05-helpers.Rmd

# Miscellaneous Helpers

If you worked through all these steps, you are almost good to go.
Here are have some additional recommendations to make your server life easier.

## byobu

`byobu` is a wrapper for your SSH session that makes it possible to close your terminal session and not loose the command running in it.
If you start long running jobs, you can safely start them in a `byobu` window without worrying about them to quit once you shut down your machine.

Run `byobu` after being logged in and a `byobu` session will be launched.

You can open multiple ones with `byobu -S <session name>`, e.g. `byobu -S session2`.
Once you have multiple ones open, an interactive prompt will ask you which one you want to start next time.

## radian {#radian}

`radian` is an optimized R command line tool. 
You will notice the benefits compared to the default `R` once you start using it.
You need to install it via `pip` which is already installed if you installed `python`.

Usually `setuptools` needs to be upgraded first.

```sh
pip3 install --user --upgrade setuptools
pip3 install --user radian
```

Now you can either always use `radian` or set an alias in your `.bashrc` , e.g. `alias r="radian"`.
Note that `radian` only works if you have set the env variable `R_HOME` correctly.
See [here](#R) for more details.

If is does not work at this moment, you might need to add the binary to your `$PATH` variable in your `~/.bashrc`.

```sh
export PATH=~/.local/bin:$PATH
```

## ccache

If you load `ccache`, you will speed-up source installations of R packages a lot.
(On Linux, all R packages are installed from source.)
Besides loading `ccache`, you also need to create the following file in your home directory (`~/.R/Makevars`):

(Note that you need to create the folder first, it does not exist by default (`mkdir ~/.R/`).)

```sh
CXX_STD = CXX14

VER=
CCACHE=ccache
CC=$(CCACHE) gcc $(VER)
CXX=$(CCACHE) g++$(VER)
C11=$(CCACHE) g++$(VER)
C14=$(CCACHE) g++$(VER)
FC=$(CCACHE) gfortran$(VER)
F77=$(CCACHE) gfortran$(VER)
```

When installing a package now, you will occasionally see that the `gcc` lines are prefixed with `ccache`.
This means that this `gcc` call was already executed once and is now loaded from the cache rather than being run again.
This saves a lot of time, especially for packages that take long to install (`dplyr`, `Rcpp`, `stringi`).

## Create a bash alias for your project {#wrapper}

Often you might want to use an {renv} library in a specific directory with a specific R version after having logged into the server.

Rather than navigating there all the time by hand and loading the R version manually, you can create an alias that does this for you.
You can of course also use this approach without {renv}  - just to load a specific version. 

```
alias my-project="cd /path/to/project && <load custom R env module> && R"
```