############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data hmdbQuery ### ############################################################################## ############################################################################## * checking for file ‘hmdbQuery/DESCRIPTION’ ... OK * preparing ‘hmdbQuery’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘hmdbQuery.Rmd’ using rmarkdown Quitting from hmdbQuery.Rmd:37-41 [lk1] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `file()`: ! cannot open the connection to 'http://www.hmdb.ca/metabolites/HMDB0000001.xml' --- Backtrace: ▆ 1. └─hmdbQuery::HmdbEntry(...) 2. └─hmdbQuery:::hmxToList(prefix = prefix, id = id) 3. └─base::readLines(.hmxPath(prefix = prefix, id = id, ...)) 4. └─base::file(con, "r") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'hmdbQuery.Rmd' failed with diagnostics: cannot open the connection to 'http://www.hmdb.ca/metabolites/HMDB0000001.xml' --- failed re-building ‘hmdbQuery.Rmd’ SUMMARY: processing the following file failed: ‘hmdbQuery.Rmd’ Error: Vignette re-building failed. Execution halted