ubuntu之R攻略

    安装依赖库

sudo aptitude -y install tcl-dev tk-dev
sudo aptitude -y install libicu-dev liblzma-dev
sudo aptitude -y install libpng12-dev libjpeg-dev libtiff4-dev libcairo2-dev

    安装R

wget http://mirrors.xmu.edu.cn/CRAN/src/base/R-3/R-3.1.1.tar.gz -nc -O ~/download/R-3.1.1.tar.gz
tar zxvf ~/download/R-3.1.1.tar.gz -C /tmp/
cd /tmp/R-3.1.1/
./configure --enable-R-shlib --with-tcl-config=/usr/lib/tclConfig.sh --with-tk-config=/usr/lib/tkConfig.sh
make
sudo make install

    安装rstudio

wget http://download1.rstudio.org/rstudio-0.98.978-amd64.deb -nc -O ~/download/rstudio-0.98.978-amd64.deb
sudo dpkg -i ~/download/rstudio-0.98.978-amd64.deb

    安装package(在R中运行)

install.packages(c("ggplot2", "DMwR", "vegan", "ade4", "geoR", "caret", "pcaPP", "rJava",
                   "indicspesies", "roxygen2", "snowfall", "rpf", "numDeriv", "psych",
                   "geosphere"), repos = "http://172.30.0.75/cran")

source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite(c("BiocInstaller", "qvalue", "DirichletMultinomial", "impute", "minet",
           "GO.db", "org.Hs.eg.db", "org.Mm.eg.db"))

install.packages("WGCNA", repos = "http://172.30.0.75/cran")

    安装源代码版OpenMx

sudo aptitude install -y curl
cd ~/download
svn checkout "http://openmx.psyc.virginia.edu/svn" OpenMx
cd OpenMx/truck
sudo make install

    .Rprofile设置

#
options(papersize="a4")
options(editor="vim")
options(tab.width = 2)
options(width = 130)

#
options(prompt="> ")
options(continue="+ ")

#
.First <- function() {
    library(utils)
    if(interactive()) try(loadhistory("~/.Rhistory"))
}

# ......
.Last <- function() {
    if(interactive()) try(savehistory("~/.Rhistory"))
}