[R-sig-Debian] Help for sources.list
Michael Friendly
friendly at yorku.ca
Sat Jun 5 19:23:02 CEST 2010
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
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