From ligges at statistik.tu-dortmund.de  Thu Oct 15 09:54:44 2009
From: ligges at statistik.tu-dortmund.de (Uwe Ligges)
Date: Thu, 15 Oct 2009 09:54:44 +0200
Subject: [Rd] MASS (and class, nnet, spatial) for R 2.10.0 ?
In-Reply-To: <4AD6C7E5.8020808@biostat.ku.dk>
References: <19158.21461.867019.783280@ron.nulle.part>	<4AD65689.5020000@stats.uwo.ca>	<19158.26517.120600.412604@ron.nulle.part>
	<4AD6C7E5.8020808@biostat.ku.dk>
Message-ID: <4AD6D544.5040104@statistik.tu-dortmund.de>



Peter Dalgaard wrote:
> 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?)


Can packages depend on VR? Untested, but at least there is no such 
package on CRAN and dependency rules should mention the package, not the 
bundle.

The PACKAGES file in src/contrib also points to the packages in 
src/contrib/2.10.0. It is up to Dirk to use the information in PACKAGES 
correctly as it is done for the Windows and Mac binaries on CRAN.

Best,
Uwe







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



[Rd] MASS (and class, nnet, spatial) for R 2.10.0 ?
Uwe Ligges