[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 20:31:27 CEST 2020 

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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> >>>>>>>>>
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> >>>>>>>>>
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> >>>>>>>>>
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> >>>>>>>>>
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> >>>>>>>>>
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> >>>>>>>>>
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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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