Install and Update R and R packages

OS:      WIN7  
R:       3.03  
RStudio: 0.98.501

updated on Tue Apr 08 14:57:09 2014, it was first post here

1. Install R

R is available at http://www.r-project.org/.

2. Update R

if (!require(installr)) {
    # load / install+load installr
    install.packages("installr")
    require(installr)
}

updateR()

3. Install R packages

3.1 Installing R packages from CRAN (http://cran.r-project.org/)

install.packages("FinCal", dependencies = TRUE)  # FinCal is the package name

or

RStudio -> Tools -> Install Packages -> Install from 'Repository (CRAN)'

3.2 Installing R packages from Package Archive File (offline)

install.packages("FinCal_0.5.zip")

or

RStudio -> Tools -> Install Packages -> Install from 'Package Archive File'

or

R CMD INSTALL FinCal_0.5.zip

3.3 Installing R packages from Bioconductor (http://www.bioconductor.org/)

source("http://bioconductor.org/biocLite.R")  # installs 'BiocInstaller'
biocLite()  # installs automatically 'Biobase' 'IRanges' 'AnnotationDbi' ‘BiocGenerics’ ‘RSQLite’
all_group()  # Get list of all packages in BioConductor
biocLite(c("GenomicFeatures", "AnnotationDbi"))  #installing GenomicFeatures &AnnotationDbi packages

3.4 Installing R packages from GitHub (https://github.com/)

install.packages("devtools")  # requires for downloading & installation of GitHub packages
require(devtools)
install_github(repo = "FinCal", username = "felixfan")  # installing FinCal package

4. Update all existing packages

4.1 Automated Re-Install of Packages (packages in the default library dir)

update.packages(ask = FALSE, repos = "http://cran.rstudio.org", checkBuilt = TRUE)

or just

update.packages(ask = FALSE)

4.2 Automated Re-Install of Packages (packages do not in the default library dir)

.libPaths()  # gets the library trees within which packages are looked for
myPath = c("C:/Users/alice/Documents/R/win-library/3.0")  # change it to your own dir
package_df <- as.data.frame(installed.packages(myPath))  #Get currently installed packages
package_list <- as.character(package_df$Package)
install.packages(package_list)  #Re-install all installed packages

4.3 Automated Re-Install of Packages (packages from Bioconductor)

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

5. Reference

Installing R packages from CRAN/Bioconductor/Omegahat/Github
R 3.0.0 is released! (what’s new, and how to upgrade)
Automated Re-Install of Packages for R 3.0