Last updated on 2024-06-08 09:49:30 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| admiral | 4 | 2 | 7 |
| admiral.test | 13 | ||
| admiraldev | 13 |
Current CRAN status: ERROR: 4, NOTE: 2, OK: 7
Version: 1.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘adsl.Rmd’ using rmarkdown
--- finished re-building ‘adsl.Rmd’
--- re-building ‘bds_exposure.Rmd’ using rmarkdown
--- finished re-building ‘bds_exposure.Rmd’
--- re-building ‘bds_finding.Rmd’ using rmarkdown
--- finished re-building ‘bds_finding.Rmd’
--- re-building ‘bds_tte.Rmd’ using rmarkdown
--- finished re-building ‘bds_tte.Rmd’
--- re-building ‘generic.Rmd’ using rmarkdown
--- finished re-building ‘generic.Rmd’
--- re-building ‘higher_order.Rmd’ using rmarkdown
--- finished re-building ‘higher_order.Rmd’
--- re-building ‘hys_law.Rmd’ using rmarkdown
--- finished re-building ‘hys_law.Rmd’
--- re-building ‘imputation.Rmd’ using rmarkdown
--- finished re-building ‘imputation.Rmd’
--- re-building ‘lab_grading.Rmd’ using rmarkdown
--- finished re-building ‘lab_grading.Rmd’
--- re-building ‘occds.Rmd’ using rmarkdown
--- finished re-building ‘occds.Rmd’
--- re-building ‘pk_adnca.Rmd’ using rmarkdown
Quitting from lines 1221-1245 [unnamed-chunk-40] (pk_adnca.Rmd)
Error: processing vignette 'pk_adnca.Rmd' failed with diagnostics:
Dataset contains duplicate records with respect to `STUDYID`, `USUBJID`, `AFRLT` and `EVID`
Run `get_duplicates_dataset()` to access the duplicate records
--- failed re-building ‘pk_adnca.Rmd’
--- re-building ‘queries_dataset.Rmd’ using rmarkdown
--- finished re-building ‘queries_dataset.Rmd’
--- re-building ‘questionnaires.Rmd’ using rmarkdown
--- finished re-building ‘questionnaires.Rmd’
--- re-building ‘visits_periods.Rmd’ using rmarkdown
--- finished re-building ‘visits_periods.Rmd’
SUMMARY: processing the following file failed:
‘pk_adnca.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.2
Check: R code for possible problems
Result: NOTE
call_derivation: no visible global function definition for ‘is_named’
params: no visible global function definition for ‘is_named’
print_named_list: no visible global function definition for ‘is_named’
Undefined global functions or variables:
is_named
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.2
Check: examples
Result: ERROR
Running examples in ‘admiral-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: call_derivation
> ### Title: Call a Single Derivation Multiple Times
> ### Aliases: call_derivation
> ### Keywords: high_order_function
>
> ### ** Examples
>
> library(dplyr, warn.conflicts = FALSE)
> adsl <- tribble(
+ ~STUDYID, ~USUBJID, ~TRTSDT, ~TRTEDT,
+ "PILOT01", "01-1307", NA, NA,
+ "PILOT01", "05-1377", "2014-01-04", "2014-01-25",
+ "PILOT01", "06-1384", "2012-09-15", "2012-09-24",
+ "PILOT01", "15-1085", "2013-02-16", "2013-08-18",
+ "PILOT01", "16-1298", "2013-04-08", "2013-06-28"
+ ) %>%
+ mutate(
+ across(TRTSDT:TRTEDT, as.Date)
+ )
>
> ae <- tribble(
+ ~STUDYID, ~DOMAIN, ~USUBJID, ~AESTDTC, ~AEENDTC,
+ "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29",
+ "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29",
+ "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29",
+ "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29",
+ "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29",
+ "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29",
+ "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29",
+ "PILOT01", "AE", "06-1384", "2012-09-15", "2012-09-29",
+ "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29",
+ "PILOT01", "AE", "06-1384", "2012-09-23", "2012-09-29",
+ "PILOT01", "AE", "16-1298", "2013-06-08", "2013-07-06",
+ "PILOT01", "AE", "16-1298", "2013-06-08", "2013-07-06",
+ "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06",
+ "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06",
+ "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06",
+ "PILOT01", "AE", "16-1298", "2013-04-22", "2013-07-06"
+ )
>
> adae <- ae %>%
+ derive_vars_merged(
+ dataset_add = adsl,
+ new_vars = exprs(TRTSDT, TRTEDT),
+ by_vars = exprs(USUBJID)
+ )
>
> ## While `derive_vars_dt()` can only add one variable at a time, using `call_derivation()`
> ## one can add multiple variables in one go
> call_derivation(
+ dataset = adae,
+ derivation = derive_vars_dt,
+ variable_params = list(
+ params(dtc = AESTDTC, date_imputation = "first", new_vars_prefix = "AST"),
+ params(dtc = AEENDTC, date_imputation = "last", new_vars_prefix = "AEN")
+ ),
+ min_dates = exprs(TRTSDT),
+ max_dates = exprs(TRTEDT)
+ )
Error in is_named(args) : could not find function "is_named"
Calls: call_derivation -> assert_list_of -> params
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [163s/279s]
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")
[ FAIL 47 | WARN 342 | SKIP 3 | PASS 681 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-derive_var_ontrtfl.R:419:3', 'test-duplicates.R:43:3',
'test-roxygen2.R:20:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-admiral_options.R:15:3'): get_admiral_option Test 3: non-character argument triggers assertion error ──
<assert_character_scalar/assert-admiraldev/rlang_error/error/condition>
Error in `get_admiral_option(subject_keys)`: Argument `option` must be a scalar of class <character>, but is a number.
Backtrace:
▆
1. ├─testthat::expect_error(get_admiral_option(subject_keys), "`option` must be a character scalar but is `1`") at test-admiral_options.R:15:3
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::get_admiral_option(subject_keys)
8. └─admiraldev::assert_character_scalar(option)
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-admiral_options.R:27:3'): set_admiral_options Test 5: unexpected function input for set gives error ──
<assert_vars/assert-admiraldev/rlang_error/error/condition>
Error in `set_admiral_options(subject_keys = rlang::quos(STUDYID, USUBJID2))`: Each element of the list in argument `subject_keys` must be class/type <symbol>.
i But, element 1 is a <quosure> object, and element 2 is a <quosure> object
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-admiral_options.R:27:3
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::set_admiral_options(subject_keys = rlang::quos(STUDYID, USUBJID2))
8. └─admiraldev::assert_vars(subject_keys)
9. └─admiraldev::assert_list_of(...)
10. └─cli::cli_abort(...)
11. └─rlang::abort(...)
── Error ('test-call_derivation.R:35:3'): call_derivation Test 1: Test that call_derivation generates expected summary ──
Error in `is_named(args)`: could not find function "is_named"
Backtrace:
▆
1. ├─admiral::call_derivation(...) at test-call_derivation.R:35:3
2. │ └─admiraldev::assert_list_of(variable_params, "params")
3. └─admiral::params(...)
── Error ('test-call_derivation.R:92:3'): call_derivation Test 2: Test that call_derivation generates expected imputation ──
Error in `is_named(args)`: could not find function "is_named"
Backtrace:
▆
1. ├─admiral::call_derivation(...) at test-call_derivation.R:92:3
2. │ └─admiraldev::assert_list_of(variable_params, "params")
3. └─admiral::params(dtc = AESTDTC, date_imputation = "first", new_vars_prefix = "AST")
── Error ('test-call_derivation.R:112:3'): call_derivation Test 3: Test that Error is thrown if ... has no arguments ──
Error in `is_named(args)`: could not find function "is_named"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-call_derivation.R:112:3
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::call_derivation(...)
8. │ └─admiraldev::assert_list_of(variable_params, "params")
9. └─admiral::params(dtc = AESTDTC, date_imputation = "first", new_vars_prefix = "AST")
── Error ('test-call_derivation.R:170:3'): call_derivation Test 6: Error is thrown if passed params are not properly named ──
Error in `is_named(args)`: could not find function "is_named"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-call_derivation.R:170:3
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::call_derivation(...)
8. │ └─admiraldev::assert_list_of(variable_params, "params")
9. └─admiral::params(XYZ)
── Error ('test-call_derivation.R:208:3'): call_derivation Test 8: Error is thrown if duplicate parameters ──
Error in `is_named(args)`: could not find function "is_named"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-call_derivation.R:208:3
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::params(dtc = VSDTC, dtc = VSDTC, new_vars_prefix = "A")
── Error ('test-consolidate_metadata.R:24:3'): consolidate_metadata Test 1: consolidation works ──
Error in `assert_list_of(datasets, class = "data.frame", named = TRUE)`: argument "cls" is missing, with no default
Backtrace:
▆
1. ├─admiraldev::expect_dfs_equal(...) at test-consolidate_metadata.R:24:3
2. │ └─diffdf::diffdf(...)
3. └─admiral::consolidate_metadata(...)
4. └─admiraldev::assert_list_of(datasets, class = "data.frame", named = TRUE)
5. └─admiraldev::assert_character_scalar(cls)
── Error ('test-consolidate_metadata.R:51:3'): consolidate_metadata Test 2: error if key vars are not unique ──
Error in `assert_list_of(datasets, class = "data.frame", named = TRUE)`: argument "cls" is missing, with no default
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-consolidate_metadata.R:51:3
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::consolidate_metadata(...)
8. └─admiraldev::assert_list_of(datasets, class = "data.frame", named = TRUE)
9. └─admiraldev::assert_character_scalar(cls)
── Failure ('test-consolidate_metadata.R:77:3'): consolidate_metadata Test 3: check_keys deprecation test ──
`try(...)` did not throw the expected warning.
── Error ('test-consolidate_metadata.R:105:3'): consolidate_metadata Test 4: warn if variables differ ──
Error in `assert_list_of(datasets, class = "data.frame", named = TRUE)`: argument "cls" is missing, with no default
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-consolidate_metadata.R:105:3
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::consolidate_metadata(...)
8. └─admiraldev::assert_list_of(datasets, class = "data.frame", named = TRUE)
9. └─admiraldev::assert_character_scalar(cls)
── Error ('test-derive_advs_params.R:222:3'): compute_bsa Test 25: an error is issued if an invalid method is specified ──
<assert_character_scalar/assert-admiraldev/rlang_error/error/condition>
Error in `compute_bsa(height = c(170, 185), weight = c(75, 90), method = "unknown-method")`: Argument `method` must be equal to one of "Mosteller", "DuBois-DuBois", "Haycock", "Gehan-George", "Boyd", "Fujimoto", or "Takahira".
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_advs_params.R:222:3
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::compute_bsa(height = c(170, 185), weight = c(75, 90), method = "unknown-method")
8. └─admiraldev::assert_character_scalar(...)
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-derive_advs_params.R:294:3'): derive_param_bmi Test 32: BMI parameter NOT added - wrong hgt unit ──
<assert_unit/assert-admiraldev/rlang_error/error/condition>
Error in `derive_param_bmi(input, by_vars = exprs(USUBJID, VISIT), get_unit_expr = VSSTRESU)`: It is expected that "HEIGHT" has unit of "cm". In the input dataset the unit is "m".
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_advs_params.R:294:3
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_param_bmi(input, by_vars = exprs(USUBJID, VISIT), get_unit_expr = VSSTRESU)
8. └─admiraldev::assert_unit(...)
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-derive_advs_params.R:312:3'): derive_param_bmi Test 33: BMI parameter NOT added - wrong wgt unit ──
<assert_unit/assert-admiraldev/rlang_error/error/condition>
Error in `derive_param_bmi(input, by_vars = exprs(USUBJID, VISIT), get_unit_expr = VSSTRESU)`: It is expected that "WEIGHT" has unit of "kg". In the input dataset the unit is "g".
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_advs_params.R:312:3
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_param_bmi(input, by_vars = exprs(USUBJID, VISIT), get_unit_expr = VSSTRESU)
8. └─admiraldev::assert_unit(...)
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-derive_advs_params.R:331:3'): derive_param_bmi Test 34: BMI parameter NOT added - multiple unit for wgt ──
<assert_unit/assert-admiraldev/rlang_error/error/condition>
Error in `derive_param_bmi(input, by_vars = exprs(USUBJID, VISIT), get_unit_expr = VSSTRESU)`: Multiple units "kg" and "g" found for "WEIGHT". Please review and update the units.
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_advs_params.R:331:3
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_param_bmi(input, by_vars = exprs(USUBJID, VISIT), get_unit_expr = VSSTRESU)
8. └─admiraldev::assert_unit(...)
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-derive_advs_params.R:348:3'): derive_param_bmi Test 35: BMI parameter NOT added - PARAMCD not set ──
<assert_varval_list/assert-admiraldev/rlang_error/error/condition>
Error in `derive_param_bmi(input, by_vars = exprs(USUBJID, VISIT), set_values_to = exprs(PARAM = "Body Mass Index"),
get_unit_expr = VSSTRESU)`: The following required elements are missing from argument `set_values_to`: "PARAMCD".
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_advs_params.R:348:3
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_param_bmi(...)
8. └─admiraldev::assert_varval_list(set_values_to, required_elements = "PARAMCD")
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-derive_advs_params.R:479:3'): derive_param_bsa Test 39: BSA parameter NOT added - wrong unit for height ──
<assert_unit/assert-admiraldev/rlang_error/error/condition>
Error in `derive_param_bsa(input, by_vars = exprs(USUBJID, VISIT), method = "Mosteller",
get_unit_expr = VSSTRESU)`: It is expected that "HEIGHT" has unit of "cm". In the input dataset the unit is "m".
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_advs_params.R:479:3
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_param_bsa(...)
8. └─admiraldev::assert_unit(...)
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-derive_advs_params.R:502:3'): derive_param_bsa Test 40: BSA parameter NOT added - wrong unit for weight ──
<assert_unit/assert-admiraldev/rlang_error/error/condition>
Error in `derive_param_bsa(input, by_vars = exprs(USUBJID, VISIT), method = "Mosteller",
get_unit_expr = VSSTRESU)`: It is expected that "WEIGHT" has unit of "kg". In the input dataset the unit is "g".
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_advs_params.R:502:3
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_param_bsa(...)
8. └─admiraldev::assert_unit(...)
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-derive_advs_params.R:526:3'): derive_param_bsa Test 41: BSA parameter NOT added - multiple unit for weight ──
<assert_unit/assert-admiraldev/rlang_error/error/condition>
Error in `derive_param_bsa(input, by_vars = exprs(USUBJID, VISIT), method = "Mosteller",
get_unit_expr = VSSTRESU)`: Multiple units "kg" and "g" found for "WEIGHT". Please review and update the units.
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_advs_params.R:526:3
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_param_bsa(...)
8. └─admiraldev::assert_unit(...)
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-derive_advs_params.R:548:3'): derive_param_bsa Test 42: BSA parameter NOT added - PARAMCD not set ──
<assert_varval_list/assert-admiraldev/rlang_error/error/condition>
Error in `derive_param_bsa(input, by_vars = exprs(USUBJID, VISIT), method = "Mosteller",
set_values_to = exprs(PARAM = "Body Surface Area"), get_unit_expr = VSSTRESU)`: The following required elements are missing from argument `set_values_to`: "PARAMCD".
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_advs_params.R:548:3
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_param_bsa(...)
8. └─admiraldev::assert_varval_list(set_values_to, required_elements = "PARAMCD")
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-derive_advs_params.R:906:3'): derive_param_map Test 52: MAP parameter NOT added - wrong DIABP unit ──
<assert_unit/assert-admiraldev/rlang_error/error/condition>
Error in `derive_param_map(input, by_vars = exprs(USUBJID, VISIT), get_unit_expr = extract_unit(PARAM))`: It is expected that "DIABP" has unit of "mmHg". In the input dataset the unit is "mHg".
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_advs_params.R:906:3
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_param_map(input, by_vars = exprs(USUBJID, VISIT), get_unit_expr = extract_unit(PARAM))
8. └─admiraldev::assert_unit(...)
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-derive_advs_params.R:927:3'): derive_param_map Test 53: MAP parameter NOT added - wrong SYSBP unit ──
<assert_unit/assert-admiraldev/rlang_error/error/condition>
Error in `derive_param_map(input, by_vars = exprs(USUBJID, VISIT), get_unit_expr = extract_unit(PARAM))`: It is expected that "SYSBP" has unit of "mmHg". In the input dataset the unit is "mHg".
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_advs_params.R:927:3
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_param_map(input, by_vars = exprs(USUBJID, VISIT), get_unit_expr = extract_unit(PARAM))
8. └─admiraldev::assert_unit(...)
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-derive_advs_params.R:949:3'): derive_param_map Test 54: MAP parameter NOT added - wrong PULSE unit ──
<assert_unit/assert-admiraldev/rlang_error/error/condition>
Error in `derive_param_map(input, by_vars = exprs(USUBJID, VISIT), hr_code = "PULSE",
get_unit_expr = extract_unit(PARAM))`: It is expected that "PULSE" has unit of "beats/min". In the input dataset the unit is "beats/m".
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_advs_params.R:949:3
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_param_map(...)
8. └─admiraldev::assert_unit(...)
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-derive_advs_params.R:971:3'): derive_param_map Test 55: MAP parameter NOT added - PARAMCD not set ──
<assert_varval_list/assert-admiraldev/rlang_error/error/condition>
Error in `derive_param_map(input, by_vars = exprs(USUBJID, VISIT), set_values_to = exprs(PARAM = "Mean Arterial Pressure"),
get_unit_expr = extract_unit(PARAM))`: The following required elements are missing from argument `set_values_to`: "PARAMCD".
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_advs_params.R:971:3
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_param_map(...)
8. └─admiraldev::assert_varval_list(set_values_to, required_elements = "PARAMCD")
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-derive_param_exist_flag.R:70:3'): derive_param_merged_exist_flag Test 2: error is issued if paramter already exists in dataset ──
<assert_param_does_not_exist/assert-admiraldev/rlang_error/error/condition>
Error in `derive_param_exist_flag(dataset = adrs, dataset_ref = adsl, dataset_add = adrs,
filter_add = PARAMCD == "OVR", condition = AVALC == "PD",
false_value = "N", set_values_to = exprs(PARAMCD = "OVR",
ANL01FL = "Y"))`: The parameter code "OVR" already exists in dataset `dataset`.
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_param_exist_flag.R:70:3
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_param_exist_flag(...)
8. └─admiraldev::assert_param_does_not_exist(dataset, set_values_to$PARAMCD)
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-derive_param_exposure.R:165:3'): derive_param_exposure Test 3: Errors ──
<assert_varval_list/assert-admiraldev/rlang_error/error/condition>
Error in `derive_param_exposure(., dataset_add = input, by_vars = exprs(USUBJID),
input_code = "DOSE", analysis_var = AVAL, summary_fun = function(x) mean(x,
na.rm = TRUE), set_values_to = exprs(PARCAT1 = "OVERALL"))`: The following required elements are missing from argument `set_values_to`: "PARAMCD".
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_param_exposure.R:165:3
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. ├─input %>% ...
8. └─admiral::derive_param_exposure(...)
9. └─admiraldev::assert_varval_list(set_values_to, required_elements = "PARAMCD")
10. └─cli::cli_abort(...)
11. └─rlang::abort(...)
── Error ('test-derive_param_extreme_record.R:133:3'): derive_param_extreme_record Test 3: Error given when sources is not in proper list format ──
<assert_list_of/assert-admiraldev/rlang_error/error/condition>
Error in `derive_param_extreme_record(dataset = aevent, sources = records_source(dataset_name = "pr",
filter = PRDECOD == "ACS", new_vars = exprs(ADT = convert_dtc_to_dt(PRSTDTC),
AVALC = PRDECOD)), source_datasets = list(pr = pr), by_vars = exprs(STUDYID,
USUBJID), order = exprs(ADT), mode = "first", set_values_to = exprs(PARAMCD = "FIRSTACT",
PARAM = "First Anti-Cancer Therapy"))`: Each element of the list in argument `sources` must be class/type <records_source>.
i But, element 1 is a string, element 2 is a call, and element 3 is a list
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_param_extreme_record.R:133:3
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_param_extreme_record(...)
8. └─admiraldev::assert_list_of(sources, "records_source")
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-derive_param_tte.R:316:3'): derive_param_tte Test 4: error is issued if DTC variables specified for date ──
<assert_date_var/assert-admiraldev/rlang_error/error/condition>
Error in `filter_date_sources(sources = event_conditions, source_datasets = source_datasets,
by_vars = by_vars, create_datetime = create_datetime, subject_keys = subject_keys,
mode = "first")`: Column "AESTDTC" in dataset `ae` must be a date or datetime, but is a character vector.
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_param_tte.R:316:3
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_param_tte(...)
8. │ ├─... %>% mutate(!!tmp_event := 1L)
9. │ └─admiral:::filter_date_sources(...)
10. │ └─admiraldev::assert_date_var(...)
11. │ └─cli::cli_abort(...)
12. │ └─rlang::abort(...)
13. └─dplyr::mutate(., `:=`(!!tmp_event, 1L))
── Error ('test-derive_param_tte.R:575:3'): derive_param_tte Test 8: errors if PARAMCD and by_vars are not one to one ──
<assert_one_to_one/assert-admiraldev/rlang_error/error/condition>
Error in `derive_param_tte(dataset_adsl = adsl, by_vars = exprs(AEDECOD),
start_date = TRTSDT, event_conditions = list(ttae), censor_conditions = list(eos),
source_datasets = list(adsl = adsl, ae = ae), set_values_to = exprs(PARAMCD = "TTAE",
PARCAT2 = AEDECOD))`: For some values of "PARAMCD" there is more than one value of "AEDECOD"
i Call `admiral::get_one_to_many_dataset()` to get all one-to-many values.
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_param_tte.R:575:3
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_param_tte(...)
8. └─admiraldev::assert_one_to_one(new_param, exprs(PARAMCD), by_vars)
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-derive_param_tte.R:638:3'): derive_param_tte Test 9: errors if set_values_to contains invalid expressions ──
Error in `process_set_values_to(., set_values_to)`: Assigning variables failed!
* `set_values_to = exprs(PARAMCD = paste0("TTAE", as.numeric(as.factor(AEDECOD))), PARAM = past("Time to First", AEDECOD, "Adverse Event"), PARCAT1 = TTAE, PARCAT2 = AEDECOD)`
See error message below:
i In argument: `PARAM = past("Time to First", AEDECOD, "Adverse Event")`. Caused by error in `past()`: ! could not find function "past"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_param_tte.R:638:3
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_param_tte(...)
8. │ └─... %>% remove_tmp_vars()
9. ├─admiraldev::remove_tmp_vars(.)
10. ├─dplyr::mutate(...)
11. └─admiraldev::process_set_values_to(., set_values_to)
12. └─base::tryCatch(...)
13. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. └─value[[3L]](cond)
16. └─cli::cli_abort(...)
17. └─rlang::abort(...)
── Error ('test-derive_param_tte.R:721:3'): derive_param_tte Test 10: error is issued if parameter code already exists ──
<assert_param_does_not_exist/assert-admiraldev/rlang_error/error/condition>
Error in `derive_param_tte(expected_output, dataset_adsl = adsl, start_date = TRTSDT,
event_conditions = list(ttae), censor_conditions = list(eos),
source_datasets = list(adsl = adsl, ae = ae), set_values_to = exprs(PARAMCD = "TTAE",
PARAM = "Time to First Adverse Event"))`: The parameter code "TTAE" already exists in dataset `dataset`.
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_param_tte.R:721:3
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_param_tte(...)
8. └─admiraldev::assert_param_does_not_exist(dataset, unique_params[i])
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-derive_summary_records.R:85:3'): derive_summary_records Test 3: Errors ──
<assert_vars/assert-admiraldev/rlang_error/error/condition>
Error in `derive_summary_records(input, by_vars = "x", set_values_to = exprs(z = mean(z)))`: Argument `by_vars` must be class <list>, but is a string.
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_summary_records.R:85:3
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_summary_records(input, by_vars = "x", set_values_to = exprs(z = mean(z)))
8. └─admiraldev::assert_vars(by_vars)
9. └─admiraldev::assert_list_of(...)
10. └─admiraldev::assert_s3_class(...)
11. └─cli::cli_abort(...)
12. └─rlang::abort(...)
── Error ('test-derive_var_extreme_date.R:202:3'): derive_var_extreme_dtm Test 5: error is issued if `--DTC` variable is specified ──
<assert_date_var/assert-admiraldev/rlang_error/error/condition>
Error in `derive_var_extreme_dtm(adsl, new_var = LSTALVDTM, source_datasets = list(ae = ae),
ae_start, mode = "last")`: Column "AESTDTC" in dataset `ae` must be a date or datetime, but is a character vector.
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_var_extreme_date.R:202:3
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_extreme_dtm(...)
8. └─admiraldev::assert_date_var(...)
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-derive_var_merged_ef_msrc.R:27:3'): derive_var_merged_ef_msrc Test 1: wihtout by_vars ──
Error in `assert_list_of(source_datasets, class = "data.frame", named = TRUE)`: argument "cls" is missing, with no default
Backtrace:
▆
1. └─admiral::derive_var_merged_ef_msrc(...) at test-derive_var_merged_ef_msrc.R:27:3
2. └─admiraldev::assert_list_of(...)
3. └─admiraldev::assert_character_scalar(cls)
── Error ('test-derive_var_merged_ef_msrc.R:74:3'): derive_var_merged_ef_msrc Test 2: with by_vars ──
Error in `assert_list_of(source_datasets, class = "data.frame", named = TRUE)`: argument "cls" is missing, with no default
Backtrace:
▆
1. └─admiral::derive_var_merged_ef_msrc(...) at test-derive_var_merged_ef_msrc.R:74:3
2. └─admiraldev::assert_list_of(...)
3. └─admiraldev::assert_character_scalar(cls)
── Error ('test-derive_vars_aage.R:19:3'): derive_vars_aage Test 2: Error is thrown when age_unit is not proper unit ──
<assert_character_scalar/assert-admiraldev/rlang_error/error/condition>
Error in `derive_vars_aage(input, age_unit = "centuries")`: Argument `age_unit` must be equal to one of "year", "years", "yr", "yrs", "y", "month", "months", "mo", "mos", "week", "weeks", "wk", "wks", "w", "day", "days", "d", "hour", ..., "secs", or "s".
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_vars_aage.R:19:3
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_aage(input, age_unit = "centuries")
8. └─admiraldev::assert_character_scalar(...)
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-derive_vars_aage.R:62:3'): derive_var_age_years Test 5: Error is thrown when age_unit is not proper unit ──
<assert_character_scalar/assert-admiraldev/rlang_error/error/condition>
Error in `derive_var_age_years(input, AGE, age_unit = "month", new_var = AAGE)`: Argument `age_unit` must be equal to one of "years", "months", "weeks", "days", "hours", "minutes", or "seconds".
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-derive_vars_aage.R:62:3
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_age_years(input, AGE, age_unit = "month", new_var = AAGE)
8. └─admiraldev::assert_character_scalar(...)
9. └─cli::cli_abort(...)
10. └─rlang::abort(...)
── Error ('test-restrict_derivation.R:15:3'): restrict_derivation Test 1: restrict derivation with parameters ──
Error in `is_named(args)`: could not find function "is_named"
Backtrace:
▆
1. ├─admiral::restrict_derivation(...) at test-restrict_derivation.R:15:3
2. │ └─admiraldev::assert_s3_class(args, "params", optional = TRUE)
3. └─admiral::params(by_vars = exprs(USUBJID))
── Error ('test-restrict_derivation.R:74:5'): restrict_derivation Test 3: access functions from the parent environment ──
Error in `is_named(args)`: could not find function "is_named"
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-restrict_derivation.R:73:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. ├─admiral::restrict_derivation(...) at test-restrict_derivation.R:74:5
10. │ └─admiraldev::assert_s3_class(args, "params", optional = TRUE)
11. └─admiral::params(new_var = X)
── Error ('test-restrict_derivation.R:98:3'): restrict_derivation Test 4: allow dplyr functions ──
Error in `is_named(args)`: could not find function "is_named"
Backtrace:
▆
1. ├─admiral::restrict_derivation(...) at test-restrict_derivation.R:98:3
2. │ └─admiraldev::assert_s3_class(args, "params", optional = TRUE)
3. └─admiral::params(AVAL = AVAL + 1)
── Error ('test-slice_derivation.R:10:3'): slice_derivation Test 1: slice derivation ──
Error in `is_named(args)`: could not find function "is_named"
Backtrace:
▆
1. ├─admiral::slice_derivation(...) at test-slice_derivation.R:10:3
2. │ └─admiraldev::assert_s3_class(args, "params", optional = TRUE)
3. └─admiral::params(dtc = VSDTC, new_vars_prefix = "A")
── Error ('test-slice_derivation.R:48:3'): slice_derivation Test 2: non matching observations ──
Error in `is_named(args)`: could not find function "is_named"
Backtrace:
▆
1. ├─admiral::slice_derivation(...) at test-slice_derivation.R:48:3
2. │ └─admiraldev::assert_s3_class(args, "params", optional = TRUE)
3. └─admiral::params(dtc = VSDTC, new_vars_prefix = "A")
── Error ('test-slice_derivation.R:82:3'): slice_derivation Test 3: empty slice ──
Error in `is_named(args)`: could not find function "is_named"
Backtrace:
▆
1. ├─admiral::slice_derivation(...) at test-slice_derivation.R:82:3
2. │ └─admiraldev::assert_s3_class(args, "params", optional = TRUE)
3. └─admiral::params(dtc = VSDTC, new_vars_prefix = "A")
── Error ('test-slice_derivation.R:120:3'): slice_derivation Test 4: slice without arguments ──
Error in `is_named(args)`: could not find function "is_named"
Backtrace:
▆
1. ├─admiral::slice_derivation(...) at test-slice_derivation.R:120:3
2. │ └─admiraldev::assert_s3_class(args, "params", optional = TRUE)
3. └─admiral::params(dtc = VSDTC, new_vars_prefix = "A", time_imputation = "last")
── Error ('test-user_utils.R:150:3'): print.source Test 13: `source` objects are printed as intended ──
Error in `is_named(list[[name]])`: could not find function "is_named"
Backtrace:
▆
1. ├─testthat::expect_identical(capture.output(print(ttae)), expected_print_output) at test-user_utils.R:150:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─utils::capture.output(print(ttae))
5. │ └─base::withVisible(...elt(i))
6. ├─base::print(ttae)
7. └─admiral:::print.source(ttae)
8. └─admiral::print_named_list(x, indent = indent)
── Error ('test-user_utils.R:155:3'): print.source Test 14: `source` objects containing `source` objects ──
Error in `is_named(args)`: could not find function "is_named"
Backtrace:
▆
1. ├─admiral::derivation_slice(filter = AVISITN > 0, args = params(new_var = CHG)) at test-user_utils.R:155:3
2. │ └─admiraldev::assert_s3_class(args, "params", optional = TRUE)
3. └─admiral::params(new_var = CHG)
── Error ('test-user_utils.R:229:3'): print_named_list Test 18: named list with unamed list ──
Error in `is_named(list[[name]])`: could not find function "is_named"
Backtrace:
▆
1. └─testthat::expect_snapshot(...) at test-user_utils.R:229:3
2. └─rlang::cnd_signal(state$error)
[ FAIL 47 | WARN 342 | SKIP 3 | PASS 681 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘adsl.Rmd’ using rmarkdown
--- finished re-building ‘adsl.Rmd’
--- re-building ‘bds_exposure.Rmd’ using rmarkdown
Quitting from lines 397-437 [unnamed-chunk-25] (bds_exposure.Rmd)
Error: processing vignette 'bds_exposure.Rmd' failed with diagnostics:
could not find function "is_named"
--- failed re-building ‘bds_exposure.Rmd’
--- re-building ‘bds_finding.Rmd’ using rmarkdown
Quitting from lines 611-622 [unnamed-chunk-41] (bds_finding.Rmd)
Error: processing vignette 'bds_finding.Rmd' failed with diagnostics:
could not find function "is_named"
--- failed re-building ‘bds_finding.Rmd’
--- re-building ‘bds_tte.Rmd’ using rmarkdown
Quitting from lines 431-502 [unnamed-chunk-22] (bds_tte.Rmd)
Error: processing vignette 'bds_tte.Rmd' failed with diagnostics:
could not find function "is_named"
--- failed re-building ‘bds_tte.Rmd’
--- re-building ‘generic.Rmd’ using rmarkdown
--- finished re-building ‘generic.Rmd’
--- re-building ‘higher_order.Rmd’ using rmarkdown
Quitting from lines 116-126 [unnamed-chunk-6] (higher_order.Rmd)
Error: processing vignette 'higher_order.Rmd' failed with diagnostics:
could not find function "is_named"
--- failed re-building ‘higher_order.Rmd’
--- re-building ‘hys_law.Rmd’ using rmarkdown
--- finished re-building ‘hys_law.Rmd’
--- re-building ‘imputation.Rmd’ using rmarkdown
Quitting from lines 480-502 [unnamed-chunk-22] (imputation.Rmd)
Error: processing vignette 'imputation.Rmd' failed with diagnostics:
could not find function "is_named"
--- failed re-building ‘imputation.Rmd’
--- re-building ‘lab_grading.Rmd’ using rmarkdown
--- finished re-building ‘lab_grading.Rmd’
--- re-building ‘occds.Rmd’ using rmarkdown
Quitting from lines 386-403 [unnamed-chunk-18] (occds.Rmd)
Error: processing vignette 'occds.Rmd' failed with diagnostics:
could not find function "is_named"
--- failed re-building ‘occds.Rmd’
--- re-building ‘pk_adnca.Rmd’ using rmarkdown
Quitting from lines 1221-1245 [unnamed-chunk-40] (pk_adnca.Rmd)
Error: processing vignette 'pk_adnca.Rmd' failed with diagnostics:
Dataset contains duplicate records with respect to `STUDYID`, `USUBJID`, `AFRLT` and `EVID`
Run `get_duplicates_dataset()` to access the duplicate records
--- failed re-building ‘pk_adnca.Rmd’
--- re-building ‘queries_dataset.Rmd’ using rmarkdown
--- finished re-building ‘queries_dataset.Rmd’
--- re-building ‘questionnaires.Rmd’ using rmarkdown
Quitting from lines 203-229 [unnamed-chunk-12] (questionnaires.Rmd)
Error: processing vignette 'questionnaires.Rmd' failed with diagnostics:
could not find function "is_named"
--- failed re-building ‘questionnaires.Rmd’
--- re-building ‘visits_periods.Rmd’ using rmarkdown
--- finished re-building ‘visits_periods.Rmd’
SUMMARY: processing the following files failed:
‘bds_exposure.Rmd’ ‘bds_finding.Rmd’ ‘bds_tte.Rmd’ ‘higher_order.Rmd’
‘imputation.Rmd’ ‘occds.Rmd’ ‘pk_adnca.Rmd’ ‘questionnaires.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.0
Check: data for non-ASCII characters
Result: NOTE
Note: found 12 marked UTF-8 strings
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.1.0
Check: running R code from vignettes
Result: ERROR
Errors in running code in vignettes:
when running code in ‘concepts_conventions.Rmd’
...
> adcm
STUDYID USUBJID CMTRT
1 XXX XXX-1 ASPIRIN
> adcm %>% select(get_admiral_option("subject_keys"))
When sourcing ‘concepts_conventions.R’:
Error: Can't select columns with `get_admiral_option("subject_keys")`.
✖ `get_admiral_option("subject_keys")` must be numeric or character, not a list.
Execution halted
‘adsl.Rmd’ using ‘UTF-8’... [5s/5s] OK
‘bds_exposure.Rmd’ using ‘UTF-8’... [2s/2s] OK
‘bds_finding.Rmd’ using ‘UTF-8’... [4s/4s] OK
‘bds_tte.Rmd’ using ‘UTF-8’... [4s/4s] OK
‘concepts_conventions.Rmd’ using ‘UTF-8’... failed
‘generic.Rmd’ using ‘UTF-8’... [3s/3s] OK
‘higher_order.Rmd’ using ‘UTF-8’... [3s/3s] OK
‘hys_law.Rmd’ using ‘UTF-8’... [1s/1s] OK
‘imputation.Rmd’ using ‘UTF-8’... [1s/2s] OK
‘lab_grading.Rmd’ using ‘UTF-8’... [2s/2s] OK
‘occds.Rmd’ using ‘UTF-8’... [2s/3s] OK
‘pk_adnca.Rmd’ using ‘UTF-8’... [4s/4s] OK
‘queries_dataset.Rmd’ using ‘UTF-8’... [1s/1s] OK
‘questionnaires.Rmd’ using ‘UTF-8’... [3s/3s] OK
‘visits_periods.Rmd’ using ‘UTF-8’... [2s/2s] OK
Flavor: r-oldrel-macos-arm64
Version: 1.1.0
Check: running R code from vignettes
Result: ERROR
Errors in running code in vignettes:
when running code in ‘concepts_conventions.Rmd’
...
> adcm
STUDYID USUBJID CMTRT
1 XXX XXX-1 ASPIRIN
> adcm %>% select(get_admiral_option("subject_keys"))
When sourcing ‘concepts_conventions.R’:
Error: Can't select columns with `get_admiral_option("subject_keys")`.
✖ `get_admiral_option("subject_keys")` must be numeric or character, not a list.
Execution halted
‘adsl.Rmd’ using ‘UTF-8’... [8s/19s] OK
‘bds_exposure.Rmd’ using ‘UTF-8’... [3s/7s] OK
‘bds_finding.Rmd’ using ‘UTF-8’... [5s/8s] OK
‘bds_tte.Rmd’ using ‘UTF-8’... [7s/9s] OK
‘concepts_conventions.Rmd’ using ‘UTF-8’... failed
‘generic.Rmd’ using ‘UTF-8’... [4s/7s] OK
‘higher_order.Rmd’ using ‘UTF-8’... [4s/6s] OK
‘hys_law.Rmd’ using ‘UTF-8’... [2s/2s] OK
‘imputation.Rmd’ using ‘UTF-8’... [2s/3s] OK
‘lab_grading.Rmd’ using ‘UTF-8’... [3s/4s] OK
‘occds.Rmd’ using ‘UTF-8’... [4s/6s] OK
‘pk_adnca.Rmd’ using ‘UTF-8’... [7s/10s] OK
‘queries_dataset.Rmd’ using ‘UTF-8’... [1s/1s] OK
‘questionnaires.Rmd’ using ‘UTF-8’... [5s/6s] OK
‘visits_periods.Rmd’ using ‘UTF-8’... [3s/4s] OK
Flavor: r-oldrel-macos-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13