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I updated my Mac to OS X El Capitan and knitr doesn't work on it. Before the update everything was fine. Now LyX is saying : "The module knitr requires a package that is not available in your LaTex installation". But before the update it was available!

So I can't compile my documents. Can someone help me?

2

I had the same problem with El Capitan, knitr and TeXShop. The issue is related to new security features of El Capitan that restrict access to the /usr folder. I reinstalled the latest versions of MacTeX and R and now am able to compile knitr files just fine.

For additional detail, see this explanation (though it doesn't address knitr): https://tug.org/mactex/UpdatingForElCapitan.pdf

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I also had this problem thanks to the restrictions on writing to /usr in El Capitan. Redownloading R and MacTex does solve the problem, as mentioned in another answer, but you can avoid re-downloading MacTex by entering this into terminal:

cd /Library/TeX
sudo ln -s Distributions/Programs/texbin texbin
echo "/Library/TeX/texbin" >~/Desktop/TeX
sudo cp ~/Desktop/TeX /etc/paths.d/TeX

Rscript is off limits now though, thanks to the changes. Try checking in Terminal: which Rscript. I had to re-download R though, which worked. Now when I do which Rscript I get:

/usr/local/bin/Rscript

Alternatively, try running in Rstudio, which accesses R directly.

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