Re: [Rd] Hidden files problem in R CMD check

2015-09-27 Thread cstrato 

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 -@l' I get e.g. in directory /R:

s$ ls -@l
total 1232
-rw-r--r--@ 1 rabbitus  staff4691 Apr 10 22:07 AffyRNAdeg.R
com.apple.quarantine26
-rw-r--r--@ 1 rabbitus  staff3629 Apr 10 22:07 Constructors.R
com.apple.quarantine26
-rw-r--r--@ 1 rabbitus  staff   26283 Apr 10 22:07 TreeSetClasses.R
com.apple.quarantine26
...

Thank you and
Best regards,
Christian


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


On Sep 26, 2015, at 5:06 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?



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








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Re: [Rd] Hidden files problem in R CMD check

2015-09-26 Thread Ista Zahn 
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"  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  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@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
> David Winsemius
> Alameda, CA, USA
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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Re: [Rd] Hidden files problem in R CMD check

2015-09-26 Thread cstrato 

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



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Re: [Rd] Hidden files problem in R CMD check

2015-09-26 Thread David Winsemius 

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  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@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

David Winsemius
Alameda, CA, USA

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Re: [Rd] Hidden files problem in R CMD check

2015-09-26 Thread cstrato 

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



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Re: [Rd] Hidden files problem in R CMD check

2015-09-26 Thread Dirk Eddelbuettel 

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

-- 
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Re: [Rd] Hidden files problem in R CMD check

2015-09-26 Thread Simon Urbanek 
Christian,

those are resource forks from your files - possibly maintained by your (likey 
very old?) editor.

First, is seems that you are not creating the tar ball correctly - the correct 
way is to use R CMD build which should not include resource forks nor files on 
the ignore list.

That said, if for some reason you intend to create is by hand (not 
recommended), you may want to set COPYFILE_DISABLE=1 so it doesn't include 
resource forks.

Cheers,
Simon


On Sep 26, 2015, at 3:30 PM, cstrato  wrote:

> Dear all,
> 
> When running R CMD check on my Mac (Yosemite 10.10.5) I get suddenly NOTEs 
> and WARNINGs
> that my tar.gz file does contain hidden files.
> 
> However, when checking the corresponding directories with 'ls -al' (or with 
> mc)
> none of these files does exist!! (with exception .BBSoptions).
> 
> Here is a partial output of 00check.log:
> 
> * using log directory '/Volumes/LumiData/CRAN/xps.Rcheck'
> * using R version 3.2.0 (2015-04-16)
> * using platform: x86_64-apple-darwin13.4.0 (64-bit)
> * using session charset: ASCII
> * checking for file 'xps/DESCRIPTION' ... OK
> * this is package 'xps' version '1.29.2'
> * checking package namespace information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking if there is a namespace ... OK
> * checking for executable files ... OK
> * checking for hidden files and directories ... NOTE
> Found the following hidden files and directories:
>  .BBSoptions
>  ._.BBSoptions
>  ._DESCRIPTION
>  ._NAMESPACE
>  ._R
>  ._README
>  ._build
>  ._inst
>  ._man
>  ._src
>  ._vignettes
>  R/._AffyRNAdeg.R
>  R/._Constructors.R
>  R/._TreeSetClasses.R
>  R/._bgcorrect.R
>  R/._dabg.call.R
> ...
>  man/._AffyRNAdeg.Rd
>  man/._AnalysisTreeSet-class.Rd
>  man/._CallTreeSet-class.Rd
>  man/._DataTreeSet-class.Rd
>  man/._ExprTreeSet-class.Rd
> ...
>  src/._rwrapper.cxx
>  src/._rwrapper.h
>  src/._xps.def
>  src/._xpsLinkDef.h
>  vignettes/._APTvsXPS.Rnw
>  vignettes/._BoxPlot_BgrdGC_bgrd.png
>  vignettes/._BoxPlot_BgrdMAS5_bgrd.png
>  vignettes/._BoxPlot_BgrdRMA.png
> ...
> * checking package subdirectories ... WARNING
> Subdirectory 'R' contains invalid file names:
>  '._AffyRNAdeg.R' '._Constructors.R' '._TreeSetClasses.R'
>  '._bgcorrect.R' '._dabg.call.R' '._dfw.R' '._export.R' '._express.R'
> ...
> Subdirectory 'man' contains invalid file names:
>  '._AffyRNAdeg.Rd' '._AnalysisTreeSet-class.Rd'
>  '._CallTreeSet-class.Rd' '._DataTreeSet-class.Rd'
>  '._ExprTreeSet-class.Rd' '._Filter-class.Rd'
>  ...
> 
> 
> Does anyone know why these files are listed?
> For some reason all these hidden files start with '._'
> 
> My suspicion was that maybe there is something wrong with Spotlight (i.e. 
> mdutil)
> so I excluded the whole volume from Spotlight. This did not help. Adding the 
> volume
> again and thus forcing a rebuild for Spotlight did not help either.
> 
> What could I do to remove these apparently non-existing hidden files?
> 
> Best regards
> Christian
> _._._._._._._._._._._._._._._._._._
> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
> V.i.e.n.n.a   A.u.s.t.r.i.a
> e.m.a.i.l:cstrato at aon.at
> _._._._._._._._._._._._._._._._._._
> 
> __
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> https://stat.ethz.ch/mailman/listinfo/r-devel
> 

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Re: [Rd] Hidden files problem in R CMD check

2015-09-26 Thread cstrato 

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.


However, I must admit that I do not understand it.

Since  more than ten years I am running the 'tar' command on my Macs
(using Leopard, Snow Leopard, Lion and now Yosemite) and running
R CMD check did never give these warning messages.
Even two weeks ago everything was ok.

Could it be that upgrading from OS X 10.10.3 to 10.10.5 did change the 
behaviour?

(However, the link above is already from 2011)


Maybe one word regarding the editor I am using:
Yes, I am using 'nedit-5.5-Darwin-i386/nedit' which is pretty old,
but in my opinion the best and fastest editor I know:
- When I open a C++ file containing more than 10,000 lines it opens it
  immediately with all C++ instructions highlighted immediately
  (in contrast to emacs)
- I can open the huge (>500 MB) Affymetrix annotation files containing
  more than one million lines in few seconds and scroll fast from
  beginning to end
- It does even have a Language Mode for R

I do not believe that 'nedit' does  create these hidden files, since it 
never did.



Thank you once again.
Best regards,
Christian


On 09/26/15 21:44, Simon Urbanek wrote:

Christian,

those are resource forks from your files - possibly maintained by your (likey 
very old?) editor.

First, is seems that you are not creating the tar ball correctly - the correct 
way is to use R CMD build which should not include resource forks nor files on 
the ignore list.

That said, if for some reason you intend to create is by hand (not 
recommended), you may want to set COPYFILE_DISABLE=1 so it doesn't include 
resource forks.

Cheers,
Simon


On Sep 26, 2015, at 3:30 PM, cstrato  wrote:


Dear all,

When running R CMD check on my Mac (Yosemite 10.10.5) I get suddenly NOTEs and 
WARNINGs
that my tar.gz file does contain hidden files.

However, when checking the corresponding directories with 'ls -al' (or with mc)
none of these files does exist!! (with exception .BBSoptions).

Here is a partial output of 00check.log:

* using log directory '/Volumes/LumiData/CRAN/xps.Rcheck'
* using R version 3.2.0 (2015-04-16)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: ASCII
* checking for file 'xps/DESCRIPTION' ... OK
* this is package 'xps' version '1.29.2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
  ._.BBSoptions
  ._DESCRIPTION
  ._NAMESPACE
  ._R
  ._README
  ._build
  ._inst
  ._man
  ._src
  ._vignettes
  R/._AffyRNAdeg.R
  R/._Constructors.R
  R/._TreeSetClasses.R
  R/._bgcorrect.R
  R/._dabg.call.R
...
  man/._AffyRNAdeg.Rd
  man/._AnalysisTreeSet-class.Rd
  man/._CallTreeSet-class.Rd
  man/._DataTreeSet-class.Rd
  man/._ExprTreeSet-class.Rd
...
  src/._rwrapper.cxx
  src/._rwrapper.h
  src/._xps.def
  src/._xpsLinkDef.h
  vignettes/._APTvsXPS.Rnw
  vignettes/._BoxPlot_BgrdGC_bgrd.png
  vignettes/._BoxPlot_BgrdMAS5_bgrd.png
  vignettes/._BoxPlot_BgrdRMA.png
...
* checking package subdirectories ... WARNING
Subdirectory 'R' contains invalid file names:
  '._AffyRNAdeg.R' '._Constructors.R' '._TreeSetClasses.R'
  '._bgcorrect.R' '._dabg.call.R' '._dfw.R' '._export.R' '._express.R'
...
Subdirectory 'man' contains invalid file names:
  '._AffyRNAdeg.Rd' '._AnalysisTreeSet-class.Rd'
  '._CallTreeSet-class.Rd' '._DataTreeSet-class.Rd'
  '._ExprTreeSet-class.Rd' '._Filter-class.Rd'
  ...


Does anyone know why these files are listed?
For some reason all these hidden files start with '._'

My suspicion was that maybe there is something wrong with Spotlight (i.e. 
mdutil)
so I excluded the whole volume from Spotlight. This did not help. Adding the 
volume
again and thus forcing a rebuild for Spotlight did not help either.

What could I do to remove these apparently non-existing hidden files?

Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a   A.u.s.t.r.i.a
e.m.a.i.l:cstrato at aon.at
_._._._._._._._._._._._._._._._._._

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Re: [Rd] Hidden files problem in R CMD check

2015-09-26 Thread Dirk Eddelbuettel 

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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Re: [Rd] Hidden files problem in R CMD check

2015-09-26 Thread Simon Urbanek 

On Sep 26, 2015, at 5:06 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?
> 

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
>> 
> 

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[Rd] Hidden files problem in R CMD check

2015-09-26 Thread cstrato 

Dear all,

When running R CMD check on my Mac (Yosemite 10.10.5) I get suddenly 
NOTEs and WARNINGs

that my tar.gz file does contain hidden files.

However, when checking the corresponding directories with 'ls -al' (or 
with mc)

none of these files does exist!! (with exception .BBSoptions).

Here is a partial output of 00check.log:

* using log directory '/Volumes/LumiData/CRAN/xps.Rcheck'
* using R version 3.2.0 (2015-04-16)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: ASCII
* checking for file 'xps/DESCRIPTION' ... OK
* this is package 'xps' version '1.29.2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
  ._.BBSoptions
  ._DESCRIPTION
  ._NAMESPACE
  ._R
  ._README
  ._build
  ._inst
  ._man
  ._src
  ._vignettes
  R/._AffyRNAdeg.R
  R/._Constructors.R
  R/._TreeSetClasses.R
  R/._bgcorrect.R
  R/._dabg.call.R
...
  man/._AffyRNAdeg.Rd
  man/._AnalysisTreeSet-class.Rd
  man/._CallTreeSet-class.Rd
  man/._DataTreeSet-class.Rd
  man/._ExprTreeSet-class.Rd
...
  src/._rwrapper.cxx
  src/._rwrapper.h
  src/._xps.def
  src/._xpsLinkDef.h
  vignettes/._APTvsXPS.Rnw
  vignettes/._BoxPlot_BgrdGC_bgrd.png
  vignettes/._BoxPlot_BgrdMAS5_bgrd.png
  vignettes/._BoxPlot_BgrdRMA.png
...
* checking package subdirectories ... WARNING
Subdirectory 'R' contains invalid file names:
  '._AffyRNAdeg.R' '._Constructors.R' '._TreeSetClasses.R'
  '._bgcorrect.R' '._dabg.call.R' '._dfw.R' '._export.R' '._express.R'
...
Subdirectory 'man' contains invalid file names:
  '._AffyRNAdeg.Rd' '._AnalysisTreeSet-class.Rd'
  '._CallTreeSet-class.Rd' '._DataTreeSet-class.Rd'
  '._ExprTreeSet-class.Rd' '._Filter-class.Rd'
  ...


Does anyone know why these files are listed?
For some reason all these hidden files start with '._'

My suspicion was that maybe there is something wrong with Spotlight 
(i.e. mdutil)
so I excluded the whole volume from Spotlight. This did not help. Adding 
the volume

again and thus forcing a rebuild for Spotlight did not help either.

What could I do to remove these apparently non-existing hidden files?

Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a   A.u.s.t.r.i.a
e.m.a.i.l:cstrato at aon.at
_._._._._._._._._._._._._._._._._._

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