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

Mon May 4 14:08:41 CEST 2020

I'll try to scrounge time today (but def have some Tue) to setup fresh
Catalina VM with 4GB memory and see if I can reproduce there and
capture some more logs.

On Mon, May 4, 2020 at 7:29 AM Hiroshi Hakoyama
<hiroshi-hakoyama using nagano.ac.jp> wrote:
>
> 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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