R.app GUI 1.71 (7827) crashes on Catalina
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 <bob at 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://eclecticlight.co/taccy-signet-precize-alifix-utiutility-alisma/) 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-hakoyama at 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://hako.space/R/devices_log_for_test_R.txt https://hako.space/R/devices_log_for_test2_R.txt Best regards, Hiroshi
2020/05/04 20:29?Hiroshi Hakoyama <hiroshi-hakoyama at nagano.ac.jp>????:
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.hurr at gmail.com>????: 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://gist.github.com/bhive01/2a48fa3e6fd70ae1b974184ad7b947ba#file-r-gui_pid4422_working_console-log 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.hurr at 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://gist.github.com/bhive01/5efa02237085c7a3ccf6d137e04f7c45 Here is the full Apple Crash Log that came up after I force quit R: https://gist.github.com/bhive01/0eeb32d0a666f875e83440268b69aefd 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 <bob at 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.hurr at 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-hakoyama at 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 at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac