This chapter describes the installation of R packages and servers to create a data science workbench. Deployments using Docker, e.g. https://github.com/rocker-org/rocker, are easier to install, however, using system users (e.g. AD users provided via winbind) for the RStudio user management requires a non-docker install.
Assuming the VM runs Ubuntu 14.04 "Trusty Tahr":
add R repo to
/etc/apt/sources.listinstall system packagegs
install R libraries
download and install RStudio Server and RWhiny Server
sudo su
echo "deb http://cran.csiro.au/bin/linux/ubuntu trusty/" >> /etc/apt/sources.list
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 apt-get update && apt-get -y upgrade apt-get -y dist-upgrade reboot
apt-get -y install r-base r-base-dev gdebi-core texlive-full htop ncdu libcurl4-openssl-dev libxml2-dev
sudo su - -c "R -e "install.packages(c('shiny', 'shinyIncubator','markdown','whisker','Hmisc','dplyr','tidyr','lubridate','qcc','httr','RCurl','curl','devtools'), repos='http://cran.rstudio.com/');devtools::install_github("ropensci/ckanr")""
wget -O /tmp/rstudio.deb https://download2.rstudio.org/rstudio-server-0.99.467-amd64.deb gdebi -n /tmp/rstudio.deb wget -O /tmp/shiny.deb https://download3.rstudio.org/ubuntu-12.04/x86_64/shiny-server-1.4.0.721-amd64.deb gdebi -n /tmp/shiny.deb
/home/ubuntu/shiny-serve$ git clone [email protected]:florianm/shiny-timeseries.git
Configure as in :doc:`workbench`.
Notes on Shiny's app dir:
- RStudio Server lets ubuntu access files only in own home directory
/home/ubuntu. - RShiny Server can use any directory as app directory, default is
/srv/shiny-server. - The external volume has enough space (100GB) and can be snapshotted (btrfs).
- The correct folders have already been created in the DevOps chapter.
/srv/shiny-serveris a symlink to/mnt/btrfsvol/shiny-server.- The user ubuntu's home directory contains another symlink to
/srv/shiny-server.