Linux Installation

Install xcms, CAMERA, and LOBSTAHS under Linux (Debian Jessie)

Warning: this installation takes a very long time.

Install prereqs

You will need to have superuser privileges or use sudo to run the apt-key and apt-get commands.

apt-get install -y libnetcdf-dev libssl-dev software-properties-common libcurl4-openssl-dev

Install R from CRAN Debian repository

This is necessary. The versions of R in the Debian package repositories are not new enough.

apt-key adv --keyserver keys.gnupg.net --recv-key 6212B7B7931C4BB16280BA1306F90DE5381BA480
add-apt-repository 'deb http://cran.rstudio.com/bin/linux/debian jessie-cran3/'
apt-get update
apt-get install r-base

The keyserver and repository for Ubuntu are different, see this link for details

Install Bioconductor prereqs

In R:

source("https://bioconductor.org/biocLite.R")
biocLite()
biocLite("devtools")
biocLite("CAMERA")

The last step above will take a very long time, as large packages such as mzR are built from source.

Install LOBSTAHS from GitHub

In R:

library(devtools)
install_github("vanooylipidomics/LOBSTAHS")