Note: We recommend use the 2.15 version of R
For Mac users you will need to have installed the tcltk add-on for R. This can be downloaded from http://cran.r-project.org/bin/macosx/tools/tcltk-8.5.5-x11.dmg.
Open R console.
First install the dependencies which are required for the DvD package. Download the R script DvDdependencies.R, this script will automatically check for and if necessary install R packages required by DvD.
source("~/DvDdependencies.R") #where "~/" should be the directory where the source file is stored
install.packages("~/DrugVsDiseasedata_0.99.2.tar.gz",type="source") #note "~/" should point to the directory where the file is saved library(DrugVsDiseasedata)
install.packages("~/cMap2data_0.99.1.tar.gz",type="source") #note "~/" should point to the directory where the file is saved library(cMap2data)
install.packages("~/DrugVsDisease_1.1.2.tar.gz",type="source") #note "~/" should point to the directory where the file is saved library(DrugVsDisease)
install.packages("Rserve") # This command only needs to be typed once library(Rserve) Rserve(args="--vanilla")
Note: Rserve is only disabled if you restart your pc. Thus, if you want to use Rserve after reboot you have to call it again.
On Windows Rserve may also stop working if an error is encountered.
Note: We recommend use the 2.8.3 version of Cytoscape
IMPORTANT: Before using DvD on Ubuntu you need to type on Terminal
sudo apt-get install libcairo2-dev sudo apt-get install libxt-dev