[BioC] Upgrading to 1.7.0 under R 2.2.0

[Jonathan Arthur]

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)

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

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?

Thanks for your help.

Regards,

Jonathan

-- 
Dr Jonathan Arthur
Sesqui Lecturer in Bioinformatics
Central Clinical School, Faculty of Medicine and SUBIT
Medical Foundation Building, K25
University of Sydney
Ph: +61 2 9036 3132
Email: jarthur at med.usyd.edu.au