Simon Urbanek <simon.urba...@r-project.org> writes: >> On Dec 8, 2016, at 11:51 AM, Rainer M Krug <rai...@krugs.de> wrote: >> >> Simon Urbanek <simon.urba...@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.
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 <rai...@krugs.de> wrote: >>>> >>>> Karl Thomaseth <karl.thomas...@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@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@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >> >> Brandon Hurr <brandon.h...@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.urba...@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 <rai...@krugs.de> wrote: >>>>> >>>>> Karl Thomaseth <karl.thomas...@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@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@r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>> >>>> _______________________________________________ >>>> R-SIG-Mac mailing list >>>> R-SIG-Mac@r-project.org >>>> 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
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