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Welcome to the ONION wiki!
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 *.
- 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
To build MulEA with vignettes you need to follow instructions in Build process. Some known issues are describe in Known problems part.
- download, update sources by cloning, pulling this repository: https://github.com/wjurkowski/ONION.git
- Install all dependencies of ONION package from R console:
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()
If you see some similar message to that:
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’
You need to manually install each dependency for package GenomicFeatures. To do it for example for RCurl put into R console:
biocLite("RCurl")
Then you can see what is the problem with instalation of that library. In our case important part of the message looks like that:
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/usr/users/TGAC_ga002/turekc/R/x86_64-pc-linux-gnu-library/3.3/RCurl’
After a short research you will find that you do not have required lib on your system. In this case you need to install it by run this command in terminal:
sudo apt-get install libcurl4-gnutls-dev
Then try to install Rcurl again by performing biocLite("RCurl") in R console.
In case of XML or rtracklayer packages, the fastest way is install R package from Advanced Packaging Tool (apt). If you see message like that:
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
You probably should run this command in terminal:
sudo apt-get install r-cran-xml
As you can see some R packages are available in this way.
click Build $ Reload in RStudio again and execute the following: vignette("ONION")