By default, rmarkdown::render uses the directory of the template (.Rmd) file for temporary files. For phenoptrReports, this is the inst/rmd directory, which may not be writable. Use the intermediates_dir argument to render to put temp files in the output directory, which must be writable.
By default,
rmarkdown::renderuses the directory of the template (.Rmd) file for temporary files. For phenoptrReports, this is theinst/rmddirectory, which may not be writable. Use theintermediates_dirargument torenderto put temp files in the output directory, which must be writable.