############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data mitch ### ############################################################################## ############################################################################## * checking for file ‘mitch/DESCRIPTION’ ... OK * preparing ‘mitch’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘infiniumMethArrayWorkflow.Rmd’ using rmarkdown trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt' Quitting from lines 89-95 [genenames] (infiniumMethArrayWorkflow.Rmd) Error: processing vignette 'infiniumMethArrayWorkflow.Rmd' failed with diagnostics: cannot open URL 'ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt' --- failed re-building ‘infiniumMethArrayWorkflow.Rmd’ --- re-building ‘mitchWorkflow.Rmd’ using rmarkdown trying URL 'https://reactome.org/download/current/ReactomePathways.gmt.zip' Content type 'application/zip' length 274586 bytes (268 KB) ================================================== downloaded 268 KB 2024-06-27 17:16:43.332 R[59571:198540806] XType: com.apple.fonts is not accessible. 2024-06-27 17:16:43.333 R[59571:198540806] XType: XTFontStaticRegistry is enabled. Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "mitch Workflow", and the latter is "mitch". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check. --- finished re-building ‘mitchWorkflow.Rmd’ SUMMARY: processing the following file failed: ‘infiniumMethArrayWorkflow.Rmd’ Error: Vignette re-building failed. Execution halted