Kevin had a suggestion that I toggle disk access in the Security settings, building on Bob's original comment to give R full disk access. As soon as I turned it off, it no longer crashed upon load. I turned it back on and it didn't crash then either. I have been testing for a few days now and I can no longer cause it to crash like it used to.
Hiroshi, I suggest trying that as well and see if it solves your problem too. Thanks for helping dig on this issue. Brandon On Wed, May 20, 2020 at 4:24 PM Simon Urbanek <simon.urba...@r-project.org> wrote: > Unfortunately I cannot reproduce it. When opening a file in one of the > protected folders with R 4.0.0 release on Catalina I get '"R" would like to > access files in your Documents folder' - which you have to agree to (one of > those Catalina annoyances). It only asks once - we don't explicitly control > it, so I wonder if there is some interaction … > > Cheers, > Simon > > > > > On May 21, 2020, at 10:58 AM, Brandon Hurr <brandon.h...@gmail.com> > wrote: > > > > 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 > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
