[R-SIG-Mac] R.app GUI 1.71 (7827) crashes on Catalina

John Helly he||yj @end|ng |rom uc@d@edu
Sat May 23 21:08:15 CEST 2020 

Aloha.

I have the same problem.  Have deleted all the .R* files I can find and
still no joy.  FWIW, RStudio works fine.

I assume R.app was tested before it was released and wonder if it was
tested on a brand-new Catalina or an upgrade (or both)?   I have a few
of these systems and could test on a 'clean' install if that would help.

J.

On 5/23/20 11:44, Brandon Hurr wrote:
> I jumped the gun on this. I rebooted and the pinwheel of death is back when
> I open a second file in the editor.
>
> Bummer.
>
> On Sat, May 23, 2020 at 11:31 AM Brandon Hurr <brandon.hurr using gmail.com>
> wrote:
>
>> Kevin had a suggestion that I toggle disk access in the Security settings,
>> building on Bob's original comment to give R full disk access. As soon as I
>> turned it off, it no longer crashed upon load. I turned it back on and it
>> didn't crash then either. I have been testing for a few days now and I can
>> no longer cause it to crash like it used to.
>>
>> Hiroshi, I suggest trying that as well and see if it solves your problem
>> too.
>>
>> Thanks for helping dig on this issue.
>> Brandon
>>
>> On Wed, May 20, 2020 at 4:24 PM Simon Urbanek <simon.urbanek using r-project.org>
>> wrote:
>>
>>> Unfortunately I cannot reproduce it. When opening a file in one of the
>>> protected folders with R 4.0.0 release on Catalina I get '"R" would like to
>>> access files in your Documents folder' - which you have to agree to (one of
>>> those Catalina annoyances). It only asks once - we don't explicitly control
>>> it, so I wonder if there is some interaction …
>>>
>>> Cheers,
>>> Simon
>>>
>>>
>>>
>>>> On May 21, 2020, at 10:58 AM, Brandon Hurr <brandon.hurr using gmail.com>
>>> wrote:
>>>> I just want to add that this is still happening. The size of the
>>>> script seems to be irrelevant (10s of lines). If you double click
>>>> another .R file for R GUI to load it gives the beachball of death and
>>>> R maxes out 1 of my cores. Are there specific logs or files that would
>>>> be helpful beyond what has been supplied?
>>>>
>>>> Thanks,
>>>> Brandon
>>>>
>>>> On Mon, May 4, 2020 at 5:39 AM Bob Rudis <bob using rud.is> wrote:
>>>>> Aye, I should have noted that Apple's `tccd` and entire TCC (privacy)
>>>>> subsystem is super buggy/noisy. Enough of them that there are a fw
>>>>> third-party apps like Taccy
>>>>> (
>>> https://urldefense.com/v3/__https://eclecticlight.co/taccy-signet-precize-alifix-utiutility-alisma/__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjTzjfoVM$ )
>>>>> to help privacy-perms issues. The GUI code does not try to do things
>>>>> `tccd` would balk at, and this particular sandbox error shows up in
>>>>> many general apps/FOSS projects outside of R GUI.
>>>>>
>>>>> On Mon, May 4, 2020 at 8:13 AM Hiroshi Hakoyama
>>>>> <hiroshi-hakoyama using nagano.ac.jp> wrote:
>>>>>> The sandbox error also happened for test2.R that can open without
>>> trouble.
>>>>>> So, this might not be the critical error.
>>>>>>
>>>>>> I uploaded the two devices logs for test.R and test2.R:
>>>>>>
>>>>>> https://urldefense.com/v3/__https://hako.space/R/devices_log_for_test_R.txt__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTj-SyhUy8$ 
>>>>>> https://urldefense.com/v3/__https://hako.space/R/devices_log_for_test2_R.txt__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjWtZz14g$ 
>>>>>>
>>>>>> Best regards,
>>>>>>
>>>>>> Hiroshi
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>> 2020/05/04 20:29、Hiroshi Hakoyama <hiroshi-hakoyama using nagano.ac.jp
>>>> のメール:
>>>>>>> Thank you for responses.
>>>>>>>
>>>>>>> I installed the debug build R.app GUI 1.71 (7834) to MacBook Air
>>> (2012, 4G RAM, Catalina 10.15.4), and double-clicked test.R. The result is
>>> the same GUI hang. The following is a part of the device log:
>>>>>>> ...
>>>>>>> default       19:56:06.123133+0900    R        - 1 documents to open
>>>>>>> default       19:56:06.123188+0900    R        -
>>> application:openFile:/Users/hako/Desktop/test.R called
>>>>>>> default       19:56:06.123316+0900    R        - intial start,
>>> changing wd to pathname whic is /Users/hako/Desktop/
>>>>>>> error 19:56:06.126663+0900    tccd    {ID: com.apple.sandboxd,
>>> PID[155], auid: 0, euid: 0, binary path: '/usr/libexec/sandboxd'} attempted
>>> to call TCCAccessRequest without the
>>> com.apple.private.tcc.manager.check-by-audit-token entitlement
>>>>>>> default       19:56:06.127340+0900    tccd    PID[155] is checking
>>> access for target PID[655]
>>>>>>> default       19:56:06.136847+0900    tccd    -[TCCDAccessIdentity
>>> staticCode]: static code for: identifier org.R-project.R, type: 0:
>>> 0x7fa62ad38b10 at /Applications/R.app
>>>>>>> ...
>>>>>>>
>>>>>>> The error line seems to be similar with Brandon's cases.
>>>>>>>
>>>>>>>
>>>>>>> Best regards,
>>>>>>>
>>>>>>>
>>>>>>> Hiroshi
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> 2020/05/02 11:18、Brandon Hurr <brandon.hurr using gmail.com>のメール:
>>>>>>>>
>>>>>>>> I have a mac mini as well that does not show this crash. It's much
>>>>>>>> beefier (6-core i7, 32 GB RAM probably not relevant).
>>>>>>>> Here is the same boot up log with the same file and it does not
>>> crash R.
>>>>>>>>
>>> https://urldefense.com/v3/__https://gist.github.com/bhive01/2a48fa3e6fd70ae1b974184ad7b947ba*file-r-gui_pid4422_working_console-log__;Iw!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjZZHVqhs$ 
>>>>>>>> I look at the transition where the two differ and the crash happens
>>>>>>>> and the one that works is much shorter. At line 319 in the
>>> non-working
>>>>>>>> MBA (PID 889) it "makes presenter" and then stops. Making presenter
>>>>>>>> doesn't happen until line 4261 in the working file. Lots of parsing
>>> of
>>>>>>>> the file is missing (4000 lines of it).
>>>>>>>>
>>>>>>>> B
>>>>>>>>
>>>>>>>> On Fri, May 1, 2020 at 6:48 PM Brandon Hurr <brandon.hurr using gmail.com>
>>> wrote:
>>>>>>>>> Thanks Bob.
>>>>>>>>>
>>>>>>>>> I did this and it did not fix it sadly.
>>>>>>>>> I downloaded the Debug version of R-GUI and captured the following
>>>>>>>>> after clicking on the same file (which did cause it to crash again)
>>>>>>>>> Here is the console log for the R PID (889 in this instance) from
>>>>>>>>> loading R to then clicking to load the same file (which froze my
>>>>>>>>> system again):
>>>>>>>>> https://urldefense.com/v3/__https://gist.github.com/bhive01/5efa02237085c7a3ccf6d137e04f7c45__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjrmA89co$ 
>>>>>>>>> Here is the full Apple Crash Log that came up after I force quit R:
>>>>>>>>> https://urldefense.com/v3/__https://gist.github.com/bhive01/0eeb32d0a666f875e83440268b69aefd__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjfzfw5XY$ 
>>>>>>>>>
>>>>>>>>> I hope this is helpful. Please let me know if I need to dig more
>>> and
>>>>>>>>> recommendations for doing so.
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> B
>>>>>>>>>
>>>>>>>>> On Fri, May 1, 2020 at 5:54 PM Bob Rudis <bob using rud.is> wrote:
>>>>>>>>>> Suggestion: try adding R.app to "Full Disk Access" in the Privacy
>>> tab
>>>>>>>>>> under Security & Privacy system preferences.
>>>>>>>>>>
>>>>>>>>>> I'm not experiencing these issues (just now when I tried it; I
>>>>>>>>>> generally don't use R.app)
>>>>>>>>>>
>>>>>>>>>> On Fri, May 1, 2020 at 4:54 PM Brandon Hurr <
>>> brandon.hurr using gmail.com> wrote:
>>>>>>>>>>> I'm going to add to the pile on this one. It's hard to nail down
>>>>>>>>>>> though. I was able to load Hiroshi's test.R script after loading
>>> up
>>>>>>>>>>> R-GUI 7827 and just now 7832. I loaded it from multiple
>>> directories by
>>>>>>>>>>> clicking on it.
>>>>>>>>>>> That said, I've been having many issues locking up R-GUI on my
>>> 2019
>>>>>>>>>>> MBAir since upgrading to R4.0.0. I can click and load R-GUI with
>>> a
>>>>>>>>>>> script file, but if I want to load another script it gives me the
>>>>>>>>>>> colored pinwheel of death. Sometimes it will load up R-GUI, but
>>> then
>>>>>>>>>>> pinwheel of death on loading a lengthy script. I'm not sure the
>>> length
>>>>>>>>>>> is the issue.
>>>>>>>>>>>
>>>>>>>>>>> I played around with the console a bit and noticed these
>>> messages pop
>>>>>>>>>>> up when it locks up R:
>>>>>>>>>>> error    13:49:54.173449-0700    kernel    Sandbox: garcon(763)
>>>>>>>>>>> deny(1) file-read-xattr /Users/brandonhurr/Dropbox (BioLumic
>>> Ltd)/Data
>>>>>>>>>>> standardisation/Database Converts/Conversion script DEV.R
>>>>>>>>>>> error    13:49:54.243397-0700    kernel    Sandbox: garcon(763)
>>>>>>>>>>> deny(1) file-read-xattr /Users/brandonhurr/Dropbox (BioLumic
>>> Ltd)/Data
>>>>>>>>>>> standardisation/Database Converts
>>>>>>>>>>> error    13:49:54.312989-0700    kernel    Sandbox: garcon(763)
>>>>>>>>>>> deny(1) file-read-xattr /Users/brandonhurr/Dropbox (BioLumic
>>> Ltd)/Data
>>>>>>>>>>> standardisation
>>>>>>>>>>> error    13:49:54.344345-0700    kernel    Sandbox: garcon(763)
>>>>>>>>>>> deny(1) file-read-xattr /Users/brandonhurr/Dropbox (BioLumic Ltd)
>>>>>>>>>>>
>>>>>>>>>>> A rough guess here is that the sandboxing isn't working right
>>> (or is?)
>>>>>>>>>>> and is blocking access of R-GUI to the file which then locks up
>>>>>>>>>>> because it's waiting for data?
>>>>>>>>>>>
>>>>>>>>>>> Anyone else seeing this behavior and have a better idea how to
>>> pin it down?
>>>>>>>>>>> Thanks,
>>>>>>>>>>> B
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Thu, Apr 30, 2020 at 6:07 AM Hiroshi Hakoyama
>>>>>>>>>>> <hiroshi-hakoyama using nagano.ac.jp> wrote:
>>>>>>>>>>>> Dear All,
>>>>>>>>>>>>
>>>>>>>>>>>> Environment:
>>>>>>>>>>>> R version 4.0.0 (2020-04-24) -- "Arbor Day"
>>>>>>>>>>>> [R.app GUI 1.71 (7827) x86_64-apple-darwin17.0]
>>>>>>>>>>>> macOS: Mojave and Catalina
>>>>>>>>>>>> Removed file for the test: .Rapp.history
>>>>>>>>>>>>
>>>>>>>>>>>> Description:
>>>>>>>>>>>> R.app crashes when a large file (e.g., test.R) is
>>> double-clicked on Mojave and Catalina. The crash does not occur on High
>>> Sierra. Small source files (e.g., test2.R) do not cause the crash on Mojave
>>> and Catalina.
>>>>>>>>>>>> How-To-Repeat:
>>>>>>>>>>>> Double-click test.R (or open test.R using R.app) on Catalina or
>>> Mojave.
>>>>>>>>>>>> Fix:
>>>>>>>>>>>> unknown
>>>>>>>>>>>>
>>>>>>>>>>>> Crash Report is too large to paste to the email.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Best regards,
>>>>>>>>>>>>
>>>>>>>>>>>> Hiroshi Hakoyama
>>>>>>>>>>>> Nagano University
>>>>>>>>>>>>
>>>>>>>>>>>> test.R
>>>>>>>>>>>>
>>> ###############################################################################
>>> ###############################################################################
>>> ###############################################################################
>>> ###############################################################################
>>> ###############################################################################
>>> ###############################################################################
>>> ###############################################################################
>>> ###############################################################################
>>> ###############################################################################
>>> ###############################################################################
>>> ###############################################################################
>>> ###############################################################################
>>> ###############################################################################
>>> ###############################################################################
>>> ###############################################################################
>>> ###############################################################################
>>>>>>>>>>>> x <- rnorm(100000)
>>>>>>>>>>>> y <- rnorm(100000)
>>>>>>>>>>>> hist(x)
>>>>>>>>>>>> hist(y)
>>>>>>>>>>>>
>>>>>>>>>>>> test2.R
>>>>>>>>>>>> x <- rnorm(100000)
>>>>>>>>>>>> y <- rnorm(100000)
>>>>>>>>>>>> hist(x)
>>>>>>>>>>>> hist(y)
>>>>>>>>>>>>
>>>>>>>>>>>> system.log
>>>>>>>>>>>> Apr 30 20:54:40 ec7 R[1147]: assertion failed: 19E287:
>>> libxpc.dylib + 92807 [32B0E31E-9DA3-328B-A962-BC9591B93537]: 0x89
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-- 
John Helly, University of California, San Diego / San Diego Supercomputer Center / Scripps Institution of Oceanography / 760 840 8660 mobile / http://www.sdsc.edu/~hellyj
ORCID ID: orcid.org/0000-0002-3779-0603

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