README.md

In paulklemm/regression-heatmap-r-package: Regression Heat Map R Backend for Access with OpenCPU

Installation Ubuntu Single User Server

sudo apt-get update
sudo apt-get upgrade
sudo apt-get r-base
apt-get install libcurl4-gnutls-dev
sudo apt-get install openjdk-7-*
# https://stackoverflow.com/questions/16438073/unable-to-install-rjava-in-r-3-0-in-ubuntu-13-04
sudo R CMD javareconf
sudo apt-get libssl-dev
# Now we have all requirements; launch R
sudo R
install.packages('devtools')
devtools::install_github('paulklemm/regression-heatmap-r-package')
install.packages('opencpu')
# Launch OpenCPU on Port 5003
opencpu::opencpu$start(5003)

For large computations it might be necessary to replace increase the timeout (usually set to 90 seconds) under ~/.opencpu.conf ("timelimit.post": 90).

Create a fixed IP

Edit /etc/network/interfaces (http://wiki.ubuntuusers.de/interfaces)

Example

# This file describes the network interfaces available on your system
# and how to activate them. For more information, see interfaces(5).

# The loopback network interface
auto lo
iface lo inet loopback

# The primary network interface
auto eth0
# iface eth0 inet dhcp

iface eth0 inet static
address 172.27.212.10
netmask 255.255.0.0
network 172.27.0.0
broadcast 172.27.0.255
gateway 172.27.100.100
dns-nameservers 172.27.0.12 141.44.23.23
dns-search isg.intern

Optional: Install SSH and VNC

• sudo apt-get install openssh-server
• sudo apt-get install x11vnc

Old keys for the machine in the ssh client need to be replaced by running ssh-keygen -R hostname and replace the keys under ~/.ssh/known_host.

I had trouble running x11vnc under Gnome, so I've installed XFCE through sudo apt-get install xubuntu-desktop gksu leafpad synaptic and chose the xfce session at login (through the ubuntu logo).

This repository is licensed under Attribution-NonCommercial-NoDerivatives 4.0 International (see LICENCE.md)

I will change the licence to http://choosealicense.com/licenses/mit/ as soon as the associated paper gets accepted.

Workaround for Java Loading Error

rJava and OpenCPU currently don't play nice together. We start OpenCPU in single user mode to bypass this problem. To do this, simply create a R file starting OpenCPU on the correct port and then adding a CRON job for it, so it is automatically loaded on startup.

Create the Script

touch startOpenCPU.R
nano startOpenCPU.R
  # Add following code without the `#`
  # opencpu::opencpu$start(5003)
  # opencpu::opencpu$stop()
  # opencpu::opencpu$start(5003)
sudo crontab -e
  # Add `sudo R CMD BATCH [path-to-script]/startOpenCPU.R`

OpenCPU should start in single user mode on startup now. If its not, look into the log for troubleshooting using grep CRON /var/log/syslog.

Note that this is a quick-fix until the issue is resolved!

paulklemm/regression-heatmap-r-package documentation built on May 24, 2019, 8:45 p.m.