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

David Winsemius dw|n@em|u@ @end|ng |rom comc@@t@net
Wed Aug 5 03:38:59 CEST 2020 

On 8/3/20 6:25 AM, Duncan Murdoch wrote:
> Thanks. Looks like I should update.  I'm looking forward to the 
> crashes...
Fortune candidate.
>
> Duncan Murdoch
>
> On 03/08/2020 9:21 a.m., Marc Schwartz 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
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>
>>>
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