Aloha. Just tested R.app on a clean Catalina system and it opens the same file that fails on an upgraded system. So next test should be after a complete uninstall of R.app (maybe R itself as well?). How does one do a complete uninstall?
J. On 5/23/20 12:08, John Helly wrote: > 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