[BioC] Bioconductor and R 2.7

[Herve Pages]

Hi Aaron,

aaron.j.mackey at gsk.com wrote:
>> just don't try to carry over your installed packages from the 2.6.1
>> installation to the 2.7 one - please install all packages from scratch
>> using biocLite (http://www.bioconductor.org/download), which
>> automatically takes care of release version synchronisation between R
>> and Bioconductor.
> 
> Out of curiousity, won't "update.packages()" achieve the same thing 
> (assuming you've used setRepositories() to include BioC)?  I've also just 
> upgraded to 2.7.0, and today update.packages() choose to download Biobase 
> 1.99.10 (the version from "upcoming" BioC 2.2)

After you've upgraded to R 2.7.0, reinstalling Bioconductor packages (and any
other package) from scratch (i.e. in an empty library folder) is recommended.

For BioC package, this should be done with biocLite(), which is the easy and
safe way to do it. Other methods can work if you know what you are doing.
E.g. using update.packages() might work, provided that you use the proper
repositories for BioC 2.2. This can be achieved with:

   > source("http://bioconductor.org/biocLite.R")
   > biocinstallRepos()
   [1] "http://bioconductor.org/packages/2.2/bioc"
   [2] "http://bioconductor.org/packages/2.2/data/annotation"
   [3] "http://bioconductor.org/packages/2.2/data/experiment"
   [4] "http://bioconductor.org/packages/2.2/extra"
   [5] "http://cran.fhcrc.org"
   > install.packages(rep=biocinstallRepos(), ask=FALSE)

Note that updating instead of reinstalling from scratch will not get you rid
of the BioC 2.1 packages that have been discontinued in BioC 2.2. Keeping these
packages around is a potential source of problems because they might not work
properly with BioC 2.2 / R-2.7. So again, it's better to do a clean install from
scratch with biocLite().

Cheers,
H.

> 
> Thanks,
> 
> -Aaron
> 
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