Perhaps I misunderstand, but the paper you link to has an R package that implements CPCA in R as used in the paper. Ben Bolker contributes here but IIRC he has moved from Florida now so the web link in the paper is dead. Ben is now at McMaster and you can find the latest version of that package here: http://www.math.mcmaster.ca/~bolker/R/ look for the /bin folder for compiled binary or /src for the sources (for use on Linux).

Is it possible to use common principal components for assessing covariance matrix similarity in R? 
On my Windows 7 x64 computer, Firefox 4 has seamlessly downgraded itself to Firefox 3.6 twice.  I haven't determined exactly when this is occurring, but the second time was when restarting after adding GreaseMonkey.  It is possible the first time was also after adding an add-on.  

Re-upgrading to 4.0 seems to work perfectly.

How can I stop this from happening again?
