R SIG Debian - Dec 2013 - Upgrading 2.15.3 to 3.0.x on Debian Squeeze?

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.

- 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?

- 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.
  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?

If the answers to those three questions aren't simple, are there
explicit, step-by-step instructions somewhere?  I've looked
unsuccessfully.

Is this a fairly foolproof upgrade?  Minor upgrades have certainly
seemed simple on both Linux and Windows.

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/

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/
> 
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> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
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-- 
Dr. Johannes Ranke                 jranke at uni-bremen.de