[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
Simon Urbanek
simon.urbanek at r-project.org
Thu Dec 8 22:13:01 CET 2016
> 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.
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
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