From hpages at fhcrc.org  Mon Apr 11 02:05:25 2011
From: hpages at fhcrc.org (=?ISO-8859-1?Q?Herv=E9_Pag=E8s?=)
Date: Sun, 10 Apr 2011 17:05:25 -0700
Subject: [Rd] R CMD build now removes empty dirs
In-Reply-To: <BANLkTim9+O=B+hUwExw_1Af5+ojEO1w5pA@mail.gmail.com>
References: <1705062143.2814.1301464854707.JavaMail.root@zimbra4.fhcrc.org>	<849792884.2828.1301468207385.JavaMail.root@zimbra4.fhcrc.org>
	<BANLkTim9+O=B+hUwExw_1Af5+ojEO1w5pA@mail.gmail.com>
Message-ID: <4DA245C5.2060604@fhcrc.org>

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<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
>>


-- 
Herv? Pag?s

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: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



[Rd] R CMD build now removes empty dirs
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