Using the devel Version of Bioconductor

In this release cycle, the same version of R (3.0) can be used with two different versions of Bioconductor (2.12, release, and 2.13, devel). When BiocInstaller is first installed on R-3.0, it downloads release packages. To change this, run the useDevel() function.

library(BiocInstaller)
useDevel()

With argument TRUE (the default), this downloads the devel version of BiocInstaller and subsequently all packages downloaded with biocLite() are from the devel repository. Run useDevel() only once. See ?useDevel for more information.

Separate libraries

It is best to keep Bioconductor release and devel packages in separate libraries.

An easy way to do this is to have two separate installation of R-3.0.

A more complicated way is to use the R_LIBS_USER environment variable. First, create two separate directories. Suggested directory names are Linux:

~/R/x86_64-unknown-linux-gnu-library/3.0-bioc-release
~/R/x86_64-unknown-linux-gnu-library/3.0-bioc-devel

Mac OS:

~/Library/R/3.0-bioc-release/library
~/Library/R/3.0-bioc-devel/library

and Windows:

C:\Users\YOUR_NAME\Documents\R\win-library\3.0-bioc-release
C:\Users\YOUR_NAME\Documents\R\win-library\3.0-bioc-devel

(change YOUR_NAME to your user name)

Invoke "R for bioc-devel" or "R for bioc-release" from the command line on Linux:

R_LIBS_USER=~/R/x86_64-unknown-linux-gnu-library/3.0-bioc-release R
R_LIBS_USER=~/R/x86_64-unknown-linux-gnu-library/3.0-bioc-devel R

Mac OS X:

R_LIBS_USER=~~/Library/R/3.0-bioc-release/library R
R_LIBS_USER=~~/Library/R/3.0-bioc-devel/library R

and Windows (assuming that R.exe is in PATH):

cmd /C "set R_LIBS_USER=C:\Users\YOUR_NAME\Documents\R\win-library\3.0-bioc-release &&  R"
cmd /C "set R_LIBS_USER=C:\Users\YOUR_NAME\Documents\R\win-library\3.0-bioc-devel &&  R"

When correctly configured, R's .libPaths() function will return the release or devel directory as its first entry. Packages are installed to that directory, and that is the first place that library() looks for them. biocLite() and install.packages() respect this setting; update.packages() attempts to update packages in the directory where the current package is installed.

Aliases

On Linux and Mac OS X, you can create a bash alias to save typing. Add the following to your ~/bash_profile on Linux:

alias Rdevel='R_LIBS_USER=~/R/x86_64-unknown-linux-gnu-library/3.0-bioc-devel R'
alias Rrelease='R_LIBS_USER=~/R/x86_64-unknown-linux-gnu-library/3.0-bioc-release R'

or Mac OS X

alias Rdevel='R_LIBS_USER=~/Library/R/3.0-bioc-devel/library R'
alias Rrelease='R_LIBS_USER=~/Library/R/3.0-bioc-release/library R'

Invoke R from the command line as Rdevel or Rrelease.

On Windows, create two shortcuts, one for release and one for devel. For devel (do similar steps for release) go to My Computer and navigate to a directory that is in your PATH. Then right-click and choose New->Shortcut. In the "type the location of the item" box, put:

cmd /C "set R_LIBS_USER=C:\Users\YOUR_NAME\Documents\R\win-library\3.0-bioc-devel &&  R"

(again, it's assumed R.exe is in your PATH) Click "Next", and in the "Type a name for this shortcut" box, type

Rdevel

Invoke these from the command line as Rdevel.lnk.

Because R_LIBS_USER is an environment variable, its value should be inherited by any subprocesses started by R, so they should do the right thing as well.