[R-SIG-Mac] [External] Re: crash due to rgl and base graphics conflict
Duncan Murdoch
murdoch@dunc@n @end|ng |rom gm@||@com
Mon Aug 3 20:44:31 CEST 2020
It didn't stay fixed. I get crashes about half the time now. I'll see
if I can figure out what's going wrong. My guess would be that rather
than an rgl bug this is an Xquartz bug, but maybe I can find a way to
prevent it.
Duncan Murdoch
On 03/08/2020 12:54 p.m., Duncan Murdoch wrote:
> With great trepidation, I installed Catalina. I saw the same crash as
> reported. Then I reinstalled Xquartz, shut down the Xquartz that was
> still running (should have done that in the other order!), and tried
> again: no crash. Hope it stays fixed!
>
> Duncan Murdoch
>
> On 03/08/2020 9:25 a.m., Duncan Murdoch wrote:
>> Thanks. Looks like I should update. I'm looking forward to the crashes...
>>
>> 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
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
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>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>
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