Hi, 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. > - 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. > > http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What_0027s-the-best-way-to-upgrade_003f > (admittedly for Windows) says to uninstall and reinstall R. Do I > follow the cran -> cran3 update approach, as I'm on Linux? Yes. > - 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. > - 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. > 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. > 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. > Is this a fairly foolproof upgrade? Minor upgrades have certainly > seemed simple on both Linux and Windows. I have upgraded painlessly using this approach, but it would be nice to hear about your experiences. Johannes > > Thanks, > > Bill > > PS: I'll also have to upgrade a Windows installation soon. I'm running > 2.15.3 under XP64 on one machine and under XP on another, and both will > get new installations of W7 after the disks are wiped. Is there a neat > way to reinstall all the packages I currently have when I reinstall R > (version 3.0.2 on W7)? > -- > Bill Harris > Facilitated Systems > http://makingsense.facilitatedsystems.com/ > > _______________________________________________ > R-SIG-Debian mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-debian -- Dr. Johannes Ranke [email protected] _______________________________________________ R-SIG-Debian mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-debian
