[R-SIG-Mac] R-devel segmentation fault in combination RStudio/R GUI

Simon Urbanek @|mon@urb@nek @end|ng |rom R-project@org
Thu Sep 26 05:15:52 CEST 2024 

Sebastian,

The R GUI problem has been identified (R-devel removed R_SetOptionWidth() which broke the GUI) and is now fixed (Mac-GUI r8453).

I cannot comment on RStudio issues, but you mentioned packages: check your .libPaths() and make sure you remove (or re-install) *all* packages since packages are not compatible between R versions.

Cheers,
Simon


> On 26 Sep 2024, at 11:42, Simon Urbanek <simon.urbanek using R-project.org> wrote:
> 
> Sebastian,
> 
> thanks, I can replicate the crash in the R GUI and it’s due to a missing symbol detected at run-time (I’m attaching the traceback even though it’s not very helpful). Unfortunately, the error doesn’t say which symbol and from which library - and the use is inside Apple’s core library, not R itself - so I have to dig deeper to see what triggers it. This could well be some bug in R-devel, because the build of R-4.4-branch from the same nightly run works fine. I’ll try to have a more in-depth look next week.
> 
> Cheers,
> Simon
> 
> 
> * thread #1, queue = 'com.apple.main-thread', stop reason = signal SIGABRT
>    frame #0: 0x00000001972434c8 dyld`__abort_with_payload + 8
> dyld`:
> ->  0x1972434c8 <+8>:  b.lo   0x1972434e8               ; <+40>
>    0x1972434cc <+12>: pacibsp 
>    0x1972434d0 <+16>: stp    x29, x30, [sp, #-0x10]!
>    0x1972434d4 <+20>: mov    x29, sp
> Target 0: (R) stopped.
> (lldb) bt
> * thread #1, queue = 'com.apple.main-thread', stop reason = signal SIGABRT
>  * frame #0: 0x00000001972434c8 dyld`__abort_with_payload + 8
>    frame #1: 0x000000019724e0cc dyld`abort_with_payload_wrapper_internal + 104
>    frame #2: 0x000000019724e100 dyld`abort_with_payload + 16
>    frame #3: 0x00000001971df7f0 dyld`dyld4::halt(char const*, dyld4::StructuredError const*) + 304
>    frame #4: 0x00000001972144fc dyld`dyld4::APIs::_dyld_missing_symbol_abort() + 28
>    frame #5: 0x000000019879574c Foundation`__NSFireDelayedPerform + 372
>    frame #6: 0x00000001976615b8 CoreFoundation`__CFRUNLOOP_IS_CALLING_OUT_TO_A_TIMER_CALLBACK_FUNCTION__ + 32
>    frame #7: 0x000000019766125c CoreFoundation`__CFRunLoopDoTimer + 972
>    frame #8: 0x0000000197660d94 CoreFoundation`__CFRunLoopDoTimers + 356
>    frame #9: 0x00000001976441cc CoreFoundation`__CFRunLoopRun + 1856
>    frame #10: 0x0000000197643434 CoreFoundation`CFRunLoopRunSpecific + 608
>    frame #11: 0x00000001a1ded19c HIToolbox`RunCurrentEventLoopInMode + 292
>    frame #12: 0x00000001a1decfd8 HIToolbox`ReceiveNextEventCommon + 648
>    frame #13: 0x00000001a1decd30 HIToolbox`_BlockUntilNextEventMatchingListInModeWithFilter + 76
>    frame #14: 0x000000019aea2cc8 AppKit`_DPSNextEvent + 660
>    frame #15: 0x000000019b6994d0 AppKit`-[NSApplication(NSEventRouting) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 700
>    frame #16: 0x0000000100009628 R`-[RController doProcessEvents:] + 160
>    frame #17: 0x0000000100005260 R`-[RController handleReadConsole:] + 80
>    frame #18: 0x000000010000c0d8 R`Re_ReadConsole + 192
>    frame #19: 0x0000000100b76328 libR.dylib`R_ReplDLLdo1 at main.c:375:6 [opt]
>    frame #20: 0x0000000100016ea0 R`run_REngineRmainloop + 260
>    frame #21: 0x000000010000e54c R`-[REngine runREPL] + 124
>    frame #22: 0x0000000100001c2c R`main + 592
>    frame #23: 0x00000001971db154 dyld`start + 2476
> 
> 
> 
> 
> 
> 
>> On 26 Sep 2024, at 06:12, Sebastian Kreutzer <sebastian.kreutzer using uni-heidelberg.de> wrote:
>> 
>> Hello, 
>> 
>> Thanks again to Prof Ripley and Simon; however, I am afraid I have to get back 
>> to you on this because my “I am good for now" was premature.
>> 
>> The R-devel builds now appear again on https://mac.r-project.org/; thank you very much!
>> 
>> Unfortunately, I have the same issue with these builds as with the ones I have produced locally.
>> 
>> - I installed and tried the binary builds from https://mac.r-project.org/big-sur/last-success/ and 
>> https://mac.r-project.org/ but when I use RStudio (just updated before once more) and try to load
>> a package, the session crashes immediately. The same goes for the R GUI; it won’t start anymore.
>> 
>> - As before, calling R from the terminal works fine without any issue
>> 
>> - When I return to R-4.4.1-arm64.pkg (always freshly installed, no version switching), 
>> everything works as expected, with no error or issue. 
>> 
>> - I’ve looked up the RStudio GitHub issue list but found no report
>> 
>> - The console shows the following errors (shorted; I can provide full reports if wanted): 
>> 
>> RStudio:  EXC_CRASH (SIGABRT)
>> R GUI: codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":”SIGABRT"
>> 
>> - To be absolutely sure, I then tried to install the R-devel build from https://mac.r-project.org/ on my private M1 Mac mini, still running macOS 14.7 and 
>> I got the same crashes. Other than being from Apple, these two machines (the M2 and the private M1) have nothing in common 
>> regarding the setup. 
>> 
>> This observation makes me somewhat think that it is likely that someone else can perhaps reproduce this "issue"? 
>> 
>> Thanks once more for your support and kind regards, 
>> 
>> Sebastian 
>> 
>> P.S. Sorry for the HTML in my last messages. Prof Ripley was so kind as to point me to the e-mail certificate that caused these HTML tags. It should be fine now. 
>> 
>> 
>>> On 25. Sep 2024, at 11:50, Prof Brian Ripley <ripley using stats.ox.ac.uk> wrote:
>>> 
>>> On 25/09/2024 10:26, Sebastian Kreutzer wrote:
>>>> Hi Simon,
>>>> Many thanks for your prompt reply and the link; it greatly helps, and I appreciate it!
>>>> Yes, sorry for not detailing my issue further, but I did not want to
>>>> spam anybody with the log and configuration files I am using, so I cut it short.
>>>> I will also look more carefully into the differences between “my” build process and the CRAN builds;
>>>> it seems evident that I have overlooked something. My initial thought was just that with all the API
>>>> changes going on and me using a more recent version of macOS for the build than CRAN does,
>>> 
>>> The machine used for the M1mac additional issue is fully up-to-date, see https://www.stats.ox.ac.uk/pub/bdr/M1mac/README.txt
>>> 
>>> Following the instructions in the R-admin manual and not by some third party is always a good idea before posting.
>>> 
>>> Do please stop sending HTML, as required in the posting guide.
>>> 
>>>> it would not surprise me that, at some point, something
>>>> had changed in macOS, causing this “user-interface-only” crash.
>>>> Anyway, so as not to bother you further, thanks again for the help. I am good for now,
>>>> and if I figure out what has to be changed in my configuration to make it work again,  I will post it.
>>>> Kind regards,
>>>> Sebastian
>>>>> On 25. Sep 2024, at 01:40, Simon Urbanek <simon.urbanek using R-project.org> wrote:
>>>>> 
>>>>> Sebastian,
>>>>> 
>>>>> if you want to replicate the CRAN builds, you have to also use the same settings, otherwise you may have a build which is not binary compatible. It is unclear from your description how you built R (there are several variants such as framework install vs "unix"-style install and they are incompatible). You can see the flags actually used at the top of ${R_HOME}/etc/Makevars.
>>>>> 
>>>>> As for macOS R binaries, all latest builds are always available from
>>>>> https://mac.r-project.org/big-sur/last-success/
>>>>> 
>>>>> The fact that the main page itself is not showing R-devel is certainly not intentional since the binaries are there - I’ll look into that, thanks for reposting (you shouldn't wait months to report that ;)).
>>> 
>>> I did report it a month ago to Simon.
>>> 
>>>>> 
>>>>> Thanks,
>>>>> Simon
>>>>> 
>>>>> 
>>>>> 
>>>>>> On 24 Sep 2024, at 02:27, Sebastian Kreutzer <sebastian.kreutzer using uni- heidelberg.de> wrote:
>>>>>> 
>>>>>> Hello,
>>>>>> 
>>>>>> I am writing because I have been struggling for a couple of months to get R-devel to work in combination with
>>>>>> RStudio or the R GUI.
>>>>>> 
>>>>>> In the past, I had been downloading R-devel for macOS from https:// mac.r-project.org/, which
>>>>>> nearly always worked, however, for some (months I have in mind), there aren't daily R-devel builds. So I started building
>>>>>> R from source following https://stackoverflow.com/questions/75595875/ how-do-i-build-r-from-sources-on-macos
>>>>>> 
>>>>>> Adapted to my system, this worked surprisingly well, so I kept drawing R-devel from the SNV server on a regular
>>>>>> basis and built it from the source. However, it stopped working in mid-August. In a nutshell:
>>>>>> 
>>>>>> - I can build R-devel from the source without any issue flagged, and when started in the terminal, it works as expected.
>>>>>> - However, it crashes reproducibly when trying to load a package in RStudio (stable/nightly build) and the R GUI (always the latest version)
>>>>>> terminates the R session on start. Error messages in the console I get read as follows:
>>>>>> 
>>>>>>> R GUI: Termination Reason:  Namespace SIGNAL, Code 11 Segmentation fault: 11
>>>>>>> RStudio: Exception Type: EXC_CRASH (SIGABRT) ->    /usr/lib/dyld 0x0 - 0xffffffffffffffff ??? (*) <00000000-0000-0000-0000-000000000000> ???
>>>>>> 
>>>>>> I can share the full logs, but I want to keep it short for now.
>>>>>> 
>>>>>> My questions are:
>>>>>> 
>>>>>> - Did anybody encounter such an issue with the latest R-devel and R GUI, RStudio?
>>>>>> - Is this perhaps why an R-devel binary is currently not available on https://mac.r-project.org/?
>>>>>> 
>>>>>> If I know that this is a known issue, it is all good; however, if it works
>>>>>> For all others without, then the error must be on my end, and I have to keep digging further.
>>>>>> 
>>>>>> - Tested systems: M2 -> macOS 14.5 to 15.0 with the Xcode on always the latest version available at the time.
>>>>>> - SNV: Always the latest check out
>>>>>> 
>>>>>> 
>>>>>> Kind regards,
>>>>>> 
>>>>>> 
>>>>>> Sebastian Kreutzer
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
>>>> R-SIG-Mac using r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>>> 
>>> -- 
>>> Brian D. Ripley,                  ripley using stats.ox.ac.uk
>>> Emeritus Professor of Applied Statistics, University of Oxford
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