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

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

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

Brandon Hurr
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
<[hidden email]> 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
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

Bob Rudis
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 <[hidden email]> 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
> <[hidden email]> 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
> > [hidden email]
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> _______________________________________________
> R-SIG-Mac mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

Bob Rudis
Also, can you try running with the Debug build and poke around for
contextual errors if you still get errors?

On Fri, May 1, 2020 at 8:54 PM Bob Rudis <[hidden email]> 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 <[hidden email]> 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
> > <[hidden email]> 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
> > > [hidden email]
> > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > [hidden email]
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

Brandon Hurr
In reply to this post by Bob Rudis
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 <[hidden email]> 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 <[hidden email]> 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
> > <[hidden email]> 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
> > > [hidden email]
> > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > [hidden email]
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac

_______________________________________________
R-SIG-Mac mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
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Re: [R-SIG-Mac] R.app GUI 1.71 (7827) crashes on Catalina

Brandon Hurr
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> > > <[hidden email]> 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
> > > > [hidden email]
> > > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> > >
> > > _______________________________________________
> > > R-SIG-Mac mailing list
> > > [hidden email]
> > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

Hiroshi Hakoyama
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 <[hidden email]>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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
>>>> <[hidden email]> 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
>>>>> [hidden email]
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
>>>> [hidden email]
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

Bob Rudis
I'll try to scrounge time today (but def have some Tue) to setup fresh
Catalina VM with 4GB memory and see if I can reproduce there and
capture some more logs.

On Mon, May 4, 2020 at 7:29 AM Hiroshi Hakoyama
<[hidden email]> wrote:

>
> 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 <[hidden email]>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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> >>>> <[hidden email]> 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
> >>>>> [hidden email]
> >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>>>
> >>>> _______________________________________________
> >>>> R-SIG-Mac mailing list
> >>>> [hidden email]
> >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>

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

Hiroshi Hakoyama
In reply to this post by Hiroshi Hakoyama
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 <[hidden email]>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 <[hidden email]>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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
>>>>> <[hidden email]> 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
>>>>>> [hidden email]
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>
>>>>> _______________________________________________
>>>>> R-SIG-Mac mailing list
>>>>> [hidden email]
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>

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

Bob Rudis
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
<[hidden email]> 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 <[hidden email]>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 <[hidden email]>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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> >>>>> <[hidden email]> 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
> >>>>>> [hidden email]
> >>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>>>>
> >>>>> _______________________________________________
> >>>>> R-SIG-Mac mailing list
> >>>>> [hidden email]
> >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
>

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

Brandon Hurr
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 <[hidden email]> 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
> <[hidden email]> 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 <[hidden email]>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 <[hidden email]>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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
> > >>>>> <[hidden email]> 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
> > >>>>>> [hidden email]
> > >>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> > >>>>>
> > >>>>> _______________________________________________
> > >>>>> R-SIG-Mac mailing list
> > >>>>> [hidden email]
> > >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> > >
> >

_______________________________________________
R-SIG-Mac mailing list
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Re: [R-SIG-Mac] R.app GUI 1.71 (7827) crashes on Catalina

Simon Urbanek
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 <[hidden email]> 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 <[hidden email]> 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
>> <[hidden email]> 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 <[hidden email]>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 <[hidden email]>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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
>>>>>>>> <[hidden email]> 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
>>>>>>>>> [hidden email]
>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> R-SIG-Mac mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>
>>>
>
> _______________________________________________
> R-SIG-Mac mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

Brandon Hurr
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 <[hidden email]>
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 <[hidden email]>
> 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 <[hidden email]> 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
> >> <[hidden email]> 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 <[hidden email]
> >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 <[hidden email]>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 <[hidden email]>
> 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 <[hidden email]> 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 <
> [hidden email]> 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
> >>>>>>>> <[hidden email]> 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
> >>>>>>>>> [hidden email]
> >>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>>>>>>>
> >>>>>>>> _______________________________________________
> >>>>>>>> R-SIG-Mac mailing list
> >>>>>>>> [hidden email]
> >>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>>>
> >>>
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > [hidden email]
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> _______________________________________________
> R-SIG-Mac mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>

        [[alternative HTML version deleted]]

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

Brandon Hurr
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 <[hidden email]>
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 <[hidden email]>
> 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 <[hidden email]>
>> 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 <[hidden email]> 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
>> >> <[hidden email]> 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 <[hidden email]
>> >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 <[hidden email]>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 <[hidden email]>
>> 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 <[hidden email]> 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 <
>> [hidden email]> 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
>> >>>>>>>> <[hidden email]> 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
>> >>>>>>>>> [hidden email]
>> >>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> >>>>>>>>
>> >>>>>>>> _______________________________________________
>> >>>>>>>> R-SIG-Mac mailing list
>> >>>>>>>> [hidden email]
>> >>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> >>>>
>> >>>
>> >
>> > _______________________________________________
>> > R-SIG-Mac mailing list
>> > [hidden email]
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>

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

R-SIG-Mac mailing list
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 <[hidden email]>
> 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 <[hidden email]>
>> 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 <[hidden email]>
>>> 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 <[hidden email]> 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
>>>>> <[hidden email]> 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 <[hidden email]
>>>> 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 <[hidden email]>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 <[hidden email]>
>>> 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 <[hidden email]> 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 <
>>> [hidden email]> 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
>>>>>>>>>>> <[hidden email]> 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
>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ 
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> R-SIG-Mac mailing list
>>>>>>>>>>> [hidden email]
>>>>>>>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ 
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
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>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> [hidden email]
>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ 
>>>
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--
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

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

R-SIG-Mac mailing list
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 <[hidden email]>
>> 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 <[hidden email]>
>>> 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 <[hidden email]>
>>>> 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 <[hidden email]> 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
>>>>>> <[hidden email]> 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 <[hidden email]
>>>>> 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 <[hidden email]>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 <[hidden email]>
>>>> 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 <[hidden email]> 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 <
>>>> [hidden email]> 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
>>>>>>>>>>>> <[hidden email]> 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
>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ 
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> R-SIG-Mac mailing list
>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ 
>>>>> _______________________________________________
>>>>> R-SIG-Mac mailing list
>>>>> [hidden email]
>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ 
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
>>>> [hidden email]
>>>> 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
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>> 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

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

R-SIG-Mac mailing list
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 <[hidden email]>
>>> 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 <[hidden email]>
>>>> 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 <[hidden email]>
>>>>> 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 <[hidden email]> 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
>>>>>>> <[hidden email]> 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 <[hidden email]
>>>>>> 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 <[hidden email]>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 <[hidden email]>
>>>>> 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 <[hidden email]> 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 <
>>>>> [hidden email]> 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
>>>>>>>>>>>>> <[hidden email]> 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
>>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ 
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> R-SIG-Mac mailing list
>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ 
>>>>>> _______________________________________________
>>>>>> R-SIG-Mac mailing list
>>>>>> [hidden email]
>>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ 
>>>>> _______________________________________________
>>>>> R-SIG-Mac mailing list
>>>>> [hidden email]
>>>>> 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
>>> [hidden email]
>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ 

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

R-SIG-Mac mailing list
Sorry. Take it back.  It started in Xcode, not R.app.
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 <[hidden email]>
>>>> 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 <[hidden email]>
>>>>> 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 <[hidden email]>
>>>>>> 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 <[hidden email]> 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
>>>>>>>> <[hidden email]> 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 <[hidden email]
>>>>>>> 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 <[hidden email]>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 <[hidden email]>
>>>>>> 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 <[hidden email]> 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 <
>>>>>> [hidden email]> 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
>>>>>>>>>>>>>> <[hidden email]> 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
>>>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ 
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> R-SIG-Mac mailing list
>>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ 
>>>>>>> _______________________________________________
>>>>>>> R-SIG-Mac mailing list
>>>>>>> [hidden email]
>>>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ 
>>>>>> _______________________________________________
>>>>>> R-SIG-Mac mailing list
>>>>>> [hidden email]
>>>>>> 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
>>>> [hidden email]
>>>> 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

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

R-SIG-Mac mailing list
In reply to this post by R-SIG-Mac mailing list
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 <[hidden email]>
>>>> 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 <[hidden email]>
>>>>> 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 <[hidden email]>
>>>>>> 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 <[hidden email]> 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
>>>>>>>> <[hidden email]> 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 <[hidden email]
>>>>>>> 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 <[hidden email]>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 <[hidden email]>
>>>>>> 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 <[hidden email]> 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 <
>>>>>> [hidden email]> 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
>>>>>>>>>>>>>> <[hidden email]> 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
>>>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ 
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> R-SIG-Mac mailing list
>>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ 
>>>>>>> _______________________________________________
>>>>>>> R-SIG-Mac mailing list
>>>>>>> [hidden email]
>>>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ 
>>>>>> _______________________________________________
>>>>>> R-SIG-Mac mailing list
>>>>>> [hidden email]
>>>>>> 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
>>>> [hidden email]
>>>> 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

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

R-SIG-Mac mailing list
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 <[hidden email]>
>>>>> 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 <[hidden email]>
>>>>>> 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 <[hidden email]>
>>>>>>> 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 <[hidden email]> 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
>>>>>>>>> <[hidden email]> 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 <[hidden email]
>>>>>>>> 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 <[hidden email]>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 <[hidden email]>
>>>>>>> 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 <[hidden email]> 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 <
>>>>>>> [hidden email]> 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
>>>>>>>>>>>>>>> <[hidden email]> 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
>>>>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ 
>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>> R-SIG-Mac mailing list
>>>>>>>>>>>>>>> [hidden email]
>>>>>>>>>>>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ 
>>>>>>>> _______________________________________________
>>>>>>>> R-SIG-Mac mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-mac__;!!Mih3wA!RJVCh9VfCoz3T_2M05bjyLjXayhKn0WRsh2X4wrwNKDorPrQmKY4NxTjzw9O9rQ$ 
>>>>>>> _______________________________________________
>>>>>>> R-SIG-Mac mailing list
>>>>>>> [hidden email]
>>>>>>> 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
>>>>> [hidden email]
>>>>> 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

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