Install

• Install R
• Find Bioconductor Packages
• Install Bioconductor Packages
• Update Bioconductor Packages

Install R

1. Download the most recent version of R. The R FAQs and the R Installation and Administration Manual contain detailed instructions for installing R on various platforms (Linux, OS X, and Windows being the main ones).

2. Start the R program; on Windows and OS X, this will usually mean double-clicking on the R application, on UNIX-like systems, type "R" at a shell prompt.

3. As a first step with R, start the R help browser by typing help.start() in the R command window. For help on any function, e.g. the "mean" function, type ? mean.

Find Bioconductor Packages

Visit the Workflows help page and BiocViews taxonomy to discover available software.

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Install Base Bioconductor Packages

Install BioConductor packages using the biocLite.R installation script. In an R command window, type the following:

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

This installs the following packages: affy, affydata, affyPLM, affyQCReport, annaffy, annotate, Biobase, biomaRt, Biostrings, DynDoc, gcrma, genefilter, geneplotter, GenomicRanges, hgu95av2.db, limma, marray, multtest, vsn, and xtable. After downloading and installing these packages, the script prints "Installation complete" and TRUE.

The biocLite.R script has arguments that change the default behavior:

pkgs
    Character vector of BioConductor packages to install.
destdir
    File system directory for downloaded packages.
lib
    R library where packages are installed.

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Install Additional Bioconductor Packages

There are many Bioconductor and R packages in addition to those in the default installation of biocLite. A catalog of the Bioconductor packages is available at BiocViews. To install a new package, e.g., EBImage, use

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

Install "pkg1" and "pkg2" with

biocLite(c("pkg1", "pkg2"))

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Update Installed Bioconductor Packages

Bioconductor packages, especially those in the development branch, are updated fairly regularly. To identify packages requiring update, start a new session of R and enter

source("http://bioconductor.org/biocLite.R")
old.packages(repos=biocinstallRepos())

To update all installed packages that are out of date, start a new session of R and enter

source("http://bioconductor.org/biocLite.R")
update.packages(repos=biocinstallRepos(), ask=FALSE)

Read the help page for update.packages for additional details. Recompiling installed Bioconductor packages

Rarely, underlying changes in the operating system require ALL installed packages to be recompiled for source (C or Fortran) compatibility. One way to address this might be to start a new R session and enter

source("http://bioconductor.org/biocLite.R")
pkgs <- rownames(installed.packages())
biocLite(pkgs)

As this will reinstall all currently installed packages, it likely involves a significant amount of network bandwidth and compilation time. All packages are implicitly updated, and the cumulative effect might introduce wrinkles that disrupt your workflow.

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