[R-sig-Debian] Upgrading 2.15.3 to 3.0.x on Debian Squeeze?

Johannes Ranke 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
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


>   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?

> - 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

> 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.


> 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/
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Dr. Johannes Ranke                 jranke at uni-bremen.de

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