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-hakoy...@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-hakoy...@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.h...@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.h...@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 <b...@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.h...@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-hakoy...@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 > >>>>>> _______________________________________________ > >>>>>> R-SIG-Mac mailing list > >>>>>> R-SIG-Mac@r-project.org > >>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > >>>>> > >>>>> _______________________________________________ > >>>>> R-SIG-Mac mailing list > >>>>> R-SIG-Mac@r-project.org > >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
