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

Hiroshi Hakoyama h|ro@h|-h@koy@m@ @end|ng |rom n@g@no@@c@jp
Mon May 4 14:13:14 CEST 2020 

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 using 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.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
>>>>> 
>>>>> _______________________________________________
>>>>> 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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