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? 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 >
On 26 September 2015 at 23:06, cstrato wrote: | Dear Dirk, | | Yes, I know, however forget for one moment R. No we can't. Your question was about to make R CMD check happy and 'quiet'. And one answer is to feed it a properly constructed file. | | If I use tar independent of R it still should not create these hidden | files. Hm, I doubt that. We have to tell R explicitly to exclude dotfiles, directories from version control etc pp. Recall the discussion years when .git was added to the already existing .svn? In any event, R is open source so you can check what 'build' does and follow its code into the tools package. | BTW, do you know where these hidden files are stored on the Mac? Pass -- I am too pedestrian for owing one of those machines ;-) Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Dear Dirk, Please do not get me wrong. Yes, I am doing it the wrong way and I am doing it since about eight years. Nevertheless I am still allowed to be confused when something suddenly happens which did not happen before during all these years. Doing it correctly will solve the problem, but it will not explain this behavior which suddenly popped up. Best regards, Christian On 09/26/15 23:30, Dirk Eddelbuettel wrote:> > On 26 September 2015 at 23:06, cstrato wrote: > | Dear Dirk, > | > | Yes, I know, however forget for one moment R. > > No we can't. Your question was about to make R CMD check happy and > 'quiet'. And one answer is to feed it a properly constructed file. > | > | If I use tar independent of R it still should not create these hidden > | files. > > Hm, I doubt that. We have to tell R explicitly to exclude dotfiles, > directories from version control etc pp. Recall the discussion years when > .git was added to the already existing .svn? > > In any event, R is open source so you can check what 'build' does and follow > its code into the tools package. > > | BTW, do you know where these hidden files are stored on the Mac? > > Pass -- I am too pedestrian for owing one of those machines ;-) > > Dirk >
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. -- David.> > 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 >> > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-develDavid Winsemius Alameda, CA, USA
Hi Christian, This seems like a question about OSX rather than R. You will probably have more luck asking on an apple forum. Or just google: http://bfy.tw/1zhP Best, Ista On Sep 26, 2015 8:39 PM, "David Winsemius" <dwinsemius at comcast.net> wrote:> > 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. > > -- > David. > > > > > 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 > >> > > > > ______________________________________________ > > R-devel at r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > David Winsemius > Alameda, CA, USA > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >[[alternative HTML version deleted]]
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: >> | $R CMD check xps_1.29.2.tar.gz >> | now leaves only '.BBSoptions' as hidden file. >> >> No, still wrong. As Simon said, we all are supposed to use 'R CMD build xps' >> to create the tarball. "Back in the day ..." straight tar cfz ... worked, it >> more or less stopped _many_ years ago. Cf TheOneManualThatMatters: >> >> 1.3.1 Checking packages >> ----------------------- >> >> Using 'R CMD check', the R package checker, one can test whether >> _source_ R packages work correctly. It can be run on one or more >> directories, or compressed package 'tar' archives with extension >> '.tar.gz', '.tgz', '.tar.bz2' or '.tar.xz'. >> >> It is strongly recommended that the final checks are run on a 'tar' >> archive prepared by 'R CMD build'. >> >> Ie "It is strongly recommended ... 'tar' archive prepared by 'R CMD build'. >> >> Dirk >> >
Dear Simon,
As usual you are not only right but also very helpful.
It seems that I did miss your point with '._*' files.
Now, when I do 'ls - at l' I get e.g. in directory /R:
s$ 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
>>>
>>
>
>