An alternative to "official" R
By "official" R, I mean the version of R issued by the R Foundation. Revolution Analytics has been a source of information, courses and a beefed-up commercial version of R (Revolution R Enterprise). They have also produced an open-source version, Revolution R Open. It is freely available from their Managed R Archive Network (MRAN). I'll leave the description of its features to them, and just mention the one that caught my eye: coupled with the Intel Math Kernel Library, it provides out-of-the-box multithreading, which should speed up long computational runs.Revolution Analytics is now a Microsoft property, and I can't being to describe the cognitive dissonance caused by downloading open-source software from Microsoft. Nonetheless, I decided to install RROpen. One catch is that it requires reinstalling pretty much every R package I use, which can be a bit time consuming. The remainder of this post is about the other catch: how to get RROpen and "official" R (henceforth "R" without any qualifications) to coexist peacefully, on a Debian-based distribution (Mint in my case).
What's the problem?
RRO and R install in different directories, so why is anything special necessary to let them coexist? I found out the hard way. After installing RRO (on a system that already had R), I found that the command R in a terminal launched /usr/bin/R, which RRO had replaced with its R binary, making itself the default choice. That was fine for me. This morning, though, the system package manager notified me that the r-base package had been updated. I authorized the update, which among other things resulted in <sigh>/usr/bin/R being replaced by the "official" R version</sigh>.That can be fixed manually from a terminal (as root), but it appeared that I was doomed to perpetually mediating between the two versions whenever the r-base package updated. This could be why Rich Gillin ("owner" of the Google+ Statistics and R community) recommended uninstalling R before installing RRO.
What's the solution?
Debian-based distributions of Linux use the Debian alternatives system to manage contention between different programs that have the same use. In essence, the system puts a link in a directory on the system command path that points not to a specific executable but to a directory containing choices for what program should answer to that name. Applied to our case, /usr/bin/R becomes a symbolic link to /etc/alternatives/R, which in turn is a symbolic link to the version of R you want to execute when you type R at a command prompt (or when, say, the RStudio IDE launches). In my case, that link points to /usr/lib64/RRO-3.2.0/R-3.2.0/lib/R/bin/R. (How would like to have to type that every time you wanted to run RRO?)
To manage alternatives, you can either use the update-alternatives command in a terminal or the Galternatives GUI for it. On my system, though, Galternatives does not entirely work. It lets you add alternatives once a base configuration is set, but it will not let you create (or delete) the initial configuration. So I went with the command line.
Assuming you have both RRO and R installed, here are the commands to set them up as alternatives:
sudo rm /usr/bin/R sudo update-alternatives --install /usr/bin/R R /usr/lib64/RRO-3.2.0/R-3.2.0/lib/R/bin/R 200 sudo update-alternatives --install /usr/bin/R R /usr/lib/R/bin/R 100
The anatomy of the middle line is as follows:
- sudo
- Run this stuff as root.
- update-alternatives
- Run the configuration update tool.
- --install
- I want to install a new alternative for a program. Other choices include --configure to alter the default choice, --list to show alternatives for a program, and --display to show a list including priorities.
- /usr/bin/R
- Where the link to the various alternatives will go. This should be somewhere on your command path. A program (such as RStudio) trying to execute R with no path, or using the default path for R, will look here and be forwarded to the chosen version. Similarly, if you just type R in a terminal, this is the program that will run.
- R
- The name used in the alternatives directory for the symbolic link to the actual executable.
- /usr/lib64/RRO-3.2.0/R-3.2.0/lib/R/bin/R
- The executable to be run.
- 200
- A priority value. The highest priority alternative becomes the default choice, unless you manually override it.
The first time I tried this (with /usr/bin/R being the RRO executable), I omitted the first line, and update-alternatives informed me that it had not created /usr/bin/R (presumably because it was reluctant to overwrite what was already there, despite running with root privileges). So I suggest deleting the current entry before setting up the alternatives. Also, as an aside, after running the first two lines, I was able to us Galternatives to enter the third one, and I can use Galternatives to change which is the default choice for R.
I tried reinstalling the r-base package after doing this, and the default R choice remained RRO, so I think this will survive upgrades to either system. We'll see.
