[Rd] tempdir() may be deleted during long-running R session

Prof Brian Ripley ripley at stats.ox.ac.uk
Fri Apr 21 13:03:32 CEST 2017

 From the R-admin manual §5:

'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 

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,                  ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford

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