[R] R, VR, and Debian

Dirk Eddelbuettel
Mon, 07 Apr 2008 00:30:48 -0000

On 6 April 2008 at 23:58, (Ted Harding) wrote:
| Hi Folks,
| A while ago (September 2007) I set up an experimental
| Debian 4.0 Etch installation, and installed R on it,
| along with several packages -- including e1071 and
| the "Bundle" VR -- by means of the Debian package
| manager. Most of the time, R works fine. But not always.
|
| Just now, I wanted to try the code suggested by
| Johannes H?sing for "Stroparia"'s Multiset Permutation
| question.
|
| The first line is "library(e1071)" -- this failed
| because:
|
| library(e1071)
| Loading required package: class
| Error: package 'class' could not be loaded
| In addition: Warning message:
| there is no package called 'class' in: library(pkg,
| character.only = TRUE, logical = TRUE, lib.loc = lib.loc)

Looks like you may want to file a bug report against the corresponding Debian
package which be out of sync or requiring a rebuild. I'm CCing the
maintainer
of that pacage too.
|
| The Debian package manager tells me that "r-cran-vr"
| is fully installed, and that
| "The VR package contains four individuals packages:
| MASS, class, nnet and spatial."
|
| Also, that the installed version of r-cran-vr is
| 7.2.29-1 and also that this is the latest version.
| However, the version on CRAN is 7.2-41.

You made a choice of picking Debian etch for stability. This means packages
will not be updated _by design and your choice_.  So you cannot turn around
and say 'how come the VR version  is behind CRAN?'.

For Debian unstable and testing (sid and lenny, IIRC) we have current
versions.

| A search downwards from /usr/lib/R finds nothing that
| matches "class", "nnet", nor "spatial", though
MASS
| is there. 'locate class', 'locate nnet', 'locate
spatial'
| all draw blanks (as far as anything to do with R is
| concerned). So these packages, allegedly part of VR,
| have not been installed.

I have them below /usr/lib/R as you'd expect, but I ran testing.  Maybe
something happened.  I'd reinstall the package.

| I thought of uninstalling VR and re-installing, but
| after I marked it for deletion I was told that lots
| of other packages would disappear as well, so I
| backed off.

Just re-install by hand to test. Download the ,deb to /tmp and do 'sudo dpkg
--install r-cran-vr_*.deb' on it.

| It would seem, therefore, that installing R via the
| Debian repositories can be a close approximation to
| a waste of time!
|
| Additionally, in the past I have encountered a block
| when trying to install R packages from source, on this
| system, because something is wrong with 'gfortran'.
|
| I do not want to have to fight Debian in order to get
| on with using R, and (once again) feel discouraged
| about continuing to use a Linux distribution which,
| in other respects, is of high repute.

Many people are happy users of R and Debian.  Why don;t you bring your
questions to the r-sig-debian list where they are most on-topic?

Hth, Dirk

| I would be grateful for comments on the above observations,
| and particularly grateful for suggestions about how to
| overcome these problems.
|
| With best wishes to all,
| Ted.
|
| --------------------------------------------------------------------
| E-Mail: (Ted Harding) <Ted.Harding at manchester.ac.uk>
| Fax-to-email: +44 (0)870 094 0861
| Date: 06-Apr-08                                       Time: 23:58:27
| ------------------------------ XFMail ------------------------------
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--
Three out of two people have difficulties with fractions.