From mikko.korpela at helsinki.fi  Fri Apr 21 14:13:26 2017
From: mikko.korpela at helsinki.fi (Mikko Korpela)
Date: Fri, 21 Apr 2017 15:13:26 +0300
Subject: [Rd] tempdir() may be deleted during long-running R session
In-Reply-To: <15e3b0a3-e0a8-2da8-27c4-9268a5751986@stats.ox.ac.uk>
References: <c78e9022-04c2-3cda-5898-dceec8bc5e94@helsinki.fi>
 <15e3b0a3-e0a8-2da8-27c4-9268a5751986@stats.ox.ac.uk>
Message-ID: <4f0797c5-a078-67ae-3992-cd66a82b454a@helsinki.fi>

On 21/04/17 14:03, Prof Brian Ripley wrote:
> 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
> system.'

I am sorry for having missed this part of the manual, where the issue 
indeed is clearly documented.
>
>
> 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.

Despite my obvious failure to read the manual and report this properly, 
I will try to make a case. I understand that data stored in a temporary 
file may disappear, and for that reason using an alternative TMPDIR 
might be advisable. However, I think that creating a new temporary file 
is a different case, and it would be nice if `?` and `help` continued to 
work, for example. I understand if this will not be put on the R core 
list of things to do.

>>
>> 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
>>

-- 
Mikko Korpela
Department of Geosciences and Geography
University of Helsinki



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