Using system R with user installed packages

In my previous posts here and here, I showed you how to maintain your own R install, and update the libraries after you update your own R version.

Today, I’m going to cover an easier topic, how to use the system R installs.

We have a variety of versions of R on the infrastructure. By default, you are most likely to use the system version of R that comes with CentOS 7, which is found in /usr/bin/R and /bin/R, which happens to be 3.3.1 and is from 2016.

Let’s take a look at what’s available that we have installed for you:

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# davised:Linux @ waterman in ~ [22:32:26]
$ ls -1d /local/cluster/R-*
/local/cluster/R-3.2.5
/local/cluster/R-3.3.1
/local/cluster/R-3.3.1.c7
/local/cluster/R-3.3.2
/local/cluster/R-3.4.1
/local/cluster/R-3.4.2
/local/cluster/R-3.5.0
/local/cluster/R-3.5.1
/local/cluster/R-3.6.0
/local/cluster/R-3.6.1
/local/cluster/R-4.0.2

To get the latest version of R accessible to you, we’ll need to edit your .cshrc or .bashrc depending on which shell you are using.

Here are the commands to do so:

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echo 'export PATH=/local/cluster/R-4.0.2/bin:${PATH}' >> ~/.bashrc
echo 'setenv PATH /local/cluster/R-4.0.2/bin:${PATH}' >> ~/.cshrc

You can log out and log back in, or source the appropriate file to make sure the changes have taken place:

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$ R --version
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.

You can maintain your packages in your lab space the same way as I previously covered in the first post.

You might simplify the path a bit, and you can decide if you want to maintain a record of packages for each R install, e.g.

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mkdir -p /nfs3/CGRB/home/davised/opt/R/library/4.0.2
export R_LIBS=/nfs3/CGRB/home/davised/opt/R/library/4.0.2 #bash
setenv R_LIBS /nfs3/CGRB/home/davised/opt/R/library/4.0.2 #tcsh

Then, you can iterate directories when new verisons come out, e.g. if 4.0.3 is the next version:

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mkdir -p /nfs3/CGRB/home/davised/opt/R/library/4.0.3
export R_LIBS=/nfs3/CGRB/home/davised/opt/R/library/4.0.3 #bash
setenv R_LIBS /nfs3/CGRB/home/davised/opt/R/library/4.0.3 #tcsh

OR, for a more simple library variable:

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mkdir -p /nfs3/CGRB/home/davised/opt/R/library
export R_LIBS=/nfs3/CGRB/home/davised/opt/R/library #bash
setenv R_LIBS /nfs3/CGRB/home/davised/opt/R/library #tcsh

You need to add the export or setenv commands, for bash and tcsh into your .bashrc or .cshrc files, respectively, for the commands to remain after login/logout.

Load up an R session and test out the new $R_LIBS environment variable that you set:

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> install.packages("remotes", repos="https://ftp.osuosl.org/pub/cran")
Installing package into ‘/nfs3/CGRB/home/davised/opt/R/library’
(as ‘lib’ is unspecified)

You’ll see that I went with the second option. I generally copy a backup of the library dir to a backup folder on big version jumps, just in case some error really slows down my work, I have something to fall back to. But, otherwise, having a single folder for R libraries has not caused me too much trouble.

Whatever way you maintain your R, be it through the /local/cluster/R- versions or your own, you should be covered.

Feel free to request R version upgrades if we don’t get to them soon enough using the relatively new cgrb-software request form. Help us out by choosing cgrb-software from the dropdown menu.

Thanks, and good luck!