# Using system R with user installed packages


In my previous posts [here](/posts/installing-user-r-version-on-infrastructure)
and [here](/posts/updating-r-libraries-after-r-version-update), 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:

```
# 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:

```
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:

```
$ 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](/posts/installing-user-r-version-on-infrastructure).

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.

```
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:

```
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:

```
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:

```
> 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](http://shell.cgrb.oregonstate.edu/support/). Help
us out by choosing cgrb-software from the dropdown menu.

Thanks, and good luck!