• Getting The Latest Version of Bioconductor
• Install Packages
• Find Packages
• Update Packages
• Troubleshoot Package Installations
• Install R

Getting The Latest Version of Bioconductor

Install the latest release of R, then get the latest version of Bioconductor by following the steps below. The current release version of R is 3.0, and the currently released Bioconductor version is 2.12.

Install Bioconductor Packages

Use the biocLite.R script to install Bioconductor packages. To install core packages, type the following in an R command window:

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

Install specific packages, e.g., "GenomicFeatures" and "AnnotationDbi", with

biocLite(c("GenomicFeatures", "AnnotationDbi"))

The biocLite() function (in the BiocInstaller package installed by the biocLite.R script) has arguments that change its default behavior; type ?biocLite for further help.

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Find Bioconductor Packages

Visit the Workflows page and software package list to discover available packages.

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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")
biocLite()              ## R version 3.0 or later

Use the argument ask=FALSE to update old packages without being prompted. For older versions of R, use the command biocLite(NULL). Read the help page for ?biocLite 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 work flow.

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Troubleshoot Package Installations

Use the commands

library(BiocInstaller)
biocValid()             ## R version 3.0 or later

to flag packages that are either out-of-date or too new for your version of Bioconductor. The output suggests ways to solve identified problems, and the help page ?biocValid lists arguments influencing the behavior of the function.

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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.