R markdown compile error:

Question

When I try to compile an Rmarkdown document to pdf, I get this error:

    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.

Does anyone know what this means?

Answer 1

Have you tried the following? (FROM: https://bookdown.org/yihui/bookdown/html-widgets.html)

install.packages("webshot")
webshot::install_phantomjs()

It worked for me. See also: https://github.com/rstudio/bookdown/issues/440

Answer 2

I ran into this problem when using Bookdown, and the accepted solution did not work in my context. I resolved it after figuring out what the "YAML front-matter of your RMarkdown file" is. With bookdown, there is a .travis.yml file and a _bookdown.yml file, but you want to leave these two alone and these are not what the error message is referencing.

The "front-matter" would be the top of your RMarkdown file (if using bookdown it would be the "index.Rmd" file), see screenshot below:

So just add always_allow_html: yes to the YAML header as its own line and it should work as expected (or give you a different error)