The javascript included into your HTML result with rmarkdown will depend on the output format used and also the content of the document. Any feature used that requires JS or CSS will create a line in the header of the document.
With a default html_document, you will have some JS and CSS because there is some feature like table of content, boostrap theming, code folding, tabset, ... This will lead to some html dependencies being including in the doc.
The doc of html_document can give you some hints on this
You can also provide a custom template if you want to have full control over what is produced, but you need to learn about Pandoc, and some features of rmarkdown or R packages may not work unless you know how to tweak.
Hope it helps