[Rd] R CMD build now removes empty dirs

From: Pages, Herve <hpages_at_fhcrc.org>
Date: Tue, 29 Mar 2011 23:56:47 -0700 (PDT)


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.



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