Last updated on 2026-02-03 22:49:51 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3.4 | 17.89 | 302.66 | 320.55 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.3.4 | 12.75 | 103.51 | 116.26 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.3.4 | 28.00 | 229.65 | 257.65 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.3.4 | 28.00 | 238.28 | 266.28 | ERROR | |
| r-devel-windows-x86_64 | 1.3.4 | 21.00 | 352.00 | 373.00 | OK | |
| r-patched-linux-x86_64 | 1.3.4 | 16.93 | 289.41 | 306.34 | OK | |
| r-release-linux-x86_64 | 1.3.4 | 14.90 | 290.69 | 305.59 | OK | |
| r-release-macos-arm64 | 1.3.4 | OK | ||||
| r-release-macos-x86_64 | 1.3.4 | 10.00 | 306.00 | 316.00 | OK | |
| r-release-windows-x86_64 | 1.3.4 | 19.00 | 348.00 | 367.00 | OK | |
| r-oldrel-macos-arm64 | 1.3.4 | OK | ||||
| r-oldrel-macos-x86_64 | 1.3.4 | 10.00 | 305.00 | 315.00 | OK | |
| r-oldrel-windows-x86_64 | 1.3.4 | 25.00 | 424.00 | 449.00 | OK |
Version: 1.3.4
Check: examples
Result: ERROR
Running examples in ‘eHDPrep-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: apply_quality_ctrl
> ### Title: Apply quality control measures to a dataset
> ### Aliases: apply_quality_ctrl
>
> ### ** Examples
>
> data(example_data)
> require(tibble)
Loading required package: tibble
>
> # create an example class_tbl object
> # note that diabetes_type is classes as ordinal and is not modified as its
> # levels are not pre-coded
> tibble::tribble(~"var", ~"datatype",
+ "patient_id", "id",
+ "tumoursize", "numeric",
+ "t_stage", "ordinal_tstage",
+ "n_stage", "ordinal_nstage",
+ "diabetes", "factor",
+ "diabetes_type", "ordinal",
+ "hypertension", "factor",
+ "rural_urban", "factor",
+ "marital_status", "factor",
+ "SNP_a", "genotype",
+ "SNP_b", "genotype",
+ "free_text", "freetext") -> data_types
>
> data_QC <- apply_quality_ctrl(example_data, patient_id, data_types,
+ bin_cats =c("No" = "Yes", "rural" = "urban"), min_freq = 0.6)
Error in `dplyr::summarise()`:
ℹ In argument: `dplyr::across(everything(), ~!.x %in% ord_levels)`.
Caused by error:
! `dplyr::across(everything(), ~!.x %in% ord_levels)` must be size 1,
not 1000.
ℹ To return more or less than 1 row per group, use `reframe()`.
Backtrace:
▆
1. ├─eHDPrep::apply_quality_ctrl(...)
2. │ └─... %>% suppressWarnings()
3. ├─base::suppressWarnings(.)
4. │ └─base::withCallingHandlers(...)
5. ├─eHDPrep::encode_cats(...)
6. │ └─dplyr::select(data, !!!dplyr::enquos(...))
7. ├─base::suppressMessages(.)
8. │ └─base::withCallingHandlers(...)
9. ├─eHDPrep::encode_genotypes(...)
10. │ └─data %>% ...
11. ├─dplyr::mutate(., dplyr::across(c(!!!vars), encode_genotype_vec))
12. ├─eHDPrep::encode_ordinals(...)
13. │ └─... %>% dplyr::filter(.data$value > 0)
14. ├─dplyr::filter(., .data$value > 0)
15. ├─tidyr::pivot_longer(., dplyr::everything())
16. ├─dplyr::summarise(., dplyr::across(c(!!!vars), sum))
17. ├─dplyr::summarise(., dplyr::across(everything(), ~!.x %in% ord_levels))
18. ├─dplyr::select(., !!!vars)
19. ├─eHDPrep::encode_ordinals(...)
20. │ └─... %>% dplyr::filter(.data$value > 0)
21. ├─dplyr::filter(., .data$value > 0)
22. ├─tidyr::pivot_longer(., dplyr::everything())
23. ├─dplyr::summarise(., dplyr::across(c(!!!vars), sum))
24. ├─dplyr::summarise(., dplyr::across(everything(), ~!.x %in% ord_levels))
25. ├─dplyr:::summarise.data.frame(., dplyr::across(everything(), ~!.x %in% ord_levels))
26. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
27. │ └─base::withCallingHandlers(...)
28. ├─dplyr:::dplyr_internal_error(...)
29. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
30. │ └─rlang:::signal_abort(cnd, .file)
31. │ └─base::signalCondition(cnd)
32. └─dplyr (local) `<fn>`(`<dpl:::__>`)
33. └─dplyr (local) handler(cnd)
34. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Introduction_to_eHDPrep.Rmd’ using rmarkdown
Quitting from Introduction_to_eHDPrep.Rmd:245-252 [unnamed-chunk-14]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `dplyr::summarise()`:
i In argument: `dplyr::across(everything(), ~!.x %in% ord_levels)`.
Caused by error:
! `dplyr::across(everything(), ~!.x %in% ord_levels)` must be size 1,
not 1000.
i To return more or less than 1 row per group, use `reframe()`.
---
Backtrace:
x
1. +-eHDPrep::apply_quality_ctrl(...)
2. | \-... %>% suppressWarnings()
3. +-base::suppressWarnings(.)
4. | \-base::withCallingHandlers(...)
5. +-eHDPrep::encode_cats(...)
6. | \-dplyr::select(data, !!!dplyr::enquos(...))
7. +-base::suppressMessages(.)
8. | \-base::withCallingHandlers(...)
9. +-eHDPrep::encode_genotypes(...)
10. | \-data %>% ...
11. +-dplyr::mutate(., dplyr::across(c(!!!vars), encode_genotype_vec))
12. +-eHDPrep::encode_ordinals(...)
13. | \-... %>% dplyr::filter(.data$value > 0)
14. +-dplyr::filter(., .data$value > 0)
15. +-tidyr::pivot_longer(., dplyr::everything())
16. +-dplyr::summarise(., dplyr::across(c(!!!vars), sum))
17. +-dplyr::summarise(., dplyr::across(everything(), ~!.x %in% ord_levels))
18. +-dplyr::select(., !!!vars)
19. +-eHDPrep::encode_ordinals(...)
20. | \-... %>% dplyr::filter(.data$value > 0)
21. +-dplyr::filter(., .data$value > 0)
22. +-tidyr::pivot_longer(., dplyr::everything())
23. +-dplyr::summarise(., dplyr::across(c(!!!vars), sum))
24. +-dplyr::summarise(., dplyr::across(everything(), ~!.x %in% ord_levels))
25. +-dplyr:::summarise.data.frame(., dplyr::across(everything(), ~!.x %in% ord_levels))
26. | \-dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
27. | \-base::withCallingHandlers(...)
28. \-dplyr:::dplyr_internal_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Introduction_to_eHDPrep.Rmd' failed with diagnostics:
ℹ In argument: `dplyr::across(everything(), ~!.x %in% ord_levels)`.
Caused by error:
! `dplyr::across(everything(), ~!.x %in% ord_levels)` must be size 1,
not 1000.
ℹ To return more or less than 1 row per group, use `reframe()`.
--- failed re-building ‘Introduction_to_eHDPrep.Rmd’
SUMMARY: processing the following file failed:
‘Introduction_to_eHDPrep.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.4
Check: examples
Result: ERROR
Running examples in ‘eHDPrep-Ex.R’ failed
The error most likely occurred in:
> ### Name: apply_quality_ctrl
> ### Title: Apply quality control measures to a dataset
> ### Aliases: apply_quality_ctrl
>
> ### ** Examples
>
> data(example_data)
> require(tibble)
Loading required package: tibble
>
> # create an example class_tbl object
> # note that diabetes_type is classes as ordinal and is not modified as its
> # levels are not pre-coded
> tibble::tribble(~"var", ~"datatype",
+ "patient_id", "id",
+ "tumoursize", "numeric",
+ "t_stage", "ordinal_tstage",
+ "n_stage", "ordinal_nstage",
+ "diabetes", "factor",
+ "diabetes_type", "ordinal",
+ "hypertension", "factor",
+ "rural_urban", "factor",
+ "marital_status", "factor",
+ "SNP_a", "genotype",
+ "SNP_b", "genotype",
+ "free_text", "freetext") -> data_types
>
> data_QC <- apply_quality_ctrl(example_data, patient_id, data_types,
+ bin_cats =c("No" = "Yes", "rural" = "urban"), min_freq = 0.6)
Error in `dplyr::summarise()`:
ℹ In argument: `dplyr::across(everything(), ~!.x %in% ord_levels)`.
Caused by error:
! `dplyr::across(everything(), ~!.x %in% ord_levels)` must be size 1,
not 1000.
ℹ To return more or less than 1 row per group, use `reframe()`.
Backtrace:
▆
1. ├─eHDPrep::apply_quality_ctrl(...)
2. │ └─... %>% suppressWarnings()
3. ├─base::suppressWarnings(.)
4. │ └─base::withCallingHandlers(...)
5. ├─eHDPrep::encode_cats(...)
6. │ └─dplyr::select(data, !!!dplyr::enquos(...))
7. ├─base::suppressMessages(.)
8. │ └─base::withCallingHandlers(...)
9. ├─eHDPrep::encode_genotypes(...)
10. │ └─data %>% ...
11. ├─dplyr::mutate(., dplyr::across(c(!!!vars), encode_genotype_vec))
12. ├─eHDPrep::encode_ordinals(...)
13. │ └─... %>% dplyr::filter(.data$value > 0)
14. ├─dplyr::filter(., .data$value > 0)
15. ├─tidyr::pivot_longer(., dplyr::everything())
16. ├─dplyr::summarise(., dplyr::across(c(!!!vars), sum))
17. ├─dplyr::summarise(., dplyr::across(everything(), ~!.x %in% ord_levels))
18. ├─dplyr::select(., !!!vars)
19. ├─eHDPrep::encode_ordinals(...)
20. │ └─... %>% dplyr::filter(.data$value > 0)
21. ├─dplyr::filter(., .data$value > 0)
22. ├─tidyr::pivot_longer(., dplyr::everything())
23. ├─dplyr::summarise(., dplyr::across(c(!!!vars), sum))
24. ├─dplyr::summarise(., dplyr::across(everything(), ~!.x %in% ord_levels))
25. ├─dplyr:::summarise.data.frame(., dplyr::across(everything(), ~!.x %in% ord_levels))
26. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
27. │ └─base::withCallingHandlers(...)
28. ├─dplyr:::dplyr_internal_error(...)
29. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
30. │ └─rlang:::signal_abort(cnd, .file)
31. │ └─base::signalCondition(cnd)
32. └─dplyr (local) `<fn>`(`<dpl:::__>`)
33. └─dplyr (local) handler(cnd)
34. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.3.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Introduction_to_eHDPrep.Rmd’ using rmarkdown
Quitting from Introduction_to_eHDPrep.Rmd:245-252 [unnamed-chunk-14]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `dplyr::summarise()`:
i In argument: `dplyr::across(everything(), ~!.x %in% ord_levels)`.
Caused by error:
! `dplyr::across(everything(), ~!.x %in% ord_levels)` must be size 1,
not 1000.
i To return more or less than 1 row per group, use `reframe()`.
---
Backtrace:
x
1. +-eHDPrep::apply_quality_ctrl(...)
2. | \-... %>% suppressWarnings()
3. +-base::suppressWarnings(.)
4. | \-base::withCallingHandlers(...)
5. +-eHDPrep::encode_cats(...)
6. | \-dplyr::select(data, !!!dplyr::enquos(...))
7. +-base::suppressMessages(.)
8. | \-base::withCallingHandlers(...)
9. +-eHDPrep::encode_genotypes(...)
10. | \-data %>% ...
11. +-dplyr::mutate(., dplyr::across(c(!!!vars), encode_genotype_vec))
12. +-eHDPrep::encode_ordinals(...)
13. | \-... %>% dplyr::filter(.data$value > 0)
14. +-dplyr::filter(., .data$value > 0)
15. +-tidyr::pivot_longer(., dplyr::everything())
16. +-dplyr::summarise(., dplyr::across(c(!!!vars), sum))
17. +-dplyr::summarise(., dplyr::across(everything(), ~!.x %in% ord_levels))
18. +-dplyr::select(., !!!vars)
19. +-eHDPrep::encode_ordinals(...)
20. | \-... %>% dplyr::filter(.data$value > 0)
21. +-dplyr::filter(., .data$value > 0)
22. +-tidyr::pivot_longer(., dplyr::everything())
23. +-dplyr::summarise(., dplyr::across(c(!!!vars), sum))
24. +-dplyr::summarise(., dplyr::across(everything(), ~!.x %in% ord_levels))
25. +-dplyr:::summarise.data.frame(., dplyr::across(everything(), ~!.x %in% ord_levels))
26. | \-dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
27. | \-base::withCallingHandlers(...)
28. \-dplyr:::dplyr_internal_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Introduction_to_eHDPrep.Rmd' failed with diagnostics:
ℹ In argument: `dplyr::across(everything(), ~!.x %in% ord_levels)`.
Caused by error:
! `dplyr::across(everything(), ~!.x %in% ord_levels)` must be size 1,
not 1000.
ℹ To return more or less than 1 row per group, use `reframe()`.
--- failed re-building ‘Introduction_to_eHDPrep.Rmd’
SUMMARY: processing the following file failed:
‘Introduction_to_eHDPrep.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc