[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 18:54:18 CEST 2020
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
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> 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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