[R-sig-Debian] Help for sources.list
(Ted Harding)
Ted.Harding at manchester.ac.uk
Sat Jun 5 22:08:22 CEST 2010
Thanks for this, Michael. It looks useful, and I shall certainly
keep it by me for future reference.
I wish to apologise for my abrupt reaction to Dirk's response
to my initial query.
Best wishes to all,
Ted.
On 05-Jun-10 17:23:02, Michael Friendly wrote:
> For what it's worth, I found the instructions for upgrading R on debian
> linux sufficiently
> confusing, that I wrote down in a sort of script the steps I carried
> out, as a record for future reference.
> The next time, I'll just copy/paste selections of lines to a terminal
> window.
> Maybe someone else will find this useful or suggest a way to streamline
> it.
>
> -MIchael
>
>###################################
># append lenny-cran to sources.list
># see: http://cran.r-project.org/bin/linux/debian/ for details
>## NB: better to choose a local CRAN mirror
> cd /etc/apt/
> echo 'deb http://cran.R-project.org/bin/linux/debian lenny-cran/' >>
> sources.list
># see: http://cran.r-project.org/bin/linux/debian/ for details
>
>###################################
># updating R to the current release
>
>
> sudo
> aptitude update
># check policy: make sure you see the newer version
> apt-cache policy r-base
>
> aptitude install r-base r-base-core r-base-dev r-recommended
> aptitude install r-base-html
>
>###################################
># updating r-cran packages [
># NB: (a) I'm not certain of the difference between installing via
># debian packages, vs. update.packages
># (b) to install selectively via apt, it is easier to use a gui tool
># like synaptic than by specifying debian packages on the command
># line
>
># updating R packages: CRAN often has newer than debian r-cran builds
> R
>#update.packages(lib.loc="/usr/local/lib/R/site-packages")
> update.packages()
>
># install other non r-cran packages from CRAN
> nondeb <- c("heplots", "candisc", "vcdExtra")
> install.packages(nondeb)
>
># see what versions are installed where
> pkgs <- installed.packages()
> pkgs[,1:3]
>
>
>
> 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
>>> ------------------------------ XFMail ------------------------------
>>>
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>>
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>
>
> --
> Michael Friendly Email: friendly at yorku.ca
> Professor, Psychology Dept.
> York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
> 4700 Keele Street http://datavis.ca
> Toronto, ONT M3J 1P3 CANADA
>
--------------------------------------------------------------------
E-Mail: (Ted Harding) <Ted.Harding at manchester.ac.uk>
Fax-to-email: +44 (0)870 094 0861
Date: 05-Jun-10 Time: 21:08:16
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