[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 21:26:28 CEST 2020 

Aloha.

Just tested R.app on a clean Catalina system and it opens the same file
that fails on an upgraded system.  So next test should be after a
complete uninstall of R.app (maybe R itself as well?).  How does one do
a complete uninstall?

J.

On 5/23/20 12:08, John Helly wrote:
> 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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