Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-08-18 11:41 -0400 (Mon, 18 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4566
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 160/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bedbaser 1.0.3  (landing page)
Andres Wokaty
Snapshot Date: 2025-08-14 13:40 -0400 (Thu, 14 Aug 2025)
git_url: https://git.bioconductor.org/packages/bedbaser
git_branch: RELEASE_3_21
git_last_commit: cf1844d
git_last_commit_date: 2025-07-16 11:47:03 -0400 (Wed, 16 Jul 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for bedbaser on palomino7

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.

raw results


Summary

Package: bedbaser
Version: 1.0.3
Command: chmod a+r bedbaser -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data bedbaser
StartedAt: 2025-08-14 17:32:25 -0400 (Thu, 14 Aug 2025)
EndedAt: 2025-08-14 17:33:10 -0400 (Thu, 14 Aug 2025)
EllapsedTime: 44.9 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   chmod a+r bedbaser -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data bedbaser
###
##############################################################################
##############################################################################


* checking for file 'bedbaser/DESCRIPTION' ... OK
* preparing 'bedbaser':
* checking DESCRIPTION meta-information ... OK
* installing the package 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