############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biodbChebi ### ############################################################################## ############################################################################## * checking for file ‘biodbChebi/DESCRIPTION’ ... OK * preparing ‘biodbChebi’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘biodbChebi.Rmd’ using rmarkdown INFO [20:04:17.661] Loading definitions from package biodb version 1.16.1. INFO [20:04:21.079] Loading definitions from package biodbChebi version 1.14.0. INFO [20:04:21.114] Loading definitions from package biodbHmdb version 1.14.0. INFO [20:04:21.150] Loading definitions from package biodbNcbi version 1.12.0. INFO [20:04:21.178] Loading definitions from package biodbNci version 1.12.0. INFO [20:04:21.189] Loading definitions from package biodbUniprot version 1.14.0. INFO [20:04:21.467] Load 3 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. Quitting from biodbChebi.Rmd:63-65 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! XML content does not seem to be XML: '' --- Backtrace: ▆ 1. └─chebi$getEntry(c("2528", "17053", "15440")) 2. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop) 3. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 4. └─self$createEntryFromContent(...) 5. └─entry$parseContent(single.content) 6. └─private$doParseContent(content) 7. └─XML::xmlInternalTreeParse(content, asText = TRUE) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'biodbChebi.Rmd' failed with diagnostics: XML content does not seem to be XML: '' --- failed re-building ‘biodbChebi.Rmd’ SUMMARY: processing the following file failed: ‘biodbChebi.Rmd’ Error: Vignette re-building failed. Execution halted