[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 22:17:36 CEST 2020 

Well, when I retry on 'clean' system, R.app runs fine even if the
*.plist file is there. 

J.


On 5/23/20 13:14, John Helly wrote:
> 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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