Last updated on 2023-02-05 11:10:40 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.1 | 7.77 | 263.70 | 271.47 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.1 | 6.42 | 193.44 | 199.86 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.1 | 335.47 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.1 | 342.39 | ERROR | |||
| r-devel-windows-x86_64 | 0.1.1 | 45.00 | 309.00 | 354.00 | ERROR | |
| r-patched-linux-x86_64 | 0.1.1 | 9.63 | 258.73 | 268.36 | ERROR | |
| r-release-linux-x86_64 | 0.1.1 | 7.94 | 260.96 | 268.90 | ERROR | |
| r-release-macos-arm64 | 0.1.1 | 48.00 | OK | |||
| r-release-macos-x86_64 | 0.1.1 | 71.00 | OK | |||
| r-release-windows-x86_64 | 0.1.1 | 25.00 | 187.00 | 212.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.1 | 44.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.1.1 | 72.00 | OK | |||
| r-oldrel-windows-ix86+x86_64 | 0.1.1 | 19.00 | 319.00 | 338.00 | ERROR |
Version: 0.1.1
Check: examples
Result: ERROR
Running examples in ‘metacore-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: check_inconsistent_labels
> ### Title: Optional checks to consistency of metadata
> ### Aliases: check_inconsistent_labels check_inconsistent_types
> ### check_inconsistent_formats
>
> ### ** Examples
>
> ## EXAMPLE WITH DUPLICATES
> # Loads in a metacore obj called metacore
> load(metacore_example("pilot_ADaM.rda"))
> check_inconsistent_labels(metacore)
Error in `mutate()`:
ℹ In argument: `across(...)`.
ℹ In group 3: `var1 = "CHG"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
▆
1. ├─metacore::check_inconsistent_labels(metacore)
2. │ └─metacore:::basic_check(label, metacore)
3. │ └─... %>% select(variable = var1, everything())
4. ├─dplyr::select(., variable = var1, everything())
5. ├─dplyr::summarise(...)
6. ├─dplyr::group_by(...)
7. ├─dplyr::mutate(...)
8. ├─dplyr:::mutate.data.frame(...)
9. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
10. │ ├─base::withCallingHandlers(...)
11. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
12. │ ├─base::withCallingHandlers(...)
13. │ └─mask$eval_all_mutate(quo)
14. │ └─dplyr (local) eval()
15. └─dplyr:::dplyr_internal_error("dplyr:::mutate_incompatible_size", `<named list>`)
16. └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [195s/211s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(metacore)
>
> test_check("metacore")
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 67 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-checks.R:16'): Test label Checks ───────────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `mutate(., across(everything(), function(x) {
attr(x, "label") <- NULL
x
}))`: ℹ In argument: `across(...)`.
ℹ In group 3: `var1 = "CHG"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
▆
1. ├─check_inconsistent_labels(metacore) %>% ... at test-checks.R:16:3
2. ├─dplyr::arrange(., variable, label)
3. ├─metacore::check_inconsistent_labels(metacore)
4. │ └─metacore:::basic_check(label, metacore)
5. │ └─... %>% select(variable = var1, everything())
6. ├─dplyr::select(., variable = var1, everything())
7. ├─dplyr::summarise(...)
8. ├─dplyr::group_by(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr:::mutate.data.frame(...)
11. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
12. │ ├─base::withCallingHandlers(...)
13. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
14. │ ├─base::withCallingHandlers(...)
15. │ └─mask$eval_all_mutate(quo)
16. │ └─dplyr (local) eval()
17. ├─dplyr:::dplyr_internal_error(...)
18. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
19. │ └─rlang:::signal_abort(cnd, .file)
20. │ └─base::signalCondition(cnd)
21. ├─dplyr (local) `<fn>`(`<dpl:::__>`)
22. │ └─rlang::abort(msg, call = call("across"), parent = cnd)
23. │ └─rlang:::signal_abort(cnd, .file)
24. │ └─base::signalCondition(cnd)
25. └─dplyr (local) `<fn>`(`<rlng_rrr>`)
26. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
── Error ('test-checks.R:44'): Check formats and types ─────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `mutate(., across(everything(), function(x) {
attr(x, "label") <- NULL
x
}))`: ℹ In argument: `across(...)`.
ℹ In group 2: `var1 = "BASE"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
▆
1. ├─metacore::check_inconsistent_types(metacore) at test-checks.R:44:3
2. │ └─metacore:::basic_check(type, metacore)
3. │ └─... %>% select(variable = var1, everything())
4. ├─dplyr::select(., variable = var1, everything())
5. ├─dplyr::summarise(...)
6. ├─dplyr::group_by(...)
7. ├─dplyr::mutate(...)
8. ├─dplyr:::mutate.data.frame(...)
9. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
10. │ ├─base::withCallingHandlers(...)
11. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
12. │ ├─base::withCallingHandlers(...)
13. │ └─mask$eval_all_mutate(quo)
14. │ └─dplyr (local) eval()
15. ├─dplyr:::dplyr_internal_error(...)
16. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
17. │ └─rlang:::signal_abort(cnd, .file)
18. │ └─base::signalCondition(cnd)
19. ├─dplyr (local) `<fn>`(`<dpl:::__>`)
20. │ └─rlang::abort(msg, call = call("across"), parent = cnd)
21. │ └─rlang:::signal_abort(cnd, .file)
22. │ └─base::signalCondition(cnd)
23. └─dplyr (local) `<fn>`(`<rlng_rrr>`)
24. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 67 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [143s/212s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(metacore)
>
> test_check("metacore")
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 67 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-checks.R:16'): Test label Checks ───────────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `mutate(., across(everything(), function(x) {
attr(x, "label") <- NULL
x
}))`: ℹ In argument: `across(...)`.
ℹ In group 3: `var1 = "CHG"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
▆
1. ├─check_inconsistent_labels(metacore) %>% ... at test-checks.R:16:3
2. ├─dplyr::arrange(., variable, label)
3. ├─metacore::check_inconsistent_labels(metacore)
4. │ └─metacore:::basic_check(label, metacore)
5. │ └─... %>% select(variable = var1, everything())
6. ├─dplyr::select(., variable = var1, everything())
7. ├─dplyr::summarise(...)
8. ├─dplyr::group_by(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr:::mutate.data.frame(...)
11. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
12. │ ├─base::withCallingHandlers(...)
13. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
14. │ ├─base::withCallingHandlers(...)
15. │ └─mask$eval_all_mutate(quo)
16. │ └─dplyr (local) eval()
17. ├─dplyr:::dplyr_internal_error(...)
18. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
19. │ └─rlang:::signal_abort(cnd, .file)
20. │ └─base::signalCondition(cnd)
21. ├─dplyr (local) `<fn>`(`<dpl:::__>`)
22. │ └─rlang::abort(msg, call = call("across"), parent = cnd)
23. │ └─rlang:::signal_abort(cnd, .file)
24. │ └─base::signalCondition(cnd)
25. └─dplyr (local) `<fn>`(`<rlng_rrr>`)
26. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
── Error ('test-checks.R:44'): Check formats and types ─────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `mutate(., across(everything(), function(x) {
attr(x, "label") <- NULL
x
}))`: ℹ In argument: `across(...)`.
ℹ In group 2: `var1 = "BASE"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
▆
1. ├─metacore::check_inconsistent_types(metacore) at test-checks.R:44:3
2. │ └─metacore:::basic_check(type, metacore)
3. │ └─... %>% select(variable = var1, everything())
4. ├─dplyr::select(., variable = var1, everything())
5. ├─dplyr::summarise(...)
6. ├─dplyr::group_by(...)
7. ├─dplyr::mutate(...)
8. ├─dplyr:::mutate.data.frame(...)
9. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
10. │ ├─base::withCallingHandlers(...)
11. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
12. │ ├─base::withCallingHandlers(...)
13. │ └─mask$eval_all_mutate(quo)
14. │ └─dplyr (local) eval()
15. ├─dplyr:::dplyr_internal_error(...)
16. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
17. │ └─rlang:::signal_abort(cnd, .file)
18. │ └─base::signalCondition(cnd)
19. ├─dplyr (local) `<fn>`(`<dpl:::__>`)
20. │ └─rlang::abort(msg, call = call("across"), parent = cnd)
21. │ └─rlang:::signal_abort(cnd, .file)
22. │ └─base::signalCondition(cnd)
23. └─dplyr (local) `<fn>`(`<rlng_rrr>`)
24. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 67 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.1
Check: examples
Result: ERROR
Running examples in ‘metacore-Ex.R’ failed
The error most likely occurred in:
> ### Name: check_inconsistent_labels
> ### Title: Optional checks to consistency of metadata
> ### Aliases: check_inconsistent_labels check_inconsistent_types
> ### check_inconsistent_formats
>
> ### ** Examples
>
> ## EXAMPLE WITH DUPLICATES
> # Loads in a metacore obj called metacore
> load(metacore_example("pilot_ADaM.rda"))
> check_inconsistent_labels(metacore)
Error in `mutate()`:
ℹ In argument: `across(...)`.
ℹ In group 3: `var1 = "CHG"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
▆
1. ├─metacore::check_inconsistent_labels(metacore)
2. │ └─metacore:::basic_check(label, metacore)
3. │ └─... %>% select(variable = var1, everything())
4. ├─dplyr::select(., variable = var1, everything())
5. ├─dplyr::summarise(...)
6. ├─dplyr::group_by(...)
7. ├─dplyr::mutate(...)
8. ├─dplyr:::mutate.data.frame(...)
9. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
10. │ ├─base::withCallingHandlers(...)
11. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
12. │ ├─base::withCallingHandlers(...)
13. │ └─mask$eval_all_mutate(quo)
14. │ └─dplyr (local) eval()
15. └─dplyr:::dplyr_internal_error("dplyr:::mutate_incompatible_size", `<named list>`)
16. └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64
Version: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [238s/450s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(metacore)
>
> test_check("metacore")
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 67 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-checks.R:16'): Test label Checks ───────────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `mutate(., across(everything(), function(x) {
attr(x, "label") <- NULL
x
}))`: ℹ In argument: `across(...)`.
ℹ In group 3: `var1 = "CHG"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
▆
1. ├─check_inconsistent_labels(metacore) %>% ... at test-checks.R:16:3
2. ├─dplyr::arrange(., variable, label)
3. ├─metacore::check_inconsistent_labels(metacore)
4. │ └─metacore:::basic_check(label, metacore)
5. │ └─... %>% select(variable = var1, everything())
6. ├─dplyr::select(., variable = var1, everything())
7. ├─dplyr::summarise(...)
8. ├─dplyr::group_by(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr:::mutate.data.frame(...)
11. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
12. │ ├─base::withCallingHandlers(...)
13. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
14. │ ├─base::withCallingHandlers(...)
15. │ └─mask$eval_all_mutate(quo)
16. │ └─dplyr (local) eval()
17. ├─dplyr:::dplyr_internal_error(...)
18. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
19. │ └─rlang:::signal_abort(cnd, .file)
20. │ └─base::signalCondition(cnd)
21. ├─dplyr (local) `<fn>`(`<dpl:::__>`)
22. │ └─rlang::abort(msg, call = call("across"), parent = cnd)
23. │ └─rlang:::signal_abort(cnd, .file)
24. │ └─base::signalCondition(cnd)
25. └─dplyr (local) `<fn>`(`<rlng_rrr>`)
26. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
── Error ('test-checks.R:44'): Check formats and types ─────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `mutate(., across(everything(), function(x) {
attr(x, "label") <- NULL
x
}))`: ℹ In argument: `across(...)`.
ℹ In group 2: `var1 = "BASE"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
▆
1. ├─metacore::check_inconsistent_types(metacore) at test-checks.R:44:3
2. │ └─metacore:::basic_check(type, metacore)
3. │ └─... %>% select(variable = var1, everything())
4. ├─dplyr::select(., variable = var1, everything())
5. ├─dplyr::summarise(...)
6. ├─dplyr::group_by(...)
7. ├─dplyr::mutate(...)
8. ├─dplyr:::mutate.data.frame(...)
9. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
10. │ ├─base::withCallingHandlers(...)
11. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
12. │ ├─base::withCallingHandlers(...)
13. │ └─mask$eval_all_mutate(quo)
14. │ └─dplyr (local) eval()
15. ├─dplyr:::dplyr_internal_error(...)
16. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
17. │ └─rlang:::signal_abort(cnd, .file)
18. │ └─base::signalCondition(cnd)
19. ├─dplyr (local) `<fn>`(`<dpl:::__>`)
20. │ └─rlang::abort(msg, call = call("across"), parent = cnd)
21. │ └─rlang:::signal_abort(cnd, .file)
22. │ └─base::signalCondition(cnd)
23. └─dplyr (local) `<fn>`(`<rlng_rrr>`)
24. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 67 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [239s/288s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(metacore)
>
> test_check("metacore")
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 67 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-checks.R:16'): Test label Checks ───────────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `mutate(., across(everything(), function(x) {
attr(x, "label") <- NULL
x
}))`: ℹ In argument: `across(...)`.
ℹ In group 3: `var1 = "CHG"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
▆
1. ├─check_inconsistent_labels(metacore) %>% ... at test-checks.R:16:3
2. ├─dplyr::arrange(., variable, label)
3. ├─metacore::check_inconsistent_labels(metacore)
4. │ └─metacore:::basic_check(label, metacore)
5. │ └─... %>% select(variable = var1, everything())
6. ├─dplyr::select(., variable = var1, everything())
7. ├─dplyr::summarise(...)
8. ├─dplyr::group_by(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr:::mutate.data.frame(...)
11. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
12. │ ├─base::withCallingHandlers(...)
13. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
14. │ ├─base::withCallingHandlers(...)
15. │ └─mask$eval_all_mutate(quo)
16. │ └─dplyr (local) eval()
17. ├─dplyr:::dplyr_internal_error(...)
18. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
19. │ └─rlang:::signal_abort(cnd, .file)
20. │ └─base::signalCondition(cnd)
21. ├─dplyr (local) `<fn>`(`<dpl:::__>`)
22. │ └─rlang::abort(msg, call = call("across"), parent = cnd)
23. │ └─rlang:::signal_abort(cnd, .file)
24. │ └─base::signalCondition(cnd)
25. └─dplyr (local) `<fn>`(`<rlng_rrr>`)
26. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
── Error ('test-checks.R:44'): Check formats and types ─────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `mutate(., across(everything(), function(x) {
attr(x, "label") <- NULL
x
}))`: ℹ In argument: `across(...)`.
ℹ In group 2: `var1 = "BASE"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
▆
1. ├─metacore::check_inconsistent_types(metacore) at test-checks.R:44:3
2. │ └─metacore:::basic_check(type, metacore)
3. │ └─... %>% select(variable = var1, everything())
4. ├─dplyr::select(., variable = var1, everything())
5. ├─dplyr::summarise(...)
6. ├─dplyr::group_by(...)
7. ├─dplyr::mutate(...)
8. ├─dplyr:::mutate.data.frame(...)
9. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
10. │ ├─base::withCallingHandlers(...)
11. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
12. │ ├─base::withCallingHandlers(...)
13. │ └─mask$eval_all_mutate(quo)
14. │ └─dplyr (local) eval()
15. ├─dplyr:::dplyr_internal_error(...)
16. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
17. │ └─rlang:::signal_abort(cnd, .file)
18. │ └─base::signalCondition(cnd)
19. ├─dplyr (local) `<fn>`(`<dpl:::__>`)
20. │ └─rlang::abort(msg, call = call("across"), parent = cnd)
21. │ └─rlang:::signal_abort(cnd, .file)
22. │ └─base::signalCondition(cnd)
23. └─dplyr (local) `<fn>`(`<rlng_rrr>`)
24. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 67 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.1
Check: tests
Result: ERROR
Running 'testthat.R' [204s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(metacore)
>
> test_check("metacore")
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 67 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-checks.R:16'): Test label Checks ───────────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `mutate(., across(everything(), function(x) {
attr(x, "label") <- NULL
x
}))`: ℹ In argument: `across(...)`.
ℹ In group 3: `var1 = "CHG"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
▆
1. ├─check_inconsistent_labels(metacore) %>% ... at test-checks.R:16:3
2. ├─dplyr::arrange(., variable, label)
3. ├─metacore::check_inconsistent_labels(metacore)
4. │ └─metacore:::basic_check(label, metacore)
5. │ └─... %>% select(variable = var1, everything())
6. ├─dplyr::select(., variable = var1, everything())
7. ├─dplyr::summarise(...)
8. ├─dplyr::group_by(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr:::mutate.data.frame(...)
11. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
12. │ ├─base::withCallingHandlers(...)
13. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
14. │ ├─base::withCallingHandlers(...)
15. │ └─mask$eval_all_mutate(quo)
16. │ └─dplyr (local) eval()
17. ├─dplyr:::dplyr_internal_error(...)
18. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
19. │ └─rlang:::signal_abort(cnd, .file)
20. │ └─base::signalCondition(cnd)
21. ├─dplyr (local) `<fn>`(`<dpl:::__>`)
22. │ └─rlang::abort(msg, call = call("across"), parent = cnd)
23. │ └─rlang:::signal_abort(cnd, .file)
24. │ └─base::signalCondition(cnd)
25. └─dplyr (local) `<fn>`(`<rlng_rrr>`)
26. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
── Error ('test-checks.R:44'): Check formats and types ─────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `mutate(., across(everything(), function(x) {
attr(x, "label") <- NULL
x
}))`: ℹ In argument: `across(...)`.
ℹ In group 2: `var1 = "BASE"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
▆
1. ├─metacore::check_inconsistent_types(metacore) at test-checks.R:44:3
2. │ └─metacore:::basic_check(type, metacore)
3. │ └─... %>% select(variable = var1, everything())
4. ├─dplyr::select(., variable = var1, everything())
5. ├─dplyr::summarise(...)
6. ├─dplyr::group_by(...)
7. ├─dplyr::mutate(...)
8. ├─dplyr:::mutate.data.frame(...)
9. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
10. │ ├─base::withCallingHandlers(...)
11. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
12. │ ├─base::withCallingHandlers(...)
13. │ └─mask$eval_all_mutate(quo)
14. │ └─dplyr (local) eval()
15. ├─dplyr:::dplyr_internal_error(...)
16. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
17. │ └─rlang:::signal_abort(cnd, .file)
18. │ └─base::signalCondition(cnd)
19. ├─dplyr (local) `<fn>`(`<dpl:::__>`)
20. │ └─rlang::abort(msg, call = call("across"), parent = cnd)
21. │ └─rlang:::signal_abort(cnd, .file)
22. │ └─base::signalCondition(cnd)
23. └─dplyr (local) `<fn>`(`<rlng_rrr>`)
24. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 67 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [191s/226s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(metacore)
>
> test_check("metacore")
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 67 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-checks.R:16'): Test label Checks ───────────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `mutate(., across(everything(), function(x) {
attr(x, "label") <- NULL
x
}))`: ℹ In argument: `across(...)`.
ℹ In group 3: `var1 = "CHG"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
▆
1. ├─check_inconsistent_labels(metacore) %>% ... at test-checks.R:16:3
2. ├─dplyr::arrange(., variable, label)
3. ├─metacore::check_inconsistent_labels(metacore)
4. │ └─metacore:::basic_check(label, metacore)
5. │ └─... %>% select(variable = var1, everything())
6. ├─dplyr::select(., variable = var1, everything())
7. ├─dplyr::summarise(...)
8. ├─dplyr::group_by(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr:::mutate.data.frame(...)
11. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
12. │ ├─base::withCallingHandlers(...)
13. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
14. │ ├─base::withCallingHandlers(...)
15. │ └─mask$eval_all_mutate(quo)
16. │ └─dplyr (local) eval()
17. ├─dplyr:::dplyr_internal_error(...)
18. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
19. │ └─rlang:::signal_abort(cnd, .file)
20. │ └─base::signalCondition(cnd)
21. ├─dplyr (local) `<fn>`(`<dpl:::__>`)
22. │ └─rlang::abort(msg, call = call("across"), parent = cnd)
23. │ └─rlang:::signal_abort(cnd, .file)
24. │ └─base::signalCondition(cnd)
25. └─dplyr (local) `<fn>`(`<rlng_rrr>`)
26. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
── Error ('test-checks.R:44'): Check formats and types ─────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `mutate(., across(everything(), function(x) {
attr(x, "label") <- NULL
x
}))`: ℹ In argument: `across(...)`.
ℹ In group 2: `var1 = "BASE"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
▆
1. ├─metacore::check_inconsistent_types(metacore) at test-checks.R:44:3
2. │ └─metacore:::basic_check(type, metacore)
3. │ └─... %>% select(variable = var1, everything())
4. ├─dplyr::select(., variable = var1, everything())
5. ├─dplyr::summarise(...)
6. ├─dplyr::group_by(...)
7. ├─dplyr::mutate(...)
8. ├─dplyr:::mutate.data.frame(...)
9. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
10. │ ├─base::withCallingHandlers(...)
11. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
12. │ ├─base::withCallingHandlers(...)
13. │ └─mask$eval_all_mutate(quo)
14. │ └─dplyr (local) eval()
15. ├─dplyr:::dplyr_internal_error(...)
16. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
17. │ └─rlang:::signal_abort(cnd, .file)
18. │ └─base::signalCondition(cnd)
19. ├─dplyr (local) `<fn>`(`<dpl:::__>`)
20. │ └─rlang::abort(msg, call = call("across"), parent = cnd)
21. │ └─rlang:::signal_abort(cnd, .file)
22. │ └─base::signalCondition(cnd)
23. └─dplyr (local) `<fn>`(`<rlng_rrr>`)
24. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 67 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [196s/248s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(metacore)
>
> test_check("metacore")
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 67 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-checks.R:16'): Test label Checks ───────────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `mutate(., across(everything(), function(x) {
attr(x, "label") <- NULL
x
}))`: ℹ In argument: `across(...)`.
ℹ In group 3: `var1 = "CHG"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
▆
1. ├─check_inconsistent_labels(metacore) %>% ... at test-checks.R:16:3
2. ├─dplyr::arrange(., variable, label)
3. ├─metacore::check_inconsistent_labels(metacore)
4. │ └─metacore:::basic_check(label, metacore)
5. │ └─... %>% select(variable = var1, everything())
6. ├─dplyr::select(., variable = var1, everything())
7. ├─dplyr::summarise(...)
8. ├─dplyr::group_by(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr:::mutate.data.frame(...)
11. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
12. │ ├─base::withCallingHandlers(...)
13. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
14. │ ├─base::withCallingHandlers(...)
15. │ └─mask$eval_all_mutate(quo)
16. │ └─dplyr (local) eval()
17. ├─dplyr:::dplyr_internal_error(...)
18. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
19. │ └─rlang:::signal_abort(cnd, .file)
20. │ └─base::signalCondition(cnd)
21. ├─dplyr (local) `<fn>`(`<dpl:::__>`)
22. │ └─rlang::abort(msg, call = call("across"), parent = cnd)
23. │ └─rlang:::signal_abort(cnd, .file)
24. │ └─base::signalCondition(cnd)
25. └─dplyr (local) `<fn>`(`<rlng_rrr>`)
26. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
── Error ('test-checks.R:44'): Check formats and types ─────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `mutate(., across(everything(), function(x) {
attr(x, "label") <- NULL
x
}))`: ℹ In argument: `across(...)`.
ℹ In group 2: `var1 = "BASE"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
▆
1. ├─metacore::check_inconsistent_types(metacore) at test-checks.R:44:3
2. │ └─metacore:::basic_check(type, metacore)
3. │ └─... %>% select(variable = var1, everything())
4. ├─dplyr::select(., variable = var1, everything())
5. ├─dplyr::summarise(...)
6. ├─dplyr::group_by(...)
7. ├─dplyr::mutate(...)
8. ├─dplyr:::mutate.data.frame(...)
9. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
10. │ ├─base::withCallingHandlers(...)
11. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
12. │ ├─base::withCallingHandlers(...)
13. │ └─mask$eval_all_mutate(quo)
14. │ └─dplyr (local) eval()
15. ├─dplyr:::dplyr_internal_error(...)
16. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
17. │ └─rlang:::signal_abort(cnd, .file)
18. │ └─base::signalCondition(cnd)
19. ├─dplyr (local) `<fn>`(`<dpl:::__>`)
20. │ └─rlang::abort(msg, call = call("across"), parent = cnd)
21. │ └─rlang:::signal_abort(cnd, .file)
22. │ └─base::signalCondition(cnd)
23. └─dplyr (local) `<fn>`(`<rlng_rrr>`)
24. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 67 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.1.1
Check: examples
Result: ERROR
Running examples in 'metacore-Ex.R' failed
The error most likely occurred in:
> ### Name: check_inconsistent_labels
> ### Title: Optional checks to consistency of metadata
> ### Aliases: check_inconsistent_labels check_inconsistent_types
> ### check_inconsistent_formats
>
> ### ** Examples
>
> ## EXAMPLE WITH DUPLICATES
> # Loads in a metacore obj called metacore
> load(metacore_example("pilot_ADaM.rda"))
> check_inconsistent_labels(metacore)
Error in `mutate()`:
i In argument: `across(...)`.
i In group 3: `var1 = "CHG"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
x
1. +-metacore::check_inconsistent_labels(metacore)
2. | \-metacore:::basic_check(label, metacore)
3. | \-... %>% select(variable = var1, everything())
4. +-dplyr::select(., variable = var1, everything())
5. +-dplyr::summarise(...)
6. +-dplyr::group_by(...)
7. +-dplyr::mutate(...)
8. +-dplyr:::mutate.data.frame(...)
9. | \-dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
10. | +-base::withCallingHandlers(...)
11. | \-dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
12. | +-base::withCallingHandlers(...)
13. | \-mask$eval_all_mutate(quo)
14. | \-dplyr (local) eval()
15. \-dplyr:::dplyr_internal_error("dplyr:::mutate_incompatible_size", `<named list>`)
16. \-rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64
Version: 0.1.1
Check: tests
Result: ERROR
Running 'testthat.R' [221s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(metacore)
>
> test_check("metacore")
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 67 ]
== Failed tests ================================================================
-- Error ('test-checks.R:16'): Test label Checks -------------------------------
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `mutate(., across(everything(), function(x) {
attr(x, "label") <- NULL
x
}))`: i In argument: `across(...)`.
i In group 3: `var1 = "CHG"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
x
1. +-check_inconsistent_labels(metacore) %>% ... at test-checks.R:16:3
2. +-dplyr::arrange(., variable, label)
3. +-metacore::check_inconsistent_labels(metacore)
4. | \-metacore:::basic_check(label, metacore)
5. | \-... %>% select(variable = var1, everything())
6. +-dplyr::select(., variable = var1, everything())
7. +-dplyr::summarise(...)
8. +-dplyr::group_by(...)
9. +-dplyr::mutate(...)
10. +-dplyr:::mutate.data.frame(...)
11. | \-dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
12. | +-base::withCallingHandlers(...)
13. | \-dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
14. | +-base::withCallingHandlers(...)
15. | \-mask$eval_all_mutate(quo)
16. | \-dplyr (local) eval()
17. +-dplyr:::dplyr_internal_error(...)
18. | \-rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
19. | \-rlang:::signal_abort(cnd, .file)
20. | \-base::signalCondition(cnd)
21. +-dplyr (local) `<fn>`(`<dpl:::__>`)
22. | \-rlang::abort(msg, call = call("across"), parent = cnd)
23. | \-rlang:::signal_abort(cnd, .file)
24. | \-base::signalCondition(cnd)
25. \-dplyr (local) `<fn>`(`<rlng_rrr>`)
26. \-rlang::abort(message, class = error_class, parent = parent, call = error_call)
-- Error ('test-checks.R:44'): Check formats and types -------------------------
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `mutate(., across(everything(), function(x) {
attr(x, "label") <- NULL
x
}))`: i In argument: `across(...)`.
i In group 2: `var1 = "BASE"`.
Caused by error in `across()`:
! Can't compute column `variable`.
Caused by error in `dplyr_internal_error()`:
Backtrace:
x
1. +-metacore::check_inconsistent_types(metacore) at test-checks.R:44:3
2. | \-metacore:::basic_check(type, metacore)
3. | \-... %>% select(variable = var1, everything())
4. +-dplyr::select(., variable = var1, everything())
5. +-dplyr::summarise(...)
6. +-dplyr::group_by(...)
7. +-dplyr::mutate(...)
8. +-dplyr:::mutate.data.frame(...)
9. | \-dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
10. | +-base::withCallingHandlers(...)
11. | \-dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
12. | +-base::withCallingHandlers(...)
13. | \-mask$eval_all_mutate(quo)
14. | \-dplyr (local) eval()
15. +-dplyr:::dplyr_internal_error(...)
16. | \-rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
17. | \-rlang:::signal_abort(cnd, .file)
18. | \-base::signalCondition(cnd)
19. +-dplyr (local) `<fn>`(`<dpl:::__>`)
20. | \-rlang::abort(msg, call = call("across"), parent = cnd)
21. | \-rlang:::signal_abort(cnd, .file)
22. | \-base::signalCondition(cnd)
23. \-dplyr (local) `<fn>`(`<rlng_rrr>`)
24. \-rlang::abort(message, class = error_class, parent = parent, call = error_call)
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 67 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64