Multiple platform build/check report for BioC 3.21 - BUILD results for corral on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4823
palomino7	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4565
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4603
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4544
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4579
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 corral on merida1

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

Version: 1.18.0

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

StartedAt: 2025-07-31 18:02:59 -0400 (Thu, 31 Jul 2025)

EndedAt: 2025-07-31 18:32:27 -0400 (Thu, 31 Jul 2025)

EllapsedTime: 1767.8 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 corral
###
##############################################################################
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* checking for file ‘corral/DESCRIPTION’ ... OK
* preparing ‘corral’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘corral_dimred.Rmd’ using rmarkdown

Quitting from corral_dimred.Rmd:85-92 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! subscript contains invalid names
---
Backtrace:
    ▆
 1. └─corral::plot_embedding_sce(...)
 2.   ├─SingleCellExperiment::colData(sce)[, color_attr]
 3.   └─SingleCellExperiment::colData(sce)[, color_attr]
 4.     ├─S4Vectors::extractCOLS(x, j)
 5.     └─S4Vectors::extractCOLS(x, j)
 6.       └─S4Vectors::normalizeSingleBracketSubscript(i, xstub)
 7.         ├─S4Vectors::NSBS(...)
 8.         └─S4Vectors::NSBS(...)
 9.           └─S4Vectors:::.subscript_error("subscript contains invalid ", what)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'corral_dimred.Rmd' failed with diagnostics:
subscript contains invalid names
--- failed re-building ‘corral_dimred.Rmd’

--- re-building ‘corralm_alignment.Rmd’ using rmarkdown
2025-07-31 18:31:55.233 R[12307:286244796] XType: com.apple.fonts is not accessible.
2025-07-31 18:31:55.233 R[12307:286244796] XType: XTFontStaticRegistry is enabled.
--- finished re-building ‘corralm_alignment.Rmd’

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

Error: Vignette re-building failed.
Execution halted