From cstrato at aon.at  Sat Sep 26 21:30:14 2015
From: cstrato at aon.at (cstrato)
Date: Sat, 26 Sep 2015 21:30:14 +0200
Subject: [Rd] Hidden files problem in R CMD check
Message-ID: <5606F246.20902@aon.at>

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
_._._._._._._._._._._._._._._._._._



[Rd] Hidden files problem in R CMD check
cstrato