.R:65:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::create_period_dataset(...)
4. └─admiral::derive_vars_merged(...)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-period_dataset.R:104:3'): create_period_dataset Test 3: subperiods ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-period_dataset.R:104:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::create_period_dataset(...)
4. └─admiral::derive_vars_merged(...)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-period_dataset.R:213:3'): derive_vars_period Test 7: periods ───
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-period_dataset.R:213:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_vars_period(...)
4. │ ├─... %>% rename(all_of(rename_arg))
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)
10. └─dplyr::rename(., all_of(rename_arg))
── Error ('test-period_dataset.R:252:3'): derive_vars_period Test 8: phases ────
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-period_dataset.R:252:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_vars_period(...)
4. │ ├─... %>% rename(all_of(rename_arg))
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)
10. └─dplyr::rename(., all_of(rename_arg))
── Error ('test-period_dataset.R:294:3'): derive_vars_period Test 9: subperiods ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-period_dataset.R:294:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_vars_period(...)
4. │ ├─... %>% rename(all_of(rename_arg))
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)
10. └─dplyr::rename(., all_of(rename_arg))
── Error ('test-period_dataset.R:386:3'): create_period_dataset Test 12: DT and DTM columns exist, pulls only one unique col ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-period_dataset.R:386:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::create_period_dataset(...)
4. └─admiral::derive_vars_merged(...)
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
── Error ('test-period_dataset.R:426:3'): derive_vars_period Test 13: periods ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-period_dataset.R:426:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_vars_period(...)
4. │ ├─... %>% rename(all_of(rename_arg))
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)
10. └─dplyr::rename(., all_of(rename_arg))
── Error ('test-period_dataset.R:467:3'): derive_vars_period Test 14: periods variable derived when only one variable needed ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-period_dataset.R:467:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral::derive_vars_period(adsl, dataset_ref = period_ref, new_vars = exprs(APxxSDT = APERSDT))
4. │ ├─... %>% rename(all_of(rename_arg))
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)
10. └─dplyr::rename(., all_of(rename_arg))
── Error ('test-restrict_derivation.R:15:3'): restrict_derivation Test 1: restrict derivation with parameters ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. └─admiral::restrict_derivation(...) at test-restrict_derivation.R:15:3
2. └─base::eval(call, envir = list(data_derive = data_derive), enclos = parent.frame())
3. └─base::eval(call, envir = list(data_derive = data_derive), enclos = parent.frame())
4. └─admiral::derive_var_base(data_derive, by_vars = exprs(USUBJID))
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-slice_derivation.R:169:5'): slice_derivation Test 5: calling it in a function ──
Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join"
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-slice_derivation.R:187:3
2. │ └─diffdf::diffdf(...)
3. ├─admiral (local) my_merge(dataset = select(expected, -MVAL), my_b_data = b_data)
4. │ └─admiral::slice_derivation(...) at test-slice_derivation.R:169:5
5. │ └─rlang::eval_tidy(call, env = eval_env)
6. └─admiral (local) `<fn>`(...)
7. └─base::tryCatch(...)
8. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
[ FAIL 175 | WARN 0 | SKIP 112 | PASS 663 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc