[R-SIG-Mac] R.app crashes with non existing object - WAS: CONFIRMED - R.app crashes at startup on MacOS Sierra, Re: CONFIRMED - R.app crashes at startup on MacOS Sierra
Karl Thomaseth
karl.thomaseth at gmail.com
Sat Dec 10 11:07:43 CET 2016
One possible problem seems to be with Sierra, because R crashes with the following line written on the Console:
R[788]: BUG in libdispatch client: kevent[EVFILT_MACHPORT] monitored resource vanished before the source cancel handler was invoked
which is an old known problem
Cheers,
Karl
> On 9 Dec 2016, at 09:24, Rainer M Krug <Rainer at krugs.de> wrote:
>
> Simon Urbanek <simon.urbanek at r-project.org <mailto:simon.urbanek at r-project.org>> writes:
>
>>> On Dec 8, 2016, at 11:51 AM, Rainer M Krug <Rainer at krugs.de> wrote:
>>>
>>> Simon Urbanek <simon.urbanek at r-project.org> writes:
>>>
>>>> Karl,
>>>>
>>>> unfortunately I cannot reproduce it on 10.12.1. How exactly can you
>>>> trigger it? I have tried dragging a file on the R icon and open -a
>>>> /Applications/R.app test.R and neither crashed on me. Does it depend
>>>> on the R file opened or its location?
>>>>
>>>> Rainer,
>>>> it seems that your build is broken - I have seen crashes on error in
>>>> builds that don't compile longjmp correctly so errors blow up the
>>>> event loop - which seems to be the case in your build. How did you
>>>> build it?
>>>
>>> I installed via homebrew and I used the bottled version, i.e. the
>>> pre-compiled one. At the moment I am installing from source and see how
>>> that one works ... done ... Same problem. I assume it is one of the dependencies?
>>> Any suggestions?
>>>
>>
>> Since that is not our binary I fear you'll have to take it up with
>> whoever does the homebrew recipe for it. I can only vouch for the CRAN
>> binary, you're on your own with 3rd party binaries - they often have
>> issues that are not under our control.
>
> That's why I said initially that I don't expect any help on this :).
>
> But it also occurs when I install from source via homebrew. Can you give
> me any hint on how I can debug this (when I have time)?
>
> Thanks,
>
> Rainer
>
>
>>
>> Cheers,
>> Simon
>>
>>
>>
>>
>>> Rainer
>>>
>>>
>>>
>>>>
>>>> Cheers,
>>>> Simon
>>>>
>>>>
>>>>
>>>>> On Dec 8, 2016, at 5:45 AM, Rainer M Krug <Rainer at krugs.de> wrote:
>>>>>
>>>>> Karl Thomaseth <karl.thomaseth at gmail.com> writes:
>>>>>
>>>>>> Hello all,
>>>>>>
>>>>>> I regret to bother you, but since I upgraded to MacOS Sierra more than a month ago, I am experiencing
>>>>>> that whenever I open any “file.R”, which launches automatically R.app GUI the GUI crashes (see info below),
>>>>>> I removed also all .RData and .Rapp.history from my system with
>>>>>> sudo find / -name “.RData” -delete
>>>>>> sudo find / -name “.Rapp*” -delete
>>>>>> If I start R directly from the Dock, everything works fine.
>>>>>
>>>>> First attempt: Nope - works. Then I realized it opened in emacs...
>>>>>
>>>>> OK.
>>>>>
>>>>> Opening a .R file via clicking on it actually results in the crash as
>>>>> well. The file is opened, but R crashes.
>>>>>
>>>>>
>>>>> How did you install R? I installed via homebrew (And no, I don't expect
>>>>> any help here for my case).
>>>>>
>>>>> But I might add: maybe related - but R crashes in the GUI if I use
>>>>> e.g. a non-existing function - maybe related?
>>>>>
>>>>> ,----
>>>>> | > version
>>>>> | _
>>>>> | platform x86_64-apple-darwin16.1.0
>>>>> | arch x86_64
>>>>> | os darwin16.1.0
>>>>> | system x86_64, darwin16.1.0
>>>>> | status
>>>>> | major 3
>>>>> | minor 3.2
>>>>> | year 2016
>>>>> | month 10
>>>>> | day 31
>>>>> | svn rev 71607
>>>>> | language R
>>>>> | version.string R version 3.3.2 (2016-10-31)
>>>>> | nickname Sincere Pumpkin Patch
>>>>> | > version()
>>>>> | Error: could not find function "version"
>>>>> |
>>>>> | *** caught segfault ***
>>>>> | address 0x18, cause 'memory not mapped'
>>>>> |
>>>>> | Possible actions:
>>>>> | 1: abort (with core dump, if enabled)
>>>>> | 2: normal R exit
>>>>> | 3: exit R without saving workspace
>>>>> | 4: exit R saving workspace
>>>>> | Selection:
>>>>> `----
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Rainer
>>>>>
>>>>>>
>>>>>> Thank you
>>>>>>
>>>>>> Karl Thomaseth
>>>>>>
>>>>>>
>>>>>>
>>>>>> R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
>>>>>> Copyright (C) 2016 The R Foundation for Statistical Computing
>>>>>> Platform: x86_64-apple-darwin13.4.0 (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.
>>>>>>
>>>>>> [R.app GUI 1.68 (7288) x86_64-apple-darwin13.4.0]
>>>>>>
>>>>>> *** caught segfault ***
>>>>>> address 0x7f8bf2637f8, cause 'memory not mapped'
>>>>>>
>>>>>> Possible actions:
>>>>>> 1: abort (with core dump, if enabled)
>>>>>> 2: normal R exit
>>>>>> 3: exit R without saving workspace
>>>>>> 4: exit R saving workspace
>>>>>>>
>>>>>> Selection:
>>>>>>
>>>>>> =======================================
>>>>>>> sessionInfo()
>>>>>> R version 3.3.2 (2016-10-31)
>>>>>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>>>>> Running under: macOS Sierra 10.12.1
>>>>>>
>>>>>> locale:
>>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>>>
>>>>>> attached base packages:
>>>>>> [1] stats graphics grDevices utils datasets methods base
>>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> R-SIG-Mac mailing list
>>>>>> R-SIG-Mac at r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>
>>>>>
>>>>> --
>>>>> Rainer M. Krug
>>>>> email: Rainer<at>krugs<dot>de
>>>>> PGP: 0x0F52F982
>>>>> _______________________________________________
>>>>> R-SIG-Mac mailing list
>>>>> R-SIG-Mac at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>
>>>
>>> Brandon Hurr <brandon.hurr at gmail.com> writes:
>>>
>>>> Simon,
>>>>
>>>> I have been experiencing this error for quite some time. If I load a r
>>>> script by double clicking it, it happens nearly 100% of the time. If I
>>>> load R itself first then it doesn't happen. If I clear the "recent"
>>>> files area it doesn't happen until I fill it again. The file opened
>>>> seems irrelevant, as does the location of the file (admittedly, all in
>>>> user space or external drives).
>>>>
>>>> Despite the dire warning, if I hit escape I can continue working
>>>> nearly indefinitely without issue (my script save rate increases to
>>>> compensate for risk).
>>>>
>>>> This was reported by CW on Nov 4th (perhaps others before), email
>>>> entitled: "[R-SIG-Mac] R segfault at startup, causing R crash". I
>>>> worked a little bit with Kevin Ushey offline to get to the bottom of
>>>> it further and I thought he pinned it down or at least got closer to
>>>> the cause.
>>>>
>>>> "
>>>> After playing around with R.app for a bit, I was able to get myself
>>>> into a state where R.app was either dying or hanging on startup. I did
>>>> the following:
>>>>
>>>> 1. Open R.app,
>>>> 2. Open a new R document (using the icon in the top menu bar --
>>>> 'Create a new, empty document in the editor' ),
>>>> 3. Write and execute some code -- in my case, 'x <- 1; print(x)',
>>>> executed with Cmd + Enter,
>>>> 4. (optionally) Repeat steps 2 and 3, creating new documents and
>>>> executing more code,
>>>> 5. Focus a different application,
>>>> 6. Attempt to open an R document (using the menu bar again --
>>>> 'Source script or load data in R',
>>>> 7. Observe that R.app is now hanging.
>>>>
>>>> Note that if you run these repro steps, you may see R segfault / die
>>>> on startup (although in some cases all was fine). Note that step 5 is
>>>> necessary (IIUC) to force R.app to attempt to save the application
>>>> state.
>>>>
>>>> It looks like R.app stores session state in the folder
>>>>
>>>> ~/Library/Saved Application State/org.R-project.R.savedState
>>>>
>>>> My hypothesis at this point is that this saved state is somehow
>>>> getting corrupted. Removing that folder seems to resolve any startup
>>>> crashes I see.
>>>>
>>>> As for the 'Open File' dialog hang, here's what I believe are the
>>>> relevant bits of an lldb stack trace I see:
>>>>
>>>> * frame #0: 0x00007fffce2a7cba libsystem_kernel.dylib`__psynch_mutexwait + 10
>>>> frame #1: 0x00007fffce390f6a
>>>> libsystem_pthread.dylib`_pthread_mutex_lock_wait + 100
>>>> frame #2: 0x00007fffc573faee
>>>> FinderKit`+[FI_TFloatingInputWindowController singleton] + 34
>>>> frame #3: 0x00007fffc57edd5b FinderKit`-[FI_TBrowserTableView
>>>> inputContext] + 29
>>>> frame #4: 0x00007fffb6d397dc AppKit`+[NSTextInputContext
>>>> currentInputContext] + 145
>>>> frame #5: 0x00007fffb6e7a272 AppKit`+[_NSAutomaticFocusRing
>>>> setActiveFirstResponderChanged] + 37
>>>> frame #6: 0x00007fffb6e7a1d9
>>>> AppKit`___NSPostActiveFirstResponderChanged_block_invoke + 29
>>>> frame #7: 0x00007fffb90cdec7
>>>> CoreFoundation`__CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__
>>>> + 23
>>>> frame #8: 0x00007fffb90cde37 CoreFoundation`__CFRunLoopDoObservers + 391
>>>> frame #9: 0x00007fffb90aead9 CoreFoundation`__CFRunLoopRun + 873
>>>> frame #10: 0x00007fffb90ae514 CoreFoundation`CFRunLoopRunSpecific + 420
>>>> frame #11: 0x00007fffbaaabcb2 Foundation`-[NSRunLoop(NSRunLoop)
>>>> runMode:beforeDate:] + 277
>>>> frame #12: 0x000000010b21f43e R`-[RDocumentWinCtrl
>>>> setStatusLineText:](self=0x00006180001e7c00,
>>>> _cmd="setStatusLineText:", text=@"print(x, ...)") + 910 at
>>>> RDocumentWinCtrl.m:465
>>>> frame #13: 0x000000010b21f03d R`-[RDocumentWinCtrl
>>>> RDocumentDidResize:](self=0x00006180001e7c00,_cmd="RDocumentDidResize:",
>>>> notification=@"NSWindowDidResizeNotification") + 77 at
>>>> RDocumentWinCtrl.m:431
>>>>
>>>> with context from frame 12:
>>>>
>>>> frame #12: 0x000000010b21f43e R`-[RDocumentWinCtrl
>>>> setStatusLineText:](self=0x00006180001e7c00,
>>>> _cmd="setStatusLineText:", text=@"print(x, ...)") + 910 at
>>>> RDocumentWinCtrl.m:465
>>>> 462 [statusLine setStringValue:text];
>>>> 463 [statusLine setNeedsDisplay:YES];
>>>> 464 // Run NSDefaultRunLoopMode to allow to update status line
>>>> -> 465 [[NSRunLoop currentRunLoop] runMode:NSDefaultRunLoopMode
>>>> 466
>>>> beforeDate:[NSDate distantPast]];
>>>> 467
>>>> 468 }
>>>>
>>>> Hopefully this helps...
>>>>
>>>> Best,
>>>> Kevin
>>>> "
>>>>
>>>> B
>>>>
>>>> On Thu, Dec 8, 2016 at 6:28 AM, Simon Urbanek
>>>> <simon.urbanek at r-project.org> wrote:
>>>>> Karl,
>>>>>
>>>>> unfortunately I cannot reproduce it on 10.12.1. How exactly can you
>>>>> trigger it? I have tried dragging a file on the R icon and open -a
>>>>> /Applications/R.app test.R and neither crashed on me. Does it depend
>>>>> on the R file opened or its location?
>>>>>
>>>>> Rainer,
>>>>> it seems that your build is broken - I have seen crashes on error in
>>>>> builds that don't compile longjmp correctly so errors blow up the
>>>>> event loop - which seems to be the case in your build. How did you
>>>>> build it?
>>>>>
>>>>> Cheers,
>>>>> Simon
>>>>>
>>>>>
>>>>>
>>>>>> On Dec 8, 2016, at 5:45 AM, Rainer M Krug <Rainer at krugs.de> wrote:
>>>>>>
>>>>>> Karl Thomaseth <karl.thomaseth at gmail.com> writes:
>>>>>>
>>>>>>> Hello all,
>>>>>>>
>>>>>>> I regret to bother you, but since I upgraded to MacOS Sierra more than a month ago, I am experiencing
>>>>>>> that whenever I open any “file.R”, which launches automatically R.app GUI the GUI crashes (see info below),
>>>>>>> I removed also all .RData and .Rapp.history from my system with
>>>>>>> sudo find / -name “.RData” -delete
>>>>>>> sudo find / -name “.Rapp*” -delete
>>>>>>> If I start R directly from the Dock, everything works fine.
>>>>>>
>>>>>> First attempt: Nope - works. Then I realized it opened in emacs...
>>>>>>
>>>>>> OK.
>>>>>>
>>>>>> Opening a .R file via clicking on it actually results in the crash as
>>>>>> well. The file is opened, but R crashes.
>>>>>>
>>>>>>
>>>>>> How did you install R? I installed via homebrew (And no, I don't expect
>>>>>> any help here for my case).
>>>>>>
>>>>>> But I might add: maybe related - but R crashes in the GUI if I use
>>>>>> e.g. a non-existing function - maybe related?
>>>>>>
>>>>>> ,----
>>>>>> | > version
>>>>>> | _
>>>>>> | platform x86_64-apple-darwin16.1.0
>>>>>> | arch x86_64
>>>>>> | os darwin16.1.0
>>>>>> | system x86_64, darwin16.1.0
>>>>>> | status
>>>>>> | major 3
>>>>>> | minor 3.2
>>>>>> | year 2016
>>>>>> | month 10
>>>>>> | day 31
>>>>>> | svn rev 71607
>>>>>> | language R
>>>>>> | version.string R version 3.3.2 (2016-10-31)
>>>>>> | nickname Sincere Pumpkin Patch
>>>>>> | > version()
>>>>>> | Error: could not find function "version"
>>>>>> |
>>>>>> | *** caught segfault ***
>>>>>> | address 0x18, cause 'memory not mapped'
>>>>>> |
>>>>>> | Possible actions:
>>>>>> | 1: abort (with core dump, if enabled)
>>>>>> | 2: normal R exit
>>>>>> | 3: exit R without saving workspace
>>>>>> | 4: exit R saving workspace
>>>>>> | Selection:
>>>>>> `----
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> Rainer
>>>>>>
>>>>>>>
>>>>>>> Thank you
>>>>>>>
>>>>>>> Karl Thomaseth
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
>>>>>>> Copyright (C) 2016 The R Foundation for Statistical Computing
>>>>>>> Platform: x86_64-apple-darwin13.4.0 (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.
>>>>>>>
>>>>>>> [R.app GUI 1.68 (7288) x86_64-apple-darwin13.4.0]
>>>>>>>
>>>>>>> *** caught segfault ***
>>>>>>> address 0x7f8bf2637f8, cause 'memory not mapped'
>>>>>>>
>>>>>>> Possible actions:
>>>>>>> 1: abort (with core dump, if enabled)
>>>>>>> 2: normal R exit
>>>>>>> 3: exit R without saving workspace
>>>>>>> 4: exit R saving workspace
>>>>>>>>
>>>>>>> Selection:
>>>>>>>
>>>>>>> =======================================
>>>>>>>> sessionInfo()
>>>>>>> R version 3.3.2 (2016-10-31)
>>>>>>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>>>>>> Running under: macOS Sierra 10.12.1
>>>>>>>
>>>>>>> locale:
>>>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>>>>
>>>>>>> attached base packages:
>>>>>>> [1] stats graphics grDevices utils datasets methods base
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> R-SIG-Mac mailing list
>>>>>>> R-SIG-Mac at r-project.org
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> Rainer M. Krug
>>>>>> email: Rainer<at>krugs<dot>de
>>>>>> PGP: 0x0F52F982
>>>>>> _______________________________________________
>>>>>> R-SIG-Mac mailing list
>>>>>> R-SIG-Mac at r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>
>>>>> _______________________________________________
>>>>> R-SIG-Mac mailing list
>>>>> R-SIG-Mac at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>
>>> --
>>> Rainer M. Krug
>>> email: Rainer<at>krugs<dot>de
>>> PGP: 0x0F52F982
>>
>
> --
> Rainer M. Krug
> email: Rainer<at>krugs<dot>de
> PGP: 0x0F52F982
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