Home

Welcome to the ONION wiki!

Environment Set Up

To develop, build and etc. ONION on your own computer you have to install some necessary packages. It is also nice to set up some optional one to help you with process of developing and so on. Optional steps are with asterix *.

Ubuntu (Debian)

• Install R on your machine:
  sudo su
  echo "deb http://www.stats.bris.ac.uk/R/bin/linux/ubuntu precise/" >> /etc/apt/sources.list
  apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
  apt-get update
  apt-get install r-base r-base-dev
  apt-get install libatlas3-base
  apt-get install libopenblas-base
• Install RStudio*:
  Go to https://www.rstudio.com/products/rstudio/download/ and download for example rstudio-1.0.136-amd64.deb
  dpkg -i rstudio-1.0.136-amd64.deb
• Install GIT and get sources of ONION project:
  sudo apt-get install git
  git clone https://github.com/wjurkowski/ONION.git

Build

To build MulEA with vignettes you need to follow instructions in Build process. Some known issues are describe in Known problems part.

Build process

• download, update sources by cloning, pulling this repository: https://github.com/wjurkowski/ONION.git
• Install all dependencies of ONION package:
  source("https://bioconductor.org/biocLite.R")
  biocLite(c("igraph", "plyr", "RCurl", "RJSONIO", "XML", "testthat", "pls", "corrplot", "yacca", "FRCC", "httr", "STRINGdb", "BiocCheck", "CCA", "gridExtra", "mygene", "ChemmineR", "ChemmineOB", "knitr", "rmarkdown"))
• open the ONION.Rproj project in R Studio
• build package

install.packages(c("devtools", "roxygen2", "testthat", "knitr", "rmarkdown"))
devtools::install_github("hadley/devtools", force = TRUE)
library(devtools)
devtools::build_vignettes()

then click Build $ Reload in RStudio under Build tab. After that follow with:
devtools::build_vignettes()

Known problems

ERROR: dependencies ‘RCurl’, ‘rtracklayer’, ‘biomaRt’ are not available for package ‘GenomicFeatures’ * removing ‘/usr/users/TGAC_ga002/turekc/R/x86_64-pc-linux-gnu-library/3.3/GenomicFeatures’

to display the vignette

click Build $ Reload in RStudio again and execute the following: vignette("MulEA")

Known Problems

rJava problem

Create the file /etc/ld.so.conf.d/java.conf with the following entries:
/usr/lib/jvm/java-8-oracle/jre/lib/amd64
/usr/lib/jvm/java-8-oracle/jre/lib/amd64/server

sudo ldconfig
apt-get install r-cran-rjava
R CMD javareconf