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downgrading to R 2.15.1-4 from sid beta 3.0.0

4 messages · Dirk Eddelbuettel, Sébastien Bihorel

Original
Sébastien Bihorel
# 
On Mon, 25 Mar 2013 18:51:24 -0500,
Dirk Eddelbuettel <edd at debian.org> wrote:

            

      
      
      
    

        
Thanks Dirk and Charles for the pointers.  I'm now running a locally
installed R 2.15.3 and packages until the dust settles with 3.0.0.

I just noticed that many sid packages have now been rebuilt against R
3.0.0.  Kudos to Dirk and the team!  However, I don't understand how
this works for packages that have an upstream Depends on R < 3.0.0.  One
of these is nlme, and yet r-cran-nlme has been rebuilt against R 3.0.0,
even though it fails to load in this latest R with:

R> library(nlme)
Error: package ?nlme? was built before R 3.0.0: please re-install it

What am I missing?

Thanks,

  
    

      
      
    

  


  


    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
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On 1 April 2013 at 14:12, Sebastian P. Luque wrote:

        
| On Mon, 25 Mar 2013 18:51:24 -0500,

        
| Dirk Eddelbuettel <edd at debian.org> wrote:

        
|

        
| > On 26 March 2013 at 07:35, Charles Plessy wrote:

        
| >> Le Mon, Mar 25, 2013 at 03:14:11PM -0500, Sebastian P. Luque a ?crit
| >> : > On Mon, 25 Mar 2013 13:14:15 -0500,

        
| >> > Dirk Eddelbuettel <edd at debian.org> wrote:

        
| >> > 
| >> > > c) If you must downgrade, I would downgrade to 2.15.3-2 from CRAN
| >> > > rather than 2.15.1.
| >> > 
| >> > Great, doing that right now.
| >> 
| >> Hi Sebastian and everybody,
| >> 
| >> Note (if it helps) that it is also available from
| >> snapshot.debian.org.
| >> 
| >> http://snapshot.debian.org/package/r-base/
| 
| > Ace -- thanks for the reminder about snapshot.d.o.
| 
| > As for Seb's query about mass-updates: what you do from ESS, I do from
| > shell via littler -- and yes, I usually control via lib.loc(). In this
| > case we may want to force it everywhere... though I can't fully
| > recommend to overwrite files owned by dpkg and apt-*.  If it breaks,
| > you keep the pieces.
| 
| > And lastly, this is of course a bug in r-base as it could potentially
| > conflict with its dependents. In practive, I don't see how we could do
| > this easily so the best bet is probably to simply upgrade the .deb
| > packages as fast as possible.
| 
| > Dirk
| 
| > My ~/bin/update.r is below, with some comments removed. A version is
| > also in the littler sources and Debian package.
| 
| Thanks Dirk and Charles for the pointers.  I'm now running a locally
| installed R 2.15.3 and packages until the dust settles with 3.0.0.
| 
| I just noticed that many sid packages have now been rebuilt against R
| 3.0.0.  Kudos to Dirk and the team!  However, I don't understand how

Yes, I kept busy over the weekend.

| this works for packages that have an upstream Depends on R < 3.0.0.  One
| of these is nlme, and yet r-cran-nlme has been rebuilt against R 3.0.0,
| even though it fails to load in this latest R with:

I don't see that in the nlme sources. 

Rather, the one I uploaded (3.1-109) has

	Depends: graphics, stats, R (>= 3.0.0)

| R> library(nlme)
| Error: package ?nlme? was built before R 3.0.0: please re-install it
| 
| What am I missing?

I *very strongly* suspect that you have an older r-cran-nlme on your system,
or that you have older nlme installation ahead of the current r-cran-nlme in
your .libPaths()

Check the result from installed.packages().

Dirk

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Sébastien Bihorel
    

    

      
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On Mon, 1 Apr 2013 15:14:46 -0500,

        
Dirk Eddelbuettel <edd at debian.org> wrote:

        

            

      
      
      
    

        
R> library(nlme)

            

      
      
      
    

        
Indeed, that was it!  I somehow forgot to remove the temporary local
installations of nlme and coda, so they wouldn't be found before the
Debian packages.  Sorry for the noise.

Again, thanks so much for keeping Debian so neat!

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Sébastien Bihorel
    

    

      
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On Mon, 01 Apr 2013 15:37:49 -0500,

        
"Sebastian P. Luque" <spluque at gmail.com> wrote:

        

            

      
      
      
    

        
R> library(nlme)

            

      
      
      
    

        
This prompted me to write something to check for these things:

---<--------------------cut here---------------start------------------->---
local.lib <- .libPaths()[1]
localpkgs <- installed.packages(lib.loc=local.lib)[, 1]
## The system-wide library:
sys.lib <- .libPaths()[2]
syspkgs <- installed.packages(lib.loc=sys.lib)[, 1]
## All the installed packages in local library that should be removed
dups <- localpkgs %in% syspkgs
## Check them out
localpkgs[dups]
## Remove them
if (any(dups)) remove.packages(localpkgs[dups], lib=local.lib)
---<--------------------cut here---------------end--------------------->---

Assuming the default situation in Debian that .libPaths()[1] is the
standard /usr/local/lib/R/site-library, where regular users can write.
It also assumes of course one wants to remove all duplicate packages.

If one has local R versions besides Debian, each using a library under
say /usr/local/lib/R-VERSION/site-library, then one could have:

R_LIBS_USER="/usr/local/lib/R-%V/site-library"

in ~/.Renviron, then .libPaths()[1] would always correspond to the
appropriate library, whatever local version of R is running.  This is
working neatly for me so far.  Debian R ignores ~/.Renviron presumably
because it has found /etc/R/Renviron first, so .libPaths()[1] is always
the stock /usr/local/lib/R/site-library.  Am I following this correctly?