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.
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 >
>>>>> 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