############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data sparrow ### ############################################################################## ############################################################################## * checking for file ‘sparrow/DESCRIPTION’ ... OK * preparing ‘sparrow’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘sparrow.Rmd’ using rmarkdown Quitting from sparrow.Rmd:215-217 [build-gdb] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `setkeyv()`: ! some columns are not in the data.table: [gs_cat] --- Backtrace: ▆ 1. └─sparrow::getMSigGeneSetDb(c("h", "c2"), "human", id.type = "entrez") 2. └─data.table::setkeyv(sigs.all, c("gs_cat", "gs_name")) 3. └─data.table:::stopf(...) 4. └─data.table:::raise_condition(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'sparrow.Rmd' failed with diagnostics: some columns are not in the data.table: [gs_cat] --- failed re-building ‘sparrow.Rmd’ SUMMARY: processing the following file failed: ‘sparrow.Rmd’ Error: Vignette re-building failed. Execution halted