Multiple platform build/check report for BioC 3.23 - BUILD results for nipalsMCIA on kjohnson3

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"	4875
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4583
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 nipalsMCIA on kjohnson3

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

Version: 1.9.0

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

StartedAt: 2025-12-14 17:09:21 -0500 (Sun, 14 Dec 2025)

EndedAt: 2025-12-14 17:10:35 -0500 (Sun, 14 Dec 2025)

EllapsedTime: 73.8 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data nipalsMCIA
###
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* checking for file ‘nipalsMCIA/DESCRIPTION’ ... OK
* preparing ‘nipalsMCIA’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Analysis-of-MCIA-Decomposition.Rmd’ using rmarkdown
2025-12-14 17:09:42.086 R[3569:391811042] XType: Using static font registry.
--- finished re-building ‘Analysis-of-MCIA-Decomposition.Rmd’

--- re-building ‘Predicting-New-Scores.Rmd’ using rmarkdown
--- finished re-building ‘Predicting-New-Scores.Rmd’

--- re-building ‘Single-Cell-Analysis.Rmd’ using rmarkdown

Quitting from Single-Cell-Analysis.Rmd:833-845 [seurat-markers-dot-adt]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'x' in selecting a method for function 'rownames': The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
---
Backtrace:
     ▆
  1. ├─Seurat::DotPlot(...)
  2. ├─BiocGenerics::rownames(...)
  3. ├─SeuratObject::GetAssayData(object = obj, assay = "ADT", slot = "counts")
  4. ├─SeuratObject:::GetAssayData.Seurat(...)
  5. │ └─SeuratObject::.Deprecate(...)
  6. │   └─lifecycle::deprecate_stop(...)
  7. │     └─lifecycle:::deprecate_stop0(msg)
  8. │       └─rlang::cnd_signal(...)
  9. │         └─rlang:::signal_abort(cnd)
 10. │           └─base::signalCondition(cnd)
 11. └─base (local) `<fn>`(`<lfcycl__>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Single-Cell-Analysis.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'rownames': The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
--- failed re-building ‘Single-Cell-Analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘Single-Cell-Analysis.Rmd’

Error: Vignette re-building failed.
Execution halted