[R-SIG-Mac] [External] Re: crash due to rgl and base graphics conflict

Patrick Schratz p@tr|ck@@chr@tz @end|ng |rom gm@||@com
Mon Aug 3 15:28:59 CEST 2020


Works fine in both RStudio and in the terminal for me (10.15.6).

R 4.0.2, official binary

On 3 Aug 2020, at 15:21, Marc Schwartz via R-SIG-Mac wrote:

> Hi,
>
> Just installed rgl and I get the same crash and error message from the 
> original post below, running R from the CLI.
>
> If I run R from within ESS (what I normally use), I get:
>
>   Process R abort trap: 6 at Mon Aug  3 09:15:32 2020
>
> If I run R from R.app (the default macOS GUI), the command runs fine 
> and I get the graphic.
>
> I am running R 4.0.2 (2020-06-22) on macOS 10.15.6.
>
> R was cleanly installed, and XQuartz (2.7.11) was updated afterwards.
>
> Regards,
>
> Marc Schwartz
>
>
>> On Aug 3, 2020, at 9:05 AM, Duncan Murdoch <murdoch.duncan using gmail.com> 
>> wrote:
>>
>> I just got a message from someone else using Catalina 10.15.5 who 
>> still gets a crash from
>>
>> library(rgl)
>> plot(1:10)
>>
>> I don't have Catalina, and haven't seen it.  Has anyone else?
>>
>> Duncan Murdoch
>>
>> On 31/05/2020 4:44 p.m., Richard M. Heiberger wrote:
>>> I upgraded last night to Catalina 10.15.5 (19F96).
>>> The crash has gone away and that example now works normally.
>>> On Fri, May 29, 2020 at 3:25 PM Richard M. Heiberger 
>>> <rmh using temple.edu> wrote:
>>>>
>>>> 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
>>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac using r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac using r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac



More information about the R-SIG-Mac mailing list