[R-SIG-Mac] CONFIRMED - R.app crashes at startup on MacOS Sierra
Brandon Hurr
brandon.hurr at gmail.com
Thu Dec 8 22:13:35 CET 2016
Simon,
"> 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."
This sounds exactly the same to me, but if I've misunderstood some
subtleties then apologies for the noise.
Brandon
On Thu, Dec 8, 2016 at 1:10 PM, Simon Urbanek
<simon.urbanek at r-project.org> wrote:
> 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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>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>
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