############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biodbUniprot ### ############################################################################## ############################################################################## * checking for file ‘biodbUniprot/DESCRIPTION’ ... OK * preparing ‘biodbUniprot’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘biodbUniprot.Rmd’ using rmarkdown INFO [20:15:06.531] Loading definitions from package biodb version 1.16.1. INFO [20:15:08.756] Loading definitions from package biodbChebi version 1.14.0. INFO [20:15:08.789] Loading definitions from package biodbHmdb version 1.14.0. INFO [20:15:08.825] Loading definitions from package biodbNcbi version 1.12.0. INFO [20:15:08.852] Loading definitions from package biodbNci version 1.12.0. INFO [20:15:08.861] Loading definitions from package biodbUniprot version 1.14.0. INFO [20:15:09.106] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/uniprot-958d776f924f3e7a3bae586fa731b40c. Quitting from biodbUniprot.Rmd:83-86 [unnamed-chunk-6] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `conn$wsSearch()`: ! object 'BiodbUrl' not found --- Backtrace: ▆ 1. └─conn$wsSearch(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'biodbUniprot.Rmd' failed with diagnostics: object 'BiodbUrl' not found --- failed re-building ‘biodbUniprot.Rmd’ SUMMARY: processing the following file failed: ‘biodbUniprot.Rmd’ Error: Vignette re-building failed. Execution halted