From p.dalgaard at biostat.ku.dk  Thu Oct 15 08:57:41 2009
From: p.dalgaard at biostat.ku.dk (Peter Dalgaard)
Date: Thu, 15 Oct 2009 08:57:41 +0200
Subject: [Rd] MASS (and class, nnet, spatial) for R 2.10.0 ?
In-Reply-To: <19158.26517.120600.412604@ron.nulle.part>
References: <19158.21461.867019.783280@ron.nulle.part>	<4AD65689.5020000@stats.uwo.ca>
	<19158.26517.120600.412604@ron.nulle.part>
Message-ID: <4AD6C7E5.8020808@biostat.ku.dk>

Dirk Eddelbuettel wrote:
> On 14 October 2009 at 18:54, Duncan Murdoch wrote:
> | On 14/10/2009 6:42 PM, Dirk Eddelbuettel wrote:
> | > Maybe I missed an announcement somewhere but having started with the usual
> | > practice of putting R pre-releases into Debian unstable leading up to the
> | > release of the next R version, I now find myself unable to do my daily
> | > package maintenance as I only see VR 7.2-49 with its
> | > 
> | > 	Depends: 	R (? 2.5.0), R (? 2.9.2)
> | > 
> | > preventing use on R 2.10.0.   That stopped the update of the Debian package
> | > r-cran-effects (which wants MASS) in its tracks.   
> | > 
> | > I see the somewhat hidden MASS 7.3-0 and 7.3-1 in
> | > 
> | > 	http://cran.r-project.org/src/contrib/Archive/MASS/
> | > 
> | > so should I be using these?  Along with the other components of VR ?
> | 
> | Yes, see this news item:
> | 
> |      o	Bundles of packages are deprecated.  See 'Writing R
> | 	Extensions' for the steps needed to unbundle a bundle.
> 
> That of course I knew as a reader of both your NEWS feed [1] as well as my
> own CRANberries [2] which carried e.g. Paul Gilbert's dse unbundling.
> 
> But that still does not answer my new MASS, nnet, spatial, class release are
> not on CRAN in the usual location (eg $CRAN/src/contrib/) but socked away in
> the Archive/ subdir.
> 
> | The VR bundle contained packages class, MASS, nnet, and spatial, which 
> | are now separate recommended packages, whose source is included in the R 
> | source tarball, or on CRAN in
> | 
> | http://cran.r-project.org/src/contrib/2.10.0/Recommended/
> 
> I guess the fact that VR is special and included in R itself explains part of
> it.  I forget about that angle.

I don't think that's it. Rather, the point is that packages directly 
under src/contrib/ refers to the CURRENT version of R and gets updated 
only on release of the next version. The MASS in src/contrib/2.10.0 has

Depends: R (>= 2.10.0), grDevices, graphics, stats, utils

which means that trouble will occur if it gets put into src/contrib at 
this stage and someone tries to install it.

This does occasionally also affect non-recommended packages, currently: 
orientlib, which is in src/contrib/2.10.0/Other.

So, the point is that if you are building stuff for unreleased versions, 
the process should be taught to look in the appropriate part of CRAN.

As I'm never quite sure what you're up to, I can't tell whether the 
issue is on your side or ours. There does seem to be some potential 
issues, both with dependency searches and with the effects of 
unbundling. (Do we, e.g., want a virtual VR package which just depends 
on the packages that used to be inside, for the benefit of packages that 
depends on VR?)

-p

> Dirk
> 
> [1] http://developer.r-project.org/blosxom.cgi/R-devel
> [2] http://dirk.eddelbuettel.com/cranberries/


-- 
    O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
   c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
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[Rd] MASS (and class, nnet, spatial) for R 2.10.0 ?
Peter Dalgaard