Johannes Ranke <jra...@uni-bremen.de> writes: > On Mon, Dec 09, 2013 at 09:27:11PM -0800, Bill Harris wrote: >> I'm running Debian Squeeze on an amd64 machine and currently have R >> 2.15.3. Some packages have been installed with aptitude and some with >> install.packages(). Now I'd like to update R to 3.0.2 (I upgraded arm >> to a version that requires 3.0 :-( ), and I'm a confused. > > The only critical point is that R packages that belong to Debian squeeze > will not work with the new R. So the question is wether you rely on any > such packages.
Yes, for better or worse. I once thought Dirk recommended that; I now see that he seems more ambivalent than I recall. >> - http://cran.us.r-project.org/bin/linux/debian/ seems to say I just >> change the sources list to point to '...cran3' instead of to '...cran' >> and then update / upgrade. Yet > > Correct. Great. That's easy enough. >> - http://cran.us.r-project.org/bin/linux/debian/ says I should run >> "`dpkg -get-selections | grep r-cran` and compare with the list of >> packages supported below." I've done that, but I don't know what to >> do with that knowledge: do I `aptitude remove` all of those packages >> /not/ listed below or do something else? > > Well these are the packages that will not work after the upgrade to R > 3.0.x. You can leave them on your system, but I would recommend to > remove them and install them from within R using install.packages() > after the upgrade. But just to be clear: you do not need to remove those > that are in the list of supported packages in the README as these will > be upgraded together with base R. `dpkg -get-selections | grep r-cran | wc -l` shows 100 such packages, but synaptic shows 25 packages installed from squeeze-cran/main. So I have 25 packages to remove (easy) and 100 to reinstall later (a bit more of a chore :-) ). >> - http://www.r-bloggers.com/upgrading-r-and-packages/ suggests a script >> that updates installed packages. I've used that on minor upgrades on >> XP successfully. I don't see documentation that suggests it's needed >> for major upgrades or perhaps on Linux. > > I do not think that this is helpful, unless the number of R packages > installed stemming from Debian squeeze is large. I'm going to ignore it. >> http://www.r-bloggers.com/r-3-0-0-is-released-whats-new-and-how-to-upgrade/ >> seems to suggest that running `update.packages(checkBuilt=TRUE)` is >> sufficient (except perhaps for what aptitude has to do). What is the >> right thing to do? > > Yes, this should be enough, except for the packages from Debian squeeze > mentioned above, that need special care. Again, easy enough. >> If the answers to those three questions aren't simple, are there >> explicit, step-by-step instructions somewhere? I've looked >> unsuccessfully. > > Feel free to make suggestions to improve the Debian README on CRAN. I > tried to make it as clear as possible, but needless to say it could be > improved. The two things I didn't understand were - what to do when I identified packages that were installed in Debian (I guessed right, but I didn't have the guts to try it and see) - what to do when I read seemingly contradictory instructions, even if they were potentially for different platforms You helped. > I have upgraded painlessly using this approach, but it would be nice to > hear about your experiences. I'll check back in. Vielen Dank! Bill -- Bill Harris Facilitated Systems http://makingsense.facilitatedsystems.com/ _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
