[R-sig-Debian] Help for sources.list

(Ted Harding) Ted.Harding at manchester.ac.uk
Sat Jun 5 19:49:57 CEST 2010 

Many thanks, Doug, for trying to help! I have entered the line you
suggested into /etc/apt/sources.txt:

  deb http://cran.uk.r-project.org/bin/linux/debian lenny-cran/

After that, starting up Synaptic Package Manager (after "Reload")
gives the following result:

=============
  The repository may no longer be available or could not be
  contacted because of network problems. If available an older
  version of the failed index will be used. Otherwise the
  repository will be ignored. Check your network connection and
  ensure the repository address in the preferences is correct.

http://cran.uk.r-project.org/bin/linux/debian/lenny-cran/
Packages: 301 Moved Permanently
=============

However, when I visit the URL returned above:

  http://cran.uk.r-project.org/bin/linux/debian/lenny-cran

I find a webpage with a long list of R packages, all very recently dated
(e.g. r-base-core_2.11.1-1~lennycran.0_amd64.deb  01-Jun-2010 05:57 13M)

So the stuff is there! But the Debian package manager thinks otherwise.
This (and that was the reason why I wrote my original query as I did)
reminds me of the time I went through a similar exercise on a Debian
Etch a couple of years ago. It took me a week to get it to work. The
solution which Dirk then suggested (which he said worked for him) did
not work for me.

On that machine, sources.list includes the following:
##deb http://cran.uk.r-project.org/bin/linux/debian /stable
##deb http://www.stats.bris.ac.uk/R/bin/linux/debian stable/
### See Dirk Eddelbuettel on r-sig-debian 28/04/2008 02:53:21 CEST ###
##deb http://cran.us.r-project.org/bin/linux/debian stable/
deb http://cran.us.r-project.org/bin/linux/debian etch-cran/
##deb http://cran.uk.r-project.org/bin/linux/debian etch-cran/
##deb http://www.stats.bris.ac.uk/R/bin/linux/debian etch-cran/

[unsuccessful attempts commented out].

Your suggestion, Doug, is similar to the last line but one but with
"lenny-cran" instead of "etch-cran". Since that did not work then,
but did when "uk.r-project" was changed to "us.r-project", I tried
the same change to your suggested line, therefore now:

  deb http://cran.uk.r-project.org/bin/linux/debian lenny-cran/

The result was:

  An error occurred
  The following details are provided:

  W: GPG error: http://www.debian-multimedia.org lenny Release:
  The following signatures couldn't be verified because the public
  key is not available: NO_PUBKEY 07DC563D1F41B907

  W: GPG error: http://cran.us.r-project.org lenny-cran/ Release:
  The following signatures couldn't be verified because the public
  key is not available: NO_PUBKEY 06F90DE5381BA480

Then package manager aborted.

This sort of thing is why I was hoping that a (preferably UK-based)
Debian Lenny user who has a suitable R-cran entry in their sources.list,
which works, would simply tell me what it is!

Thanks again, and hoping for further enlightenment.
Ted.

On 05-Jun-10 16:16:31, Douglas Bates wrote:
> As both you and Dirk have made considerable contributions to the R
> project, although in different contexts, I will try to smooth out some
> of the wrinkles in the communication.  The thing to realize is that
> the Debian packages for R on the Debian archives are updated only when
> a new release of Debian is prepared, and that is infrequent.  On the
> other hand the Debian packages for R on the CRAN archives are updated
> frequently.  It is not uncommon to have them updated within a few
> hours of a new release of R.
> 
> This is why many respondents have suggested something like the
> explanation at
> 
> http://cran.uk.r-project.org/bin/linux/debian
> 
> which says, in effect, that you should add the line
> 
> deb http://cran.uk.r-project.org/bin/linux/debian lenny-cran/
> 
> to your sources.list file.
> 
> 
> 
> On Sat, Jun 5, 2010 at 10:07 AM, Ted Harding
> <Ted.Harding at manchester.ac.uk> wrote:
>> On 05-Jun-10 15:03:55, Ted Harding wrote:
>>> On 05-Jun-10 14:34:24, Dirk Eddelbuettel wrote:
>>>>
>>>> Ted,
>>>>
>>>> On 5 June 2010 at 14:23, (Ted Harding) wrote:
>>>>| Greetings!
>>>>| I would be very grateful if someone could supply a suitable
>>>>| line to enter into /etc/apt/sources.list for the benefit of
>>>>| a complete dummy user (i.e. me -- I do not want to have to
>>>>| do any interpretation, guesswork, reading of docs, etc.;
>>>>| I want to just copy it in).
>>>>|
>>>>| The machine in question is an Intel laptop, wuth Debian Lenny
>>>>| (according to the Debian website the current stable version
>>>>| as of 12 Feb 2010). The current contents of /etc/apt/sources.list
>>>>| are:
>>>>| =======
>>>>| deb http://ftp.uk.debian.org/debian/ lenny main contrib non-free
>>>>| deb-src http://ftp.uk.debian.org/debian/ lenny main contrib
>>>>| non-free
>>>>|
>>>>| deb http://security.debian.org/ lenny/updates main contrib non-free
>>>>| deb-src http://security.debian.org/ lenny/updates main contrib
>>>>| non-free
>>>>|
>>>>| deb http://volatile.debian.org/debian-volatile lenny/volatile main
>>>>| deb-src http://volatile.debian.org/debian-volatile lenny/volatile
>>>>| main
>>>>|
>>>>| deb http://www.debian-multimedia.org lenny main
>>>>| =======
>>>>|
>>>>| I had not been using this machine for running R, until I tried it
>>>>| yesterday and was shocked to find that the R version installed is
>>>>|
>>>>| _ R 2.7.1 (2008-06-23)
>>>>|
>>>>| compared with the version I have on my regular machine, which is
>>>>| R 2.11.0 (2010-04-22). Then I was shocked, on visiting the Debian
>>>>| Lenny webpage, to find that the currently held version of R is
>>>>
>>>> What part of "stable" is unclear? _When you opt for "stable", you
>>>> ask
>>>> Debian
>>>> not to change your packages.
>>>>
>>>> So remarking that it doesn't update your R package, or preferred
>>>> editor, or
>>>> whatever, is inconsistent with what _you_ have chosen. A _stable_
>>>> selection
>>>> of packages. _I am not a native speaker of English but stable seems
>>>> to
>>>> imply
>>>> 'does not change' reasonably well.
>>>>
>>>> So I am puzzled why this is so hard to explain.
>>>>
>>>> Now, maybe you are complaining that Debian has too few releases
>>>> which
>>>> is a
>>>> different matter and requires a bit more of a meta-discussion. _Too
>>>> many,
>>>> Ubuntu is a reasonable compromise between stability and bi-annual
>>>> updates. I
>>>> use it myself, but I also use (and like) Debian testing. It depends.
>>>>
>>>> But by choosing Lenny you got what you asked for. _Now, as you
>>>> asked,
>>>> ...
>>>>
>>>>| the same as the above: "2.7.1-1+lenny" for all the basic R
>>>>| packages.
>>>>| No wonder I have not been getting updates!
>>>>|
>>>>| I am located in the UK.
>>>>|
>>>>| What should I put in /etc/apt/sources.list ? (Maybe more than one
>>>>| line, if that would be relevant to installing/updating a variety
>>>>| of R packages).
>>>>
>>>> It is all documented, and a Google search for 'debian lenny R
>>>> package'
>>>> gets
>>>> me there as a first hit. See the bin/linux/debian/ directory of any
>>>> CRAN
>>>> mirror.
>>>>
>>>> There are occassional mistakes (as Michael Friendly recently
>>>> noticed)
>>>> but the
>>>> page makes an earnest attempt at documenting this so I won't repeat
>>>> it
>>>> here.
>>>> If you have suggestions to make it clearer, please let Johannes or
>>>> us
>>>> know.
>>>>
>>>> This also gets discussed here regularly so you may find looking at
>>>> the
>>>> list
>>>> archives beneficial.
>>>>
>>>> Good luck.
>>>>
>>>> --
>>>> _ Regards, Dirk
>>>
>>> Duncan, I am sorry but your reply is of no help at all.
>>> Goodbye.
>>
>> I meant "Dirk".
>>
>> --------------------------------------------------------------------
>> E-Mail: (Ted Harding) <Ted.Harding at manchester.ac.uk>
>> Fax-to-email: +44 (0)870 094 0861
>> Date: 05-Jun-10 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Time: 16:07:18
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>>
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--------------------------------------------------------------------
E-Mail: (Ted Harding) <Ted.Harding at manchester.ac.uk>
Fax-to-email: +44 (0)870 094 0861
Date: 05-Jun-10                                       Time: 18:49:53
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