Fix r fenced block that was changed in https://github.com/lcolladotor/markdown-redcarpet.tmbundle/commit/6d8cb9d1def67910b33e17c50d93e31a5d6cf6f1 Note that the rmarkdown format uses {} to specify options for the code chunk.
Change knitrBootstrap command to make it more general by using rmarkdown::render()