Dirk Eddelbuettel sent the following at 20/09/11 21:37:
Welcome!
Thanks!
On 20 September 2011 at 21:20, Chris Evans wrote:
| I am moving from windoze on a Dell laptop to Debian but I seem to have
| hit a snag for R. I managed to find the information to point an
| /etc/apt/sources.list entry at my local CRAN repository and have
| installed R 2.13.1 for squeeze from the Bristol UK repository.
Good so far.
| I installed a number of the additional R packages using synaptic which
| reported no errors but when I run my first update.packages() as an
| ordinary user I get this:
*Every* interaction with the package management system in Debian or Ubuntu
has to happen as root. So do NOT say 'synaptic', say 'sudo synaptic'.
I ran synaptic from the Debian application menu which defaults to root
after askling for the root password the first time I invoke it after a
reboot. (I probably should have said that I've been using Debian for my
internet server work for about 15 years: I'm not a Debian/linux newbie,
just someone finally throwing away the reins from M$ to have a laptop
running Debian as well!)
| The downloaded packages are in
| ‘/tmp/Rtmp9LYziU/downloaded_packages’
| Warning in install.packages(update[instlib == l, "Package"], l,
| contriburl = contriburl, :
| 'lib = "/usr/lib/R/library"' is not writable
| Error in install.packages(update[instlib == l, "Package"], l, contriburl
| = contriburl, :
| unable to install packages
| In addition: Warning messages:
| 1: In install.packages(update[instlib == l, "Package"], l, contriburl =
| contriburl, :
| installation of package 'rgl' had non-zero exit status
| 2: In install.packages(update[instlib == l, "Package"], l, contriburl =
| contriburl, :
| installation of package 'XML' had non-zero exit status
If you get this, and think you used synaptic, you're confused.
Perhaps but not how you think (I think!: just not clear in what I said.
I get that from invoking update.packages() in an R session launched from
a user (chris) terminal session. Before that I had done an install of
2.13.1 from synaptic calling r-cran-base and then finding R worked and
then running synaptic again and getting those additional debs I wanted
from the ones you packaged and the Bristol CRAN repository provided
(r-cran-abind, r-cran-amelia, and others).
Synaptic gets you prebuilt binaries from the repos it knows about.
What you show here is local compilation, possibly triggered by R. Not at all
the same.
Agree and sorry I wasn't clear.
| Although all the compilations have run through, presumably with errors
| for rgl and XML, clearly the "not writable" status of /usr/lib/R/library
Both r-cran-rgl and r-cran-xml exists _as pre-built binaries_. See above, do
not build them locally unless you have to AND know how to.
I wouldn't dream of compiling locally anything I can get from a deb you
rolled!!
| has genuinely prevented the update.
|
| I thought I'd seen strong advice here recently against updating
| libraries as root so I'm intrigued about this. Can someone advise me
| what I should do?
|
| Thanks in advance and huge thanks to all who do the porting to Debian
| and generally make R so good.
It works actually really well indeed, but it is still on Linux / Unix --
which is a whole new world onto itself for people just joining. As the joke
goes: "Unix is user-friendly, but it is picky about its friends."
I like that phrase, hadn't heard it: nice. I do try to adapt to its
demands and be a good friend and in 15 years have virtually never found
it truly whimsical, it's usaully got a reason it doesn't like you even
if it doesn't always tell you clearly what you did to offend!
Is there a local user group or a colleague you could bug locally?
Good question, in 15 years I haven't needed that but if someone on the
list knows of them I could explore that.
However, I come back to feeling that there must be three separate
problems here that come from within the packages I added after the
initial r-cran-base install. My hunch is that there are things with XML
and rgl that I will be able to track down when restrict to just updating
them but that at the moment there is a more global problem which I'm
guessing is caused by one package overriding the order of library path
options seen in .libPaths() which starts with a perfectly writable local
user directory and I am guessing there is some way that package has
insisted that the install tries /usr/lib/R/library.
I don't know enough about the way that R and linux work agree the use of
those library location options. From ?.libPaths and a bit more hunting
around the R help I had the impression that the .libPath options would
be used in order. I think I can remove the /usr ones by hacking in
/etc/R but that presumably risks losing access to the main libraries
that will have been installed there so that doesn't look a good step
forward except perhaps to debug things.
I suspect that I could do a complete remove of all of R, start again
installing r-cran-base, check that R installed by that updates fine run
by a user and then I could use synaptic to add the additional deb
packages you provide but doing that one by one and running R and
update.packages() after each one to see if I don't hit this until afetr
a particular deb but that's going to take quite a long time so I
wondered if you or the list had quicker suggestions to debug this.
Sorry for length but hope that's clearer (got to try to be an acceptable
friend on R lists as well as with linux and I really, really do
appreciate the generosity of this list).
Chris
--
Chris Evans<[email protected]> Skype: chris-psyctc
Consultant Psychiatrist in Psychotherapy, Notts. PDD network;
Professor, Psychotherapy, Nottingham University
*If I am writing from one of those roles, it will be clear. Otherwise*
*my views are my own and not representative of those institutions *
If you have difficulty Emailing me on this address or getting a reply,
send again but cc to: chris dot evans at nottshc dot nhs dot uk
and to: c dot evans at nottingham dot ac dot uk
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