############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data zenith ### ############################################################################## ############################################################################## * checking for file ‘zenith/DESCRIPTION’ ... OK * preparing ‘zenith’: * checking DESCRIPTION meta-information ... OK * installing the package to process help pages Loading required namespace: zenith * saving partial Rd database * creating vignettes ... ERROR --- re-building ‘loading_genesets.Rmd’ using rmarkdown --- finished re-building ‘loading_genesets.Rmd’ --- re-building ‘zenith.Rmd’ using rmarkdown Quitting from zenith.Rmd:34-73 [standard] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `msigdbr_check_data()`: ! Please run the following command to install the 'msigdbdf' package: install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev') --- Backtrace: ▆ 1. └─zenith::get_MSigDB("H", to = "ENSEMBL") 2. └─base::lapply(...) 3. └─zenith (local) FUN(X[[i]], ...) 4. └─EnrichmentBrowser::getGenesets(...) 5. └─EnrichmentBrowser:::.getMSigDb(...) 6. ├─base::unique(msigdbr::msigdbr_collections()$gs_cat) 7. └─msigdbr::msigdbr_collections() 8. └─msigdbr:::msigdbr_check_data() ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'zenith.Rmd' failed with diagnostics: Please run the following command to install the 'msigdbdf' package: install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev') --- failed re-building ‘zenith.Rmd’ SUMMARY: processing the following file failed: ‘zenith.Rmd’ Error: Vignette re-building failed. Execution halted