I jumped the gun on this. I rebooted and the pinwheel of death is back when I open a second file in the editor.
Bummer. On Sat, May 23, 2020 at 11:31 AM Brandon Hurr <brandon.h...@gmail.com> wrote: > 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
