[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
Thu Dec 8 17:51:14 CET 2016
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?
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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