############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 spatialHeatmap ### ############################################################################## ############################################################################## * 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 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 = ``) 9. └─SeuratObject (local) `[[<-`(`*tmp*`, image, value = ``) 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