Multiple platform build/check report for BioC 3.22 - BUILD results for epiregulon on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4810
palomino8	Windows Server 2022 Datacenter	x64	4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"	4548
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4528
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4493
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*

BUILD results for epiregulon on kjohnson3

To the developers/maintainers of the epiregulon package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epiregulon.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: epiregulon

Version: 1.5.1

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data epiregulon

StartedAt: 2025-06-18 16:14:27 -0400 (Wed, 18 Jun 2025)

EndedAt: 2025-06-18 16:15:07 -0400 (Wed, 18 Jun 2025)

EllapsedTime: 39.4 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data epiregulon
###
##############################################################################
##############################################################################


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

Quitting from multiome.mae.Rmd:66-91 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `validObject()`:
! invalid class "SingleCellAccessibilityExperiment" object: superclass "ExpData" not defined in the environment of the object's class
---
Backtrace:
     ▆
  1. └─scMultiome::reprogramSeq()
  2.   └─scMultiome:::retrieve(...)
  3.     └─scMultiome::loadMAE(file = eh[[1]], experiments, verbose)
  4.       └─base::lapply(experiments, loadExp, file = file, verbose = verbose)
  5.         └─scMultiome (local) FUN(X[[i]], ...)
  6.           ├─SingleCellExperiment::`reducedDims<-`(...)
  7.           └─SingleCellExperiment::`reducedDims<-`(...)
  8.             └─SingleCellExperiment:::.set_internal_all(...)
  9.               └─BiocGenerics::updateObject(x)
 10.                 └─methods::validObject(result)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'multiome.mae.Rmd' failed with diagnostics:
invalid class "SingleCellAccessibilityExperiment" object: superclass "ExpData" not defined in the environment of the object's class
--- failed re-building ‘multiome.mae.Rmd’

SUMMARY: processing the following file failed:
  ‘multiome.mae.Rmd’

Error: Vignette re-building failed.
Execution halted