[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
Rainer M Krug
Rainer at krugs.de
Fri Dec 9 09:24:59 CET 2016
Simon Urbanek <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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