inst/staticdocs/INSTALLATIONs_pre.md

In supraHex: supraHex: a supra-hexagonal map for analysing tabular omics data

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) has been installed in your local machine. The current version 3.1.0 can be installed following quick 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 for R installation 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-3.1.0.tar.gz
tar xvfz R-3.1.0.tar.gz
cd R-3.1.0
./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-3.1.0.tar.gz
tar xvfz R-3.1.0.tar.gz
cd R-3.1.0
./configure --prefix=/home/hfang/R-3.1.0
make
make check
make install
/home/hfang/R-3.1.0/bin/R # start R

2. Install the package from Bioconductor and R-Forge

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

To install stable release version, run:

source("http://bioconductor.org/biocLite.R")
biocLite("supraHex")

To install latest development version (highly recommended for benefits of latest improvements), run:

if(!require(hexbin)) install.packages("hexbin",repos="http://www.stats.bris.ac.uk/R")
if(!require(ape)) install.packages("ape",repos="http://www.stats.bris.ac.uk/R")
install.packages("supraHex",repos="http://R-Forge.R-project.org", type="source")

To install latest development version (highly recommended for benefits of latest improvements), run:

library(BiocInstaller) 
useDevel(devel=T)
source("http://bioconductor.org/biocLite.R")
biocLite("supraHex")
# After intallation, it is very important to reset back to the release version of Bioconductor
# Otherwise, packages to be installed will come from the development version (might be instable)
useDevel(devel=F)

supraHex documentation built on Nov. 26, 2020, 2:01 a.m.