From ripley at stats.ox.ac.uk  Tue Apr 16 15:20:21 2013
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Tue, 16 Apr 2013 14:20:21 +0100
Subject: [Rd] package file permissions problem R 3.0.0/Windows OS
In-Reply-To: <web-453468600@cgpsrv2.cis.mcmaster.ca>
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Message-ID: <516D5015.8090300@stats.ox.ac.uk>

John,

Taking this off-list.   I suspect this is pretty much unique to you, but 
we will see.  I am about to add a para to 'Writing R Extensions' along 
the lines of

'Where a non-POSIX file system is in use which does not utilize execute 
permissions, some care is needed with permissions. This applies on 
Windows and to e.g. FAT-formatted drives and SMB-mounted file systems on 
other OSes. The ?mode? of the file recorded in the tarball will be 
whatever file.info() returns. On Windows this will record only 
directories with execute permission and on other OSes it is likely that 
all files have reported ?mode? 0777. A particular issue is packages 
being built on Windows which are intended to contain executable scripts 
such as configure and cleanup: it is difficult to include these from 
Windows but where Cygwin has been used to set a POSIX-like mode, using 
environment variable R_BUILD_TAR=tar.exe may provide a workaround.'

Brian

On 15/04/2013 21:28, John Fox wrote:
> Dear Brian,
>
> I hope that I can clarify the issue and not confuse it further. I apologize if I was less than clear.
>
> I originally built the tarball for the sem package on my Windows 7 system using "R CMD build" via RStudio with R 3.0.0. Both my Windows 7 system and the Windows 8 system that I subsequently also used to build the package tarball use the NTFS file system. Of course, these are Windows file systems and don't use the Unix permission scheme, but there are apparently permissions recorded in the tarball, and they caused problems for you when I submitted the package to CRAN. The permissions are visible when I look inside the tarball, e.g., with 7zip.
>
> When I rebuilt the package using "R CMD build" with R 2.15.2 (as opposed to 3.0.0) on both of these Windows systems, the permissions inside the tarball were correct.
>
> I never built the package on my Linux system, although I did try building it on my Mac. I obtained correct permissions inside the tarball when I did, which isn't surprising.
>
> If it's the case that package tarballs built under Windows don't have execute permissions set where these are needed (as for cleanup), won't you have the same problem when such tarballs are submitted to CRAN that you had with the sem package?
>
> Also, I'm still not clear why the execute permissions were set properly when I created the tarball having set R_BUILD_TAR=tar or using R 2.15.2.
>
> To reiterate, if this issue is unique to me, I can certainly work around it. I know that it's hard to diagnose this kind of problem long-distance via email.
>
> Best,
>   John
>
> On Mon, 15 Apr 2013 20:19:21 +0100
>   Prof Brian Ripley <ripley at stats.ox.ac.uk> 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.
>>
>>> 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
>>
>>
>> --
>> 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
>>
>> ______________________________________________
>> 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



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