[R-sig-Debian] Upgrading 2.15.3 to 3.0.x on Debian Squeeze?
jranke at uni-bremen.de
Tue Dec 10 06:58:39 CET 2013
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
> - 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
> (admittedly for Windows) says to uninstall and reinstall R. Do I
> follow the cran -> cran3 update approach, as I'm on Linux?
> - 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.
> 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
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
> 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.
> 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
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
Dr. Johannes Ranke jranke at uni-bremen.de
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