Re: [Rd] R CMD build now removes empty dirs

From: Henrik Bengtsson <hb_at_biostat.ucsf.edu>
Date: Wed, 30 Mar 2011 20:04:32 -0700

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?).

/Henrik

On Tue, Mar 29, 2011 at 11:56 PM, Pages, Herve <hpages_at_fhcrc.org> wrote:
> Hi,
>
> 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
> inst/:
>
> [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?
>
> Thanks,
> H.
>
> PS: This page
>
>  http://stat.ethz.ch/R-manual/R-devel/doc/html/NEWS.html
>
> (referenced from http://developer.r-project.org/) has not been
> updated for months.
>
> ______________________________________________
> R-devel_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>



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