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

Michael Dewey info at aghmed.fsnet.co.uk
Sun Jun 6 15:35:59 CEST 2010 

At 18:23 05/06/2010, 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,
See comment inline below


>-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

I think an explanation of this has recently been added to the welcome 
page you see after R binaries, linux, debian

>#     (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
>
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Michael Dewey
http://www.aghmed.fsnet.co.uk

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