| Back to Build/check report for BioC 3.23: simplified long |
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This page was generated on 2025-11-01 11:33 -0400 (Sat, 01 Nov 2025).
| 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" | 4774 |
| 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 2049/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| spatialHeatmap 2.17.0 (landing page) Jianhai Zhang
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
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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. |
| Package: spatialHeatmap |
| Version: 2.17.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data spatialHeatmap |
| StartedAt: 2025-10-31 20:21:49 -0400 (Fri, 31 Oct 2025) |
| EndedAt: 2025-10-31 20:25:44 -0400 (Fri, 31 Oct 2025) |
| EllapsedTime: 235.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data spatialHeatmap
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* checking for file ‘spatialHeatmap/DESCRIPTION’ ... OK
* preparing ‘spatialHeatmap’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed 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]
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<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