| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-17 11:34 -0400 (Tue, 17 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4845 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4060 |
| 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 218/2367 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biomformat 1.39.16 (landing page) Paul J. McMurdie
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| See other builds for biomformat in R Universe. | ||||||||||||||
|
To the developers/maintainers of the biomformat package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biomformat.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: biomformat |
| Version: 1.39.16 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biomformat |
| StartedAt: 2026-03-16 15:34:54 -0400 (Mon, 16 Mar 2026) |
| EndedAt: 2026-03-16 15:35:08 -0400 (Mon, 16 Mar 2026) |
| EllapsedTime: 14.1 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 biomformat
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* checking for file ‘biomformat/DESCRIPTION’ ... OK
* preparing ‘biomformat’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘biomformat.Rmd’ using rmarkdown
2026-03-16 15:35:06.349 R[95312:164086152] XType: Using static font registry.
Quitting from biomformat.Rmd:402-413 [named_subsetting]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'columns' in selecting a method for function 'biom_data': argument "columns" is missing, with no default
---
Backtrace:
▆
1. ├─biomformat::biom_data(x, rows = "GG_OTU_3")
2. ├─biomformat::biom_data(x, rows = "GG_OTU_3")
3. │ └─biomformat::biom_data(x, rows, columns)
4. └─base (local) `<fn>`(`<gtvrErrr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'biomformat.Rmd' failed with diagnostics:
error in evaluating the argument 'columns' in selecting a method for function 'biom_data': argument "columns" is missing, with no default
--- failed re-building ‘biomformat.Rmd’
SUMMARY: processing the following file failed:
‘biomformat.Rmd’
Error: Vignette re-building failed.
Execution halted