############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data CytoML ### ############################################################################## ############################################################################## * checking for file ‘CytoML/DESCRIPTION’ ... OK * preparing ‘CytoML’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘HowToExportGatingSet.Rmd’ using rmarkdown Quitting from HowToExportGatingSet.Rmd:52-71 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `add_ggcyto()`: ! object '+.gg' not found --- Backtrace: ▆ 1. ├─ggplot2::autoplot(gs[[1]]) 2. └─ggcyto:::autoplot.GatingHierarchy(gs[[1]]) 3. ├─BiocGenerics::lapply(...) 4. └─base::lapply(...) 5. └─ggcyto (local) FUN(X[[i]], ...) 6. └─ggcyto:::autoplot.GatingSet(object, gate, y = y, ...) 7. ├─ggcyto::ggcyto(object, mapping, ...) 8. └─ggcyto:::ggcyto.GatingHierarchy(object, mapping, ...) 9. ├─ggcyto::ggcyto(data, ...) 10. └─ggcyto:::ggcyto.GatingSet(data, ...) 11. └─ggcyto:::ggcyto.flowSet(data = data, mapping = mapping, ...) 12. ├─p + ggcyto_par_default() 13. └─p + ggcyto_par_default() 14. └─ggcyto:::add_ggcyto(e1, e2, e2name) 15. ├─e1 + e2.new 16. └─e1 + e2.new 17. └─ggcyto:::add_ggcyto(e1, e2, e2name) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'HowToExportGatingSet.Rmd' failed with diagnostics: object '+.gg' not found --- failed re-building ‘HowToExportGatingSet.Rmd’ --- re-building ‘cytobank2GatingSet.Rmd’ using rmarkdown Quitting from cytobank2GatingSet.Rmd:58-64 [unnamed-chunk-6] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `add_ggcyto()`: ! object '+.gg' not found --- Backtrace: ▆ 1. ├─ggplot2::autoplot(gs[[1]]) 2. └─ggcyto:::autoplot.GatingHierarchy(gs[[1]]) 3. ├─BiocGenerics::lapply(...) 4. └─base::lapply(...) 5. └─ggcyto (local) FUN(X[[i]], ...) 6. └─ggcyto:::autoplot.GatingSet(object, gate, y = y, ...) 7. ├─ggcyto::ggcyto(object, mapping, ...) 8. └─ggcyto:::ggcyto.GatingHierarchy(object, mapping, ...) 9. ├─ggcyto::ggcyto(data, ...) 10. └─ggcyto:::ggcyto.GatingSet(data, ...) 11. └─ggcyto:::ggcyto.flowSet(data = data, mapping = mapping, ...) 12. ├─p + ggcyto_par_default() 13. └─p + ggcyto_par_default() 14. └─ggcyto:::add_ggcyto(e1, e2, e2name) 15. ├─e1 + e2.new 16. └─e1 + e2.new 17. └─ggcyto:::add_ggcyto(e1, e2, e2name) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'cytobank2GatingSet.Rmd' failed with diagnostics: object '+.gg' not found --- failed re-building ‘cytobank2GatingSet.Rmd’ --- re-building ‘flowjo_to_gatingset.Rmd’ using rmarkdown --- finished re-building ‘flowjo_to_gatingset.Rmd’ SUMMARY: processing the following files failed: ‘HowToExportGatingSet.Rmd’ ‘cytobank2GatingSet.Rmd’ Error: Vignette re-building failed. Execution halted