From all installed packages, I only had issues with 5 of them, which require installation from their respective websites: Acinonyx, INLA (and AnimalINLA) and asreml. Package graph is now available from bioconductor.org. INLA can be installed really easily from inside R (see below), while I did not bother downloading again asreml and just copied the folder from ~/Library/R/OldVersion/library/asreml to ~/Library/R/CurrentVersion/library/asreml.