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This page was generated on 2025-12-13 11:47 -0500 (Sat, 13 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4874
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4582
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 285/2332HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CatsCradle 1.5.1  (landing page)
Michael Shapiro
Snapshot Date: 2025-12-12 13:40 -0500 (Fri, 12 Dec 2025)
git_url: https://git.bioconductor.org/packages/CatsCradle
git_branch: devel
git_last_commit: 032f58b
git_last_commit_date: 2025-11-04 07:21:19 -0500 (Tue, 04 Nov 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for CatsCradle on kjohnson3

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.

raw results


Summary

Package: CatsCradle
Version: 1.5.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CatsCradle
StartedAt: 2025-12-12 15:49:54 -0500 (Fri, 12 Dec 2025)
EndedAt: 2025-12-12 15:52:59 -0500 (Fri, 12 Dec 2025)
EllapsedTime: 185.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
###
###   /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 (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘CatsCradle.Rmd’ using rmarkdown
2025-12-12 15:50:19.700 R[80850:375513865] 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()`:
! Consider running UpdateSeuratObject; invalid class "FOV" object: slots in class definition but not in object: "coords_x_orientation"
---
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.           └─SeuratObject:::safeValidityCheck(object = x)
 10.             └─base::tryCatch(...)
 11.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 12.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13.                   └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'CatsCradleExampleData.Rmd' failed with diagnostics:
Consider running UpdateSeuratObject; invalid class "FOV" object: slots in class definition but not in object: "coords_x_orientation"
--- failed re-building ‘CatsCradleExampleData.Rmd’

--- re-building ‘CatsCradleQuickStart.Rmd’ using rmarkdown
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
--- finished re-building ‘CatsCradleQuickStart.Rmd’

--- re-building ‘CatsCradleSingleCellExperimentQuickStart.Rmd’ using rmarkdown
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
--- finished re-building ‘CatsCradleSingleCellExperimentQuickStart.Rmd’

--- re-building ‘CatsCradleSpatial.Rmd’ using rmarkdown
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
--- finished re-building ‘CatsCradleSpatial.Rmd’

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

Error: Vignette re-building failed.
Execution halted