[R-SIG-Mac] [External] Re: crash due to rgl and base graphics conflict
Richard M. Heiberger
rmh @end|ng |rom temp|e@edu
Fri May 29 21:25:44 CEST 2020
my 12:35 email and the attached tmp.txt are from the Terminal.app,
No emacs/ESS involved.
On Fri, May 29, 2020 at 3:13 PM Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
>
> On 29/05/2020 2:21 p.m., Richard M. Heiberger wrote:
> > I attempted to update xquartz when I updated to Catalina, and the same
> > number is still the current version number.
> >
> > Here is a related issue, attached tmp2.txt is the R transcript.
> > The interesting thing here is that rgl.quit() prevents rgl from being
> > reattached.
>
> Generally speaking rgl doesn't want to be reloaded in the same R
> session: detaching it doesn't clean up everything. That's not
> something that I'd put any priority on fixing, whereas I would look at
> the problems you're having on startup if I could reproduce them.
>
> I wonder if ESS is involved somehow: your sessionInfo listed ESSR on
> the search list. Do you have the same issues with plain R from the
> console, or R.app?
>
> > Is there an rgl equivalent for dev.cur()?
>
> There's rgl.cur(). rgl only supports two kinds of devices: on a Mac or
> Linux they'd be displayed as glX or null. Windows also supports the
> null device (which doesn't display anything), and a different one to
> display within R: I forget how the name is displayed.
>
> It might be that you'll need to set options(rgl.useNULL) before starting
> rgl, and only use the null device. It won't display anything in R, but
> allows you to call rglwidget() for a display in a browser.
>
> Duncan Murdoch
>
> > On Fri, May 29, 2020 at 1:51 PM Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
> >>
> >> On 29/05/2020 12:35 p.m., Richard M. Heiberger wrote:
> >>> I have the same Xquartz as you.
> >>
> >> I'd guess it should be updated. Generally XQuartz needs updates with
> >> every MacOS release, and your 10.15.4 is two releases further along than
> >> my 10.13.6.
> >>
> >>> I have rgl-0.100.50 from CRAN
> >>
> >> You could update that, but I doubt if it would make any difference.
> >>
> >>> Apple is macOS Catalina, Version 10.15.4
> >>> Do you need hardware information?
> >>> MacBpok Air (13 -inch, Mid 2012)
> >>> Processor 2GHz Dual-Core Intel Core i7
> >>> Memory 8 GB 1600 MHz DDR3
> >>> Graphics Intel HD Graphics 4000 1536 MB
> >>
> >> I think the XQuartz issue is most likely to help, but if it doesn't, I'm
> >> not sure what I could suggest: I don't have Catalina.
> >>
> >> Duncan Murdoch
> >>>
> >>>
> >>> from the Terminal App:
> >>> The Apple Crash Report is in the attached tmp.txt
> >>> I didn't send it to Apple.
> >>>
> >>> R version 4.0.0 (2020-04-24) -- "Arbor Day"
> >>>
> >>> Copyright (C) 2020 The R Foundation for Statistical Computing
> >>>
> >>> Platform: x86_64-apple-darwin17.0 (64-bit)
> >>>
> >>>
> >>> R is free software and comes with ABSOLUTELY NO WARRANTY.
> >>>
> >>> You are welcome to redistribute it under certain conditions.
> >>>
> >>> Type 'license()' or 'licence()' for distribution details.
> >>>
> >>>
> >>> Natural language support but running in an English locale
> >>>
> >>>
> >>> R is a collaborative project with many contributors.
> >>>
> >>> Type 'contributors()' for more information and
> >>>
> >>> 'citation()' on how to cite R or R packages in publications.
> >>>
> >>>
> >>> Type 'demo()' for some demos, 'help()' for on-line help, or
> >>>
> >>> 'help.start()' for an HTML browser interface to help.
> >>>
> >>> Type 'q()' to quit R.
> >>>
> >>>
> >>>> library(rgl)
> >>>
> >>>> plot(1:10)
> >>>
> >>>> 2020-05-29 12:30:00.536 R[24961:3275889] *** Assertion failure in BOOL NSScreenConfigurationInvalidateIfNeededForReason(_NSScreenConfigurationUpdateReason)(), /AppleInternal/BuildRoot/Library/Caches/com.apple.xbs/Sources/AppKit/AppKit-1894.40.150/AppKit.subproj/NSScreenConfiguration.m:473
> >>>
> >>> 2020-05-29 12:30:00.543 R[24961:3275889] *** Terminating app due to
> >>> uncaught exception 'NSInternalInconsistencyException', reason:
> >>> 'NSScreen reconfig must only happen on the main thread.'
> >>>
> >>> *** First throw call stack:
> >>>
> >>> (
> >>>
> >>> 0 CoreFoundation 0x00007fff371698d7
> >>> __exceptionPreprocess + 250
> >>>
> >>> 1 libobjc.A.dylib 0x00007fff6ff47a9e
> >>> objc_exception_throw + 48
> >>>
> >>> 2 CoreFoundation 0x00007fff37192bb0
> >>> +[NSException raise:format:arguments:] + 88
> >>>
> >>> 3 Foundation 0x00007fff398de456
> >>> -[NSAssertionHandler
> >>> handleFailureInFunction:file:lineNumber:description:] + 166
> >>>
> >>> 4 AppKit 0x00007fff34503083
> >>> +[_NSScreenConfiguration invalidateConfigurationIfNeededForReason:] +
> >>> 361
> >>>
> >>> 5 AppKit 0x00007fff34e4bda8
> >>> _NSApplicationInvalidateScreenConfigurationMaybeIfNeeded + 243
> >>>
> >>> 6 AppKit 0x00007fff34502c85
> >>> -[NSApplication(ScreenHandling) _reactToDockChanged] + 144
> >>>
> >>> 7 AppKit 0x00007fff345024dc
> >>> _NSCGSDockMessageReceive + 268
> >>>
> >>> 8 HIToolbox 0x00007fff35d34a3c
> >>> _ZL12DockCallbackjjPvS_ + 1987
> >>>
> >>> 9 HIServices 0x00007fff3539c8ec
> >>> dockClientNotificationProc + 217
> >>>
> >>> 10 SkyLight 0x00007fff6626f174
> >>> _ZN12_GLOBAL__N_123notify_datagram_handlerEj15CGSDatagramTypePvmS1_ +
> >>> 1002
> >>>
> >>> 11 SkyLight 0x00007fff6626de71
> >>> CGSSnarfAndDispatchDatagrams + 1671
> >>>
> >>> 12 SkyLight 0x00007fff6649d5a5
> >>> SLSGetNextEventRecordInternal + 83
> >>>
> >>> 13 SkyLight 0x00007fff6633bfbe
> >>> SLEventCreateNextEvent + 136
> >>>
> >>> 14 libXplugin.1.dylib 0x000000010686df0c
> >>> ___xp_init_service_cg_event_port_block_invoke + 104
> >>>
> >>> 15 libdispatch.dylib 0x00007fff7108d658
> >>> _dispatch_client_callout + 8
> >>>
> >>> 16 libdispatch.dylib 0x00007fff7108f818
> >>> _dispatch_continuation_pop + 414
> >>>
> >>> 17 libdispatch.dylib 0x00007fff7109f4be
> >>> _dispatch_source_invoke + 2084
> >>>
> >>> 18 libdispatch.dylib 0x00007fff71092af6
> >>> _dispatch_lane_serial_drain + 263
> >>>
> >>> 19 libdispatch.dylib 0x00007fff710935d6
> >>> _dispatch_lane_invoke + 363
> >>>
> >>> 20 libdispatch.dylib 0x00007fff7109cc09
> >>> _dispatch_workloop_worker_thread + 596
> >>>
> >>> 21 libsystem_pthread.dylib 0x00007fff712eba3d
> >>> _pthread_wqthread + 290
> >>>
> >>> 22 libsystem_pthread.dylib 0x00007fff712eab77 start_wqthread + 15
> >>>
> >>> )
> >>>
> >>> libc++abi.dylib: terminating with uncaught exception of type NSException
> >>>
> >>> zsh: abort R
> >>>
> >>> rmh using rmhs-Air ~ %
> >>>
> >>>
> >>> On Fri, May 29, 2020 at 12:16 PM Duncan Murdoch
> >>> <murdoch.duncan using gmail.com> wrote:
> >>>>
> >>>> I'm not seeing that with R-patched r78557, run from the console. I'm
> >>>> not sure I have the same MacOS version as you (R prints the same thing,
> >>>> Apple says High Sierra 10.13.6). I tried with the CRAN binary of rgl
> >>>> 0.100.54. I'd guess the version of XQuartz may be important: I'm not
> >>>> seeing rgl in the call stack, but libXplugin is there. Mine is "XQuartz
> >>>> 2.7.11 (xorg-server 1.18.4)".
> >>>>
> >>>> Duncan Murdoch
> >>>>
> >>>>
> >>>>
> >>>> On 29/05/2020 11:44 a.m., Richard M. Heiberger wrote:
> >>>>> R version 4.0.0 (2020-04-24) -- "Arbor Day"
> >>>>> Copyright (C) 2020 The R Foundation for Statistical Computing
> >>>>> Platform: x86_64-apple-darwin17.0 (64-bit)
> >>>>>
> >>>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
> >>>>> You are welcome to redistribute it under certain conditions.
> >>>>> Type 'license()' or 'licence()' for distribution details.
> >>>>>
> >>>>> Natural language support but running in an English locale
> >>>>>
> >>>>> R is a collaborative project with many contributors.
> >>>>> Type 'contributors()' for more information and
> >>>>> 'citation()' on how to cite R or R packages in publications.
> >>>>>
> >>>>> Type 'demo()' for some demos, 'help()' for on-line help, or
> >>>>> 'help.start()' for an HTML browser interface to help.
> >>>>> Type 'q()' to quit R.
> >>>>>
> >>>>>> if(identical(getOption('pager'), file.path(R.home('bin'), 'pager'))) options(pager='cat') # rather take the ESS one
> >>>>>> options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', show.error.locations=TRUE)
> >>>>>> version
> >>>>> _
> >>>>> platform x86_64-apple-darwin17.0
> >>>>> arch x86_64
> >>>>> os darwin17.0
> >>>>> system x86_64, darwin17.0
> >>>>> status
> >>>>> major 4
> >>>>> minor 0.0
> >>>>> year 2020
> >>>>> month 04
> >>>>> day 24
> >>>>> svn rev 78286
> >>>>> language R
> >>>>> version.string R version 4.0.0 (2020-04-24)
> >>>>> nickname Arbor Day
> >>>>>>
> >>>>>> library(rgl)
> >>>>>> plot(1:10)
> >>>>>>
> >>>>>
> >>>>> Process R abort trap: 6 at Fri May 29 11:32:59 2020
> >>>>> 2020-05-29 11:32:59.542 R[24448:3255600] *** Assertion failure in BOOL
> >>>>> NSScreenConfigurationInvalidateIfNeededForReason(_NSScreenConfigurationUpdateReason)(),
> >>>>> /AppleInternal/BuildRoot/Library/Caches/com.apple.xbs/Sources/AppKit/AppKit-1894.40.150/AppKit.subproj/NSScreenConfiguration.m:473
> >>>>> 2020-05-29 11:32:59.560 R[24448:3255600] *** Terminating app due to
> >>>>> uncaught exception 'NSInternalInconsistencyException', reason:
> >>>>> 'NSScreen reconfig must only happen on the main thread.'
> >>>>> *** First throw call stack:
> >>>>> (
> >>>>> 0 CoreFoundation 0x00007fff371698d7
> >>>>> __exceptionPreprocess + 250
> >>>>> 1 libobjc.A.dylib 0x00007fff6ff47a9e
> >>>>> objc_exception_throw + 48
> >>>>> 2 CoreFoundation 0x00007fff37192bb0
> >>>>> +[NSException raise:format:arguments:] + 88
> >>>>> 3 Foundation 0x00007fff398de456
> >>>>> -[NSAssertionHandler
> >>>>> handleFailureInFunction:file:lineNumber:description:] + 166
> >>>>> 4 AppKit 0x00007fff34503083
> >>>>> +[_NSScreenConfiguration invalidateConfigurationIfNeededForReason:] +
> >>>>> 361
> >>>>> 5 AppKit 0x00007fff34e4bda8
> >>>>> _NSApplicationInvalidateScreenConfigurationMaybeIfNeeded + 243
> >>>>> 6 AppKit 0x00007fff34502c85
> >>>>> -[NSApplication(ScreenHandling) _reactToDockChanged] + 144
> >>>>> 7 AppKit 0x00007fff345024dc
> >>>>> _NSCGSDockMessageReceive + 268
> >>>>> 8 HIToolbox 0x00007fff35d34a3c
> >>>>> _ZL12DockCallbackjjPvS_ + 1987
> >>>>> 9 HIServices 0x00007fff3539c8ec
> >>>>> dockClientNotificationProc + 217
> >>>>> 10 SkyLight 0x00007fff6626f174
> >>>>> _ZN12_GLOBAL__N_123notify_datagram_handlerEj15CGSDatagramTypePvmS1_ +
> >>>>> 1002
> >>>>> 11 SkyLight 0x00007fff6626de71
> >>>>> CGSSnarfAndDispatchDatagrams + 1671
> >>>>> 12 SkyLight 0x00007fff6649d5a5
> >>>>> SLSGetNextEventRecordInternal + 83
> >>>>> 13 SkyLight 0x00007fff6633bfbe
> >>>>> SLEventCreateNextEvent + 136
> >>>>> 14 libXplugin.1.dylib 0x000000010ffa5f0c
> >>>>> ___xp_init_service_cg_event_port_block_invoke + 104
> >>>>> 15 libdispatch.dylib 0x00007fff7108d658
> >>>>> _dispatch_client_callout + 8
> >>>>> 16 libdispatch.dylib 0x00007fff7108f818
> >>>>> _dispatch_continuation_pop + 414
> >>>>> 17 libdispatch.dylib 0x00007fff7109f4be
> >>>>> _dispatch_source_invoke + 2084
> >>>>> 18 libdispatch.dylib 0x00007fff71092af6
> >>>>> _dispatch_lane_serial_drain + 263
> >>>>> 19 libdispatch.dylib 0x00007fff710935d6
> >>>>> _dispatch_lane_invoke + 363
> >>>>> 20 libdispatch.dylib 0x00007fff7109cc09
> >>>>> _dispatch_workloop_worker_thread + 596
> >>>>> 21 libsystem_pthread.dylib 0x00007fff712eba3d
> >>>>> _pthread_wqthread + 290
> >>>>> 22 libsystem_pthread.dylib 0x00007fff712eab77 start_wqthread + 15
> >>>>> )
> >>>>> libc++abi.dylib: terminating with uncaught exception of type NSException
> >>>>>
> >>>>> _______________________________________________
> >>>>> R-SIG-Mac mailing list
> >>>>> R-SIG-Mac using r-project.org
> >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>>>>
> >>>>
> >>
>
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