Skip to content

How to install R 2.2.0 Debian 'unstable' package in otherwise 'sarge' system

7 messages · Dan Davison, Christian T. Steigies, Dirk Eddelbuettel +3 more

Original
Dan Davison
# 
I would like to install the latest version of R (the statistical computing 
software). This is package r-base version 2.2.0 and is in the debian 
'unstable' repository. Otherwise my system has 'sarge' packages, including 
r-base 2.1.0. What is the best way to do this? If I don't want to upgrade 
to unstable, must I compile R myself, or is there some way to install this 
as a debian package?

I have tried:

(i) pointing /etc/apt/sources.list at unstable, apt-get updating and then 
apt-get install r-base. This results in

[... full output at bottom of email ...]

E: This installation run will require temporarily removing the essential
package e2fsprogs due to a Conflicts/Pre-Depends loop. This is often bad,
but if you really want to do it, activate the APT::Force-LoopBreak option.
E: Internal Error, Could not early remove e2fsprogs

which scares me into desisting with this course of action.

(ii) apt-get install -t unstable r-base, but it replies that 
r-base is already the newest version. Have I not invoked this command 
correctly, or does the -t switch not do what I was thinking it did?


Thanks very much for any help,

Dan


dd:/home/dan# apt-get install r-base
Reading Package Lists... Done
Building Dependency Tree... Done
The following extra packages will be installed:
   e2fslibs e2fsprogs gcc-3.4-base libblkid1 libc6 libc6-dev libg2c0 
libgcc1 libss2
   libuuid1 locales r-base-core r-base-dev r-recommended
Suggested packages:
   gpart parted e2fsck-static glibc-doc ess libpaper-utils
The following NEW packages will be installed:
   e2fslibs gcc-3.4-base libblkid1 libss2 libuuid1
The following packages will be upgraded:
   e2fsprogs libc6 libc6-dev libg2c0 libgcc1 locales r-base r-base-core 
r-base-dev
   r-recommended
10 upgraded, 5 newly installed, 0 to remove and 536 not upgraded.
Need to get 0B/21.4MB of archives.
After unpacking 5886kB of additional disk space will be used.
Do you want to continue? [Y/n] Y
E: This installation run will require temporarily removing the essential 
package e2fsprogs due to a Conflicts/Pre-Depends loop. This is often bad, 
but if you really want to do it, activate the APT::Force-LoopBreak option.
E: Internal Error, Could not early remove e2fsprogs
Christian T. Steigies
#
On Wed, Oct 12, 2005 at 04:04:50PM -0500, Dan Davison wrote:
http://cran.r-project.org/doc/FAQ/R-FAQ.html#Are-there-Unix-binaries-for-R_003f

I haven't build 2.2.0 yet, but I will probably do it next weekend. R 2.1.1
is available and you should be able to install it without too many problems
(you might have to remove a lot of r-cran packages which I all put into the
r-recommended package for the backport, I'll try to fix that for the next
version).

Christian
Dirk Eddelbuettel
# 
Dan,

First off, there is even a r-sig-debian list in the universe of R mailing
lists (c.f. the R FAQ). That probably provides a more focused readership
than the union of r-help (where many won't know Debian) and debian-user
(where many won't know R).
On Wed, Oct 12, 2005 at 04:04:50PM -0500, Dan Davison wrote:
Short answers: 

i) In general, and especially between 'testing' and 'unstable', use
apt-pinning, explained in the apt-howto packages, esp apt-howto-en for
English; and on various places across the Net; try Google'ing for
apt-pinning.

That way you get the option of installing selected parts of unstable without
being forced to upgrade wholesale.  Myself and countless other have used
this for years between testing and unstable.  However, I am not so sure how
well it works between stable and unstable. It may work now as stable is
fairly recent, but may fail further down the road.

ii) In this particular case, and as explained in the R FAQ, the CRAN
archives have an apt-get'able section for Debian stable. However, Christian,
the (CC'ed) maintainer of this backport was traveling between conferences in
the US and has not yet provided R 2.2.0 (which was released less than a week
ago, after all).  It should appear shortly.
You can also recompile locally using one of two ways:

iii) as a local Debian package, and apt-get source makes that almost automatic
(provided you have source URIs in /etc/apt/sources.list, and that the
Build-Depends are actually satisfiable under Debian stable), or

iv) as non-Debian compile into /usr/local

If you're in a hurry, iv) is your way.  If you're intrigued by iii), try it.
If you can wait a few days, ii) is probably your best bet.
I'd agree. Don't force things against warnings like this.
Did you run 'apt-get update' after altering /etc/apt/sources.list ?

Try 'apt-cache policy r-base-core' which will tell you about the versions it
knows, where they are from, and how they are prioritized (aka "pinned").
Pleasure. Let me know in private mail if this is clear enough, and we could
even follow up on a local phone call.

Greetings from across town to Hyde Park,  Dirk

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Thomas Friedrichsmeier
    

    

      
      #
    

  


  

      
Hi,

2005/10/12, Christian T. Steigies <cts at debian.org>:

            

      
      
      
    

        
I used the line proposed in this linked document (cut and paste) and
got an error of missformed line by apt get. Anything wrong with this?

            

      
      
      
    

        
Regards
Thomas

  
  


  


      

    

    

      
      

        


  

        

      Kjetil Kjernsmo
    

    

      
      #
    

  


  

      
On onsdag 12 oktober 2005, 23:04, Dan Davison wrote:

            

      
      
      
    

        
Then, I'd recommend using the R's own backports, this line would 
probably do the trick:
deb http://cran.us.r-project.org/bin/linux/debian stable/
and allthough it isn't there yet, it'll probably be there soon.

However, I played with apt-build the other day, and produced my own 
build. It was quite fun, so reading up on apt-build can be a nice 
exercise.

Cheers,

Kjetil

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Vincent Goulet
    

    

      
      #
    

  


  

      
Le 12 Octobre 2005 18:03, Dirk Eddelbuettel a ??crit??:

            

      
      
      
    

        
Dear Dirk,

I'll jump in because I've been wondering how to do this for some time. 

Is there any way to pin a whole series of packages using wildcards? I can 
otherwise pin r-base and r-recommended, but the packages they depend on will 
not be pinned themselves. 

It thus seems the only way to have 'unstable' R packages on my 'testing' 
system is to list them all in /etc/apt/preferences. It is neither convenient 
nor "safe" since I will eventually miss unlisted packages.

Thanks in advance!

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
      #
    

  


  

      
Vincent,

        
On 13 October 2005 at 13:06, Vincent Goulet wrote:

        
| Le 12 Octobre 2005 18:03, Dirk Eddelbuettel a ??crit??:
| > i) In general, and especially between 'testing' and 'unstable', use
| > apt-pinning, explained in the apt-howto packages, esp apt-howto-en for
| > English; and on various places across the Net; try Google'ing for
| > apt-pinning.
| 
| Dear Dirk,
| 
| I'll jump in because I've been wondering how to do this for some time. 
| 
| Is there any way to pin a whole series of packages using wildcards? I can 
| otherwise pin r-base and r-recommended, but the packages they depend on will 
| not be pinned themselves. 
| 
| It thus seems the only way to have 'unstable' R packages on my 'testing' 
| system is to list them all in /etc/apt/preferences. It is neither convenient 
| nor "safe" since I will eventually miss unlisted packages.

Good question, and I don't have an answer.  This may be a question for
debian-user ...  On my machines, I have a local archive containing my builds
for Debian so I get packages such as R and the r-cran-* packages from there.

Amicalement,  Dirk