Multiple platform build/check report for BioC 3.22 - BUILD results for epiregulon.extra on lconway

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"	4797
palomino8	Windows Server 2022 Datacenter	x64	4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"	4538
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4571
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4515
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4483
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.extra on lconway

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

Version: 1.5.0

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

StartedAt: 2025-06-12 16:52:04 -0400 (Thu, 12 Jun 2025)

EndedAt: 2025-06-12 16:53:28 -0400 (Thu, 12 Jun 2025)

EllapsedTime: 84.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data epiregulon.extra
###
##############################################################################
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* checking for file ‘epiregulon.extra/DESCRIPTION’ ... OK
* preparing ‘epiregulon.extra’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Data_visualization.Rmd’ using rmarkdown

Quitting from Data_visualization.Rmd:37-57 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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 'Data_visualization.Rmd' failed with diagnostics:
invalid class "SingleCellAccessibilityExperiment" object: superclass "ExpData" not defined in the environment of the object's class
--- failed re-building ‘Data_visualization.Rmd’

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

Error: Vignette re-building failed.
Execution halted