[Rd] package file permissions problem R 3.0.0/Windows OS

Paul Gilbert pgilbert902 at gmail.com
Mon Apr 15 22:07:02 CEST 2013

On 13-04-15 03:19 PM, Prof Brian Ripley wrote:
> On 15/04/2013 14:11, John Fox wrote:
>> Dear Brian,
>> On Mon, 15 Apr 2013 06:56:26 +0100
>>   Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
>>> POSIX-style execute permission isn't a Windows concept, so it was
>>> fortuitous this ever worked.  One possibility is that Cygwin was
>>> involved, and a Cygwin emulation got set when tar unpacked the file
>>> and converted back to the tar representation when Cygwin tar produced
>>> the tarball. (The tar in Rtools is a fixed version of Cygwin tar,
>>> fixed to use Windows file paths.)
>> Recall that the problem was first detected when I submitted to CRAN
>> a
> new version of the sem package that I built on one of my Windows
> systems. I'm guessing that you unpacked that on a Linux system. Perhaps
> I misunderstand the point, but if the problem is in unpacking, then
> shouldn't I see it when the package is built on R 2.15.2 (not 2.5.2 --
> sorry, my typo)?
> The puzzle is how you got execute permissions recorded for files on your
> Windows system.  They are not part of the Windows file system: Cygwin
> uses ACLs to emulate them.  Once the ACLs are there, a Cygwin-based tar
> will put them as permissions into the tarball.  But a native Windows
> tool would not (it might or might not capture the ACLs using a tar
> extension, but those would be ignored by most unpacking tools on a
> Unix-alike).
> The issue is not really Windows: if you use a FAT file system on a
> Unix-alike you have the same problem -- this is why SMB mounts at least
> did not work on OS X for building R (and much else), and you need to be
> careful transferring directories via USB sticks (which are usually
> FAT-formatted).  That route usually makes the opposite compromise: to
> assume everything is executable.
>>> What are those screen shots of?
>> 7zip, which I use on Windows to manage file archives.
> Ah, so that's a listing of the .tar.gz, a graphical form of tar -tvf.
>>> R 2.5.2 was a very long time ago.  A recent change is
>> Indeed. Again, that is my unfortunate typo -- I used 2.15.2. I wanted
>> to confirm that I can build packages with the correct permissions on
>> my Windows systems using an older (but recent) version of R.
>>>       • R CMD build by default uses the internal method of tar() to
>>>         prepare the tarball.  This is more likely to produce a tarball
>>>         compatible with R CMD INSTALL and R CMD check: an external tar
>>>         program, including options, can be specified _via_ the
>>>         environment variable R_BUILD_TAR.
>> I saw that but didn't understand its import. That makes sense of a
>> difference between R 2.15.2 and 3.0.0, though I'm not sure why this
>> change would introduce a problem with the permissions.
>>> Can you try using an external tar?  (Using the internal tar on
>>> Windows was first trialled in 2.15.3.)
>> Yes, when I "set R_BUILD_TAR=tar" on my Windows 8 system, the tarball
>> for the package is built with the correct permissions under R 3.0.0.
>> The tar should be found in the Rtools\bin directory, which is first on
>> my path. I don't have Cygwin installed on this machine independently
>> of Rtools.
>> What's curious to me is that I'm seeing the problem on two different
>> Windows system but, AFAIK, no one else has experienced a similar problem.
> Very few Windows users will ever get a file that appears to 'tar' to
> have execute permissions.  For example, svn checkouts on Windows lose
> execute permissions, something which has caught me for time to time over
> the years.

I am just having the opposite problem, sliksvn is adding x permission on 
checkout, to some but not all files. Not sure why and I don't want it 
to, so would be happy to hear suggestions.


>> Thanks for your help,
>>   John
>>> On 14/04/2013 22:17, John Fox wrote:
>>>> Dear list members,
>>>> I'm experiencing a file permissions problem with a package built under
>>>> Windows with R 3.0.0. I've encountered the problem on two Windows
>>>> computers,
>>>> one running Windows 7 and the other Windows 8, and both when I build
>>>> the
>>>> package under RStudio or directly in a Windows console via "R CMD
>>>> build".
>>>> In particular, the cleanup file for the package, which as I
>>>> understand it
>>>> should have permissions set at rwx-r-r, instead has permissions
>>>> rw-rw-rw.
>>>> I've attached two .png screen shots showing how the permissions are
>>>> set when
>>>> the package is built under R 2.5.2 and R 3.0.0.
>>>> I think that my two Windows systems are reasonably vanilla. Here are
>>>> the
>>>> system and session info from R 3.0.0 run from a Windows console:
>>>>> Sys.info()
>>>>                        sysname                      release
>>>>                      "Windows"                      "7 x64"
>>>>                        version                     nodename
>>>> "build 7601, Service Pack 1"              "JOHN-DELL-XPS"
>>>>                        machine                        login
>>>>                          "x86"                       "User"
>>>>                           user               effective_user
>>>>                         "User"                       "User"
>>>>> sessionInfo()
>>>> R version 3.0.0 (2013-04-03)
>>>> Platform: i386-w64-mingw32/i386 (32-bit)
>>>> locale:
>>>> [1] LC_COLLATE=English_United States.1252
>>>> [2] LC_CTYPE=English_United States.1252
>>>> [3] LC_MONETARY=English_United States.1252
>>>> [4] LC_NUMERIC=C
>>>> [5] LC_TIME=English_United States.1252
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>> I have the latest Rtools30 installed and on my path:
>>>>> Sys.which("tar.exe")
>>>>                      tar.exe
>>>> "c:\\Rtools\\bin\\tar.exe"
>>>> Is this a general problem or is it possible that there's something
>>>> about my
>>>> Windows configurations that's causing it?
>>>> Any information would be appreciated.
>>>> John
>>>> -----------------------------------------------
>>>> John Fox
>>>> Senator McMaster Professor of Social Statistics
>>>> Department of Sociology
>>>> McMaster University
>>>> Hamilton, Ontario, Canada
>>>> ______________________________________________
>>>> R-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>> --
>>> Brian D. Ripley,                  ripley at 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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