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Emil Bode

2018-Sep-14 17:52 UTC

[Rd] Bug when calling system/system2 (and request for Bugzilla account)

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

Kevin Ushey

2018-Sep-14 17:58 UTC

head link

[Rd] Bug when calling system/system2 (and request for Bugzilla account)

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-tier@ey m@ili@g off uiow@@edu

2018-Sep-14 19:18 UTC

head link

[Rd] Bug when calling system/system2 (and request for Bugzilla account)

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

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