[Bioc-devel] biocLite.R has been modified (BiocInstaller package)

[Dan Tenenbaum]

Hi all,

Our new package for installing packages, BiocInstaller, is now used by
default (in recent versions of R-devel) when you:

source("http://bioconductor.org/biocLite.R")

As mentioned below, a major difference is that now, the biocLite()
function will attempt to update out-of-date packages. You can control
this behavior; see the documentation:

?biocLite

for more information.

Please let us know on this list if you have questions, concerns, or issues.

Thanks,
Dan



---------- Forwarded message ----------
From: Martin Morgan <mtmorgan at fhcrc.org>
Date: Tue, Jun 14, 2011 at 3:21 PM
Subject: [Bioc-devel] Updated biocLite -- please try!
To: "bioc-devel at stat.math.ethz.ch" <bioc-devel at stat.math.ethz.ch>


Hi BiocDevelopers --

As mentioned previously, we have revised how biocLite works. Please try

  source("http://bioconductor.org/scratch-repos/biocLite.R")

and then installing your favorite package

 biocLite("MyFavoritePackage")

The 'source()' command will download, install (first time only!) and
load the 'BiocInstaller' package.

biocLite does behave differently. It'll check for out-of-date packages
and ask, after installing MyFavoritePackage, whether you'd like to
update them. With no arguments, biocLite() installs just Biobase,
IRanges, and AnnotationDbi. biocLite(character()) will look for
out-of-date packages to update. And ?biocLite will provide a help
page(!).

The revised behavior should only occur in the 'devel' version of R,
R-2.13 should behave as before.

Any feedback most welcome.

Martin
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel