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

Bob Rudis bob @end|ng |rom rud@|@
Mon May 4 14:38:49 CEST 2020 

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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> >>>>>
> >>>>> _______________________________________________
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> >
>

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