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 <b...@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-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
