From maechler at stat.math.ethz.ch  Mon Apr 11 12:00:04 2011
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Mon, 11 Apr 2011 12:00:04 +0200
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: <19874.53540.989258.136667@stat.math.ethz.ch>

>>>>> Pages, Herve <hpages at fhcrc.org>
>>>>>     on Tue, 29 Mar 2011 23:56:47 -0700 (PDT) writes:

    > 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.

Thank you, Herve.
I've only now read your e-mail.
(and I now also agree that --keep-empty-dirs should *not* be needed
 to keep an empty inst/ !)

Thanks for the heads up about NEWS.html.
It's finally current again, and hopefully remains so:
It got outdated accidentally, as it was removed from the default
'make' target, and now needs an extra make call.

Martin Maechler, ETH Zurich



[Rd] R CMD build now removes empty dirs
Martin Maechler