From rossini at blindglobe.net  Mon Sep 20 16:04:36 2004
From: rossini at blindglobe.net (A.J. Rossini)
Date: Mon Sep 20 16:04:44 2004
Subject: [Rd] R-2.0.0 Install problem for pkg bundle w inter-dependent
	namespaces
In-Reply-To: <16718.42417.822821.357884@gargle.gargle.HOWL> (Martin
	Maechler's message of "Mon, 20 Sep 2004 11:41:05 +0200")
References: <D7A3CFD7825BD6119B880002A58F06C20C521C2E@groexmb02.pfizer.com>
	<16718.42417.822821.357884@gargle.gargle.HOWL>
Message-ID: <85d60hox3f.fsf@servant.blindglobe.net>


I recall that we (the BioC group) ended up shying away from bundles,
since there were so few successful ones in existence; hence the work
put into the reposTools package (for making repositories).  That might
be a better approach, Greg (i.e. make a 3rd party repository, rather
than a bundle, and make sure that the dependencies are not circular,
which was a nasty problem for an (unreleased) while with BioC).

best,
-tony


Martin Maechler <maechler@stat.math.ethz.ch> writes:

>>>>>> "Greg" == Warnes, Gregory R <gregory_r_warnes@groton.pfizer.com>
>>>>>>     on Fri, 17 Sep 2004 14:18:29 -0400 writes:
>
>     Greg> I have a revised version of the gregmisc package,
>     Greg> which I've converted into a package bundle each of
>     Greg> which has a namespace: gplots, gmodels, gdata,
>     Greg> gtoools.  Of course, there are interdependencies among
>     Greg> these namespaces:
>
>     Greg> gsun374: /tmp [11]> cd gregmisc/
>     Greg> gsun374: gregmisc [12]> grep import */NAMESPACE
>     Greg>   gdata/NAMESPACE:importFrom(gtools, odd, invalid, mixedsort)
>     Greg> gmodels/NAMESPACE:importFrom(MASS, ginv)
>     Greg>  gplots/NAMESPACE:importFrom(gtools, invalid)
>     Greg>  gplots/NAMESPACE:importFrom(gtools, odd)
>     Greg>  gplots/NAMESPACE:importFrom(gdata, nobs)
>
> since nobody else has answered yet (and a considerable portion
> of R-core is traveling this week) :
>
> If I understand correctly, your basic package 'gtools' and the
> dependency you need is
>
>  gplots --> gdata --> gtools
>         \----->----/
>
> Have you made sure to use the proper  'Depends: ' entries in
> the DESCRIPTION(.in) files of your bundle packages ?
>
> This works fine if the packages are *not* in a bundle, right?
>
>     Greg> Under R-1.9.1, this package bundle passes R CMD check
>     Greg> and installs happily.  However, under yesterday's
>     Greg> R-2.0.0-alpha, the package fails to install (& hence
>     Greg> pass CMD CHECK) with the error
>
>     Greg> ** preparing package for lazy loading
>     Greg> Error in loadNamespace(i[[1]], c(lib.loc, .libPaths()), keep.source)
>     Greg> : 
>     Greg> There is no package called 'gdata'
>     Greg> Execution halted
>     Greg> ERROR: lazy loading failed for package 'gplots'
>
>     Greg> because the gdata package is the last in the bundle to
>     Greg> be installed, so it is not yet present.
>
>     Greg> So, what is the proper way to handle this?  Is there
>     Greg> some way to manually specify the package install order?
>
> Well, isn't the order in the 'Contains:' field of the bundle
> DESCRIPTION file used?  
> If not, please consider sending patches for  
> src/scripts/INSTALL.in
>
> There are not too many bundles AFAIK, and conceptually
> (inspite of the recommended VR one) the improved package
> management tools that we (and the bioconductor project) have
> been adding to R for a while noe
> really aim for "R package objects" and clean version /
> dependency handling of inidividual packages in many different concepts.
>
> If bundle installation etc could rely entirely on the package
> tools, bundles would "work automagically".  But probably, for
> this a bundle would have to be treated as a "package repository"
> which it isn't currently AFAIK.
>
> Regards,
> Martin Maechler
>
> ______________________________________________
> R-devel@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
Anthony Rossini			    Research Associate Professor
rossini@u.washington.edu            http://www.analytics.washington.edu/ 
Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
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[Rd] R-2.0.0 Install problem for pkg bundle w inter-dependent namespaces
A.J. Rossini