[R-SIG-Mac] hidden files and directories

Marc Schwartz marc_schwartz at me.com
Wed Aug 7 15:17:24 CEST 2013

You should be running R CMD check on the package *tarball*, not on the source folder tree. So:

  R CMD check pkgName_X.1.tar.gz

or perhaps:

  R CMD check --as-cran pkgName_X.1.tar.gz

after running:

  R CMD build pkgName

to create the source tarball.

The output regarding the .DS_Store files is a NOTE regarding the package folder tree, not on the tarball contents and is not a warning or an error. Don't worry about .DS_Store or other version control system files (eg. for SVN or Git) as they will be ignored when building the package tarball, as R excludes them by default.

Other hidden files however, may be problematic, so you should avoid explicitly creating them, just as you should remove other non-essential files that may have been created by editors, GUIs, etc. that should not be part of the source package content.

More generally, don't worry about the .DS_Store files on OSX. They contain metadata that is useful for Finder and are arguably an annoyance, but that's about it. There are parallel files on other OS's as well.


Marc Schwartz

On Aug 6, 2013, at 9:59 AM, Rohmatul Fajriyah <rfajriyah at yahoo.com> wrote:

> Dear All,
> Apologise for late reply. I tried to clean some files from my laptop and it took time.
> Prof. Ripley: I already checked it and untarbut it still produces the .DS_Store 
> Dr. Hansen: I did it as follows: R CMD build pkgName, then R CMD install pkgName_X.1.tar.gz and R CMD check pkgName.
> After the last step, the results was
> NOTE: There was 1 note.
> See
>   ‘/Users/rfajriyah/Desktop/pkgName.Rcheck/00check.log’
> for details.
> It because of this :
> * checking for hidden files and directories ... NOTE
> Found the following hidden files and directories:
>   .DS_Store
>   man/.DS_Store
> These were most likely included in error. See section ‘Package
> structure’ in the ‘Writing R Extensions’ manual.
> The man/Rapp.history is gone now, after I deleted it manually.
> I suppose, I need to know how to clean the .DS_Store from my laptop. 
> Prof. Dalgaard Prof. Winsemius: if I type defaults write com.apple.Finder AppleShowAllFiles TRUE in terminal session, yes, I can see the .DS_Store by using ls or Finder.app.
> But still don't know how to clear/remove it.
> Many thanks for all your respond and suggestion.
> With kind regards,
> Ema
> ________________________________
> From: peter dalgaard <pdalgd at gmail.com>
> To: Prof Brian Ripley <ripley at stats.ox.ac.uk> 
> Cc: David Winsemius <dwinsemius at comcast.net>; "r-sig-mac at r-project.org" <r-
> Sent: Tuesday, August 6, 2013 2:55 PM
> Subject: Re: [R-SIG-Mac] hidden files and directories
> On Aug 6, 2013, at 08:06 , Prof Brian Ripley wrote:
>>> Those files would both be invisible when using the Finder.app unless you used ls in a terminal session, but I guess you figured that out
>> invisible *by default*: it is a Finder setting.
> They're trying their damndest to hide it, though. It's only settable by "defaults write ..." in a Terminal. (And if you know how to do that, you might as well be using "ls".) 
> -- 
> Peter Dalgaard, Professor
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com
> 	[[alternative HTML version deleted]]
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