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Using the RStudio image

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eitsupi edited this page Sep 10, 2021 · 25 revisions

Getting started

Here we outline how to use the rstudio image, which enables you to use RStudio in your browser via docker. These instructions also apply to using RStudio via the tidyverse images, just replace rocker/rstudio with rocker/tidyverse in the examples below.

Install the most current version of docker software as indicated for your platform.

Note: RStudio requires docker version >= 1.2 Some Linux repositories may have only older versions available, to ensure you get the latest version run curl -sSL https://get.docker.com/ubuntu/ | sudo sh. Fresh installs of the Docker Toolkit on Mac/Windows following the instructions above should be fine.

Running RStudio Server

  1. From the docker window, run:
$ sudo docker run -d -p 8787:8787 -e PASSWORD=<password> --name rstudio rocker/rstudio # replace <password> with a password of your choice

That will take a while to download the image the first time you run it. Linux users might want to add their user to the docker group to avoid having to use sudo. To do so, just run sudo usermod -a -G docker <username>. You may need to login again to refresh your group membership. (Mac and Windows users do not need to use sudo.)

  1. Once the download is finished RStudio-Server will launch invisibly. To connect to it, open a browser and enter in the ip address noted above followed by :8787, e.g. http://localhost:8787, and you should be greeted by the RStudio welcome screen. Log in using:
  • username: rstudio
  • password: <password>

and you should be able to work with RStudio in your browser in much the same way as you would on your desktop.

Folder sharing

To share files and folders between your docker image and your host OS you can use the -v option. This acts much like running RStudio in the working directory. More detailed instructions on running docker with folder sharing can be found on this wiki page.

Custom use

  • To customize the username and password: (important for publicly hosted/cloud instances)
$ docker run -d -p 8787:8787 -e USER=<username> -e PASSWORD=<password> rocker/rstudio
  • Launch an R terminal session instead of using RStudio. While not strictly necessary, we recommend always running interactive sessions with --user rstudio to avoid working as root. This is primarily a concern if you are linking local volumes (see below).
$ docker run --rm -it --user rstudio rocker/rstudio R
  • You can also launch a plain bash session
$ docker run --rm -it --user rstudio rocker/rstudio bash

Enable root

By default, the RStudio user does not have access to root, such that users cannot install binary libraries with apt-get without first entering the container (see docker exec as described below). To enable root from within RStudio, launch the container with the flag -e ROOT=TRUE, e.g.

$ docker run -d -p 8787:8787 -e PASSWORD=<password> -e ROOT=TRUE rocker/rstudio

You can now open a shell from RStudio (see the "Tools" menu), or directly from the R console using system(), e.g.

> system("sudo apt-get install -y libgsl0-dev")

(Note that the system() commands are non-interactive, hence the -y flag to accept the install.)

Multiple users

Once your RStudio-server instance is up and running on a publicly accessible web server, you may want to allow other users (such as collaborators or students) to access the same instance as well. The default configuration declares only a single user. Assuming that your container is already up and running with Docker version >= 1.3, you can use the following command to log into the running container:

$ docker exec -it <container-id> bash

where <container-id> is the container name or id assigned to your running RStudio instance (see docker ps). We can now do the usual linux root administration steps to add new users and passwords, e.g. run:

$ adduser <username>

to interactively create each new user and password (adding user contact details in the prompt is optional). You can then exit the prompt (type exit); your RStudio container is still running and now has the new users added.

Note: you should not link any shared volumes to the host on a container in which you are configuring multiple users.

Dependencies external to the R system

Many R packages have dependencies external to R, for example GSL, GDAL, JAGS and so on. To install these on a running rocker container you need to go to the docker command line and type the following:

$ docker ps # or docker image ls, find the ID of the running container you want to add a package to
$ docker exec -it <container-id> bash # a docker command to start a bash shell in your container
$ apt-get install libgsl0-dev # install the package, in this case GSL

The apt-get install line is a Debian command, and if you want to install library foo, the thing to install usually takes the form libfoo-dev.

Note: If you get an error such as "E: The value 'testing' is invalid for APT::Default-Release as such a release is not available in the sources", you should run apt-get update. In general with docker images you are expected to run apt-get update before installing.

Adding super users

rstudio (or any other specific user(s)) can be added to the sudoers file (using visudo) and given rights to run apt-get. This will make it possible to install system packages via the terminal in RStudio. These users can have root access depending on how permissive the sudoers settings are, so this approach should be used with caution.

Troubleshooting

Known Issues

With The Red Hat family derivatives, mainly CentOS and Fedora, the rstudio-based images may be unusable. This issue will prevent you from connecting to RStudio via your browser on the URL http://localhost:8787. When debugging with the curl command, you will notice that access is forbidden.

# curl localhost:8787
curl: (7) Failed to connect to localhost port 8787: Connection refused

Container log will print this output: s6-supervise (child): fatal: unable to exec run: Permission denied s6-supervise rstudio: warning: unable to spawn ./run - waiting 10 seconds

Until this issue is fix, a workable and clean solution is to start your container and log into. Then, from inside it, start rstudio-server.

# docker run -it -p 8787:8787 <RStudio image> /bin/bash
root@XXXYYY:/# rstudio-server start

Suggestions

Using docker via boot2docker can be a slightly less smooth experience than using docker on Linux. General strategies for making it work include:

  • Deleting the .boot2docker, .VirtualBox and VirtualBox VMs folders (take care to preserve your other VM images unrelated to boot2docker, if any). They will be replaced with new copies when you next run boot2docker.
  • Downgrading your version of Oracle VirtualBox to an earlier version. We've had success with VirtualBox 4.3.12 with boot2docker 1.3.0 on Windows 7.
  • If boot2docker is running ok but you get a connection error when trying to access RStudio in your browser, try quitting boot2docker, opening a regular terminal window and running boot2docker ssh -L 8787:localhost:8787 to force a port open, then run sudo docker run -d -p 8787:8787 rocker/rstudio and then point your browser to http://localhost:8787
  • If none of that helps, ask a question to the maintainers of this repository or on StackOverflow
  • To access the instance on <host_machine_ip>:8787 rather than <virtual_machine_ip>:8787 (forwarding host traffic to guest), do the following: (refer to https://github.com/docker/for-win/issues/204 for more info)
    • Go to VirtualBox -> Your BOX -> Settings -> Network ->
    • Choose NAT
    • Open Advanced
    • Click Port Forwarding
    • Add new rule to map whatever port you need from host to guest
    • Click OK, OK
    • Restart the docker instance if necessary (in case the running instance is not picking up the new config)

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