############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r spicyWorkflow -R && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe 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 Quitting from spicyWorkflow.Rmd:275-284 [unnamed-chunk-8] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `serialize()`: ! error writing to connection --- Backtrace: ▆ 1. └─cytomapper::measureObjects(...) 2. ├─BiocParallel::bpmapply(...) 3. └─BiocParallel::bpmapply(...) 4. ├─BiocParallel::bplapply(...) 5. └─BiocParallel::bplapply(...) 6. └─BiocParallel:::.bpinit(...) 7. ├─BiocParallel::bpstop(BPPARAM) 8. └─BiocParallel::bpstop(BPPARAM) 9. └─BiocParallel::.bpstop_impl(x) 10. └─BiocParallel:::.bpstop_nodes(x) 11. ├─BiocParallel::.manager_send_all(manager, .DONE()) 12. └─BiocParallel::.manager_send_all(manager, .DONE()) 13. ├─BiocParallel::.send_all(manager$backend, value) 14. └─BiocParallel::.send_all(manager$backend, value) 15. ├─BiocParallel::.send_to(backend, node, value) 16. └─BiocParallel::.send_to(backend, node, value) 17. ├─parallel:::sendData(backend[[node]], value) 18. └─parallel:::sendData.SOCKnode(backend[[node]], value) 19. └─base::serialize(data, node$con) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'spicyWorkflow.Rmd' failed with diagnostics: error writing to connection --- failed re-building 'spicyWorkflow.Rmd' SUMMARY: processing the following file failed: 'spicyWorkflow.Rmd' Error: Vignette re-building failed. Execution halted Error in serialize(data, node$con) : error writing to connection Calls: ... .send_to -> -> sendData.SOCKnode -> serialize