Last updated on 2026-02-15 09:51:11 CET.
| Package | ERROR | OK |
|---|---|---|
| batchtma | 9 | 5 |
| rifttable | 14 | |
| risks | 14 |
Current CRAN status: ERROR: 9, OK: 5
Version: 0.1.6
Check: examples
Result: ERROR
Running examples in ‘batchtma-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adjust_batch
> ### Title: Adjust for batch effects
> ### Aliases: adjust_batch
>
> ### ** Examples
>
> # Data frame with two batches
> # Batch 2 has higher values of biomarker and confounder
> df <- data.frame(
+ tma = rep(1:2, times = 10),
+ biomarker = rep(1:2, times = 10) +
+ runif(max = 5, n = 20),
+ confounder = rep(0:1, times = 10) +
+ runif(max = 10, n = 20)
+ )
>
> # Adjust for batch effects
> # Using simple means, ignoring the confounder:
> adjust_batch(
+ data = df,
+ markers = biomarker,
+ batch = tma,
+ method = simple
+ )
tma biomarker confounder biomarker_adj2
1 1 2.327543 9.3470523 2.916216
2 2 3.860619 3.1214252 3.271947
3 1 3.864267 6.5167377 4.452939
4 2 6.541039 2.2555510 5.952366
5 1 2.008410 2.6722067 2.597082
6 2 6.491948 4.8611409 5.903276
7 1 5.723376 0.1339033 6.312049
8 2 5.303989 4.8238796 4.715316
9 1 4.145570 8.6969085 4.734243
10 2 2.308931 4.4034900 1.720259
11 1 2.029873 4.8208012 2.618546
12 2 2.882784 6.9956583 2.294111
13 1 4.435114 4.9354131 5.023787
14 2 3.920519 2.8621760 3.331846
15 1 4.849207 8.2737332 5.437880
16 2 4.488496 7.6846674 3.899824
17 1 4.588093 7.9423986 5.176765
18 2 6.959530 2.0794363 6.370858
19 1 2.900176 7.2371095 3.488849
20 2 5.887226 5.1127443 5.298553
> # Returns data set with new variable "biomarker_adj2"
>
> # Use quantile regression, include the confounder,
> # change suffix of returned variable:
> adjust_batch(
+ data = df,
+ markers = biomarker,
+ batch = tma,
+ method = quantreg,
+ confounders = confounder,
+ suffix = "_batchadjusted"
+ )
Error in `purrr::map()`:
ℹ In index: 1.
Caused by error in `dplyr::filter()`:
ℹ In argument: `dplyr::across(dplyr::all_of("confounder"),
~!is.na(.x))`.
Caused by error:
! `..1` must be a logical vector, not a <tbl_df/tbl/data.frame> object.
ℹ If you used `across()` to generate this data frame, please use `if_any()` or
`if_all()` instead.
Backtrace:
▆
1. ├─batchtma::adjust_batch(...)
2. │ ├─purrr::map(...)
3. │ │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
4. │ │ ├─purrr:::with_indexed_errors(...)
5. │ │ │ └─base::withCallingHandlers(...)
6. │ │ ├─purrr:::call_with_cleanup(...)
7. │ │ └─batchtma (local) .f(.x[[i]], ...)
8. │ │ └─... %>% ...
9. │ └─data %>% ...
10. ├─dplyr::mutate(...)
11. ├─tidyr::nest(., data = dplyr::everything())
12. ├─dplyr::mutate(., .batchvar = factor_drop(.data$.batchvar))
13. ├─dplyr::filter(., !is.na(.data$variable))
14. ├─dplyr::rename(...)
15. ├─dplyr::filter(...)
16. ├─dplyr:::filter.data.frame(...)
17. │ └─dplyr:::filter_impl(...)
18. │ └─dplyr:::filter_rows(...)
19. │ └─dplyr:::filter_eval(...)
20. │ ├─base::withCallingHandlers(...)
21. │ └─mask$eval_all_filter(dots_expanded, invert, env_filter)
22. │ └─dplyr (local) eval()
23. ├─dplyr:::dplyr_internal_error(...)
24. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
25. │ └─rlang:::signal_abort(cnd, .file)
26. │ └─base::signalCondition(cnd)
27. └─dplyr (local) `<fn>`(`<dpl:::__>`)
28. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.1.6
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘batchtma.Rmd’ using rmarkdown
Quitting from batchtma.Rmd:115-120 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/purrr_error_indexed>
Error in `purrr::map()`:
ℹ In index: 1.
Caused by error in `dplyr::filter()`:
ℹ In argument: `dplyr::across(dplyr::all_of(confounders), ~!is.na(.x))`.
Caused by error:
! `..1` must be a logical vector, not a <tbl_df/tbl/data.frame> object.
ℹ If you used `across()` to generate this data frame, please use `if_any()` or
`if_all()` instead.
---
Backtrace:
▆
1. ├─... %>% ...
2. ├─batchtma::plot_batch(...)
3. │ ├─dplyr::n_distinct(...)
4. │ │ └─vctrs::df_list(...)
5. │ │ └─rlang::list2(...)
6. │ └─dplyr::select(...)
7. ├─batchtma::adjust_batch(...)
8. │ └─batchtma:::batchmean_ipw(...)
9. │ ├─purrr::map(...)
10. │ │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
11. │ │ ├─purrr:::with_indexed_errors(...)
12. │ │ │ └─base::withCallingHandlers(...)
13. │ │ ├─purrr:::call_with_cleanup(...)
14. │ │ └─batchtma (local) .f(.x[[i]], ...)
15. │ │ └─... %>% ...
16. │ └─data %>% ...
17. ├─dplyr::mutate(., .batchvar = factor_drop(.data$.batchvar))
18. ├─dplyr::filter(., !is.na(.data$variable))
19. ├─dplyr::rename(., variable = dplyr::one_of(variable))
20. ├─dplyr::filter(., dplyr::across(dplyr::all_of(confounders), ~!is.na(.x)))
21. ├─dplyr:::filter.data.frame(., dplyr::across(dplyr::all_of(confounders), ~!is.na(.x)))
22. │ └─dplyr:::filter_impl(...)
23. │ └─dplyr:::filter_rows(...)
24. │ └─dplyr:::filter_eval(...)
25. │ ├─base::withCallingHandlers(...)
26. │ └─mask$eval_all_filter(dots_expanded, invert, env_filter)
27. │ └─dplyr (local) eval()
28. └─dplyr:::dplyr_internal_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'batchtma.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `dplyr::filter()`:
ℹ In argument: `dplyr::across(dplyr::all_of(confounders), ~!is.na(.x))`.
Caused by error:
! `..1` must be a logical vector, not a <tbl_df/tbl/data.frame> object.
ℹ If you used `across()` to generate this data frame, please use `if_any()` or
`if_all()` instead.
--- failed re-building ‘batchtma.Rmd’
SUMMARY: processing the following file failed:
‘batchtma.Rmd’
Error: Vignette re-building failed.
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: 0.1.6
Check: examples
Result: ERROR
Running examples in ‘batchtma-Ex.R’ failed
The error most likely occurred in:
> ### Name: adjust_batch
> ### Title: Adjust for batch effects
> ### Aliases: adjust_batch
>
> ### ** Examples
>
> # Data frame with two batches
> # Batch 2 has higher values of biomarker and confounder
> df <- data.frame(
+ tma = rep(1:2, times = 10),
+ biomarker = rep(1:2, times = 10) +
+ runif(max = 5, n = 20),
+ confounder = rep(0:1, times = 10) +
+ runif(max = 10, n = 20)
+ )
>
> # Adjust for batch effects
> # Using simple means, ignoring the confounder:
> adjust_batch(
+ data = df,
+ markers = biomarker,
+ batch = tma,
+ method = simple
+ )
tma biomarker confounder biomarker_adj2
1 1 2.327543 9.3470523 2.916216
2 2 3.860619 3.1214252 3.271947
3 1 3.864267 6.5167377 4.452939
4 2 6.541039 2.2555510 5.952366
5 1 2.008410 2.6722067 2.597082
6 2 6.491948 4.8611409 5.903276
7 1 5.723376 0.1339033 6.312049
8 2 5.303989 4.8238796 4.715316
9 1 4.145570 8.6969085 4.734243
10 2 2.308931 4.4034900 1.720259
11 1 2.029873 4.8208012 2.618546
12 2 2.882784 6.9956583 2.294111
13 1 4.435114 4.9354131 5.023787
14 2 3.920519 2.8621760 3.331846
15 1 4.849207 8.2737332 5.437880
16 2 4.488496 7.6846674 3.899824
17 1 4.588093 7.9423986 5.176765
18 2 6.959530 2.0794363 6.370858
19 1 2.900176 7.2371095 3.488849
20 2 5.887226 5.1127443 5.298553
> # Returns data set with new variable "biomarker_adj2"
>
> # Use quantile regression, include the confounder,
> # change suffix of returned variable:
> adjust_batch(
+ data = df,
+ markers = biomarker,
+ batch = tma,
+ method = quantreg,
+ confounders = confounder,
+ suffix = "_batchadjusted"
+ )
Error in `purrr::map()`:
ℹ In index: 1.
Caused by error in `dplyr::filter()`:
ℹ In argument: `dplyr::across(dplyr::all_of("confounder"),
~!is.na(.x))`.
Caused by error:
! `..1` must be a logical vector, not a <tbl_df/tbl/data.frame> object.
ℹ If you used `across()` to generate this data frame, please use `if_any()` or
`if_all()` instead.
Backtrace:
▆
1. ├─batchtma::adjust_batch(...)
2. │ ├─purrr::map(...)
3. │ │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
4. │ │ ├─purrr:::with_indexed_errors(...)
5. │ │ │ └─base::withCallingHandlers(...)
6. │ │ ├─purrr:::call_with_cleanup(...)
7. │ │ └─batchtma (local) .f(.x[[i]], ...)
8. │ │ └─... %>% ...
9. │ └─data %>% ...
10. ├─dplyr::mutate(...)
11. ├─tidyr::nest(., data = dplyr::everything())
12. ├─dplyr::mutate(., .batchvar = factor_drop(.data$.batchvar))
13. ├─dplyr::filter(., !is.na(.data$variable))
14. ├─dplyr::rename(...)
15. ├─dplyr::filter(...)
16. ├─dplyr:::filter.data.frame(...)
17. │ └─dplyr:::filter_impl(...)
18. │ └─dplyr:::filter_rows(...)
19. │ └─dplyr:::filter_eval(...)
20. │ ├─base::withCallingHandlers(...)
21. │ └─mask$eval_all_filter(dots_expanded, invert, env_filter)
22. │ └─dplyr (local) eval()
23. ├─dplyr:::dplyr_internal_error(...)
24. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
25. │ └─rlang:::signal_abort(cnd, .file)
26. │ └─base::signalCondition(cnd)
27. └─dplyr (local) `<fn>`(`<dpl:::__>`)
28. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 0.1.6
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘batchtma.Rmd’ using rmarkdown
Quitting from batchtma.Rmd:115-120 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/purrr_error_indexed>
Error in `purrr::map()`:
ℹ In index: 1.
Caused by error in `dplyr::filter()`:
ℹ In argument: `dplyr::across(dplyr::all_of(confounders), ~!is.na(.x))`.
Caused by error:
! `..1` must be a logical vector, not a <tbl_df/tbl/data.frame> object.
ℹ If you used `across()` to generate this data frame, please use `if_any()` or
`if_all()` instead.
---
Backtrace:
▆
1. ├─... %>% ...
2. ├─batchtma::plot_batch(...)
3. │ ├─dplyr::n_distinct(...)
4. │ │ └─vctrs::df_list(...)
5. │ │ └─rlang::list2(...)
6. │ └─dplyr::select(...)
7. ├─batchtma::adjust_batch(...)
8. │ └─batchtma:::batchmean_ipw(...)
9. │ ├─purrr::map(...)
10. │ │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
11. │ │ ├─purrr:::with_indexed_errors(...)
12. │ │ │ └─base::withCallingHandlers(...)
13. │ │ ├─purrr:::call_with_cleanup(...)
14. │ │ └─batchtma (local) .f(.x[[i]], ...)
15. │ │ └─... %>% ...
16. │ └─data %>% ...
17. ├─dplyr::mutate(., .batchvar = factor_drop(.data$.batchvar))
18. ├─dplyr::filter(., !is.na(.data$variable))
19. ├─dplyr::rename(., variable = dplyr::one_of(variable))
20. ├─dplyr::filter(., dplyr::across(dplyr::all_of(confounders), ~!is.na(.x)))
21. ├─dplyr:::filter.data.frame(., dplyr::across(dplyr::all_of(confounders), ~!is.na(.x)))
22. │ └─dplyr:::filter_impl(...)
23. │ └─dplyr:::filter_rows(...)
24. │ └─dplyr:::filter_eval(...)
25. │ ├─base::withCallingHandlers(...)
26. │ └─mask$eval_all_filter(dots_expanded, invert, env_filter)
27. │ └─dplyr (local) eval()
28. └─dplyr:::dplyr_internal_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'batchtma.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `dplyr::filter()`:
ℹ In argument: `dplyr::across(dplyr::all_of(confounders), ~!is.na(.x))`.
Caused by error:
! `..1` must be a logical vector, not a <tbl_df/tbl/data.frame> object.
ℹ If you used `across()` to generate this data frame, please use `if_any()` or
`if_all()` instead.
--- failed re-building ‘batchtma.Rmd’
SUMMARY: processing the following file failed:
‘batchtma.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Current CRAN status: OK: 14
Current CRAN status: OK: 14
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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