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 <[EMAIL PROTECTED]> writes: >>>>>> "Greg" == Warnes, Gregory R <[EMAIL PROTECTED]> >>>>>> 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 > > ______________________________________________ > [EMAIL PROTECTED] mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Anthony Rossini Research Associate Professor [EMAIL PROTECTED] 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 FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}} ______________________________________________ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
