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This page was generated on 2026-01-01 11:35 -0500 (Thu, 01 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4808 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2183/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| tidybulk 2.1.0 (landing page) Stefano Mangiola
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the tidybulk package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tidybulk.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: tidybulk |
| Version: 2.1.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data tidybulk |
| StartedAt: 2025-12-31 17:54:14 -0500 (Wed, 31 Dec 2025) |
| EndedAt: 2025-12-31 18:00:09 -0500 (Wed, 31 Dec 2025) |
| EllapsedTime: 355.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data tidybulk
###
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* checking for file ‘tidybulk/DESCRIPTION’ ... OK
* preparing ‘tidybulk’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to process help pages)
* creating vignettes ... ERROR
--- re-building ‘comparison_coding.Rmd’ using rmarkdown
Loading required namespace: AnnotationDbi
2025-12-31 17:54:41.902 R[14008:599724705] XType: Using static font registry.
--- finished re-building ‘comparison_coding.Rmd’
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning: ggrepel: 15750 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 15790 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 15780 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 15789 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 15790 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 784 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Quitting from introduction.Rmd:937-953 [enrichment-gene-rank-analysis]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/dplyr:::mutate_error>
Error in `mutate()`:
ℹ In argument: `fit = map(...)`.
Caused by error in `map()`:
ℹ In index: 1.
Caused by error in `[.data.frame`:
! undefined columns selected
---
Backtrace:
▆
1. ├─tidybulk::test_gene_rank(...)
2. ├─tidybulk::test_gene_rank(...)
3. │ ├─(function(result_obj) {...
4. │ │ └─tidybulk:::memorise_methods_used(result_obj, "msigdbr")
5. │ │ └─methods::is(object_containing_methods, "SummarizedExperiment")
6. │ ├─tidybulk:::memorise_methods_used(...)
7. │ │ └─tidybulk:::attach_to_metadata(.data, methods_used, "methods_used")
8. │ │ └─methods::is(.data, "SummarizedExperiment")
9. │ └─tidybulk:::entrez_rank_to_gsea(...)
10. │ ├─dplyr::select(...)
11. │ ├─dplyr::mutate(...)
12. │ ├─dplyr::mutate(...)
13. │ └─dplyr:::mutate.data.frame(...)
14. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
15. │ ├─base::withCallingHandlers(...)
16. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
17. │ └─mask$eval_all_mutate(quo)
18. │ └─dplyr (local) eval()
19. └─purrr::map(...)
20. └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
21. ├─purrr:::with_indexed_errors(...)
22. │ └─base::withCallingHandlers(...)
23. ├─purrr:::call_with_cleanup(...)
24. └─tidybulk (local) .f(.x[[i]], ...)
25. └─clusterProfiler::GSEA(...)
26. └─enrichit::gsea_gson(...)
27. ├─gsea_res[, c(expected_cols, other_cols)]
28. └─base::`[.data.frame`(gsea_res, , c(expected_cols, other_cols))
29. └─base::stop("undefined columns selected")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
ℹ In argument: `fit = map(...)`.
Caused by error in `map()`:
ℹ In index: 1.
Caused by error in `[.data.frame`:
! undefined columns selected
--- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following file failed:
‘introduction.Rmd’
Error: Vignette re-building failed.
Execution halted