Back to Build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMN[O]PQRSTUVWXYZ

This page was generated on 2026-01-22 11:58 -0500 (Thu, 22 Jan 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4886
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 1500/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmicsMLRepoR 1.4.0  (landing page)
Sehyun Oh
Snapshot Date: 2026-01-19 13:45 -0500 (Mon, 19 Jan 2026)
git_url: https://git.bioconductor.org/packages/OmicsMLRepoR
git_branch: RELEASE_3_22
git_last_commit: c5f091e
git_last_commit_date: 2025-10-29 11:32:50 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped

BUILD results for OmicsMLRepoR on nebbiolo2

To the developers/maintainers of the OmicsMLRepoR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmicsMLRepoR.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: OmicsMLRepoR
Version: 1.4.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 OmicsMLRepoR
StartedAt: 2026-01-19 19:12:51 -0500 (Mon, 19 Jan 2026)
EndedAt: 2026-01-19 19:14:00 -0500 (Mon, 19 Jan 2026)
EllapsedTime: 69.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 OmicsMLRepoR
###
##############################################################################
##############################################################################


* checking for file ‘OmicsMLRepoR/DESCRIPTION’ ... OK
* preparing ‘OmicsMLRepoR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Quickstart.Rmd’ using rmarkdown

Quitting from Quickstart.Rmd:66-69 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (bfcneedsupdate(bfc, rid)) ...`:
! missing value where TRUE/FALSE needed
---
Backtrace:
    ▆
 1. └─OmicsMLRepoR::getMetadata("cBioPortal")
 2.   └─OmicsMLRepoR:::s2p_cached_url(fpath)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Quickstart.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘Quickstart.Rmd’

SUMMARY: processing the following file failed:
  ‘Quickstart.Rmd’

Error: Vignette re-building failed.
Execution halted