Chapter 6 OpenCPU deployment

6.1 Objective

This chapter describes how to install JAMES on the server that run OpenCPU. This is the classic way to install and run OpenCPU applications, and has the advantage that AppArmor prevents various types of malicious behaviour. In the future, we will replace this procedure by containerised deployment using Docker.

6.2 Pre-requisites

The server runs Ubuntu 18.04 (or later, not tested on Ubuntu 20.04).
The user needs sudo access to the server that run OpenCPU.

6.3 Installation of JAMES in

Here is a set of commands that removes R and its libraries, installs the latest R fresh from source, install JAMES and puts the machine to work.

A lot can go wrong. Please be patient to check each step.

#!/bin/bash
# Re-install opencpu-server, R and the libs

# make system up to date
sudo apt-get update
sudo apt-get upgrade

# disable opencpu
sudo a2dissite opencpu
sudo apachectl restart

# disable pubertyplot & webtool (only on testserver)
sudo a2dissite puberty
sudo a2dissite webtool
sudo apachectl restart

# save configuration files
mkdir conf
cp -rv /etc/opencpu/ ~/conf/
cp -rv /etc/apache2/ ~/conf/

# uninstall opencpu server & full
sudo apt-get purge opencpu-server
sudo apt-get purge opencpu-full

# remove all R libs
R -e '.libPaths()'
sudo rm -rf /usr/local/lib/R/site-library
sudo rm -rf /usr/lib/R/site-library
sudo rm -rf /usr/lib/R/library

# remove R
sudo apt-get purge r-base-core
sudo apt-get purge r-base
sudo apt-get autoremove

# add backport repositories for Ubuntu packages required by some R packages
sudo add-apt-repository 'deb https://mirror.nl.datapacket.com/ubuntu/ bionic main'
sudo add-apt-repository 'deb-src https://mirror.nl.datapacket.com/ubuntu/ bionic main'

# install R. See https://cran.r-project.org/bin/linux/ubuntu/
# update indices
sudo apt update -qq
# install two helper packages we need
sudo apt install --no-install-recommends software-properties-common dirmngr
# import the signing key (by Michael Rutter) for these repo
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
# we use R 4.0 (however note this actually installs R 4.1!! (May 2021))
sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/'
# in the future: use cran-41
sudo apt install r-base
# install r-base-dev because we want to compile from source
sudo apt-get install r-base-dev

# install opencpu-server
sudo add-apt-repository -y ppa:opencpu/opencpu-2.2
sudo apt-get update
sudo apt-get upgrade
sudo apt-get install -y opencpu-server

# restart opencpu
sudo a2ensite opencpu
sudo apachectl restart

# manually check https://vps.stefvanbuuren.nl/ocpu 
# or https://www.groeidiagrammen.nl/ocpu

# install application package: pubertyplot - only on dev server
sudo R -e 'install.packages("/home/stef/packages/pubertyplot_1.3.tar.gz", repos = NULL)'
sudo a2ensite puberty
sudo apachectl restart

# install application package: webtool - only on dev server
sudo R -e 'install.packages("RMySQL")'
sudo R -e 'install.packages("/home/stef/packages/webtool_1.1.tar.gz", repos = NULL)'
sudo a2ensite webtool
sudo apachectl restart

# install JAMES packages - this may take a while - you need the right priveledges
sudo R -e 'install.packages("remotes")'
sudo R -e 'remotes::install_github("growthcharts/james")'

# remove duplicate packages
# evade errors: "namespace 'vctrs' 0.3.6 is already loaded, but >= 0.3.8 is required"
sudo R -e 'remove.packages(c("ellipsis", "pillar", "vctrs"), "/usr/lib/opencpu/library")'

# copy back opencpu configuration for JAMES (if they were OK, otherwise tweak)
sudo rm -rf /etc/opencpu
sudo cp -rv ~/conf/opencpu /etc/opencpu/

# active JAMES
sudo apachectl restart

# check on https://tnochildhealthstatistics.shinyapps.io/james_tryout/ 

# clean up: delete ~/conf/ after everything works
rm -rf conf