[Bioc-devel] Updated biocLite -- please try!

[Laurent Gatto]

Dear Martin,

On 14 June 2011 23:21, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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 It'll check for out-of-date packages and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 biocLite(character()) will look for out-of-date packages to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.

Just tested package updating with the new biocLite revision
(sessionInfo below) and everything worked well.

Could you clarify the distinction between the Bioconductor and
BiocInstaller packages? These look very similar.

Best wishes,

Laurent

> sessionInfo()
R version 2.14.0 Under development (unstable) (2011-06-07 r56076)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C
 [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8
 [5] LC_MONETARY=en_GB.utf8    LC_MESSAGES=en_GB.utf8
 [7] LC_PAPER=C                LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BiocInstaller_1.1.11

loaded via a namespace (and not attached):
[1] tools_2.14.0

> 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
>
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