Installation

1. R requirement

R (http://www.r-project.org) is a language and environment for statistical computing and graphics. We assume R (version 3.1.0 or higher) has been installed in your local machine. The latest version can be installed following instructions below for different platforms (Windows, Mac, and Linux).

• Quick link for Windows: Download R for Windows.

• Quick link for Mac: Download R for Mac OS X 10.6 (Snow Leopard or higher).

• Below are shell command lines in Terminal (for Linux):

Assume you have a ROOT (sudo) privilege:

sudo su
wget http://www.stats.bris.ac.uk/R/src/base/R-3/R-3.2.0.tar.gz
tar xvfz R-3.2.0.tar.gz
cd R-3.2.0
./configure
make
make check
make install
R # start R

Assume you do not have a ROOT privilege and want R installation under your home directory (below /home/hfang should be replaced with yours):

wget http://www.stats.bris.ac.uk/R/src/base/R-3/R-3.2.0.tar.gz
tar xvfz R-3.2.0.tar.gz
cd R-3.2.0
./configure --prefix=/home/hfang/R-3.2.0
make
make check
make install
/home/hfang/R-3.2.0/bin/R # start R

2. Installation of the package

Notes: below are R command lines (NOT shell command lines in Terminal).

First, install dependant/imported/suggested packages:

source("http://bioconductor.org/biocLite.R")
biocLite(c("hexbin","ape","supraHex","graph","Rgraphviz","igraph","foreach","doMC","dnet","devtools"))

Second, install the package dcGOR under stable release version hosted in CRAN:

install.packages("dcGOR",repos="http://cran.r-project.org",type="source")

Third (highly recommended), update the package dcGOR from latest development version hosted in GitHub:

library(devtools)
for(pkg in c("dnet","dcGOR")){
    if(pkg %in% rownames(installed.packages())) remove.packages(pkg)
    install_github(repo=paste("hfang-bristol",pkg,sep="/"))
}