[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 22:03:04 CEST 2020 

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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