Aloha. I have the same problem. Have deleted all the .R* files I can find and still no joy. FWIW, RStudio works fine.
I assume R.app was tested before it was released and wonder if it was tested on a brand-new Catalina or an upgrade (or both)? I have a few of these systems and could test on a 'clean' install if that would help. J. On 5/23/20 11:44, Brandon Hurr wrote: > 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://urldefense.com/v3/__https://eclecticlight.co/taccy-signet-precize-alifix-utiutility-alisma/__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjTzjfoVM$ >>> ) >>>>> 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://urldefense.com/v3/__https://hako.space/R/devices_log_for_test_R.txt__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTj-SyhUy8$ >>>>>> >>>>>> https://urldefense.com/v3/__https://hako.space/R/devices_log_for_test2_R.txt__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjWtZz14g$ >>>>>> >>>>>> >>>>>> 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://urldefense.com/v3/__https://gist.github.com/bhive01/2a48fa3e6fd70ae1b974184ad7b947ba*file-r-gui_pid4422_working_console-log__;Iw!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjZZHVqhs$ >>> >>>>>>>> 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://urldefense.com/v3/__https://gist.github.com/bhive01/5efa02237085c7a3ccf6d137e04f7c45__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjrmA89co$ >>>>>>>>> >>>>>>>>> Here is the full Apple Crash Log that came up after I force quit R: >>>>>>>>> https://urldefense.com/v3/__https://gist.github.com/bhive01/0eeb32d0a666f875e83440268b69aefd__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjfzfw5XY$ >>>>>>>>> >>>>>>>>> >>>>>>>>> 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://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ >>>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> R-SIG-Mac mailing list >>>>>>>>>>> R-SIG-Mac@r-project.org >>>>>>>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ >>>>>>>>>>> >>>> _______________________________________________ >>>> R-SIG-Mac mailing list >>>> R-SIG-Mac@r-project.org >>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ >>>> >>> _______________________________________________ >>> R-SIG-Mac mailing list >>> R-SIG-Mac@r-project.org >>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ >>> >>> > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ > -- John Helly, University of California, San Diego / San Diego Supercomputer Center / Scripps Institution of Oceanography / 760 840 8660 mobile / http://www.sdsc.edu/~hellyj ORCID ID: orcid.org/0000-0002-3779-0603 _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
