R SIG Debian - Jun 2008 - best way to update packages when using Debian packages of R

After some frustrations with installing some R packages from source,
usually related to library dependencies or suspected kernel problems
(recent one with Ubuntu and Rmpi) I decided to give Debian a try. I'm
working through the tutorial found at
http://cran.r-project.org/bin/linux/debian/ and I have a couple
questions about how packages are best updated between releases of R.
Many R packages are updated between major releases to fix bugs. How
often are the .deb versions of packages updated? If often, would
apt-get update be preferable to "update.packages"? If I am not
mistaken, the later will download and compile from source. If this is
true, and there is a problem compiling from source because of a
missing dependency or other distribution related problem, would not
this cause a problem when updating? OTOH, I have been firmly told that
one should always update packages before reporting a problem to R-help
or R-devel.

As an aside, now that Lenny is in beta2 stage, has anyone tested the
current .debs against Lenny? If so, problems?

I hope I haven't missed something obvious in the tutorial that answers
these questions.

Thanks,
Mark

-- 
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN 46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)

On 18 June 2008 at 12:45, Mark Kimpel wrote:
| After some frustrations with installing some R packages from source,
| usually related to library dependencies or suspected kernel problems

[ Are you really sure 'kernel problems' affect R ? ]

| (recent one with Ubuntu and Rmpi) I decided to give Debian a try. I'm

Ubuntu had broken Open MPI in 'hardy'. 

A couple of people had reported that to launchpad with no apparent reaction.
After some more prodding and complaining from my end, they have now
recognised and understood the mistake (due to linker options on their end,
which don't work with Open MPI having code split over three libraries) and
now provide fixed Open MPI packages for 'intrepid' and
'hardy-proposed',
possibly soon in hardy-updates too.  So cheers to Ubuntu for fixing this.

Hence, you may actually be able to get back to Ubuntu and get on with work.

| working through the tutorial found at
| http://cran.r-project.org/bin/linux/debian/ and I have a couple
| questions about how packages are best updated between releases of R.
| Many R packages are updated between major releases to fix bugs. How
| often are the .deb versions of packages updated? If often, would

All publicly visible, eg via

    http://changelog.debian.net/$SourcePackageName

eg for mgcv or VR

    http://changelog.debian.net/mgcv
    http://changelog.debian.net/vr

I tend to update them as soon as they hit CRAN.  Which is nice -- but
consider a few caveats.  First, this only affects 'unstable' and not
immediately 'testing'.  Second, there are only about 60 CRAN packages in
Debian.

| apt-get update be preferable to "update.packages"? If I am not

It is still an open question, for both Ubuntu and Debian. Different people
use different methods.  At work, and on Ubuntu, I tend to run a short littler
script that updates /usr/local/lib/R/site-library directly using R's
update.packages().  At home under Debian I use a mix.  It really depends on
your preferences and style.

The basic littler script is in the examples directory of littler which you
get via apt-get as usual.

| mistaken, the later will download and compile from source. If this is
| true, and there is a problem compiling from source because of a
| missing dependency or other distribution related problem, would not
| this cause a problem when updating? OTOH, I have been firmly told that

Yes. Which is why we try help with pre-built versions of 'difficult'
packages for
folks who likely to stumble when trying it themselves.

Hth, Dirk

| one should always update packages before reporting a problem to R-help
| or R-devel.
| 
| As an aside, now that Lenny is in beta2 stage, has anyone tested the
| current .debs against Lenny? If so, problems?
| 
| I hope I haven't missed something obvious in the tutorial that answers
| these questions.
| 
| Thanks,
| Mark
| 
| -- 
| Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
| Indiana University School of Medicine
| 
| 15032 Hunter Court, Westfield, IN 46074
| 
| (317) 490-5129 Work, & Mobile & VoiceMail
| (317) 663-0513 Home (no voice mail please)
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

-- 
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