[R-SIG-Mac] R.app GUI 1.71 (7827) crashes on Catalina
Brandon Hurr
br@ndon@hurr @end|ng |rom gm@||@com
Thu May 21 00:58:45 CEST 2020
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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