[Rd] Hidden files problem in R CMD check

David Winsemius dwinsemius at comcast.net
Sun Sep 27 02:38:13 CEST 2015

On Sep 26, 2015, at 2:06 PM, cstrato wrote:

> Dear Dirk,
> Yes, I know, however forget for one moment R.
> If I use tar independent of R it still should not create these hidden files.
> BTW, do you know where these hidden files are stored on the Mac?

Your first posting showed which of several different directories they were in. Do you understand that any file whose name starts with a <period> is called a "hidden file"? It is "hidden", i.e not displayed in a Finder window, from people who are using Finder.app unless you change the default settings. It's easy to look up the code that is needed to be pasted into a Terminal session. I never remember it. I just leave Finder set up to display these 'dotfiles' as they are also called.

defaults write com.apple.finder AppleShowAllFiles YES

killall Finder

#The second command restarts Finder.app or you could try to restart the Finder by option (=alt) + rightclicking the Finder icon in the Dock and selecting Relaunch.


> Best regards,
> Christian
> On 09/26/15 23:01, Dirk Eddelbuettel wrote:
>> On 26 September 2015 at 22:41, cstrato wrote:
>> | 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.
>> No, still wrong. As Simon said, we all are supposed to use 'R CMD build xps'
>> to create the tarball.  "Back in the day ..." straight tar cfz ... worked, it
>> more or less stopped _many_ years ago.  Cf TheOneManualThatMatters:
>>    1.3.1 Checking packages
>>    -----------------------
>>    Using 'R CMD check', the R package checker, one can test whether
>>    _source_ R packages work correctly.  It can be run on one or more
>>    directories, or compressed package 'tar' archives with extension
>>    '.tar.gz', '.tgz', '.tar.bz2' or '.tar.xz'.
>>       It is strongly recommended that the final checks are run on a 'tar'
>>    archive prepared by 'R CMD build'.
>> Ie "It is strongly recommended ... 'tar' archive prepared by 'R CMD build'.
>> Dirk
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David Winsemius
Alameda, CA, USA

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