[Rd] R CMD build now removes empty dirs
hb at biostat.ucsf.edu
Thu Mar 31 05:04:32 CEST 2011
I am also in favor for keeping the ability of installing directory
structures that are partly empty. I've used it before to setup
templates that can conveniently be copied recursively to a local path.
I did noticed that R CMD INSTALL gave a warning about empty
directories before (or was it a NOTE by R CMD check?).
On Tue, Mar 29, 2011 at 11:56 PM, Pages, Herve <hpages at fhcrc.org> wrote:
> It's unfortunate that with recent revisions of R 2.13 (this
> appeared in revision 54640, March 2), 'R CMD build' now removes
> empty dirs in the package. People might have good reasons for
> having empty dirs in their packages. For example, in Bioconductor,
> we have some tools to automatically generate annotation packages
> and those tools are implemented in software packages that use
> templates for the annotation packages to be generated. Those
> package templates are stored under the inst/ folder of the
> software package. One of those software packages is the
> AnnotationDbi package: it contains 41 package templates under
> [hpages at latitude Rpacks]$ ls AnnotationDbi/inst/AnnDbPkg-templates/
> AFFYHUEX.DB CHIMP.DB MALARIA.DB WORM.DB
> ANOPHELES.DB COELICOLOR.DB MOUSECHIP.DB XENOPUSCHIP.DB
> ARABIDOPSISCHIP.DB ECOLICHIP.DB MOUSE.DB XENOPUS.DB
> ARABIDOPSIS.DB ECOLI.DB ORGANISM.DB YEASTCHIP.DB
> BASEPKG.DB FLYCHIP.DB PFAM.DB YEAST.DB
> BOVINECHIP.DB FLY.DB PIGCHIP.DB YEASTNCBI.DB
> BOVINE.DB GO.DB PIG.DB ZEBRAFISHCHIP.DB
> CANINECHIP.DB HUMANCHIP.DB RATCHIP.DB ZEBRAFISH.DB
> CANINE.DB HUMAN.DB RAT.DB
> CHICKENCHIP.DB INPARANOID.DB RHESUS.DB
> CHICKEN.DB KEGG.DB WORMCHIP.DB
> Those package templates are just the skeletons of the hundreds of
> annotation packages that we generate. Of course, each of them contains
> empty subfolders.
> Having 'R CMD build' remove those empty subfolders breaks all the
> tools that make use of those package templates.
> Maybe I've missed it but I didn't see any mention of this "feature"
> on this list and the fact that it was added only 6 weeks before the
> next R and Bioconductor releases is only making this worse.
> I hope this "feature" can be reverted. Why would people or our build
> system need to start using R CMD build --keep-empty-dirs just to get
> a source tarball right?
> PS: This page
> (referenced from http://developer.r-project.org/) has not been
> updated for months.
> R-devel at r-project.org mailing list
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