Getting Yosemite and R to play nice...

yosemiteR.md

Getting Yosemite and R to play nice

Here are some tips on getting R development working with Yosemite. Contribute what you know below and I'll add it in.

• Thread on R-SIG-Mac.
• October 2014 posts on R-SIG-Mac.

homebrew

I went ahead and re-installed all of my homebrew. You can find out what you have installed with

brew leaves

so you can make a note of what you want to re-install. You can then uninstall with this script.

@ateucher suggests (in the comments) that one moves the whole /usr/local/ per "Option 1" on this page.

tcltk/X11 issues

Seems like some of the libraries installed by XQuartz get hammered during installation. You need to download the package and re-install. XQuartz homepage.

(From Peter Dalgaard in R-SIG-Mac)

By default, my plot device was set to be X11 (which looks pretty horrible). Adding the following line to my .Rprofile got me back to Quartz device plotting:

options(device="quartz")

Why is happens is explained by Simon Urbanek in this R-SIG-Mac post.

LaTeX/MacTeX/TexLive

Seems to get hammered too, so need to download (the GIANT installer) again... http://tug.org/mactex/. If you haven't installed Yosemite yet, there are some tips on "avoiding the problem" (plus other tips).

knitr/pandoc

Building a PDF in RStudio gives the following error:

pandoc: pdflatex not found. pdflatex is needed for pdf output.
Error: pandoc document conversion failed with error 41
Execution halted

No TeX installation detected (TeX is required to create PDF output). You should install a recommended TeX distribution for your platform:

  Windows: MiKTeX (Complete) - http://miktex.org/2.9/setup
  (NOTE: Be sure to download the Complete rather than Basic installation)

  Mac OS X: TexLive 2013 (Full) - http://tug.org/mactex/
  (NOTE: Download with Safari rather than Chrome _strongly_ recommended)

  Linux: Use system package manager

This Stack Overflow thread gives some (short term) solutions.

The recommendation being that you run RStudio from the command line

$ open /Applications/RStudio.app

and that this will ensure that the PATH environment variable is correctly forwarded to RStudio, so it will find LaTeX.

As @hadley points out in the comments, "R 3.1.2 or latest RStudio should fix any path problems."

An option for the PATH issue could be using Sys.setenv within .Rprofile, potentially?

For the homebrew issue, I moved /usr/local out of the way, and then moved it back once Yosemite installation was finished, as per Option 1 here. Upgrade was quick, and it seems to have worked well.

@richfitz from within RStudio:

> Sys.getenv("PATH")
[1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/git/bin:/usr/texbin"

and from terminal:

dill@nibbler2 ~$ which pdflatex
/usr/texbin/pdflatex

So I think it's whatever environment that pandoc/pdflatex are using which is different and the issue?

Did you have any success with that option?

See also John Fox's comments here: https://stat.ethz.ch/pipermail/r-sig-mac/2014-October/011141.html

R 3.1.2 or latest RStudio should fix any path problems.

just updated all packages in r (well and having a recent TEX version) worked for me (Yosemite, Rstudio 3.9.2)

Still had path problems with R.app GUI after update to R_3.1.3, for example, with finding pdflatex.
R version 3.1.3 (2015-03-09) -- "Smooth Sidewalk"
Platform: x86_64-apple-darwin13.4.0 (64-bit)
[R.app GUI 1.65 (6913) x86_64-apple-darwin13.4.0]

Opening from the command line fixed:

$ open /Applications/R.app