[R-SIG-Mac] CONFIRMED - R.app crashes at startup on MacOS Sierra

Simon Urbanek simon.urbanek at r-project.org
Thu Dec 8 22:10:19 CET 2016


Brandon,

AFAICS your report is entirely unrelated to the problem reported by Karl - it's an entirely different location and cause. I may be able to look into it, we just should make sure we're not mixing unrelated reports.

Thanks,
Simon



> On Dec 8, 2016, at 11:30 AM, Brandon Hurr <brandon.hurr at gmail.com> wrote:
> 
> 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
>> 
>> _______________________________________________
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> 



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