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

Brandon Hurr br@ndon@hurr @end|ng |rom gm@||@com
Sat May 23 20:44:43 CEST 2020 

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://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
>> >>>>>>>>>
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>> >>>>>>>>> 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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>> >>>
>> >
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