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RStudio-Server install with Anaconda

Setting up RStudio-Server with the `ezj -R` function on Atmosphere

Recently we set up a ez script which is executed in the terminal or web shell to install Anaconda3 with Jupyter Notebook. One of the features is to install R kernel with Jupyter. It also installs r-essentials with numerous common R packages.

  1. Be sure to run ezj -R first. Reference documentation above if you have not. To set up RStudio-Server with the conda installation of R you need to set up the bash profile.
  • Add anaconda3 to your path

export PATH="/opt/anaconda3/bin:$PATH"

  • Change ownership of the /opt/anaconda3/ directory

sudo chown ${USER}:iplant-everyone /opt/anaconda3/ -R

  • Add a path to your ~/.bash_profile:

echo "export RSTUDIO_WHICH_R='/opt/anaconda3/bin/R'" >> ~/.bash_profile

Note

You will need to exit and restart your terminal for these to take effect

  1. Install RStudio-Server using the latest version
.. Ubuntu::
  - In a terminal, reset the symbolic link for `libfortran.so`:
  ``sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib/libgfortran.so``

  - Install Dependencies
  ``sudo apt-get install gdebi-core g++``

  - Change to the `/opt` folder
  ``cd /opt``

  ``sudo wget https://download2.rstudio.org/rstudio-server-1.0.153-amd64.deb``

  ``sudo gdebi -n rstudio-server-1.0.153-amd64.deb``


.. Centos::

  ``cd /opt``

  ``sudo wget https://download2.rstudio.org/rstudio-server-rhel-1.0.153-x86_64.rpm``

  ``sudo yum install --nogpgcheck rstudio-server-rhel-1.0.153-x86_64.rpm``

Note

This will fail on the first try:

user_name@128:/home$ sudo gdebi rstudio-server-1.0.143-amd64.deb
Reading package lists... Done
Building dependency tree
Reading state information... Done
Reading state information... Done

RStudio Server
RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax    highlighting editor that supports direct code execution, as well as tools for plotting, history, and workspace management.
Do you want to install the software package? [y/N]:y
(Reading database ... 136874 files and directories currently installed.)
 Preparing to unpack rstudio-server-1.0.143-amd64.deb ...
 Unpacking rstudio-server (1.0.143) over (1.0.143) ...
 Setting up rstudio-server (1.0.143) ...
 useradd: user 'rstudio-server' already exists
 groupadd: group 'rstudio-server' already exists
 rsession: no process found
 Created symlink from /etc/systemd/system/multi-user.target.wants/rstudio-server.service to /etc/systemd/system/rstudio- server.service.
 Job for rstudio-server.service failed because the control process exited with error code. See "systemctl status rstudio- server.service" and "journalctl -xe" for details.
 ● rstudio-server.service - RStudio Server
 Loaded: loaded (/etc/systemd/system/rstudio-server.service; enabled; vendor preset: enabled)
 Active: active (running) since Sat 2017-05-13 09:30:40 MST; 13ms ago
   Process: 2226 ExecStop=/usr/bin/killall -TERM rserver (code=exited, status=1/FAILURE)
   Process: 2233 ExecStart=/usr/lib/rstudio-server/bin/rserver (code=exited, status=0/SUCCESS)
  Main PID: 2236 (rserver)
  Tasks: 3
  Memory: 824.0K
    CPU: 10ms
 CGroup: /system.slice/rstudio-server.service
         └─2236 /usr/lib/rstudio-server/bin/rserver

 May 13 09:30:40 xxx.xxx.xx.xxx systemd[1]: rstudio-server.service: Service hold-off time over, scheduling restart.
 May 13 09:30:40 xxx.xxx.xx.xxx systemd[1]: Stopped RStudio Server.
 May 13 09:30:40 xxx.xxx.xx.xxx systemd[1]: Starting RStudio Server...
 May 13 09:30:40 xxx.xxx.xx.xxx systemd[1]: Started RStudio Server.
 May 13 09:30:40 xxx.xxx.xx.xxx rserver[2236]: ERROR Unable to find an installation of R on the system (which R didn't return  va...pp:472
 May 13 09:30:40 xxx.xxx.xx.xxx systemd[1]: rstudio-server.service: Main process exited, code=exited, status=1/FAILURE
 Hint: Some lines were ellipsized, use -l to show in full.

  1. Modify /etc/rstudio/rserver.conf

    sudo sh -c 'echo "rsession-which-r=/opt/anaconda3/bin/R" >> /etc/rstudio/rserver.conf'

  2. Restart RStudio-Server

    sudo rstudio-server start

  3. Log into RStudio-Server

    • Copy the IP address for the VM from the Atmosphere browser window.
    • Paste the IP address into a new browser window
    • add :8787 port # to the IP address
    • Log in using your CyVerse Username and Password.

Installing Packages for R and RStudio-Server

Note

Because we are using Anaconda3, it is suggested that you use conda to install your R packages from a terminal

Examples

conda install -c r r-raster

conda install -c conda-forge gdal

Summary

This documentation is intended for use with CyVerse Atmosphere featured images. It has been tested on Ubuntu 16.04 and Centos 6.8 images.

Additional information, help

Search for an answer: CyVerse Learning Center or CyVerse Wiki

Post your question to the user forum: Ask CyVerse

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