Aloha. If I setwd, the R.app works. It will not work with whatever default it is using.
J. On 5/23/20 12:26, John Helly wrote: > 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