[R-SIG-Mac] R.app GUI 1.71 (7827) crashes on Catalina

Mon May 4 13:29:01 CEST 2020

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 using 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.hurr using 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 using 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 using 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 using 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 using r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>> 
>>>> _______________________________________________
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