############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 biodbNci ### ############################################################################## ############################################################################## * checking for file ‘biodbNci/DESCRIPTION’ ... OK * preparing ‘biodbNci’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘biodbNci.Rmd’ using rmarkdown INFO [16:19:35.930] Loading definitions from package biodb version 1.17.1. INFO [16:19:37.403] Loading definitions from package biodbChebi version 1.15.1. INFO [16:19:37.434] Loading definitions from package biodbHmdb version 1.15.1. INFO [16:19:37.464] Loading definitions from package biodbNcbi version 1.13.1. INFO [16:19:37.487] Loading definitions from package biodbNci version 1.13.1. INFO [16:19:37.494] Loading definitions from package biodbUniprot version 1.15.1. INFO [16:19:37.661] Extract whole database of nci.cactus. INFO [16:19:37.662] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database.... Quitting from biodbNci.Rmd:72-75 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `private$doExtractDownload()`: ! attempt to apply non-function --- Backtrace: ▆ 1. └─conn$getEntryIds(2) 2. └─private$doGetEntryIds(max.results = max.results, ...) 3. └─self$download() 4. └─private$doExtractDownload() ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'biodbNci.Rmd' failed with diagnostics: attempt to apply non-function --- failed re-building ‘biodbNci.Rmd’ SUMMARY: processing the following file failed: ‘biodbNci.Rmd’ Error: Vignette re-building failed. Execution halted