############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data spicyWorkflow ### ############################################################################## ############################################################################## * checking for file ‘spicyWorkflow/DESCRIPTION’ ... OK * preparing ‘spicyWorkflow’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘spicyWorkflow.Rmd’ using rmarkdown 2024-07-09 13:22:37.218 R[49481:319139250] XType: com.apple.fonts is not accessible. 2024-07-09 13:22:37.219 R[49481:319139250] XType: XTFontStaticRegistry is enabled. Quitting from lines 447-460 [unnamed-chunk-13] (spicyWorkflow.Rmd) Error: processing vignette 'spicyWorkflow.Rmd' failed with diagnostics: ✖ Specified (x) is not in `cells`. ℹ `names(cells)`: imageID, object_id, s.area, s.radius.mean, m.cx, m.cy, m.majoraxis, m.eccentricity, Patient_ID, Status, Age, SUBTYPE, PAM50, Treatment, DCIS_grade, Necrosis, objectNum, and clusters --- failed re-building ‘spicyWorkflow.Rmd’ SUMMARY: processing the following file failed: ‘spicyWorkflow.Rmd’ Error: Vignette re-building failed. Execution halted