develVersion 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
release packages. To change this, run the
TRUE (the default), this downloads the
of BiocInstaller and subsequently all packages downloaded with
biocLite() are from the
devel repository. Run
?useDevel for more information.
It is best to keep Bioconductor
devel packages in
An easy way to do this is to have two separate installation of R-3.0.
A more complicated way is to use the
variable. First, create two separate directories. Suggested directory
names are Linux:
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
devel directory as its first entry. Packages are
installed to that directory, and that is the first place that
library() looks for them.
install.packages() respect this setting;
update.packages() attempts to update packages in the
directory where the current package is installed.
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
On Windows, create two shortcuts, one for
release and one 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
Invoke these from the command line as
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.