[BioC] Upgrading to 1.7.0 under R 2.2.0

[Seth Falcon]

Hi Jonathan,

On  9 Jan 2006, jarthur at med.usyd.edu.au wrote:
> Hello all,
>
> I recently decided to upgrade R and Bioconductor. Following the
> instructions on R web site, I installed R 2.2.0 and copied all my
> packages across. I then opened the RGui and selected Packages ->
> Update packages ... I assumed this would update all of my
> BioConductor packages to the latest version.
>
> However, after loading affy and limma a sessionInfo() gives versions
> as such:
>
> affy: 1.5.8-1 (compared to 1.8.1 on BioConductor 1.7 package list)
> limma: 2.4.7 (compared to 2.2.0 on BioConductor 1.7 package list)

Did you select the Bioconductor repository (along with CRAN) before
running the update?  It looks to me like you only got updates from
CRAN.

limma is in both CRAN and Bioconductor repositories and the most
up-to-date version is on CRAN, so that part of the update worked, I
think.

> Hence, it seems the update has failed for some packages and got the 
> version from the 1.8 developmental release for others?

Are you referring to limma?  Otherwise, please give us more detail.
It seems unlikely that you would be able to get devel packages using
R-2.2.x and the update mechanism from the Windows GUI.

> Information regarding *upgrading* packages on the Bioconductor site
> seems to refer only to *installing* packages. Do I take this to mean
> the best way to upgrade to a later version of Bioconductor is to
> re-run the installation procedure (ie biocLite or getBioC.R)? Or is
> there a distinct *upgrade* procedure?

Indeed.  Right now there is no update procedure other than
update.packages and it is not recommended (we need to improve the
documentation on this).

I *do* recommend using biocLite to install desired packages.  The
biocLite script will pickup required dependencies.

Thanks for posting and let us know if you encounter further
difficulties.

+ seth