Aloha. If I delete:
/Users/<user>/Library/Preferences/org.R-project.R.plist then R.app will work. If that file is present it will not open anything. Something is wrong with that file. I assume on the clean Catalina system I tested on, it worked because that file did not yet exist. I will confirm. J. On 5/23/20 13:03, John Helly wrote: > 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
