From hb at biostat.ucsf.edu  Thu Mar 31 05:04:32 2011
From: hb at biostat.ucsf.edu (Henrik Bengtsson)
Date: Wed, 30 Mar 2011 20:04:32 -0700
Subject: [Rd] R CMD build now removes empty dirs
In-Reply-To: <849792884.2828.1301468207385.JavaMail.root@zimbra4.fhcrc.org>
References: <1705062143.2814.1301464854707.JavaMail.root@zimbra4.fhcrc.org>
	<849792884.2828.1301468207385.JavaMail.root@zimbra4.fhcrc.org>
Message-ID: <BANLkTim9+O=B+hUwExw_1Af5+ojEO1w5pA@mail.gmail.com>

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
>



[Rd] R CMD build now removes empty dirs
Henrik Bengtsson