I was trying to upgrade to Bioconductor 3.4 and in order to do so I had to make an R upgrade (3.2.2 to 3.3.2). When running biocLite("BiocUpgrade") I get the error:
Bioconductor version 3.4 cannot be upgraded with R version 3.3.2
I already tried to remove BiocInstaller with
from all paths listed with .libPaths()  "/home/f/R/x86_64-pc-linux-gnu-library/3.3"  "/usr/local/lib/R/site-library"  "/usr/lib/R/site-library"  "/usr/lib/R/library"
Didn't work. I came across a post asking for a similar solution and a comment saying the problem might be caused by installing the new R version over the old one. I think this might be the problem in my case, but I don't no how to clean up the mess...
Does the existence of both "/usr/local/lib/R/site-library" AND "/usr/lib/R/site-library" mean, that I made the installation of the two R versions in two different ways does the old library interfere with the new installation? If this is true, do I have to remove R completely or what should I do? Just deleting old libraries or will that cause additional problems?
> sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 15.10 locale:  LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C  LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8  LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8  LC_PAPER=de_DE.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  BiocInstaller_1.24.0 loaded via a namespace (and not attached):  tools_3.3.2
Thank you for any suggestions.