R 3.1 -> 3.2 upgrade notes

My machines upgraded from R version 3.1.3 to version 3.2.0 last week, which means that existing code suddenly cannot find packages and so fails. Some notes to myself, possibly useful to others, for what to do when this happens. Relevant to Ubuntu-based systems (I use Linux Mint).

1. Update packages

cp ~/R/x86_64-pc-linux-gnu-library/3.1 ~/R/x86_64-pc-linux-gnu-library/3.2
update.packages(checkBuilt=TRUE, ask=FALSE)

1.1. rJava issues
My rJava installation failed because code was trying to compile against jni.h which was not present on my system. Solution:

sudo apt-get install openjdk-7-jdk
sudo R CMD javareconf

and then in R:

install.packages("rJava")

2. Update Bioconductor
Bioconductor is also upgraded so requires more than a package update.

remove.packages("BiocInstaller")
source("http://bioconductor.org/biocLite.R")
biocLite()

2.1. ChemmineR
My Bioconductor Chemminer update failed because package gridExtra was absent:

install.packages("gridExtra")
biocLite("ChemmineR")

3. General issues
When R is installed on Linux Mint, some packages are installed by default in /usr/lib/R/library. When performing updates as a non-root user, you’ll see messages telling you that this location is not writable and asking if you want to use your own library location. If you reply “yes”, you’ll have packages in both system and user locations. It’s probably better to say “no” and let the Ubuntu package management system handle the package upgrades.

And now we are all done so (careful!):

rm -rf ~/R/x86_64-pc-linux-gnu-library/3.1