Get the 'devel' version of the BiocInstaller package.
Downloads the 'devel' version of the BiocInstaller package
so that all subsequent invocations of
biocinstallRepos use the devel repositories.
Displays the URLs of the repositories used by
to install Bioconductor and CRAN packages.
Should only be used with a release (or patched) version of R,
With R going to a yearly release schedule and Bioconductor keeping its
twice-yearly release schedule, the same version of R (3.2) can be used
with two different versions of Bioconductor (3.1, release, and 3.2, devel).
The version number of the BiocInstaller package is what is used to determine
whether to download packages from the BioC 3.1 or 3.2 repositories.
In keeping with Bioconductor versioning conventions, if the middle number
(y in x.y.z) is even, the package is part of a release version; if odd, it's
part of a devel version.
By default, when BiocInstaller is first installed on R-3.2, it will be
set up to download BioC 3.1 packages.
If you want to change this, you can run the
function. With argument
TRUE (the default), it will download
the devel version of BiocInstaller and subsequently all packages
biocLite will be from the BioC 3.2
(devel) repository. You should run
useDevel only once.
It is possible to keep BioC 3.1 and 3.2 libraries separate, within
the same installation of R.
The trick is to use the
R_LIBS_USER environment variable.
First, create two separate directories for your BioC release
and devel packages. Suggested directory names are as follows:
Mac OS: ~/Library/R/3.2-bioc-release/library ~/Library/R/3.2-bioc-devel/library
Windows: C:\Users\YOUR_USER_NAME\Documents\R\win-library\3.2-bioc-release C:\Users\YOUR_USER_NAME\Documents\R\win-library\3.2-bioc-devel (change YOUR_USER_NAME to your user name)
You can then invoke "R for bioc-devel" or "R for bioc-release" from the command line as follows:
Linux: R_LIBS_USER=~/R/x86_64-unknown-linux-gnu-library/3.2-bioc-release R R_LIBS_USER=~/R/x86_64-unknown-linux-gnu-library/3.2-bioc-devel R Mac OS X: R_LIBS_USER=~~/Library/R/3.2-bioc-release/library R R_LIBS_USER=~~/Library/R/3.2-bioc-devel/library R
Windows: cmd /C "set R_LIBS_USER=C:\Users\YOUR_USER_NAME\Documents\R\win-library\3.2-bioc-release && R" cmd /C "set R_LIBS_USER=C:\Users\YOUR_USER_NAME\Documents\R\win-library\3.2-bioc-devel && R" (Note: this assumes that R.exe is in your PATH.)
If you launch R in this way and then invoke
you'll see that the first item is your special release or
devel directory. Packages will be installed to that directory and that
is the first place that
library will look for them.
update.packages and friends all respect this
On Linux and Mac OS X, you can create a bash alias to save typing. Add the following to your ~/bash_profile:
Linux alias Rdevel='R_LIBS_USER=~/R/x86_64-unknown-linux-gnu-library/3.2-bioc-devel R'
alias Rrelease='R_LIBS_USER=~/R/x86_64-unknown-linux-gnu-library/3.2-bioc-release R' Mac OS X alias Rdevel='R_LIBS_USER=~/Library/R/3.2-bioc-devel/library R' alias Rrelease='R_LIBS_USER=~/Library/R/3.2-bioc-release/library R'
You can then invoke these from the command line as Rdevel ...and... Rrelease
On Windows, you can create two shortcuts, one for devel and one 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_USER_NAME\Documents\R\win-library\3.2-bioc-release && R" ...for release and cmd /C "set R_LIBS_USER=C:\Users\YOUR_USER_NAME\Documents\R\win-library\3.0-bioc-devel && R"
(again, it's assumed R.exe is in your PATH)
In the "Type a name for this shortcut" box, type
You can invoke these from the command line as
(You must type in the .lnk extension.)
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.
biocinstallRepos returns the Bioconductor and CRAN
repositories used by
biocLite Installs/updates Bioconductor/CRAN packages.
install.packages installs the packages themselves.
chooseBioCmirror lets you choose from a list of all
public Bioconductor mirror URLs.
chooseCRANmirror lets you choose from a list of all
public CRAN mirror URLs.
## Not run: # useDevel() # ## End(Not run)