[R-SIG-Mac] R segfault at startup, causing R crash

Kevin Ushey kevinushey at gmail.com
Sun Nov 6 01:08:26 CET 2016 

It might be worth trying to launch R with lldb attached. You can run
the following command from the terminal:

    /usr/bin/lldb -w -n R

Then, try launching R (or R.app) -- 'lldb' should then detect that R
has been launched, and you can enter 'c' in the 'lldb' terminal window
to continue execution. Once R crashes / segfaults, you should
hopefully get a nice backtrace that may provide some actionable
information on how the bug could be fixed. The backtrace can normally
be printed using 'bt' in the lldb console. If lucky, that backtrace
should show exactly what code is causing the crash, and could give
some hints on how the crash could be resolved.

If you're not familiar with lldb, http://lldb.llvm.org/tutorial.html
gives a nice tutorial.

Best,
Kevin

On Sat, Nov 5, 2016 at 8:55 AM, C W <tmrsg11 at gmail.com> wrote:
> Hi Bryan,
>
> Right after I wrote the email, I restarted R and the problem came back.  I
> guess I jinx-ed my luck. ;)
>
> The funny thing is, I did not even have a Rscript, it was just the stand
> alone R console.  I was actually using it as a calculator.
>
> I always thought OS X is more compatible with R than Windows, who knows. :(
>
> On Sat, Nov 5, 2016 at 11:47 AM, Bryan Hanson <hanson at depauw.edu> wrote:
>
>> No problem, glad to try to help.
>>
>> There probably isn’t a problem with R.gui itself (when you “run R” on a
>> Mac by clicking the icon you are causing your computer to actually run the
>> R.gui which in turn is running R under the hood).
>>
>> So if the problem re-occurs, note the name of the most recent file (it
>> probably was opened when you launched R prior to R faulting).  Then find
>> that file and change the extension (temporarily).  Then try to launch R
>> again and I expect it will not have a problem.
>>
>> Bryan
>>
>> > On Nov 5, 2016, at 11:43 AM, C W <tmrsg11 at gmail.com> wrote:
>> >
>> > Hi Bryan,
>> >
>> > I appreciate your detailed explanation.  I am not an R expert, I do not
>> know how to fix the R.gui you mentioned.
>> >
>> > I kept on opening and closing R, after a dozen tries, the error went
>> away temporarily.  I still get the error, but it was not every time.
>> >
>> > Since then, I have upgraded to R version 3.3.2 (2016-10-31).
>> >
>> > I think this problem may come back, please let me know when you find a
>> solution.  Thank you!
>> >
>> > On Fri, Nov 4, 2016 at 8:28 PM, Bryan Hanson <hanson at depauw.edu> wrote:
>> > Sorry, I should add that when you rename the offending file you need to
>> change its extension, otherwise R will follow the file.
>> >
>> > >>> Original Message:
>> >
>> > I had something similar earlier this week (also on Sierra).  I was in
>> touch with Simon who suggested it might be a bad workspace image, so you
>> can try to remove any .RData or .rda files.  However, in my case it was not
>> that (I don’t save workspace images or histories for that matter).  But I
>> removed all of those from my entire computer anyway and the problem
>> remained (a few were left on shared drives by others who were saving
>> workspace images).
>> >
>> > Ultimately I was able to trace the problem to something being wrong with
>> the “recent” list.  In my case R.gui was trying to open the most recent
>> file in the list, but something about the link to it was corrupted.  I
>> verified this by running R from the command line and sourcing the file that
>> seemed to be associated with the crash.  It worked fine, so the file was
>> not the problem.
>> >
>> > So, here’s what worked for me: When R.gui is asking you for a
>> “selection” to close down, see if the File -> Open Recent… option can still
>> be selected, and if so, go all the way down to the clear menu item.  Once
>> this list of recently opened files was empty, R.gui ran fine.  In my case
>> not all files would clear from the list.  There was one left, and it was
>> the one apparently causing the problem.  I renamed it so R.gui couldn’t use
>> it/find it, and then the problem was gone.  Again, there was nothing wrong
>> with the file, there was something wrong with the “remembering”.
>> >
>> > A few days later, I had to repeat this process when the problem
>> re-occurred.  There may be something genuinely conflicted between Sierra
>> and R.gui, only time will tell.  If it proves to be a widespread problem
>> more observations should help narrow it down.  But this is what I
>> experienced and how I fixed it.
>> >
>> > Bryan
>> >
>> >
>> > > On Nov 4, 2016, at 7:31 PM, C W <tmrsg11 at gmail.com> wrote:
>> > >
>> > > Dear R list,
>> > >
>> > > Every time I start R, the following error message come up:
>> > >
>> > > *** caught segfault ***
>> > > address 0x0, cause 'unknown'
>> > >
>> > > 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:
>> > >
>> > >
>> > > Sometimes I get this error message instead,
>> > >
>> > > 2016-11-04 16:50:08.446 R[23372:326103] -[NSDrawerWindow
>> > > setRuleThickness:]: unrecognized selector sent to instance
>> 0x7fabc94a74b0
>> > > 2016-11-04 16:50:08.454 R[23372:326103] *** RController: caught ObjC
>> > > exception while processing system events. Update to the latest GUI
>> version
>> > > and consider reporting this properly (see FAQ) if it persists and is
>> not
>> > > known.
>> > > *** reason: -[NSDrawerWindow setRuleThickness:]: unrecognized selector
>> sent
>> > > to instance 0x7fabc94a74b0
>> > > *** name: NSInvalidArgumentException, info: (null)
>> > > *** Version: R 3.3.2 (71607) R.app R 3.3.2 GUI 1.68 Mavericks build
>> > > Consider saving your work soon in case this develops into a problem.
>> > > Here's the sessionInfo(),
>> > >
>> > >> 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
>> > > [7] base
>> > >
>> > >
>> > > I would appreciate any help,  thank you!
>> > >
>> > >       [[alternative HTML version deleted]]
>> > >
>> > > _______________________________________________
>> > > R-SIG-Mac mailing list
>> > > R-SIG-Mac at r-project.org
>> > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> >
>> >
>>
>>
>
>         [[alternative HTML version deleted]]
>
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