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://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-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://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-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://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.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://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 <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://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> R-SIG-Mac mailing list >>>>>>>> R-SIG-Mac@r-project.org >>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>> >>> > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
