############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CatsCradle ### ############################################################################## ############################################################################## * 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 2025-09-02 16:13:45.475 R[92625:180485165] XType: com.apple.fonts is not accessible. 2025-09-02 16:13:45.476 R[92625:180485165] XType: XTFontStaticRegistry is enabled. --- finished re-building ‘CatsCradle.Rmd’ --- re-building ‘CatsCradleExampleData.Rmd’ using rmarkdown Quitting from CatsCradleExampleData.Rmd:74-82 [[Ex4]] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 = ``) 8. └─SeuratObject (local) `[[<-`(`*tmp*`, i, value = ``) 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 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