From hpages at fhcrc.org  Wed Mar 30 08:56:47 2011
From: hpages at fhcrc.org (Pages, Herve)
Date: Tue, 29 Mar 2011 23:56:47 -0700 (PDT)
Subject: [Rd] R CMD build now removes empty dirs
In-Reply-To: <1705062143.2814.1301464854707.JavaMail.root@zimbra4.fhcrc.org>
Message-ID: <849792884.2828.1301468207385.JavaMail.root@zimbra4.fhcrc.org>

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.



[Rd] R CMD build now removes empty dirs
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