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I'm trying to update R from 3.2.2 (Fire safety) to 3.3.1 (Bug in your hair) on MacOS 10.11.15 (El Capitan).

Initially I tried to use the R-3.3.1.pkg from CRAN, which allowed me to use the new version in R.app. However when trying to access R through terminal, and through Sublime REPL, the previous version appears even though the installation should have deleted previous copies of R.

How do I fully delete the old copy? In El Capitan, the Frameworks folder is no longer present, so the previous fix:

rm -rf /Library/Frameworks/R.framework /Applications/R.app \    
/usr/bin/R /usr/bin/Rscript

Does not work.

P.S. (meta) how can I fireproof myself against these OS conflicts in future? Should I just run R through a VM?

Czeslaw
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1 Answers1

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This was the problem for me.

Anaconda, the python distribution provided by continuum analytics, contains a copy of R for some reason.

Therefore, if you delete your copy of R from CRAN, that (outdated) copy of R will become the default R for use in terminal, sublimeREPL, etc.

In general, booting up R and running R.home() will reveal the installation directory.

Since I want to use R and python, and update them independently, I will stop using Anaconda.

Czeslaw
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  • https://www.continuum.io/content/preliminary-support-r-conda (which means you could just update it through conda, too) – hrbrmstr Jul 09 '16 at 09:58
  • That is good to know. However this has highlighted for me that using big distributions like anaconda, given the potential for unexpected conflicts like this, is not worth it for me. – Czeslaw Jul 09 '16 at 12:34