From luke-tier@ey m@ili@g off uiow@@edu  Fri Sep 14 21:18:22 2018
From: luke-tier@ey m@ili@g off uiow@@edu (luke-tier@ey m@ili@g off uiow@@edu)
Date: Fri, 14 Sep 2018 14:18:22 -0500 (CDT)
Subject: [Rd] Bug when calling system/system2 (and request for Bugzilla
 account)
In-Reply-To: <CAJXgQP2zXr_udq1nt7CtxBdDvr3rfjmZG95TBPok0vUW5iC9Hg@mail.gmail.com>
References: <1A6E24FE-022E-44F1-9AB0-58B2DC8A2DB9@dans.knaw.nl>
 <alpine.OSX.2.21.1809141037560.55702@lukes-macbook-air.local>
 <8F2C26BE-4F8B-4C17-9EE8-6FD35A3B0E04@dans.knaw.nl>
 <CAJXgQP2zXr_udq1nt7CtxBdDvr3rfjmZG95TBPok0vUW5iC9Hg@mail.gmail.com>
Message-ID: <alpine.DEB.2.21.1809141409450.16079@luke-Latitude-7480>

Thanks to you both -- I see it now on Ubuntu. A typo in the code for
restoring the SIGINT handler in the timeout cleanup was installing the
wrong handler. Fixed in R-devel and R-patched.

Best,

luke

On Fri, 14 Sep 2018, Kevin Ushey wrote:

> FWIW I can reproduce on macOS with R 3.5.1. A smaller example:
>
>    system2("ls", timeout = 5); x <- sample(1:1E8)
>
> If I try to interrupt R while that sample call is running, R itself is closed.
>
> Best,
> Kevin
>
> On Fri, Sep 14, 2018 at 10:53 AM Emil Bode <emil.bode at dans.knaw.nl> wrote:
>>
>> I hope it's not too specific in my setup...
>> I've tried with system2 added on the first line, so:
>>
>> Example.R:
>> system2('ls', timeout=5)
>> cat('Start non-interruptable functions\n')
>> sample_a <- sample(1:1e7)
>> sample_b <- sample(1:2e7)
>> matching <- match(sample_a, sample_b)
>> cat('Finished\n')
>> Sys.sleep(10)
>>
>> And in terminal/bash:
>> R --vanilla
>> source('Example.R')
>> Send ^C between the messages (Start...  until Finished)
>>
>> Or if you have a more powerful CPU you can increase the samples, the exact code doesn't matter very much.
>> As soon as you restart and source again with the system2 call outcommented, the behaviour is different, there is a pause, and your return to the R-prompt.
>>
>> Best, Emil
>>
>>
>>
>> ?On 14/09/2018, 17:39, "luke-tierney at uiowa.edu" <luke-tierney at uiowa.edu> wrote:
>>
>>     I can't reproduce this. Can you be more precise: exactly where are you
>>     putting the system2 call and exactly where are you sending the
>>     interrupt signal with ^C?
>>
>>     Best,
>>
>>     luke
>>
>>     On Fri, 14 Sep 2018, Emil Bode wrote:
>>
>>    > Hi all,
>>    >
>>    > I found some strange behaviour, which I think is a bug. Could someone make an account for me on Bugzilla or pass on my report?
>>    >
>>    > The problem:
>>    > When pressing Ctrl-C when a file is sourced in R, run from Terminal (macOS), sometimes the entire session is ended right away, while I just want to stop the script. This is the case when I press Ctrl-C while some functions are running that don?t catch the interrupt. However, the behaviour is different whether I?m in a clean session (in which case some time is allowed to pass, so that when the function returns the script can be interrupted), or whether I have called base::system() or system2() with timeout other than 0.
>>    >
>>    > Reproducible example:
>>    > cat('Start non-interruptable functions\n')
>>    > sample_a <- sample(1:1e7)
>>    > sample_b <- sample(1:2e7)
>>    > matching <- match(sample_a, sample_b)
>>    > cat('Finished\n')
>>    > Sys.sleep(10)
>>    >
>>    > Observed behaviour:
>>    > In a clean session, when I hit Ctrl-C during the execution of match, there is a delay, and as soon as Sys.sleep() is invoked, the script is interrupted, I get back my R ?>?-prompt (unless options(error=?) is set)
>>    > But If I add the line system2("ls", timeout = 5), or something similar, when I try to break during the first part of the script, my Rsession ends, I get thrown back to my terminal-prompt.
>>    >
>>    > Desired behaviour:
>>    > The best setup would probably be if Ctrl-C would always try to break from the sourced file, and only if that doesn?t success in n seconds, break the rsession altogether, ideally with a customizable option. But maybe that?s too hard, so maybe the most pragmatic would be to have 2 hotkeys: one to break from a hanging/broken rsession, and one to gently try to break from a script. But at least I think it should be:
>>    >
>>    > Expected behaviour:
>>    > Consistent behaviour for Ctrl-C: either trying to break the script, or end the session altogether.
>>    >
>>    > Some observations:
>>    >
>>    >  *   I can still break cleanly during the Sys.sleep(). But for larger scripts, it is largely a matter of luck if I hit Ctrl-C during the right moment.
>>    >  *   I don?t notice any difference between using system or system2, or any of the arguments other than timeout provided
>>    >  *   I don?t notice any difference whether the timeout is actually exhausted or not.
>>    >  *   Later calls to system/system2 don?t change anything (i.e. later calling system(?, timeout=0) does not revert back to the old situation)
>>    >
>>    > My setup:
>>    > R 3.5.1 (Feather Spray), run with ?vanilla option
>>    > GNU bash, version 3.2.57(1)-release (x86_64-apple-darwin17)
>>    > macOS High Sierra 10.13.6
>>    >
>>    > Best regards,
>>    > Emil Bode
>>    >
>>    > Data-analyst
>>    >
>>    > +31 6 43 83 89 33
>>    > emil.bode at dans.knaw.nl<mailto:emil.bode at dans.knaw.nl>
>>    >
>>    > DANS: Netherlands Institute for Permanent Access to Digital Research Resources
>>    > Anna van Saksenlaan 51 | 2593 HW Den Haag | +31 70 349 44 50 | info at dans.knaw.nl<mailto:info at dans.kn> | dans.knaw.nl<applewebdata://71F677F0-6872-45F3-A6C4-4972BF87185B/www.dans.knaw.nl>
>>    > DANS is an institute of the Dutch Academy KNAW<http://knaw.nl/nl> and funding organisation NWO<http://www.nwo.nl/>.
>>    >
>>    >   [[alternative HTML version deleted]]
>>    >
>>    > ______________________________________________
>>    > R-devel at r-project.org mailing list
>>    > https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>     --
>>     Luke Tierney
>>     Ralph E. Wareham Professor of Mathematical Sciences
>>     University of Iowa                  Phone:             319-335-3386
>>     Department of Statistics and        Fax:               319-335-3017
>>         Actuarial Science
>>     241 Schaeffer Hall                  email:   luke-tierney at uiowa.edu
>>     Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:   luke-tierney at uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu


[Rd] Bug when calling system/system2 (and request for Bugzilla account)
luke-tier@ey m@ili@g off uiow@@edu