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I have recently upgraded to El Capitan and I can't make knitr work with texmaker anymore. I have red all the issue concerning MacTex and the change in the path from /usr to /Library/Tex but here I can't figure out what is happening.

I have set up a knitr command : Rscript -e "knitr::knit2pdf('%.Rnw')" but texmaker refuses to run it. When I copy and paste the error message into the terminal it works fine so there is no typo error. I don't understand what's going on!

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    @noname Not a Mac user, but do run knitr with texmaker in Windows. Suggestion. verify that you can run that specific command Rscript -e "knitr::knit2pdf('%.Rnw')" with the replacement of the % with an existing (in the current folder) Rnw file. If you cannot run it from a command shell, then the problem is one of paths in the operating system.
    – R. Schumacher
    Nov 23, 2015 at 5:24
  • Thanks for the comment it makes me look onto Rscript localisation, and then finally fix the bug ! I add the anwser below
    – ClementWalter
    Nov 23, 2015 at 12:06

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The solution is to specify the full path to the Rscript command and to modify the .Rprofile file as well to add latex to your R session:

  • in texmaker I have now /Library/Frameworks/R.framework/Resources/Rscript -e "knitr::knit2pdf('%.Rnw')" (this is default location on Mac, but you can get yours by typing R.home() in a R session)
  • in my .Rprofile I used the solution from this SO post, ie I write Sys.setenv("PATH" = paste(Sys.getenv("PATH"),"/Library/TeX/texbin",sep=":")) (the .Rprofile is a hidden file on /Users/my_user_name directory`)

Hope this can help !

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