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This page was generated on 2025-11-13 11:32 -0500 (Thu, 13 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4013 |
| 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 2176/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| tidybulk 2.1.0 (landing page) Stefano Mangiola
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | ||||||||
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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: 2025-11-12 17:22:42 -0500 (Wed, 12 Nov 2025) |
| EndedAt: 2025-11-12 17:23:16 -0500 (Wed, 12 Nov 2025) |
| EllapsedTime: 34.4 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
Quitting from comparison_coding.Rmd:240-242 [normalise]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument '.data' in selecting a method for function 'scale_abundance': The package "edgeR" is required.
---
Backtrace:
▆
1. ├─tidybulk::scale_abundance(identify_abundant(airway, factor_of_interest = dex))
2. ├─tidybulk::identify_abundant(airway, factor_of_interest = dex)
3. ├─tidybulk::identify_abundant(airway, factor_of_interest = dex)
4. │ └─tidybulk:::check_and_install_packages("edgeR")
5. │ └─rlang::check_installed(...)
6. │ └─base::stop(cnd)
7. └─base (local) `<fn>`(`<rlb_r___>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'comparison_coding.Rmd' failed with diagnostics:
error in evaluating the argument '.data' in selecting a method for function 'scale_abundance': The package "edgeR" is required.
--- failed re-building ‘comparison_coding.Rmd’
--- re-building ‘introduction.Rmd’ using rmarkdown
Loading required namespace: AnnotationDbi
2025-11-12 17:23:10.641 R[73730:3618303] XType: Using static font registry.
Quitting from introduction.Rmd:256-266 [filtering-abundance-methods]
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NULL
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Error: processing vignette 'introduction.Rmd' failed with diagnostics:
The package "edgeR" is required.
--- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following files failed:
‘comparison_coding.Rmd’ ‘introduction.Rmd’
Error: Vignette re-building failed.
Execution halted