[Rd] Hidden files problem in R CMD check

cstrato
2015-09-27T07:30:08Z

Dear Simon,

As  usual you are not only right but also very helpful.
It seems that I did miss your point with '._*' files.

Now, when I do 'ls - at l' I get e.g. in directory /R:

s$ ls - at l
total 1232
-rw-r--r--@ 1 rabbitus  staff    4691 Apr 10 22:07 AffyRNAdeg.R
         com.apple.quarantine        26
-rw-r--r--@ 1 rabbitus  staff    3629 Apr 10 22:07 Constructors.R
         com.apple.quarantine        26
-rw-r--r--@ 1 rabbitus  staff   26283 Apr 10 22:07 TreeSetClasses.R
         com.apple.quarantine        26
...

Thank you and
Best regards,
Christian


On 09/27/15 03:36, Simon Urbanek wrote:
>
> 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
>>>
>>
>
>