# New guidance on using system R and R libraries


# New R version updates

I've written on the topic of R libraries before:
- [Using system R installs](/posts/using-system-r-with-user-installed-packages)
- [Updating R libraries after updating](/posts/updating-r-libraries-after-r-version-update)

With the latest update to [R-4.3.1](../../../updates/r-4.3.1), we've had
to change the install location and type, so we felt that an update post was in
order.

Let's cover how to activate these new installs and how we are suggesting folks
manage their R libraries going forward.

## New install locations

New R installations will be managed using `micromamba`, which is a sort of
extension and alternative implementation of a subset of `conda` commands and
`conda` channels. Installs will be subdirectories here:

```console
/local/cluster/micromamba/envs/R-x.x.x
```

## Activating the R install

You will identify the R version you wish to activate, e.g. `4.3.1` and
determine if an install is made for this version:

```console
$ ls /local/cluster/micromamba/envs/R-4.3.1
 activate.sh   conda-meta   fonts     libexec   scripts   var
 bin           doc          include   man       share     x86_64-conda-linux-gnu
 cmake         etc          lib       sbin      ssl       x86_64-conda_cos6-linux-gnu
```

If the version is not installed, please
[submit a support request](https://shell.cqls.oregonstate.edu/support/)

{{< admonition tip "Submitting good support requests" true >}}
<https://software.cqls.oregonstate.edu/tips/posts/faq/#support-tickets>
{{< /admonition >}}

To activate `R-4.3.1` temporarily, you can check out a node with `qrsh` and run:

```console
bash
source /local/cluster/micromamba/envs/R-4.3.1/activate.sh
```

Then, you can just run `R` and give it a trial to see if you are satisfied with
the new version. To make the changes permanent across logins, you'll need to
modify your `$PATH` environment variable in your `~/.bashrc` or `~/.cshrc` e.g.

```console
echo 'export PATH=/local/cluster/micromamba/envs/R-4.3.1/scripts:${PATH}' >> ~/.bashrc
echo 'setenv PATH /local/cluster/micromamba/envs/R-4.3.1/scripts:${PATH}' >> ~/.cshrc
```

Then, when you log in next time, you'll have access to `R` and `Rscript` for
that R version.

## Managing R libraries

One difficulty with managing R libraries across different R installs is that
sometimes a R library installed for the system will be incompatible with
R libraries installed in a conda environment. In the past, I've suggested a
method to install R libraries in a particular directory and set the `R_LIBS`
variable to point to that R library directory, and unset `R_LIBS_USER`.

At the time, this information and plan made sense because managing R installs
was easier and R could be compiled using CentOS system `gcc` and other standard
system libraries. Now, using the system `gcc` to compile R and libraries is not
possible because it is too out-of-date.

At this time, we are going to use a multi-tiered approach to managing R libraries:

1. Some R libraries will be managed with `conda` because the CentOS 7 binaries
   and c/c++ libraries are incompatible.
   - These R libraries will be found in e.g.
     `/local/cluster/micromamba/envs/R-4.3.1/lib/R/library`
2. Some R libraries are commonly used and will be installed in the site libraries
   directory. This allows CQLS employees easy access to install packages for
   folks and to help troubleshoot issues.
   - These R libraries will be found in e.g.
     `/local/cluster/R/x86_64-conda-linux-gnu-library/4.3`
3. Some R libraries will be required by some users and will be managed by users
   pointing R to their own user-managed directories using either `$R_LIBS` or
   `$R_LIBS_USER`.
   - These R libraries will be found in e.g.
     `/nfs/dept/lab/home/user/opt/R/...`
     
The conda libraries and R site libraries should be accessible to you with no
additional actions of your own. To set up your user-managed R libraries, we
suggest a novel (to us) method based on the
[R documentation](https://rdrr.io/r/base/libPaths.html).

The novelty is that you do not need to specify a single directory to house your
R libs, but take advantage of some variable expansion that is built in to how
R parses the `$R_LIBS_SITE` and `$R_LIBS_USER` environment variables. As an
example, we set `R_LIBS_SITE='/local/cluster/R/%p-library/%v'` for you, and R
will be able to identify a major.minor version specific R library folder based
on if the R was installed using conda or the system.

Users can take advantage of this as well.

As an example, I set my R library environment variables like this:

```console
unset R_LIBS
export PATH=/local/cluster/micromamba/envs/R-4.3.1/scripts:${PATH}
export R_LIBS_USER='/nfs4/core/home/davised/opt/R/%p-library/%v'
```

The caveat to using this approach is that directories that are not generated
prior to starting R will not be used for R library installs. To determine if
a directory is present and being used:

```console
$ Rscript -e '.libPaths()'
[1] "/nfs4/core/home/davised/opt/R/x86_64-conda-linux-gnu-library/4.3"
[2] "/local/cluster/R/x86_64-conda-linux-gnu-library/4.3"
[3] "/local/cluster/micromamba/envs/R-4.3.1/lib/R/library"
```

If you do not see your own user directory, but only the conda libraries and site
libraries, then you can see where R is expecting to find a directory, and then
generate that directory like this:

```console
$ Rscript -e 'Sys.getenv("R_LIBS_USER")'
[1] "/nfs4/core/home/davised/opt/R/x86_64-conda-linux-gnu-library/4.3"
$ mkdir -p /nfs4/core/home/davised/opt/R/x86_64-conda-linux-gnu-library/4.3
```

## Common issues

If you cannot install new R libraries, ensure the directory that R is expecting
to find exists, as above. If you are certain that part is correct, send a
[support ticket](https://shell.cqls.oregonstate.edu/support/) with the R
library, R version, and R install location.

If you are having issues with incompatible R libraries, make sure you have unset
your `$R_LIBS` or `$R_LIBS_USER` as appropriate and/or they are not pointing to
a directory with libraries from a different R version.

If you cannot update a particular R library that you really need updated 
because, e.g. the library is installed in the conda env libraries or site
libraries, send a
[support ticket](https://shell.cqls.oregonstate.edu/support/) with the R
library, R version, and R install location.