One possible problem seems to be with Sierra, because R crashes with the following line written on the Console:
R[788]: BUG in libdispatch client: kevent[EVFILT_MACHPORT] monitored resource vanished before the source cancel handler was invoked which is an old known problem Cheers, Karl > On 9 Dec 2016, at 09:24, Rainer M Krug <[email protected]> wrote: > > Simon Urbanek <[email protected] > <mailto:[email protected]>> writes: > >>> On Dec 8, 2016, at 11:51 AM, Rainer M Krug <[email protected]> wrote: >>> >>> Simon Urbanek <[email protected]> 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 <[email protected]> wrote: >>>>> >>>>> Karl Thomaseth <[email protected]> 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 >>>>>> [email protected] >>>>>> 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 >>>>> [email protected] >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>> >>> >>> Brandon Hurr <[email protected]> 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 >>>> <[email protected]> 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 <[email protected]> wrote: >>>>>> >>>>>> Karl Thomaseth <[email protected]> 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 >>>>>>> [email protected] >>>>>>> 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 >>>>>> [email protected] >>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>>> >>>>> _______________________________________________ >>>>> R-SIG-Mac mailing list >>>>> [email protected] >>>>> 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 [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
