useDevel: Get the 'devel' version of the BiocInstaller package.

In BiocInstaller: Install/Update Bioconductor, CRAN, and github Packages

Description

Downloads the 'devel' version of the BiocInstaller package so that all subsequent invocations of biocLite and biocinstallRepos use the devel repositories.

Displays the URLs of the repositories used by biocLite to install Bioconductor and CRAN packages.

Should only be used with a release (or patched) version of R, freshly installed.

Usage

isDevel()
useDevel(devel=TRUE)

Arguments

devel

Whether to look in the devel (TRUE) or release (FALSE) repositories in subsequent invocations of biocLite and biocinstallRepos.

Details

Bioconductor has a 'release' branch and a 'devel' branch. The branch in use depends on the version of R and the version of the BiocInstaller.

useDevel() installs the correct version of the BiocInstaller package for use of the devel version of Bioconductor, provided it is supported by the version of R in use.

isDevel() returns TRUE when the version of BiocInstaller in use corresponds to the 'devel' version of Bioconductor.

In more detail, the version number of the BiocInstaller package determines whether to download packages from the release or devel repositories of Bioconductor. 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 and when the version of R supports the current release version of Bioconductor, BiocInstaller will use the release repository.

To change the version of BiocInstaller to support the 'devel' branch of Bioconductor, run useDevel(). With argument TRUE (the default), it will download the devel version of BiocInstaller and subsequently all packages downloaded with biocLite will be from the devel repository. You should run useDevel only once.

During release cycles where both the release and devel version of Bioconductor use the same version of R, it is possible to use release and devel versions of Bioconductor with the same installation of R. To do this, 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:

Linux:

~/R/x86_64-unknown-linux-gnu-library/3.2-bioc-release

~/R/x86_64-unknown-linux-gnu-library/3.2-bioc-devel

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)

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 .libPaths, 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. biocLite, install.packages, update.packages and friends all respect this setting.

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"

...for devel.

(again, it's assumed R.exe is in your PATH)

Click "Next".

In the "Type a name for this shortcut" box, type

Rdevel

or

Rrelease

You can invoke these from the command line as

Rdevel.lnk

...and...

Rrelease.lnk

(You must type in the .lnk extension.)

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.

Value

useDevel(): Invisible NULL.

isDevel(): logical(1) TRUE or FALSE.

See Also

biocinstallRepos returns the Bioconductor and CRAN repositories used by biocLite.

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.

Examples

isDevel()

## Not run: useDevel()

BiocInstaller documentation built on May 1, 2019, 11:36 p.m.