Re: [R-SIG-Mac] hidden files and directories

2013-08-06 Thread Rohmatul Fajriyah 


It was suggested by Prof. Ripley at the first place to check the tar ball.
But I missed the hint. (never checked the tar ball previously)
Thank you Prof. Ripley! 
Apologise for not spotting it in the beginning. :)

Many thanks for all your help.
It's much appreciated.

With kind regards,
Ema




 From: peter dalgaard 

Cc: Prof Brian Ripley ; David Winsemius 
; "r-sig-mac@r-project.org" ; 
"kasperdanielhan...@gmail.com"  
Sent: Tuesday, August 6, 2013 6:17 PM
Subject: Re: [R-SIG-Mac] hidden files and directories



On Aug 6, 2013, at 16:59 , Rohmatul Fajriyah wrote:

> 
> Dear All,
> 
> Apologise for late reply. I tried to clean some files from my laptop and it 
> took time.
> 
> Prof. Ripley: I already checked it and untar but it still produces the 
> .DS_Store 
> Dr. Hansen: I did it as follows: R CMD build pkgName, then R CMD install 
> pkgName_X.1.tar.gz and R CMD check pkgName.
> After the last step, the results was
>  
> NOTE: There was 1 note.
> See
>   ‘/Users/rfajriyah/Desktop/pkgName.Rcheck/00check.log’
> for details.
> 
> It because of this :
> * checking for hidden files and directories ... NOTE
> Found the following hidden files and directories:
>   .DS_Store
>   man/.DS_Store
> These were most likely included in error. See section ‘Package
> structure’ in the ‘Writing R Extensions’ manual.
> 
> The man/Rapp.history is gone now, after I deleted it manually.
> 
> I suppose, I need to know how to clean the .DS_Store from my laptop. 
> 
> Prof. Dalgaard Prof. Winsemius: if I type defaults write com.apple.Finder 
> AppleShowAllFiles TRUE in terminal session, yes, I can see the .DS_Store by 
> using ls or Finder.app.
> 
> But still don't know how to clear/remove it.

You can do it with rm in a terminal, but as I understand it, .DS_store files 
are created _by_ Finder, so it is a bit of a fight against windmills. It'll be 
there again next time you view the directory. 

The key is to do what Kasper said. Exactly what he said, not what you think he 
meant to say! I.e., 

R CMD build pkgName
R CMD check pkgName_X_Y_Z.tar.gz

I.e., do not install, build and run check on the .tar.gz file. R CMD build 
should take care of skipping the .DS_store files.


> 
> Many thanks for all your respond and suggestion.
> 
> With kind regards,
> Ema
> 
> From: peter dalgaard 
> To: Prof Brian Ripley  
> Cc: David Winsemius ; "r-sig-mac@r-project.org" <
> Sent: Tuesday, August 6, 2013 2:55 PM
> Subject: Re: [R-SIG-Mac] hidden files and directories
> 
> 
> On Aug 6, 2013, at 08:06 , Prof Brian Ripley wrote:
> 
> >> 
> >> Those files would both be invisible when using the Finder.app unless you 
> >> used ls in a terminal session, but I guess you figured that out
> > 
> > invisible *by default*: it is a Finder setting.
> > 
> 
> They're trying their damndest to hide it, though. It's only settable by 
> "defaults write ..." in a Terminal. (And if you know how to do that, you 
> might as well be using "ls".) 
> 
> -- 
> Peter Dalgaard, Professor
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Email: pd@cbs.dk  Priv: pda...@gmail.com
> 
> 
> 

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk  Priv: pda...@gmail.com
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Re: [R-SIG-Mac] hidden files and directories

2013-08-06 Thread Rohmatul Fajriyah 
Dear All,

:)
The suggestion from Dr. Hansen is working properly. Thank you!
Prof. Dalgaard, thank you for pointing out about 'exactly what he said'. 
Many thanks ... to all of you!

With kind regards,
Ema




 From: peter dalgaard 

Cc: Prof Brian Ripley ; David Winsemius 
; "r-sig-mac@r-project.org" ; 
"kasperdanielhan...@gmail.com"  
Sent: Tuesday, August 6, 2013 6:17 PM
Subject: Re: [R-SIG-Mac] hidden files and directories



On Aug 6, 2013, at 16:59 , Rohmatul Fajriyah wrote:

> 
> Dear All,
> 
> Apologise for late reply. I tried to clean some files from my laptop and it 
> took time.
> 
> Prof. Ripley: I already checked it and untar but it still produces the 
> .DS_Store 
> Dr. Hansen: I did it as follows: R CMD build pkgName, then R CMD install 
> pkgName_X.1.tar.gz and R CMD check pkgName.
> After the last step, the results was
>  
> NOTE: There was 1 note.
> See
>   ‘/Users/rfajriyah/Desktop/pkgName.Rcheck/00check.log’
> for details.
> 
> It because of this :
> * checking for hidden files and directories ... NOTE
> Found the following hidden files and directories:
>   .DS_Store
>   man/.DS_Store
> These were most likely included in error. See section ‘Package
> structure’ in the ‘Writing R Extensions’ manual.
> 
> The man/Rapp.history is gone now, after I deleted it manually.
> 
> I suppose, I need to know how to clean the .DS_Store from my laptop. 
> 
> Prof. Dalgaard Prof. Winsemius: if I type defaults write com.apple.Finder 
> AppleShowAllFiles TRUE in terminal session, yes, I can see the .DS_Store by 
> using ls or Finder.app.
> 
> But still don't know how to clear/remove it.

You can do it with rm in a terminal, but as I understand it, .DS_store files 
are created _by_ Finder, so it is a bit of a fight against windmills. It'll be 
there again next time you view the directory. 

The key is to do what Kasper said. Exactly what he said, not what you think he 
meant to say! I.e., 

R CMD build pkgName
R CMD check pkgName_X_Y_Z.tar.gz

I.e., do not install, build and run check on the .tar.gz file. R CMD build 
should take care of skipping the .DS_store files.


> 
> Many thanks for all your respond and suggestion.
> 
> With kind regards,
> Ema
> 
> From: peter dalgaard 
> To: Prof Brian Ripley  
> Cc: David Winsemius ; "r-sig-mac@r-project.org" <
> Sent: Tuesday, August 6, 2013 2:55 PM
> Subject: Re: [R-SIG-Mac] hidden files and directories
> 
> 
> On Aug 6, 2013, at 08:06 , Prof Brian Ripley wrote:
> 
> >> 
> >> Those files would both be invisible when using the Finder.app unless you 
> >> used ls in a terminal session, but I guess you figured that out
> > 
> > invisible *by default*: it is a Finder setting.
> > 
> 
> They're trying their damndest to hide it, though. It's only settable by 
> "defaults write ..." in a Terminal. (And if you know how to do that, you 
> might as well be using "ls".) 
> 
> -- 
> Peter Dalgaard, Professor
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Email: pd@cbs.dk  Priv: pda...@gmail.com
> 
> 
> 

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk  Priv: pda...@gmail.com
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Re: [R-SIG-Mac] hidden files and directories

2013-08-06 Thread peter dalgaard 

On Aug 6, 2013, at 16:59 , Rohmatul Fajriyah wrote:

> 
> Dear All,
> 
> Apologise for late reply. I tried to clean some files from my laptop and it 
> took time.
> 
> Prof. Ripley: I already checked it and untar but it still produces the 
> .DS_Store 
> Dr. Hansen: I did it as follows: R CMD build pkgName, then R CMD install 
> pkgName_X.1.tar.gz and R CMD check pkgName.
> After the last step, the results was
>  
> NOTE: There was 1 note.
> See
>   ‘/Users/rfajriyah/Desktop/pkgName.Rcheck/00check.log’
> for details.
> 
> It because of this :
> * checking for hidden files and directories ... NOTE
> Found the following hidden files and directories:
>   .DS_Store
>   man/.DS_Store
> These were most likely included in error. See section ‘Package
> structure’ in the ‘Writing R Extensions’ manual.
> 
> The man/Rapp.history is gone now, after I deleted it manually.
> 
> I suppose, I need to know how to clean the .DS_Store from my laptop. 
> 
> Prof. Dalgaard Prof. Winsemius: if I type defaults write com.apple.Finder 
> AppleShowAllFiles TRUE in terminal session, yes, I can see the .DS_Store by 
> using ls or Finder.app.
> 
> But still don't know how to clear/remove it.

You can do it with rm in a terminal, but as I understand it, .DS_store files 
are created _by_ Finder, so it is a bit of a fight against windmills. It'll be 
there again next time you view the directory. 

The key is to do what Kasper said. Exactly what he said, not what you think he 
meant to say! I.e., 

 R CMD build pkgName
 R CMD check pkgName_X_Y_Z.tar.gz

I.e., do not install, build and run check on the .tar.gz file. R CMD build 
should take care of skipping the .DS_store files.


> 
> Many thanks for all your respond and suggestion.
> 
> With kind regards,
> Ema
> 
> From: peter dalgaard 
> To: Prof Brian Ripley  
> Cc: David Winsemius ; "r-sig-mac@r-project.org" 
> ; Rohmatul Fajriyah  
> Sent: Tuesday, August 6, 2013 2:55 PM
> Subject: Re: [R-SIG-Mac] hidden files and directories
> 
> 
> On Aug 6, 2013, at 08:06 , Prof Brian Ripley wrote:
> 
> >> 
> >> Those files would both be invisible when using the Finder.app unless you 
> >> used ls in a terminal session, but I guess you figured that out
> > 
> > invisible *by default*: it is a Finder setting.
> > 
> 
> They're trying their damndest to hide it, though. It's only settable by 
> "defaults write ..." in a Terminal. (And if you know how to do that, you 
> might as well be using "ls".) 
> 
> -- 
> Peter Dalgaard, Professor
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Email: pd@cbs.dk  Priv: pda...@gmail.com
> 
> 
> 

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R-SIG-Mac] hidden files and directories

2013-08-06 Thread Rohmatul Fajriyah 


Dear All,

Apologise for late reply. I tried to clean some files from my laptop and it 
took time.

Prof. Ripley: I already checked it and untarbut it still produces the 
.DS_Store 
Dr. Hansen: I did it as follows: R CMD build pkgName, then R CMD install 
pkgName_X.1.tar.gz and R CMD check pkgName.
After the last step, the results was
 
NOTE: There was 1 note.
See
  ‘/Users/rfajriyah/Desktop/pkgName.Rcheck/00check.log’
for details.

It because of this :
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .DS_Store
  man/.DS_Store
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

The man/Rapp.history is gone now, after I deleted it manually.

I suppose, I need to know how to clean the .DS_Store from my laptop. 

Prof. Dalgaard Prof. Winsemius: if I type defaults write com.apple.Finder 
AppleShowAllFiles TRUE in terminal session, yes, I can see the .DS_Store by 
using ls or Finder.app.

But still don't know how to clear/remove it.

Many thanks for all your respond and suggestion.

With kind regards,
Ema



 From: peter dalgaard 
To: Prof Brian Ripley  
Cc: David Winsemius ; "r-sig-mac@r-project.org" > 
>> Those files would both be invisible when using the Finder.app unless you 
>> used ls in a terminal session, but I guess you figured that out
> 
> invisible *by default*: it is a Finder setting.
> 

They're trying their damndest to hide it, though. It's only settable by 
"defaults write ..." in a Terminal. (And if you know how to do that, you might 
as well be using "ls".) 

-- 
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk  Priv: pda...@gmail.com
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Re: [R-SIG-Mac] hidden files and directories

2013-08-06 Thread peter dalgaard 

On Aug 6, 2013, at 08:06 , Prof Brian Ripley wrote:

>> 
>> Those files would both be invisible when using the Finder.app unless you 
>> used ls in a terminal session, but I guess you figured that out
> 
> invisible *by default*: it is a Finder setting.
> 

They're trying their damndest to hide it, though. It's only settable by 
"defaults write ..." in a Terminal. (And if you know how to do that, you might 
as well be using "ls".) 

-- 
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R-SIG-Mac] hidden files and directories

2013-08-06 Thread Kasper Daniel Hansen 
Rohmatul,

Check by doing
  R CMD build pkgName
  R CMD check pkgName_X_Y_Z.tar.gz

The building step excludes many common files, and is recommended.

Kasper


On Tue, Aug 6, 2013 at 3:43 AM, Prof Brian Ripley wrote:

> On 06/08/2013 08:41, Rohmatul Fajriyah wrote:
>
>> Dear Prof. Ripley and Prof. Winsemius,
>>
>> I have deleted the .Rapp.history (hope, it was all of them), but still
>> got the same message when run the R CMD check PkgName.
>> I'll shutdown the laptop, start a fresh session and will rename the R
>> functions for the package and the package itself differently.
>> Then I will see what happened and report it here.
>>
>
> You are supposed to check the tarball produced by R CMD build 
>
>>
>> Many thanks for the respond and thoughts.
>>
>> With kind regards,
>> Ema
>>
>>
>> --**--**
>> 
>> *From:* Prof Brian Ripley 
>> *To:* David Winsemius 
>> *Cc:* Rohmatul Fajriyah ; "r-sig-mac@r-project.org"
>> 
>> *Sent:* Tuesday, August 6, 2013 8:06 AM
>> *Subject:* Re: [R-SIG-Mac] hidden files and directories
>>
>>
>> On 06/08/2013 01:16, David Winsemius wrote:
>>  >
>>  > On Aug 5, 2013, at 5:00 PM, Rohmatul Fajriyah wrote:
>>  >
>>  >> Dear All,
>>  >>
>>  >> I tried to build an R package (from the terminal) and everything was
>> ok until R CMD check PackageName and I got this message:
>>  >> ..
>>  >> * checking for hidden files and directories ... NOTE
>>  >> Found the following hidden files and directories:
>>  >>.DS_Store
>>  >>man/.Rapp.history
>>  >
>>  > Those files would both be invisible when using the Finder.app unless
>> you used ls in a terminal session, but I guess you figured that out
>>
>> invisible *by default*: it is a Finder setting.
>>
>>  >
>>  >> These were most likely included in error. See section ‘Package
>>  >> structure’ in the ‘Writing R Extensions’ manual.
>>  >> ..
>>  >>
>>  >> I, then:
>>  >> a. went through the archives of this mailing list (until January
>> 2011) and I could not find a similar problem.
>>  >> (apologise, if I missed it)
>>  >
>>  > In 2008 it was reported in the NEWS for R 2.7.1 that:
>>  >
>>  >
>> http://markmail.org/search/?q=**list%3Aorg.r-project.r-help+**
>> DS_Store#query:list%3Aorg.r-**project.r-help%20DS_Store+**
>> page:1+mid:cx3hryqssis2slx7+**state:results
>>  >
>>  > o R CMD build tries harder to clean up the inst/doc directory from
>> the remnants of earlier builds.
>>  >
>>  > It also removes any directories with extension .Rcheck, and files
>> .DS_Store and ._* (created by tar on Mac OS X under some circumstances:
>> it now sets environment variables to ask for such files not to be
>> created by that tar.)
>>  >
>>  > So we need to ask if this was just a warning message. It appears that
>> there are mechanisms in place to remove those files.
>>  >
>>  > (It's arguably an R-devel topic.)
>>
>> It seems the OP did not use R CMD build, rather R CMD check.
>>
>> But files like man/.Rapp.history will need to be removed manually.
>>
>>
>>
>>
>> --
>> Brian D. Ripley, rip...@stats.ox.ac.uk 
>>
>> Professor of Applied Statistics, 
>> http://www.stats.ox.ac.uk/~**ripley/
>> University of Oxford,   Tel:  +44 1865 272861 (self)
>> 1 South Parks Road,+44 1865 272866 (PA)
>> Oxford OX1 3TG, UKFax:  +44 1865 272595
>>
>>
>>
>
> --
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> Professor of Applied Statistics,  
> http://www.stats.ox.ac.uk/~**ripley/
> University of Oxford, Tel:  +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UKFax:  +44 1865 272595
>
> __**_
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/**listinfo/r-sig-mac
>

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Re: [R-SIG-Mac] hidden files and directories

2013-08-06 Thread Prof Brian Ripley 

On 06/08/2013 08:41, Rohmatul Fajriyah wrote:

Dear Prof. Ripley and Prof. Winsemius,

I have deleted the .Rapp.history (hope, it was all of them), but still
got the same message when run the R CMD check PkgName.
I'll shutdown the laptop, start a fresh session and will rename the R
functions for the package and the package itself differently.
Then I will see what happened and report it here.


You are supposed to check the tarball produced by R CMD build 


Many thanks for the respond and thoughts.

With kind regards,
Ema



*From:* Prof Brian Ripley 
*To:* David Winsemius 
*Cc:* Rohmatul Fajriyah ; "r-sig-mac@r-project.org"

*Sent:* Tuesday, August 6, 2013 8:06 AM
*Subject:* Re: [R-SIG-Mac] hidden files and directories

On 06/08/2013 01:16, David Winsemius wrote:
 >
 > On Aug 5, 2013, at 5:00 PM, Rohmatul Fajriyah wrote:
 >
 >> Dear All,
 >>
 >> I tried to build an R package (from the terminal) and everything was
ok until R CMD check PackageName and I got this message:
 >> ..
 >> * checking for hidden files and directories ... NOTE
 >> Found the following hidden files and directories:
 >>.DS_Store
 >>man/.Rapp.history
 >
 > Those files would both be invisible when using the Finder.app unless
you used ls in a terminal session, but I guess you figured that out

invisible *by default*: it is a Finder setting.

 >
 >> These were most likely included in error. See section ‘Package
 >> structure’ in the ‘Writing R Extensions’ manual.
 >> ..
 >>
 >> I, then:
 >> a. went through the archives of this mailing list (until January
2011) and I could not find a similar problem.
 >> (apologise, if I missed it)
 >
 > In 2008 it was reported in the NEWS for R 2.7.1 that:
 >
 >
http://markmail.org/search/?q=list%3Aorg.r-project.r-help+DS_Store#query:list%3Aorg.r-project.r-help%20DS_Store+page:1+mid:cx3hryqssis2slx7+state:results
 >
 > o R CMD build tries harder to clean up the inst/doc directory from
the remnants of earlier builds.
 >
 > It also removes any directories with extension .Rcheck, and files
.DS_Store and ._* (created by tar on Mac OS X under some circumstances:
it now sets environment variables to ask for such files not to be
created by that tar.)
 >
 > So we need to ask if this was just a warning message. It appears that
there are mechanisms in place to remove those files.
 >
 > (It's arguably an R-devel topic.)

It seems the OP did not use R CMD build, rather R CMD check.

But files like man/.Rapp.history will need to be removed manually.




--
Brian D. Ripley, rip...@stats.ox.ac.uk 
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford,   Tel:  +44 1865 272861 (self)
1 South Parks Road,+44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595





--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595

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Re: [R-SIG-Mac] hidden files and directories

2013-08-06 Thread Rohmatul Fajriyah 
Dear Prof. Ripley and Prof. Winsemius,

I have deleted the .Rapp.history (hope, it was all of them), but still got the 
same message when run the R CMD check PkgName.
I'll shutdown the laptop, start a fresh session and will rename the R functions 
for the package and the package itself differently.
Then I will see what happened and report it here.

Many thanks for the respond and thoughts.

With kind regards,
Ema




 From: Prof Brian Ripley 
To: David Winsemius  

ig-...@r-project.org> 
Sent: Tuesday, August 6, 2013 8:06 AM
Subject: Re: [R-SIG-Mac] hidden files and directories


On 06/08/2013 01:16, David Winsemius wrote:
>
> On Aug 5, 2013, at 5:00 PM, Rohmatul Fajriyah wrote:
>
>> Dear All,
>>
>> I tried to build an R package (from the terminal) and everything was ok 
>> until R CMD check PackageName and I got this message:
>> ..
>> * checking for hidden files and directories ... NOTE
>> Found the following hidden files and directories:
>>    .DS_Store
>>    man/.Rapp.history
>
> Those files would both be invisible when using the Finder.app unless you used 
> ls in a terminal session, but I guess you figured that out

invisible *by default*: it is a Finder setting.

>
>> These were most likely included in error. See section ‘Package
>> structure’ in the ‘Writing R Extensions’ manual.
>> ..
>>
>> I, then:
>> a. went through the archives of this mailing list (until January 2011) and I 
>> could not find a similar problem.
>> (apologise, if I missed it)
>
> In 2008 it was reported in the NEWS for R 2.7.1 that:
>
> http://markmail.org/search/?q=list%3Aorg.r-project.r-help+DS_Store#query:list%3Aorg.r-project.r-help%20DS_Store+page:1+mid:cx3hryqssis2slx7+state:results
>
> o R CMD build tries harder to clean up the inst/doc directory from the 
> remnants of earlier builds.
>
> It also removes any directories with extension .Rcheck, and files .DS_Store 
> and ._* (created by tar on Mac OS X under some circumstances: it now sets 
> environment variables to ask for such files not to be created by that tar.)
>
> So we need to ask if this was just a warning message. It appears that there 
> are mechanisms in place to remove those files.
>
> (It's arguably an R-devel topic.)

It seems the OP did not use R CMD build, rather R CMD check.

But files like man/.Rapp.history will need to be removed manually.




-- 
Brian D. Ripley,                  rip...@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595
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