Multiple platform build/check report for BioC 3.22 - BUILD results for spatialHeatmap on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4898
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4688
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4634
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4658
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 spatialHeatmap on nebbiolo2

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

Version: 2.15.2

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 spatialHeatmap

StartedAt: 2025-10-23 20:17:45 -0400 (Thu, 23 Oct 2025)

EndedAt: 2025-10-23 20:21:46 -0400 (Thu, 23 Oct 2025)

EllapsedTime: 241.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 spatialHeatmap
###
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* checking for file ‘spatialHeatmap/DESCRIPTION’ ... OK
* preparing ‘spatialHeatmap’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... ERROR
--- re-building ‘covisualize.Rmd’ using rmarkdown

Quitting from covisualize.Rmd:516-521 [unnamed-chunk-40]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `validObject()`:
! invalid class "VisiumV1" object: slots in class definition but not in object: "misc"
---
Backtrace:
     ▆
  1. ├─spatialHeatmap::covis(...)
  2. └─spatialHeatmap::covis(...)
  3.   └─spatialHeatmap (local) .local(data, ...)
  4.     └─spatialHeatmap:::shm_covis(...)
  5.       └─spatialHeatmap:::check_srsc(...)
  6.         ├─base::subset(cell, features = inter)
  7.         └─SeuratObject:::subset.Seurat(cell, features = inter)
  8.           ├─methods (local) `[[<-`(`*tmp*`, image, value = `<VisiumV1[,600]>`)
  9.           └─SeuratObject (local) `[[<-`(`*tmp*`, image, value = `<VisiumV1[,600]>`)
 10.             └─methods::validObject(object = value)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'covisualize.Rmd' failed with diagnostics:
invalid class "VisiumV1" object: slots in class definition but not in object: "misc"
--- failed re-building ‘covisualize.Rmd’

--- re-building ‘custom_SVGs.Rmd’ using rmarkdown
--- finished re-building ‘custom_SVGs.Rmd’

--- re-building ‘spatialHeatmap.Rmd’ using rmarkdown
--- finished re-building ‘spatialHeatmap.Rmd’

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

Error: Vignette re-building failed.
Execution halted