Build/check report for BioC 3.23 - BUILD results for OmicsMLRepoR on nebbiolo1

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"	4428
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BUILD results for OmicsMLRepoR on nebbiolo1

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: 1.5.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OmicsMLRepoR

StartedAt: 2025-10-30 18:14:53 -0400 (Thu, 30 Oct 2025)

EndedAt: 2025-10-30 18:15:18 -0400 (Thu, 30 Oct 2025)

EllapsedTime: 25.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OmicsMLRepoR
###
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* checking for file ‘OmicsMLRepoR/DESCRIPTION’ ... OK
* preparing ‘OmicsMLRepoR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Quickstart.Rmd’ using rmarkdown

Quitting from Quickstart.Rmd:47-54 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! package or namespace load failed for 'cBioPortalData':
 object 'microRNAs' is not exported by 'namespace:GenomicFeatures'
---
Backtrace:
    ▆
 1. ├─base::suppressPackageStartupMessages(...)
 2. │ └─base::withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
 3. └─base::library(cBioPortalData)
 4.   └─base::tryCatch(...)
 5.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.         └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Quickstart.Rmd' failed with diagnostics:
package or namespace load failed for 'cBioPortalData':
 object 'microRNAs' is not exported by 'namespace:GenomicFeatures'
--- failed re-building ‘Quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted