From simon.urbanek at r-project.org  Sat Sep 26 21:44:48 2015
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Sat, 26 Sep 2015 15:44:48 -0400
Subject: [Rd] Hidden files problem in R CMD check
In-Reply-To: <5606F246.20902@aon.at>
References: <5606F246.20902@aon.at>
Message-ID: <1B413D74-CCFD-4E5B-B6F0-B42D4C1B46E1@r-project.org>

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
Simon Urbanek