Re: [R] R "sumo" package suggestion

Andrew Beckerman Fri, 12 Nov 2004 02:33:09 -0800

One place to look, linked to the R development community, is the Bioconductor project where their GetBioC() function has package groupings (see http://www.bioconductor.org/getBioC.R) as an option. Perhaps, because of the specific focus of the Bioconductor suite, this is easier, but at least a template with R functionality already exists.

andrew

On 12 Nov 2004, at 09:48, Philippe Grosjean wrote:

Hello,
I think Achim suggestion is more realistic: it does not imply automatic
installation of all packages, but just a restricted list of packages
available on CRAN about a specific topic.
An easy way to get this result is to propose separate lists of packages. It means separate lists than http://cran.r-project.org/src/contrib/PACKAGES.html (and 'PACKAGES' in the Windows packages binaries). I don't see the problem to propose other lists that could be called 'SpatialStats.html' (in packages sources)/'SpatialStats' (in Windows binaries)... and the same for 'MachineLearning', 'Biostats', etc...

Then, of course the various functions that install packages should be adapted to use these lists. It does not look like an unsurmontable task.

Of course, if this is not done yet by the R Core Team, I presume that there must be difficulties that I don't see. It is obvious that, either we need a list maintainer for each topic, or we have to propose keywords for packages (similar to the keywords for functions) that will be used to automatically generate those separate lists.

An alternative that can currently be used for groups of users in an institution is to maintain a local copy of R packages repository, which contains only the packages of interest for this group. I do so for my students. Under Windows, in the new R 2.0.1 beta, there is a new menu entry in packages -> Set CRAN mirror... (in my version it does not work yet, looking for a missing .\doc\CRAN_mirrors.csv file), but I can easily figure out how it works and how I could append my own repository to the list to ease installation of a restricted list of R packages by my students. This is only for Windows, but a similar approach can also be used on other platforms with a little bit of coding.
Best,
Philippe
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-----Original Message-----
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Achim Zeileis
Sent: Thursday, November 11, 2004 10:21 PM
To: Liaw, Andy
Cc: [EMAIL PROTECTED]; [EMAIL PROTECTED]
Subject: Re: [R] R "sumo" package suggestion
On Thu, 11 Nov 2004 15:59:09 -0500 Liaw, Andy wrote:
Good idea, IMHO, but there are some practical difficulties:
I guess the XEmacs packages are (most, if not all) pure elisp code,
and do not need other stuff to work.  However, quite a few CRAN
packages depend on external libraries or programs, and do not
necessarily work on all platforms that R runs on.  How would such
dependencies be resolved in such a kitchen sink bundle?
I have a somewhat related idea: Start labelling packages
with a set
of pre-defined categories, and a package can be labelled with more
than one categories (especially those *misc type packages).  It is
then possible to have facility to let people install all
packages that
fall in a particular category (e.g., `spatial statistics').
I believe
several systems have such facilities, Debian being one of them,
TeXLive being another.
This is similar to idea that has been discussed from time to
time for several years now: it would be nice to have
maintained "CRAN task views"
(or something like that), i.e., we could have a maintainer
for, say "spatial stats", another one for "machine learning",
"biostats" which can of course be overlapping. Then the
maintainers would have to produce some sort of list of
packages (in a standardized format) with a little bit of
markup such that a web page can be generated from it and that
the information could be used by install.packages().
I think most users would profit from that, but nobody has
done the work to provide the infrastructure so far. I've just
discussed this with Kurt again, a week ago or so...I wanted
to play around with some ideas, but didn't get round to
really do something yet. But hopefully, I'll get round to
work on this in the next weeks.
Z
Just my $0.02...
Andy
From: Rodney Sparapani
r-help:
I have an R package suggestion.  After spending several hours the
other day installing about a dozen packages, I had an idea.  In
xemacs, there is a "sumo" package which allows me to
install a large
bundle of xemacs packages at one time (about a 120 modes
including
ESS). I think R should have a similar bundle. It would
be so much
easier than hunting/downloading/installing. Martin
encouraged me to
send this suggestion to r-help. In addition, he put
together a few
comments relating to the previous times that this, or a similar
suggestion, has been brought up here.
Martin wrote:
If you search for "install all CRAN packages"
on
        http://maths.newcastle.edu.au/~rking/R/
(the URL which is quickly found from the [Search] sidebar of
http://www.R-project.org/)
You find things like Greg Warnes 'Makefile'
http://tolstoy.newcastle.edu.au/R/help/04/04/0723.html
and
http://tolstoy.newcastle.edu.au/R/help/04/04/0616.html
which is from Tony and has the following small function:
  installNewCRANPackages <- function() {
    ## (C) A.J. Rossini, 2002--2004
    test2 <- packageStatus()$avail["Status"]
install.packages(row.names(test2)[which(test2$Status=="not
installed")])
  }
----------
Rodney Sparapani              Medical College of Wisconsin
Sr. Biostatistician           Patient Care & Outcomes Research
[EMAIL PROTECTED]              http://www.mcw.edu/pcor
Was 'Name That Tune' rigged?  WWLD -- What Would Lombardi Do
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------------------------------------------------------------------------ --------- Dr. Andrew Beckerman Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK ph +44 (0)114 222 0026; fx +44 (0)114 222 0002 http://www.shef.ac.uk/beckslab ------------------------------------------------------------------------ ----------

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Re: [R] R "sumo" package suggestion

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