Dear Chris, Dirk, dear list,
let me add some thoughts here:
Zitat von Dirk Eddelbuettel <[email protected]>:
Welcome!
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.
So you are using the R binary packages I am maintaining for CRAN.
| 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:
As Dirk pointed out, updating packages from within R under Linux/Unix
requires a bit more than under Windows. However it is not a black art.
Basically you need to have r-base-dev installed plus development
packages for any libraries your R package is linking against.
*Every* interaction with the package management system in Debian or Ubuntu
has to happen as root. So do NOT say 'synaptic', say 'sudo synaptic'.
@Dirk: He said he used update.packages() as an ordinary user.
| 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.
Synaptic gets you prebuilt binaries from the repos it knows about.
It seems to me that Chris has r-cran-rgl and r-cran-xml from Debian
squeeze, and R 2.13.1 from CRAN.
What you show here is local compilation, possibly triggered by R. Not at all
the same.
| 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 agree that I would not recommend upgrading them if there is no good
reason for doing so.
| 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."
Is there a local user group or a colleague you could bug locally?
If you really want to upgrade R packages like rgl and XML that are
available in Debian, I would recommend to do it the Debian way. This
means adding the unstable sources to your /etc/apt/sources.list,
running as root (using aptitude/apt as I am not familiar with synaptic)
aptitude build-dep r-cran-rgl r-cran-xml
which gets build dependencies, then as a normal user go to some
location where you want to build, i.e. ~/tmp and
apt-get source -b r-cran-rgl r-cran-xml
You will find, if all goes well, updated .deb packages in your working
directory that you can then install (again as root) e.g. using dpkg -i.
In this way you do not mix the packaging systems of Debian and R.
If you really want to do regular upgrades of all packages from within
R (even though you decided to use Debian stable), you can get the
build dependencies as above, but I believe Dirk would agree it would
be better to remove the Debian packages first and then install R
packages from within R in the first place.
Kind regards,
Johannes
Dirk
| 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
|
| _______________________________________________
| R-SIG-Debian mailing list
| [email protected]
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian
--
New Rcpp master class for R and C++ integration is scheduled for
San Francisco (Oct 8), more details / reg.info available at
http://www.revolutionanalytics.com/products/training/public/rcpp-master-class.php
_______________________________________________
R-SIG-Debian mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-debian
_______________________________________________
R-SIG-Debian mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-debian
