From jfox at mcmaster.ca  Mon Apr 15 15:11:18 2013
From: jfox at mcmaster.ca (John Fox)
Date: Mon, 15 Apr 2013 09:11:18 -0400
Subject: [Rd] package file permissions problem R 3.0.0/Windows OS
In-Reply-To: <516B968A.8070704@stats.ox.ac.uk>
References: <002201ce3955$7ff88580$7fe99080$@mcmaster.ca>
	<516B968A.8070704@stats.ox.ac.uk>
Message-ID: <web-453347265@cgpsrv2.cis.mcmaster.ca>

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)?

> What are those screen shots of?

7zip, which I use on Windows to manage file archives.

> 
> 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.

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



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