############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/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 [16:26:57.979] Loading definitions from package biodb version 1.16.1. INFO [16:26:59.515] Loading definitions from package biodbChebi version 1.14.0. INFO [16:26:59.545] Loading definitions from package biodbHmdb version 1.14.0. INFO [16:26:59.576] Loading definitions from package biodbNcbi version 1.12.0. INFO [16:26:59.607] Loading definitions from package biodbNci version 1.12.0. INFO [16:26:59.615] Loading definitions from package biodbUniprot version 1.14.0. INFO [16:26:59.727] Load 3 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649. Quitting from biodbChebi.Rmd:94-96 [unnamed-chunk-8] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `self$wsWsdl()`: ! object 'BiodbUrl' not found --- Backtrace: ▆ 1. └─chebi$searchCompound(name = "aspartic", max.results = 3) 2. └─self$searchForEntries(list(name = name), max.results = max.results) 3. └─private$doSearchForEntries(fields = fields, max.results = max.results) 4. └─self$wsGetLiteEntity(...) 5. ├─chk::chk_subset(search.category, self$getSearchCategories()) 6. │ └─chk::vld_subset(x, values) 7. │ └─x %in% values 8. └─self$getSearchCategories() 9. └─self$getWsdlEnumeration("SearchCategory") 10. ├─XML::xpathSApply(...) 11. │ └─XML::xpathApply(...) 12. └─self$getWsdl() 13. └─self$wsWsdl(retfmt = "parsed") 14. └─self$makeRequest(...) 15. └─sched::Request$new(...) 16. └─sched (local) initialize(...) 17. └─chk::chk_is(url, "URL") 18. └─chk::vld_is(x, class) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'biodbChebi.Rmd' failed with diagnostics: object 'BiodbUrl' not found --- failed re-building ‘biodbChebi.Rmd’ SUMMARY: processing the following file failed: ‘biodbChebi.Rmd’ Error: Vignette re-building failed. Execution halted