Well, when I retry on 'clean' system, R.app runs fine even if the *.plist file is there.
J. On 5/23/20 13:14, John Helly wrote: > 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
