| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-30 12:07 -0400 (Sat, 30 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 283/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CatsCradle 1.3.0 (landing page) Michael Shapiro
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the CatsCradle package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CatsCradle.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: CatsCradle |
| Version: 1.3.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CatsCradle |
| StartedAt: 2025-08-29 15:48:57 -0400 (Fri, 29 Aug 2025) |
| EndedAt: 2025-08-29 15:52:08 -0400 (Fri, 29 Aug 2025) |
| EllapsedTime: 190.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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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 CatsCradle
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* checking for file ‘CatsCradle/DESCRIPTION’ ... OK
* preparing ‘CatsCradle’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘CatsCradle.Rmd’ using rmarkdown
2025-08-29 15:49:23.482 R[85360:121119163] XType: Using static font registry.
--- finished re-building ‘CatsCradle.Rmd’
--- re-building ‘CatsCradleExampleData.Rmd’ using rmarkdown
Quitting from CatsCradleExampleData.Rmd:74-82 [[Ex4]]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `validObject()`:
! invalid class "FOV" object: slots in class definition but not in object: "misc"
---
Backtrace:
▆
1. └─CatsCradle (local) getExample("smallXenium", toy = TRUE)
2. ├─answer[, xeniumCells]
3. └─SeuratObject:::`[.Seurat`(answer, , xeniumCells)
4. └─SeuratObject:::subset.Seurat(...)
5. ├─base::subset(x = x[[image]], cells = cells.from.image)
6. └─SeuratObject:::subset.FOV(x = x[[image]], cells = cells.from.image)
7. ├─methods (local) `[[<-`(`*tmp*`, i, value = `<Centrods>`)
8. └─SeuratObject (local) `[[<-`(`*tmp*`, i, value = `<Centrods>`)
9. └─methods::validObject(object = x)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'CatsCradleExampleData.Rmd' failed with diagnostics:
invalid class "FOV" object: slots in class definition but not in object: "misc"
--- failed re-building ‘CatsCradleExampleData.Rmd’
--- re-building ‘CatsCradleQuickStart.Rmd’ using rmarkdown
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--- finished re-building ‘CatsCradleQuickStart.Rmd’
--- re-building ‘CatsCradleSingleCellExperimentQuickStart.Rmd’ using rmarkdown
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[----|----|----|----|----|----|----|----|----|----|
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--- finished re-building ‘CatsCradleSingleCellExperimentQuickStart.Rmd’
--- re-building ‘CatsCradleSpatial.Rmd’ using rmarkdown
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--- finished re-building ‘CatsCradleSpatial.Rmd’
SUMMARY: processing the following file failed:
‘CatsCradleExampleData.Rmd’
Error: Vignette re-building failed.
Execution halted