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This page was generated on 2026-03-20 22:25 -0400 (Fri, 20 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2026-03-12 r89611) -- "Unsuffered Consequences" 920
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Package 42/230HostnameOS / ArchINSTALLBUILDCHECK
biomformat 1.39.16  (landing page)
Paul J. McMurdie
Snapshot Date: 2026-03-20 18:00 -0400 (Fri, 20 Mar 2026)
git_url: https://git.bioconductor.org/packages/biomformat
git_branch: devel
git_last_commit: 68ba178
git_last_commit_date: 2026-03-15 15:21:42 -0400 (Sun, 15 Mar 2026)
teran2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped

BUILD results for biomformat on teran2

To the developers/maintainers of the biomformat package:
- 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.

raw results


Summary

Package: biomformat
Version: 1.39.16
Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data biomformat
StartedAt: 2026-03-20 18:36:26 -0400 (Fri, 20 Mar 2026)
EndedAt: 2026-03-20 18:36:58 -0400 (Fri, 20 Mar 2026)
EllapsedTime: 31.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/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

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