On Mon, Feb 25, 2013 at 2:10 AM, Ulrike Gr?mping
<groemping at bht-berlin.de> wrote:
Gabor,
thanks for your patient answers! I have adjusted the Rtools path to consist
of both
the bin and the gcc-4.6.3 sub directory, and that did it. The R path was set
by R as it was,
presumably because this is only a 32-bit system, and everything worked with
that R path, as there is also an R.exe in the path without the i386.
I have no idea what these path settings might have to do with write
permissions on the temp directory, but as long as it works ...
Best, Ulrike
Am 25.02.2013 01:29, schrieb Gabor Grothendieck:
On Sun, Feb 24, 2013 at 6:34 PM, Ulrike Gr?mping
<groemping at bht-berlin.de> wrote:
Am 24.02.2013 23:50, schrieb Gabor Grothendieck:
On Sun, Feb 24, 2013 at 4:00 PM, Ulrike Gr?mping
<groemping at bht-berlin.de> wrote:
Dear helpeRs,
on my Windows 7 laptop, I have problems getting R CMD check to work. I
believe it did work completely before, but I am not sure.
Yesterday it almost worked, except for the tests: These were aborted
because
of a complaint that the temporary directory wasn't available. I played
with
windows environment variables for the temporary directory, but that
didn't
solve it. Apparently I did something that made things worse:
Today, R CMD check completely refuses to work, with the error message
"Fatal
error: creation of tmpfile failed -- set TMPDIR suitably?" This is the
same
for current R and R-devel. Changes to the TEMP or TMP environment
variable
don't influence this behavior.
The path:
C:\Rtools;C:\Program Files\Dell\DW WLAN Card;C:\Program
Files\R\R-2.15.2\bin;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program
Files\Intel\OpenCL SDK\2.0\bin\x86;C:\Program Files\WIDCOMM\Bluetooth
Software\;C:\Program Files\Calibre2\;C:\Program Files\MiKTeX
2.9\miktex\bin\;C:\Program Files\TortoiseSVN\bin
Any ideas what I can do to fix this?
Perhaps also relevant: I run R CMD check from a DOS window that is
opened
with administrator rights.
1. Remove the paths to Rtools and to R in PATH since they don't look
correct.
2. Enter this from the Windows cmd line:
SET U
SET T
and it should show that TMP is set to %userprofile%\AppData\Local\Temp
and that TEMP is set to the same thing and TMPDIR is not listed.
If not change them so that it so reads.
3. Once you have done all the above then place this file anywhere on
your
path
https://batchfiles.googlecode.com/svn/trunk/R.bat
The following will find R using the registry or if its not there it
will look in the usual places and then run it so you can then try:
R.bat CMD ...whatever...
If that still does not work proceed to the following manual alternative:
4. If the above did not fix the problem download this file
https://batchfiles.googlecode.com/svn/trunk/Rpathset.bat
5. edit the SET statements in it and then place it on your Windows path.
6. Now run it from the cmd line:
Rpathset.bat
and for the rest of that cmd line session your path should be set up
correctly.
Also you might want to read:
https://batchfiles.googlecode.com/svn/trunk/batchfiles.md
There is also a new discussion group just set up at
https://groups.google.com/forum/?fromgroups#!forum/sqldf
that is also being used for the batchfiles.
Thanks, I followed your advice, and the check ran from the R.bat; also,
the
R Gui was usable again. After re-adding the paths to Rtools and R
manually
(I think they were correct anyway), I am back to the sunday state: R Gui
runs fine, the check is run, except for the tests where the complaint is:
cannot open file
'c:\Users\GROEMP~1\AppData\Local\Temp\Rtmp8kETwo\file15d8714c5215':
Permission denied
(Of course, the proper path is with groemping instead of GROEMP~1; the
abbreviation is done automatically by R CMD check or Windows.)
From the Dos box, I can cd to that directory (both long name and
abbreviated
name), and there is a 0 byte file of the name in the complaint. From the
Windows 7 Explorer, I don't know how to change to that directory, except
for
a search for the file name. Once I have found the file name, I can edit
and
change the file without being stopped from doing so, thus this does not
seem
to be an issue of write permissions.
Any idea how to fix this, without a re-installation (that might not fix
it
either, if I am unlucky)?
And, by the way, do others agree with Jeff's advice (thanks, Jeff!) that
it
is preferrable not to install and run R with administrator rights?
Best, Ulrike
1. There is something wrong with the permissions on the TEMP directory
unrelated to R. Remove everything in that directory and make sure that
you have write permission on TEMP. Its probably easier to do that
through Windows Explorer.
2. Regarding the comment on the paths, I don't think the Tools or R
paths were correct. The tools path should end end in bin but it did
not. Also there are additional components for gcc that I think were
missing. Also the R path ends in x64 (or i386 if you want 32 bit)
but yours ended in bin. Note that if you use R.bat or Rpathset.bat
consistently you don't have to set up your path in the first place.
Its basically configuration-free.
R.bat show
will show the values its heuristic found.
3. Regarding Admin rights I think its best to keep everything as
standard as possible which means installing R itself into C:\Program
Files\... tree which is where it goes by default and that requires
Admin rights to do.
On my machine Rgui.exe is found in ..\bin\x64 and the 32 bit version
is found in ..\bin\i386 and there is no Rgui.exe in ...\bin . Ditto
for RSetReg.exe, Rterm.exe and maybe a few others. Thus if yours is
the same then using a path to R ending in bin still won't let you run
Rgui.exe (and ditto for a few other executables) from the cmd line.
--
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com