On 15/04/2013 14:11, John Fox wrote:
Dear Brian,
On Mon, 15 Apr 2013 06:56:26 +0100
Prof Brian Ripley <rip...@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
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--
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
--
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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