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

Simon Urbanek @|mon@urb@nek @end|ng |rom R-project@org
Thu May 21 01:17:39 CEST 2020 

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://eclecticlight.co/taccy-signet-precize-alifix-utiutility-alisma/)
>> 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://hako.space/R/devices_log_for_test_R.txt
>>> https://hako.space/R/devices_log_for_test2_R.txt
>>> 
>>> 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://gist.github.com/bhive01/2a48fa3e6fd70ae1b974184ad7b947ba#file-r-gui_pid4422_working_console-log
>>>>> 
>>>>> 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://gist.github.com/bhive01/5efa02237085c7a3ccf6d137e04f7c45
>>>>>> Here is the full Apple Crash Log that came up after I force quit R:
>>>>>> https://gist.github.com/bhive01/0eeb32d0a666f875e83440268b69aefd
>>>>>> 
>>>>>> 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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>>>>>>>>> R-SIG-Mac using r-project.org
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>>>>>>>> 
>>>>>>>> _______________________________________________
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>>> 
> 
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