“long vectors not supported yet” error in Rmd but not in R Script

I also ran into this today, and fixed it by using cache.lazy = FALSE in the setup chunk in my .Rmd.

So what is inside of the first chunk in my R Markdown file looks like this:

library(knitr)
knitr::opts_chunk$set(cache = TRUE, warning = FALSE, 
                      message = FALSE, cache.lazy = FALSE)