• using R version 4.4.3 (2025-02-28 ucrt)
• using platform: x86_64-w64-mingw32
• R was compiled by     gcc.exe (GCC) 13.3.0     GNU Fortran (GCC) 13.3.0
• running under: Windows Server 2022 x64 (build 20348)
• using session charset: UTF-8
• checking for file 'batchtma/DESCRIPTION' ... OK
• this is package 'batchtma' version '0.1.6'
• package encoding: UTF-8
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• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for hidden files and directories ... OK
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• checking whether package 'batchtma' can be installed ... OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking 'build' directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
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• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [2s] OK
• checking whether the package can be loaded with stated dependencies ... [2s] OK
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• checking whether the namespace can be loaded with stated dependencies ... [2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s] OK
• checking loading without being on the library search path ... [2s] OK
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• checking for unstated dependencies in examples ... OK
• checking installed files from 'inst/doc' ... OK
• checking files in 'vignettes' ... OK
• checking examples ... [4s] 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$eval_all_filter(dots_expanded, invert, env_filter)  22. │ └─dplyr (local) eval()  23. ├─dplyr:::dplyr_internal_error(...)  24. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)  25. │ └─rlang:::signal_abort(cnd, .file)  26. │ └─base::signalCondition(cnd)  27. └─dplyr (local) `<fn>`(`<dpl:::__>`)  28. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [10s] ERROR Error(s) in re-building vignettes: --- re-building 'batchtma.Rmd' using rmarkdown Quitting from batchtma.Rmd:115-120 [unnamed-chunk-10] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/purrr_error_indexed> Error in `purrr::map()`: ℹ In index: 1. Caused by error in `dplyr::filter()`: ℹ In argument: `dplyr::across(dplyr::all_of(confounders), ~!is.na(.x))`. Caused by error: ! `..1` must be a logical vector, not a <tbl_df/tbl/data.frame> object. ℹ If you used `across()` to generate this data frame, please use `if_any()` or   `if_all()` instead. --- Backtrace:      ▆   1. ├─... %>% ...   2. ├─batchtma::plot_batch(...)   3. │ ├─dplyr::n_distinct(...)   4. │ │ └─vctrs::df_list(...)   5. │ │ └─rlang::list2(...)   6. │ └─dplyr::select(...)   7. ├─batchtma::adjust_batch(...)   8. │ └─batchtma:::batchmean_ipw(...)   9. │ ├─purrr::map(...)  10. │ │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)  11. │ │ ├─purrr:::with_indexed_errors(...)  12. │ │ │ └─base::withCallingHandlers(...)  13. │ │ ├─purrr:::call_with_cleanup(...)  14. │ │ └─batchtma (local) .f(.x[[i]], ...)  15. │ │ └─... %>% ...  16. │ └─data %>% ...  17. ├─dplyr::mutate(., .batchvar = factor_drop(.data$.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
• checking PDF version of manual ... [19s] OK
• checking HTML version of manual ... [1s] OK
• DONE

Status: 2 ERRORs