Rendering both PDF and HTML is only possible interactively, not via script

[jemus42]

Describe the bug
I have some Rmd documents (weekly assignments) I want to render both as PDF (for turning them in) and HTML (for sharing them with classmates), and to make it easier, I use a simple build script that calls rmarkdown:render() for both formats:

#!/usr/bin/env Rscript

rmarkdown::render(input = "testing.Rmd", output_format = "html_document")
rmarkdown::render(input = "testing.Rmd", output_format = "pdf_document")

However, when used in a script, the commands yield an error when building the PDF:

Error: Functions that produce HTML output found in document targeting latex output.
Please change the output type of this document to HTML. Alternatively, you can allow
HTML output in non-HTML formats by adding this option to the YAML front-matter of
your rmarkdown file:

  always_allow_html: yes

Note however that the HTML output will not be visible in non-HTML formats.

Since it is possible to render both PDF and HTML interactively in RStudio through the "knit" button, I am confused as to what exactly I'm doing wrong. Also, your previous comments on Stackoverflow I found through googling suggest that kabelExtra functions are "smart" enough to decide for themselves which output format is required.

To Reproduce

I have prepared a demo project here: https://github.com/jemus42/Rmd-pdf-html-debug
You can clone the project, interactively render the testing.Rmd to PDF and HTML, and then execute the lines in the build.R script which should yield the described error.

I would like to know if this is some bug somewhere or if my understanding of the knitr/RMarkdown/kableExtra internals is merely insufficient.

Edit:
Tested this on macOS Mojave and Ubuntu 16.04, each with current R 3.5.1 and up to date packages (CRAN)

[haozhu233]

Hi, @jemus42 this question is kind of related with this SO question. The trick this time is to add envir = new.env(). I put the detailed explanation in my updated answer there.

In your case,

rmarkdown::render(input = "testing.Rmd", output_format = "html_document", envir = new.env())
rmarkdown::render(input = "testing.Rmd", output_format = "pdf_document", envir = new.env())

[jemus42]

Thank you! You have now solved my first and only problem with kableExtra so far! :)

[haozhu233]

@jemus42 👍👍👍