[R] R "sumo" package suggestion

Andrew Beckerman a.beckerman at sheffield.ac.uk
Fri Nov 12 11:28:08 CET 2004 

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
>
> ..............................................<°}))><........
>  ) ) ) ) )
> ( ( ( ( (    Prof. Philippe Grosjean
>  ) ) ) ) )
> ( ( ( ( (    Numerical Ecology of Aquatic Systems
>  ) ) ) ) )   Mons-Hainaut University, Pentagone
> ( ( ( ( (    Academie Universitaire Wallonie-Bruxelles
>  ) ) ) ) )   6, av du Champ de Mars, 7000 Mons, Belgium
> ( ( ( ( (
>  ) ) ) ) )   phone: + 32.65.37.34.97, fax: + 32.65.37.33.12
> ( ( ( ( (    email: Philippe.Grosjean at umh.ac.be
>  ) ) ) ) )
> ( ( ( ( (    web:   http://www.umh.ac.be/~econum
>  ) ) ) ) )
> ..............................................................
>
>
>> -----Original Message-----
>> From: r-help-bounces at stat.math.ethz.ch
>> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Achim Zeileis
>> Sent: Thursday, November 11, 2004 10:21 PM
>> To: Liaw, Andy
>> Cc: r-help at stat.math.ethz.ch; rsparapa at post.its.mcw.edu
>> 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
>>>> rsparapa at mcw.edu              http://www.mcw.edu/pcor
>>>> Was 'Name That Tune' rigged?  WWLD -- What Would Lombardi Do
>>>>
>>>> ______________________________________________
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>>>>
>>>>
>>>
>>> ______________________________________________
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>>
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>
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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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