Downgrade R version and R package Bioconductor [duplicate]

Question

Hello everyone I am currently running R 3.0.2 on a debian server with Bioconductor v2.13. My question is simple although searching through the internet hasn't provided me with a clear answer:

How can I downgrade from R 3.0.2. to R 2-15?

Considering i keep R 3.0.2 how can i downgrade Bioconductor to v2.12?

Thank you in advance,

Answer 1

Generally, Bioconductor is designed to work with specific versions of R, so there are no guarantees associated with using older versions of Bioconductor (or any R package) with newer versions of R. Better to ask questions about Bioconductor packages on the Bioconductor mailing list. Probably what you're saying is that there is some problem with your current Bioconductor installation, and what you'd really be better of doing is fixing the problem.

Check out the LibPath of installed.packages(), and compare to the output of .libPaths(). I have

> head(installed.packages()[,"LibPath"], 1)
                                                   affy 
"/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.0"
> .libPaths()
[1] "/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.0"
[2] "/home/mtmorgan/bin/R-3-0-branch/library"  

Good news! All my Bioc packages are in a specific library. I could then arrange (see ?.libPaths) to start R with .libPaths pointing to a new location for Bioc 2.12 packages, e.g.,

R_LIBS_USER="/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.0-2.12" R

then explicitly install the version of the BiocInstaller package I want to use, e.g.,

install.packages("BiocInstaller", 
    repos="http://bioconductor.org/packages/2.12/bioc")

and library(BiocInstaller); biocLite() as usual.

If my Bioconductor packages were installed in the R home directory, then I'd remove.packages() instead of setting .libPaths(), or I'd run BiocInstaller::biocValid() and follow the directions for reverting "too new" packages.