Hi Henrik,
Just to clarify, you still have the ability of installing directory
structures that are partly empty. Actually 'R CMD INSTALL pkgpath/'
does this. And if srctarball.tar.gz contains empty dirs,
'R CMD INSTALL srctarball.tar.gz' will also keep them.
The problem is that *by default* 'R CMD build' removes those empty
dirs, unless you specify --keep-empty-dirs
The fact that 'R CMD build' and 'R CMD INSTALL' now have different
default behaviors is really a bad thing since when I'm working on
a package I typically do not use 'R CMD build' before I install it.
I use 'R CMD INSTALL' directly on the package source tree.
So everything looks ok to me because then empty dirs are installed.
It's only later when I build the source tarball that it will be
broken.
It's not just --keep-empty-dirs, it's also --resave-data. These
new options don't do the right thing by default and they are not
even consistent between 'R CMD build' and 'R CMD INSTALL'.
Cheers,
H.
On 11-03-30 08:04 PM, Henrik Bengtsson wrote:
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<hpa...@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@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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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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