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

Wolfgang Huber whuber at embl.de
Wed Jun 15 21:38:57 CEST 2011

Il Jun/15/11 5:33 PM, Steve Lianoglou ha scritto:
> Hi,
> 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 It'll check for out-of-date packages and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 biocLite(character()) will look for out-of-date packages to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
> biocInstall?

Hi Steve

Bioconductor is a joint project with contributions from hundreds of 
people, while biocLite() without arguments only installed a subset of 
the packages that someone at one time had thought to be the most used 
(most prominent? most desirable?) ones. It would have been inappropriate 
to call that 'biocInstall'. Among many other good things, the new 
solution also rectifies that.

Best wishes

Wolfgang Huber

More information about the Bioc-devel mailing list