From cstrato at aon.at  Sat Sep 26 22:41:14 2015
From: cstrato at aon.at (cstrato)
Date: Sat, 26 Sep 2015 22:41:14 +0200
Subject: [Rd] Hidden files problem in R CMD check
In-Reply-To: <1B413D74-CCFD-4E5B-B6F0-B42D4C1B46E1@r-project.org>
References: <5606F246.20902@aon.at>
	<1B413D74-CCFD-4E5B-B6F0-B42D4C1B46E1@r-project.org>
Message-ID: <560702EA.7090501@aon.at>

Dear Simon,

Thank you very much for your help, it did solve my problems!! Great!

I have googled COPYFILE_DISABLE and found the following site which does 
explain the issue with tar on Mac OS X, see:
http://unix.stackexchange.com/questions/9665/create-tar-archive-of-a-directory-except-for-hidden-files

Instead of doing:
$tar czf xps_1.29.2.tar.gz xps

I did now:
$COPYFILE_DISABLE=1 tar czf xps_1.29.2.tar.gz xps

Running:
$R CMD check xps_1.29.2.tar.gz
now leaves only '.BBSoptions' as hidden file.


However, I must admit that I do not understand it.

Since  more than ten years I am running the 'tar' command on my Macs
(using Leopard, Snow Leopard, Lion and now Yosemite) and running
R CMD check did never give these warning messages.
Even two weeks ago everything was ok.

Could it be that upgrading from OS X 10.10.3 to 10.10.5 did change the 
behaviour?
(However, the link above is already from 2011)


Maybe one word regarding the editor I am using:
Yes, I am using 'nedit-5.5-Darwin-i386/nedit' which is pretty old,
but in my opinion the best and fastest editor I know:
- When I open a C++ file containing more than 10,000 lines it opens it
   immediately with all C++ instructions highlighted immediately
   (in contrast to emacs)
- I can open the huge (>500 MB) Affymetrix annotation files containing
   more than one million lines in few seconds and scroll fast from
   beginning to end
- It does even have a Language Mode for R

I do not believe that 'nedit' does  create these hidden files, since it 
never did.


Thank you once again.
Best regards,
Christian


On 09/26/15 21:44, Simon Urbanek wrote:
> Christian,
>
> those are resource forks from your files - possibly maintained by your (likey very old?) editor.
>
> First, is seems that you are not creating the tar ball correctly - the correct way is to use R CMD build which should not include resource forks nor files on the ignore list.
>
> That said, if for some reason you intend to create is by hand (not recommended), you may want to set COPYFILE_DISABLE=1 so it doesn't include resource forks.
>
> Cheers,
> Simon
>
>
> On Sep 26, 2015, at 3:30 PM, cstrato <cstrato at aon.at> wrote:
>
>> Dear all,
>>
>> When running R CMD check on my Mac (Yosemite 10.10.5) I get suddenly NOTEs and WARNINGs
>> that my tar.gz file does contain hidden files.
>>
>> However, when checking the corresponding directories with 'ls -al' (or with mc)
>> none of these files does exist!! (with exception .BBSoptions).
>>
>> Here is a partial output of 00check.log:
>>
>> * using log directory '/Volumes/LumiData/CRAN/xps.Rcheck'
>> * using R version 3.2.0 (2015-04-16)
>> * using platform: x86_64-apple-darwin13.4.0 (64-bit)
>> * using session charset: ASCII
>> * checking for file 'xps/DESCRIPTION' ... OK
>> * this is package 'xps' version '1.29.2'
>> * checking package namespace information ... OK
>> * checking package dependencies ... OK
>> * checking if this is a source package ... OK
>> * checking if there is a namespace ... OK
>> * checking for executable files ... OK
>> * checking for hidden files and directories ... NOTE
>> Found the following hidden files and directories:
>>   .BBSoptions
>>   ._.BBSoptions
>>   ._DESCRIPTION
>>   ._NAMESPACE
>>   ._R
>>   ._README
>>   ._build
>>   ._inst
>>   ._man
>>   ._src
>>   ._vignettes
>>   R/._AffyRNAdeg.R
>>   R/._Constructors.R
>>   R/._TreeSetClasses.R
>>   R/._bgcorrect.R
>>   R/._dabg.call.R
>> ...
>>   man/._AffyRNAdeg.Rd
>>   man/._AnalysisTreeSet-class.Rd
>>   man/._CallTreeSet-class.Rd
>>   man/._DataTreeSet-class.Rd
>>   man/._ExprTreeSet-class.Rd
>> ...
>>   src/._rwrapper.cxx
>>   src/._rwrapper.h
>>   src/._xps.def
>>   src/._xpsLinkDef.h
>>   vignettes/._APTvsXPS.Rnw
>>   vignettes/._BoxPlot_BgrdGC_bgrd.png
>>   vignettes/._BoxPlot_BgrdMAS5_bgrd.png
>>   vignettes/._BoxPlot_BgrdRMA.png
>> ...
>> * checking package subdirectories ... WARNING
>> Subdirectory 'R' contains invalid file names:
>>   '._AffyRNAdeg.R' '._Constructors.R' '._TreeSetClasses.R'
>>   '._bgcorrect.R' '._dabg.call.R' '._dfw.R' '._export.R' '._express.R'
>> ...
>> Subdirectory 'man' contains invalid file names:
>>   '._AffyRNAdeg.Rd' '._AnalysisTreeSet-class.Rd'
>>   '._CallTreeSet-class.Rd' '._DataTreeSet-class.Rd'
>>   '._ExprTreeSet-class.Rd' '._Filter-class.Rd'
>>   ...
>>
>>
>> Does anyone know why these files are listed?
>> For some reason all these hidden files start with '._'
>>
>> My suspicion was that maybe there is something wrong with Spotlight (i.e. mdutil)
>> so I excluded the whole volume from Spotlight. This did not help. Adding the volume
>> again and thus forcing a rebuild for Spotlight did not help either.
>>
>> What could I do to remove these apparently non-existing hidden files?
>>
>> Best regards
>> Christian
>> _._._._._._._._._._._._._._._._._._
>> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
>> V.i.e.n.n.a           A.u.s.t.r.i.a
>> e.m.a.i.l:        cstrato at aon.at
>> _._._._._._._._._._._._._._._._._._
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
>



[Rd] Hidden files problem in R CMD check
cstrato