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

In psolaimani/BiocInstaller: Install/Update Bioconductor and CRAN 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

useDevel(devel=TRUE)

Arguments

devel

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

Details

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 useDevel function. With argument TRUE (the default), it will download the devel version of BiocInstaller and subsequently all packages downloaded with 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:

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)

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 .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

Invisible NULL.

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

## Not run: 
useDevel()

## End(Not run)

psolaimani/BiocInstaller documentation built on May 26, 2019, 11:30 a.m.