[Rd] Hidden files problem in R CMD check

Simon Urbanek
2015-09-27T01:36:17Z

On Sep 26, 2015, at 5:06 PM, cstrato <cstrato at aon.at> 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?
>

Please consider reading my original reply - those are not actual files (all but
.BBSoptions which is an actual file you can see with ls -a), those are just
resource forks of files [or extended attributes in general] -- and Apple tar if
instructed to preserve resource forks encodes them as ._* in tar balls since tar
has no native way of storing resource forks. And, again, as I said in my reply
those likely come from some software you may have used (possibly the editor).
For example, some editors store the file encoding in xattr. To list them you can
use ls -l@

Cheers,
Simon



> 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
>>
>