[R-SIG-Mac] [External] [External] Xquartz started crashing today

Tue Jun 7 02:41:23 CEST 2022

Rich,

it looks like the same problem, you have some infinite loop in your fonts. No idea how that can happen, possibly recursive symlink in your font directory?

Cheers.
Simon

> On Jun 7, 2022, at 2:12 AM, Richard M. Heiberger <rmh using temple.edu> wrote:
> 
> i think i will bring it to apple this afternoon.
> what font does the default graphics device use?
> 
> this morning the time is up to 4:26.17 and the bar is still at 1%.
> 
> From: Ken Beath <ken using kjbeath.com.au>
> Sent: Monday, June 6, 2022 1:44:58 AM
> To: Richard M. Heiberger <rmh using temple.edu>
> Cc: Simon Urbanek <simon.urbanek using R-project.org>; r-sig-mac R <r-sig-mac using r-project.org>
> Subject: [External] Re: [R-SIG-Mac] [External] Xquartz started crashing today
>  
> Less than 30 seconds on my iMac, so something is very wrong with your fonts or file system.
> 
> Ken
> 
>> On 6 Jun 2022, at 2:34 pm, Richard M. Heiberger <rmh using temple.edu> wrote:
>> 
>> I am in the middle of validating fonts. The machine has been running for about 12 hours, the Activity Monitor CPU
>> time for the Font Book app is currently at 2:35.15. It keeps going up but very slowly.
>> The progress bar at the bottom of the Font Validation window has been stuck at about 1% from when it started and hasn't moved.
>> How long is this task supposed to take?
>> 
>>> On Jun 04, 2022, at 00:49, Richard M. Heiberger <rmh using temple.edu> wrote:
>>> 
>>> Simon,
>>> 
>>> Thank you for reading this.
>>> 
>>> I sent what Apple gave me. I had not previously tried reading one of these.
>>> So should I be so lucky in the future, then all you need is everything between
>>> Process: R [
>>> and the next occurence of
>>> Process: 
>>> ?
>>> 
>>> and maybe also the up front stuff before the Process: information.
>>> 
>>> I already rebooted, installed a new R, and a new Xquartz. Those didn't help.
>>> Reinstalling R is probably irrelevant because the problem occurred first in 4.1-arm64,
>>> which is why I upgraded to 4.2-arm64. And it was still there.
>>> 
>>> This suggests that the problem is with the Fonts. I have never touched them (on purpose).
>>> I will learn a little in the next frew days and see what can be done with validation.
>>> I will let you know. But what made the fonts (if that is indeed the problem) go invalid.
>>> I can't think of anything I did that could be relevant.
>>> 
>>> Rich
>>> 
>>> 
>>>> On Jun 03, 2022, at 23:32, Simon Urbanek <simon.urbanek using R-project.org> wrote:
>>>> 
>>>> Rich,
>>>> 
>>>> thanks. You sent a log of all processes on your machine, just the R report would have been fine (which is only 18k).
>>>> 
>>>> The hang occurs in ATSFontFindFromName() where the system is looking for fonts, so you could try: a) reboot he machine, b) run Font Book (in Applications), c) select all fonts (<Cmd><A>) d) in the menu select File -> Validate Fonts e) select any invalid fonts and remove them f) reboot
>>>> 
>>>> If the problem persists try re-installing the R 4.2.0 release if it makes any difference.
>>>> 
>>>> Cheers,
>>>> Simon
>>>> 
>>>> 
>>>>> On Jun 4, 2022, at 3:10 AM, Richard M. Heiberger <rmh using temple.edu> wrote:
>>>>> 
>>>>> cover letter for crash report, that also got stopped for being part of a too large email,
>>>>> 
>>>>> 
>>>>> I am doing nothing different that I know of.
>>>>> I start R within emacs using ESS with M-x R
>>>>> 
>>>>> 
>>>>> R version 4.2.0 Patched (2022-06-02 r82444) -- "Vigorous Calisthenics"
>>>>> Copyright (C) 2022 The R Foundation for Statistical Computing
>>>>> Platform: aarch64-apple-darwin20 (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.
>>>>> 
>>>>>> setwd('/Users/rmh/Rwd2/')
>>>>>> plot(1:10)
>>>>>> C-c C-c
>>>>> 
>>>>> 
>>>>> 
>>>>> ## it just sits there, completely frozen and ignores C-c C-c
>>>>> ## then I Force Quit it from the Activity Monitor
>>>>> Process R terminated: 15 at Thu Jun 2 22:39:39 2022
>>>>> 
>>>>> 
>>>>> Do you want the crash report that the Mac offers to send to Apple?
>>>>> 
>>>>> ---
>>>>> I just finished updating all my packages.
>>>>> So now the crash generation and report.
>>>>> I entered
>>>>> 
>>>>> plot(1:10)
>>>>> 
>>>>> The rotating beachball appeared. No graph, C-c C-c has no effect..
>>>>> 
>>>>> Force Quit from Activity Monitor and CrashReport attached:
>>>>> 
>>>>> 
>>>>> Just for fun, I started R.app and entered plot(1:10)
>>>>> Same freeze and I Force Quit it again.
>>>>> I am not bothering with the Crash Report unless you tell me you need it too.
>>>>> 
>>>>> Rich
>>>>> 
>>>>>> On Jun 02, 2022, at 23:02, Simon Urbanek <simon.urbanek using r-project.org> wrote:
>>>>>> 
>>>>>> Regular R does not use X11 by default, so what exactly are you doing? You'll have to provide more details, the exact way you run R, code to reproduce and where it hangs, ideally with a crash report (which macOS creates on hangs as well).
>>>>>> 
>>>>>> Cheers,
>>>>>> Simon
>>>>>> 
>>>>>> 
>>>>>>> On 3/06/2022, at 2:51 PM, Richard M. Heiberger <rmh using temple.edu> wrote:
>>>>>>> 
>>>>>>> it makes R unresponsive according to the activity monitor.
>>>>>>> The only repair I have found is to ForceQuit R from the Activity Monitor, and start fresh R session.
>>>>>>> I downloaded a fresh copy of XQuartz-2.8.1.dmg and have the same negative results.
>>>>>>> I downloaded a fresh R from https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmac.r-project.org%2F&data=05%7C01%7Crmh%40temple.edu%7C8cd7ad54610b4d9f187b08da45e59730%7C716e81efb52244738e3110bd02ccf6e5%7C0%7C0%7C637899149713117770%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=0ynIZnv7P%2FxdWyHGUZlx%2FfMFw%2F%2Bc6KdiOaYS1kTGSGM%3D&reserved=0
>>>>>>> R version 4.2.0 Patched (2022-06-02 r82444) -- "Vigorous Calisthenics"
>>>>>>> Copyright (C) 2022 The R Foundation for Statistical Computing
>>>>>>> Platform: aarch64-apple-darwin20 (64-bit)
>>>>>>> 
>>>>>>>> version
>>>>>>> _ 
>>>>>>> platform aarch64-apple-darwin20 
>>>>>>> arch aarch64 
>>>>>>> os darwin20 
>>>>>>> system aarch64, darwin20 
>>>>>>> status Patched 
>>>>>>> major 4 
>>>>>>> minor 2.0 
>>>>>>> year 2022 
>>>>>>> month 06 
>>>>>>> day 02 
>>>>>>> svn rev 82444 
>>>>>>> language R 
>>>>>>> version.string R version 4.2.0 Patched (2022-06-02 r82444)
>>>>>>> nickname Vigorous Calisthenics 
>>>>>>>> 
>>>>>>> 
>>>>>>> I have MacOS 12.3 Monterey
>>>>>>> MacBook Air (M1,2020)
>>>>>>> Chip Apple M1
>>>>>>> memory 16GB
>>>>>>> 
>>>>>>> The pdf() device works so I I can work, but casually plotting to the screen without explicitly
>>>>>>> opening pdf() is not possible.
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