############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biodbHmdb ### ############################################################################## ############################################################################## * checking for file ‘biodbHmdb/DESCRIPTION’ ... OK * preparing ‘biodbHmdb’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘biodbHmdb.Rmd’ using rmarkdown INFO [20:04:45.243] Loading definitions from package biodb version 1.16.1. INFO [20:04:47.440] Loading definitions from package biodbChebi version 1.14.0. INFO [20:04:47.474] Loading definitions from package biodbHmdb version 1.14.0. INFO [20:04:47.508] Loading definitions from package biodbNcbi version 1.12.0. INFO [20:04:47.536] Loading definitions from package biodbNci version 1.12.0. INFO [20:04:47.545] Loading definitions from package biodbUniprot version 1.14.0. INFO [20:04:47.948] Extract whole database of hmdb.metabolites. INFO [20:04:47.950] Extracting content of downloaded', ' HMDB metabolite database... Quitting from biodbHmdb.Rmd:76-78 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `private$doExtractDownload()`: ! attempt to apply non-function --- Backtrace: ▆ 1. └─conn$getNbEntries() 2. └─private$doGetNbEntries(count = count) 3. └─self$getEntryIds() 4. └─private$doGetEntryIds(max.results = max.results, ...) 5. └─self$download() 6. └─private$doExtractDownload() ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'biodbHmdb.Rmd' failed with diagnostics: attempt to apply non-function --- failed re-building ‘biodbHmdb.Rmd’ SUMMARY: processing the following file failed: ‘biodbHmdb.Rmd’ Error: Vignette re-building failed. Execution halted