> > It might still be useful if R could sometimes detect when automated
> > cleanup happened and warn the user. Perhaps a simple way could be to
> > always create an empty file inside session directory, like
> > ".tmp_cleaner_trap". R would never touch this file, but check its
> > existence time-to
> Frederick posted the way to do this in systems using systemd. We should be
> putting that in place, or the equivalent on systems using other tempfile
> cleanups. This looks to me like something that "make install" should do, or
> perhaps it should be done by people putting together packages for
On 26/04/2017 10:39 AM, Tomas Kalibera wrote:
I agree this should be solved in configuration of
systemd/tmpreaper/whatever tmp cleaner - the cleanup must be prevented
in configuration files of these tools. Moving session directories under
/var/run (XDG_RUNTIME_DIR) does not seem like a good solu
The main point of this discussion has been that deleting the tempdir() a
fixed number of days after its creation is a problem. It should be deleted
when the process that created it is done. R attempts to do this, but there
are cases in which it does not so a backup is needed.
Bill Dunlap
TIBCO S
The Ubuntu machine I use a lot (along with others) must not be cleaning
/tmp as it has a fair number of Rtmp* directories in /tmp, even when there
are no R sessions running on the machine. I would like to automate their
removal but there is no obvious way to see if the R process that created
the t
On 26 April 2017 at 16:39, Tomas Kalibera wrote:
| I agree this should be solved in configuration of
| systemd/tmpreaper/whatever tmp cleaner - the cleanup must be prevented
Yep.
| in configuration files of these tools. Moving session directories under
| /var/run (XDG_RUNTIME_DIR) does not se
> Dirk Eddelbuettel
> on Wed, 26 Apr 2017 08:40:38 -0500 writes:
> On 26 April 2017 at 08:29, Duncan Murdoch wrote:
> | This seems like the wrong approach. The problem occurs as soon as the
> | tempdir() gets cleaned up: there could be information in temp files
> |
I agree this should be solved in configuration of
systemd/tmpreaper/whatever tmp cleaner - the cleanup must be prevented
in configuration files of these tools. Moving session directories under
/var/run (XDG_RUNTIME_DIR) does not seem like a good solution to me,
sooner or later someone might c
On 26 April 2017 at 08:29, Duncan Murdoch wrote:
| This seems like the wrong approach. The problem occurs as soon as the
| tempdir() gets cleaned up: there could be information in temp files
| that gets lost at that point. So the solution should be to prevent the
| cleanup, not to continue o
On 26/04/2017 4:21 AM, Martin Maechler wrote:
on Tue, 25 Apr 2017 21:13:59 -0700 writes:
> On Tue, Apr 25, 2017 at 02:41:58PM +, Cook, Malcolm wrote:
>> Might this combination serve the purpose:
>> * R session keeps an open handle on the tempdir it creates,
>> * whate
>
> on Tue, 25 Apr 2017 21:13:59 -0700 writes:
> On Tue, Apr 25, 2017 at 02:41:58PM +, Cook, Malcolm wrote:
>> Might this combination serve the purpose:
>> * R session keeps an open handle on the tempdir it creates,
>> * whatever tempdir harvesting cron job the
Hi Gabriel,
Thanks for asking for a better solution, as far as actually preventing
temporary files from getting deleted in the first place.
I still don't know very much about other peoples' distributions, but
Arch uses Systemd which is the culprit on my system. Systemd's
'tmpfiles.d(5)' man page
On Tue, Apr 25, 2017 at 02:41:58PM +, Cook, Malcolm wrote:
> Might this combination serve the purpose:
> * R session keeps an open handle on the tempdir it creates,
> * whatever tempdir harvesting cron job the user has be made sensitive
> enough not to delete open files (includin
> Martin,
>
> Thanks for your work on this.
>
> One thing that seems to be missing from the conversation is that recreating
> the temp directory will prevent future failures when R wants to write a
> temp file, but the files will, of course, not be there. Any code written
> assuming the co
Martin,
Thanks for your work on this.
One thing that seems to be missing from the conversation is that recreating
the temp directory will prevent future failures when R wants to write a
temp file, but the files will, of course, not be there. Any code written
assuming the contract is that the temp
> Jeroen Ooms
> on Tue, 25 Apr 2017 15:05:51 +0200 writes:
> On Tue, Apr 25, 2017 at 1:00 PM, Martin Maechler
> wrote:
>> As I've found it is not at all hard to add an option
>> which checks the existence and if the directory is no
>> longer "valid", tries to recr
Chiming in late on this thread...
> > | Are there any packages which
> > | would break if a call to 'tempdir' automatically recreated this
> > | directory? (Or would it be too much of a performance hit to have
> > | 'tempdir' check and even just issue a warning when the director
On Tue, Apr 25, 2017 at 1:00 PM, Martin Maechler
wrote:
> As I've found it is not at all hard to add an option which
> checks the existence and if the directory is no longer "valid",
> tries to recreate it (and if it fails doing that it calls the
> famous R_Suicide(), as it does when R starts up a
> Dirk Eddelbuettel
> on Sun, 23 Apr 2017 09:15:18 -0500 writes:
> On 21 April 2017 at 10:34, frede...@ofb.net wrote:
> | Hi Mikko,
> |
> | I was bitten by this recently and I think some of the replies are
> | missing the point. As I understand it, the problem con
On 24 April 2017 at 12:34, frede...@ofb.net wrote:
| As it is, I don't even know what distributions are affected. I'm not
| sure how to look up the contents of a "default" configuration on other
| distributions.
So how do you think R can automate that? Hint: It can't.
Dirk
--
http://dirk.edde
Dirk,
Your message felt a bit antagonistic to me, or maybe I'm not
understanding what you're trying to say. We all seem to agree that
different configurations exist, and that some Linux distributions are
configured to delete files in /tmp/ after a certain amount of time
(seems to be 10 days for Ar
On 21 April 2017 at 10:34, frede...@ofb.net wrote:
| Hi Mikko,
|
| I was bitten by this recently and I think some of the replies are
| missing the point. As I understand it, the problem consists of these
| elements:
|
| 1. When R starts, it creates a directory like /tmp/RtmpVIeFj4
|
| 2. Right
Hi Mikko,
I was bitten by this recently and I think some of the replies are
missing the point. As I understand it, the problem consists of these
elements:
1. When R starts, it creates a directory like /tmp/RtmpVIeFj4
2. Right after R starts I can create files in this directory with no
error
On 21 April 2017 at 15:13, Mikko Korpela wrote:
| 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
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
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 w
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 he
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 fina
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
it would be ni
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