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

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Jun 15 17:33:42 CEST 2011


On Tue, Jun 14, 2011 at 6:21 PM, 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 It'll check for out-of-date packages and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 biocLite(character()) will look for out-of-date packages to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.

Very nice!

I especially like the fact that you can pass in a regex to the
suppressUpdates parameter to ignore certain packages. Especially handy
for postponing (minor in spirit but large in d/l size) updates to the
BSgenome.* packages.

A very minor suggestion would be to add a separate/convenience
function to update packages (eg. biocUpdate or something) instead of
passing in `character()` to biocLite to do a strict-update only.

And completely OT -- for the next time "bioconductor" comes up as the
topic for trivia nite at the pub: what's the story with picking the
name `biocLite` for the installer function instead of something like


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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