| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-18 12:05 -0500 (Thu, 18 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4882 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 1463/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| nipalsMCIA 1.8.0 (landing page) Maximilian Mattessich
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: nipalsMCIA |
| Version: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data nipalsMCIA |
| StartedAt: 2025-12-15 21:31:15 -0500 (Mon, 15 Dec 2025) |
| EndedAt: 2025-12-15 21:37:04 -0500 (Mon, 15 Dec 2025) |
| EllapsedTime: 349.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data nipalsMCIA
###
##############################################################################
##############################################################################
* checking for file ‘nipalsMCIA/DESCRIPTION’ ... OK
* preparing ‘nipalsMCIA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Analysis-of-MCIA-Decomposition.Rmd’ using rmarkdown
2025-12-15 21:33:20.339 R[80791:127664183] XType: com.apple.fonts is not accessible.
2025-12-15 21:33:20.341 R[80791:127664183] XType: XTFontStaticRegistry is enabled.
--- 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