[Rd] Hidden files problem in R CMD check
cstrato at aon.at
Sat Sep 26 22:41:14 CEST 2015
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:
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
$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
(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
Thank you once again.
On 09/26/15 21:44, Simon Urbanek wrote:
> 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.
> 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:
>> * 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
>> 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
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