Render your R Markdown documents in a temporary directory


Pandoc has a known bug where it will occasionally error when running on a file located on a Windows share mounted on a Linux machine. This affects R Markdown documents because they are passed to Pandoc after knitting with knitr.


A potential solution is to first copy the R Markdown file and all its supporting files to a temporary directory on the Linux machine, render the document there, and then copy everything back to the original directory in the Windows share.

tmpsite is a prototype R package that uses a custom site generator, tmp_site, to accomplish this. To start rendering in a temporary directory, install the package from GitHub and then run the one-time setup in the directory that contains the R Markdown files.


To ensure this works:

How this works

If RStudio sees a file named index.Rmd in the same working directory, it will search this for a site generator. Thus placing an otherwise empty index.Rmd file that specifies to use tmp_site as the generator is sufficient to override the normal rendering process.

Room for improvement

This is just a quick prototype. Potentially by setting the Knit Directory, it may be possible to only copy the R Markdown file to the temporary directory (as opposed to the entire directory as is currently done). This would have multiple benefits: 1) faster because less to copy and 2) paths to files outside of the project directory could be used.

Another limitation is that tmp_site currently only supports rendering one file at a time, and thus will throw an error if provided a directory. This was done out of convenience and it would be straightforward to enhance the functionality to be similar to rmarkdown::default_site.


This code is in the public domain, i.e. CC0.

jdblischak/tmpsite documentation built on Feb. 15, 2018, 1:02 p.m.