############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data dar ### ############################################################################## ############################################################################## * checking for file ‘dar/DESCRIPTION’ ... OK * preparing ‘dar’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘article.Rmd’ using rmarkdown [WARNING] This document format requires a nonempty element. Defaulting to 'article.knit' as the title. To specify a title, use 'title' in metadata or --metadata title="...". --- finished re-building ‘article.Rmd’ --- re-building ‘dar.Rmd’ using rmarkdown --- finished re-building ‘dar.Rmd’ --- re-building ‘data_import.Rmd’ using rmarkdown Quitting from lines 151-166 [unnamed-chunk-6] (data_import.Rmd) Error: processing vignette 'data_import.Rmd' failed with diagnostics: 'rank' must be a value from taxonomyRanks(). • Rename the columns from the tax_table slot of your input phyloseq with standard names. • Standard names: Kingdom, Phylum, Class, Order, Family, Genus, Species. --- failed re-building ‘data_import.Rmd’ --- re-building ‘filtering_subsetting.Rmd’ using rmarkdown --- finished re-building ‘filtering_subsetting.Rmd’ --- re-building ‘import_export_recipes.Rmd’ using rmarkdown --- finished re-building ‘import_export_recipes.Rmd’ SUMMARY: processing the following file failed: ‘data_import.Rmd’ Error: Vignette re-building failed. Execution halted