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 <cstr...@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
_._._._._._._._._._._._._._._._._._
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