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 <ripley@stats.ox.ac.uk>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 <ripley@stats.ox.ac.uk>
>> *To:* David Winsemius <dwinsemius@comcast.net>
>> *Cc:* Rohmatul Fajriyah <rfajriyah@yahoo.com>; "r-sig-mac@r-project.org"
>> <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<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, ripley@stats.ox.ac.uk <mailto:ripley@stats.ox.ac.uk>
>>
>> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~**ripley/<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
>>
>>
>>
>
> --
> Brian D. Ripley,                  ripley@stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~**ripley/<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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