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

Bill Harris bill_harris at facilitatedsystems.com
Tue Dec 10 07:31:42 CET 2013

Johannes Ranke <jranke at 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 Harris                  
Facilitated Systems

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