| Back to Multiple platform build/check report for BioC 3.23: simplified long |
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This page was generated on 2025-12-04 11:35 -0500 (Thu, 04 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 165/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bedbaser 1.3.0 (landing page) Andres Wokaty
| 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 bedbaser package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bedbaser.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: bedbaser |
| Version: 1.3.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data bedbaser |
| StartedAt: 2025-12-03 15:45:36 -0500 (Wed, 03 Dec 2025) |
| EndedAt: 2025-12-03 15:45:52 -0500 (Wed, 03 Dec 2025) |
| EllapsedTime: 16.2 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 bedbaser
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* checking for file ‘bedbaser/DESCRIPTION’ ... OK
* preparing ‘bedbaser’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘bedbaser.Rmd’ using rmarkdown
Quitting from bedbaser.Rmd:107-109 [bb_search]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `recs$count`:
! $ operator is invalid for atomic vectors
---
Backtrace:
▆
1. └─bedbaser::bb_bed_text_search(bedbase, "cancer", limit = 10)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'bedbaser.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘bedbaser.Rmd’
SUMMARY: processing the following file failed:
‘bedbaser.Rmd’
Error: Vignette re-building failed.
Execution halted