On 21/04/17 14:42, Joris Meys wrote:
In defense of the OP: I would have checked ?tmpdir and missed the
information in the manual as well. On the help page there's ample
information on the underlying processes that create the dir on multiple
platforms. I think adding the last two sentences of prof. Ripley's quote as
a warning to the help page, would be worth the effort.
I do wonder though why you would run something that lasts 10 days and still
rely on something that is called a "temporary" directory.
For me, intuitively, the temporary directory is a place for temporary
files. I mean, the directory itself does not seem as temporary as the
files in it. I think this is not entirely unsupported by the wording in
?tempdir: "per-session temporary directory". I now understand that
"per-session" rather means that tempdir() returns a constant value
during a single R session, but the directory itself may disappear due to
things not controlled by R (documented elsewhere as pointed out by Prof
Ripley).
- Mikko
Best regards
Joris
On Fri, Apr 21, 2017 at 1:03 PM, Prof Brian Ripley <rip...@stats.ox.ac.uk>
wrote:
From the R-admin manual ยง5:
'Various environment variables can be set to determine where R creates its
per-session temporary directory. The environment variables TMPDIR, TMP and
TEMP are searched in turn and the first one which is set and points to a
writable area is used. If none do, the final default is /tmp on Unix-alikes
and the value of R_USER on Windows. The path should be an absolute path not
containing spaces (and it is best to avoid non-alphanumeric characters such
as +).
Some Unix-alike systems are set up to remove files and directories
periodically from /tmp, for example by a cron job running tmpwatch. Set
TMPDIR to another directory before starting long-running jobs on such a
system.'
On 21/04/2017 11:49, Mikko Korpela wrote:
Temporary files not accessed for a long time are automatically removed
in some Linux distributions and probably other operating systems too,
depending on system configuration. This may affect the per-session
temporary directory, the path of which is returned by tempdir(). I think
Not for those who follow the manual and know that sysadmnins have enabled
such a script.
it would be nice if R automatically tried to recreate a missing
tempdir() but this could have some performance implications.
I ran the same test (below) on R 3.3.3 patched, R 3.4.0 beta, and
R-devel, all at r72499 (2017-04-09) and compiled by myself. The results
from the test were practically identical on all of those versions, the
test platform being Ubuntu 14.04.5 LTS. This system is configured for a
/tmp cleanup threshold of 7 days of inactivity (which is the default).
After a wait of roughly 10 days, the R temporary directory had been
deleted by an automatic cleanup procedure, and a call to `?` failed.
This StackExchange question has some answers about the Ubuntu /tmp
cleanup practice: https://askubuntu.com/q/20783
a <- print(tempdir())
# [1] "/tmp/user/1069138/RtmpGc9M5z"
dir.exists(a) # TRUE
# [1] TRUE
Sys.time()
# [1] "2017-04-10 16:00:30 EEST"
## Wait for one week (Ubuntu 14.04.5 LTS)
print(Sys.time()); ?regex
# [1] "2017-04-20 14:17:29 EEST"
# Error in file(out, "wt") : cannot open the connection
# In addition: Warning message:
# In file(out, "wt") :
# cannot open file '/tmp/user/1069138/RtmpGc9M5z/Rtxt3dbb65870ad4': No
such file or directory
b <- print(tempdir())
# [1] "/tmp/user/1069138/RtmpGc9M5z"
identical(a, b)
# [1] TRUE
dir.exists(b)
# [1] FALSE
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
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