[BioC] Upgrading to 1.7.0 under R 2.2.0
jarthur at med.usyd.edu.au
Tue Jan 10 04:29:42 CET 2006
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
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.
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
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