MathJax script issue after customizing rstudio.markdownToHTML()

Question

With knit2html() from the knitr package, I can generate html pages that contain latex equations and R code. But on my system equations are not rendered when using RStudio's "knit html" button.

It is because I have modified the way the "knit html" button works. To include a table of content on my html pages, I followed the Rstudio advice on Customize Markdown Rendering. And created an .Rprofile file at the root of the project directory that overrides default markdown rendering options. My .Rprofile only contains a function that replaces the rstudio.markdownToHTML() function as such:

options(rstudio.markdownToHTML = 
  function(inputFile, outputFile) {      
    require(markdown)
    htmlOptions <- markdownHTMLOptions(defaults=TRUE)
    htmlOptions <- c(htmlOptions, "toc")
    markdownToHTML(inputFile, outputFile, options = htmlOptions) 
  }
)

With this .Rprofile, I'm happy to have an automatic table of content generated on all my .RmD documents. But equations are not rendered any more! Equations appear as plain text.

If I delete .Rprofile, reload R and click the "knit HTML" button in R Studio. Equations are rendered correctly but I don't have a table of content.
If I run :

knit2html("file.Rmd", "file.html", options = c(markdownHTMLOptions(defaults=TRUE), "toc")))

Equations are rendered correctly and I have a table of content too.

Can you help me fix rstudio.markdownToHTML() so that it renders equations?

Edit 03 April 2014: Equations are visible if I open the html page in a web browser. They are not rendered in RStudio preview HTML pane. This might be an issue with the mathjax script not taken into account anymore by the Rstudio viewer?

It would be beneficial if you showed us what code you're currently using in your .Rprofile. — Dason
Thanks Dason, all that's in my .Rprofile, is now copied above. — Paul Rougieux
R version 3.0.2 (2013-09-25) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_Ireland.1252 LC_CTYPE=English_Ireland.1252 LC_MONETARY=English_Ireland.1252 [4] LC_NUMERIC=C LC_TIME=English_Ireland.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] knitr_1.5.21 MASS_7.3-29 loaded via a namespace (and not attached): [1] evaluate_0.5.1 formatR_0.10 stringr_0.6.2 tools_3.0.2 — Paul Rougieux
You could probably move your edit to an answer since it does sort of answer the question of how to make this work. — Dason

Paul Rougieux Paul Rougieux · Accepted Answer · 2014-04-23T16:20:44

Dason suggested me to post this as an answer.

Equations are visible if I open the html page in a web browser.

Equations are not rendered in RStudio preview HTML pane. This might be an issue with the Rstudio viewer?

MathJax script issue after customizing rstudio.markdownToHTML()

1 Answers