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

John Helly he||yj @end|ng |rom uc@d@edu
Sat May 23 22:14:00 CEST 2020 

Aloha.

If I delete:

/Users/<user>/Library/Preferences/org.R-project.R.plist

then R.app will work.  If that file is present it will not open
anything.  Something is wrong with that file.  I assume on the clean
Catalina system I tested on, it worked because that file did not yet
exist.  I will confirm.

J.




On 5/23/20 13:03, John Helly wrote:
> Aloha.
>
> If I setwd, the R.app works.  It will not work with whatever default it
> is using.
>
> J.
>
> On 5/23/20 12:26, John Helly wrote:
>> 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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