Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01

[Simon Urbanek]

If it is a hang, can you get a stack trace? There are a few ways, if you're 
lucky, Apple may provide one directly when you to force-quite. Otherwise, you 
can download the GUI from mac.R-project.org, and use lldb -> attach xxx where 
xx is the PID of the GUI.

Hangs are different from crashes, they are much more annoying to debug, because 
those can be some race conditions that result from the interactions of our 
event loop and the os internal events.

Thanks,
Simon


> On Jun 27, 2020, at 4:15 AM, Carl Witthoft  wrote:
> 
> Well, dang me if today I wasn't able to open a file in R. -- but only once or 
> twice, and then I get the 100% CPU hang.  Same result if I double-clike the 
> file in Finder or use the R-menu "Open" dialog.
> 
> R- version 4.01, and to my knowledge I didn't change anything of import in my 
> Mac's system or set of applications.
> 
> If you can suggest a logfile or other tool I can pull info from to show what 
> happened, please do so.
> 
> thanks
> Carl
> 
> On 6/24/20 5:32 PM, Brandon Hurr wrote:
>> Simon,
>> 1) Yes, I use homebrew for installing python/openCV and GIS stuff. I don't 
>> recognize the others mentioned and I have a few system extensions installed 
>> (discussed below).
>> 2) I have been using Bob's Rswitch app recently and downloading the bundle 
>> rather than using the installer. The behavior is unchanged for me on two 
>> separate macs whether it's installed this way or not.
>> Related to #1, I have two separate macs where this is happening and both 
>> more or less have the same software bundle from homebrew (and most other 
>> apps).
>> brew list returns
>> gdbm openssl@1.1 python sqlite
>> jhead pandoc readline xz
>> I just wiped my homebrew install, rebooted, loaded an Rscript by double 
>> clicking into R-gui and its editor, then tried to load another script and it 
>> crashed R like before.
>> The behavior is the same with
>>  * R 4.0.2 & R.app GUI 1.72 (7846) x86_64-apple-darwin17.0 for R 4.0
>>  o Installed via PKG
>>  * R 4.1.0 (2020-06-21 r78727) & R.app GUI 1.72 (7846)
>>x86_64-apple-darwin17.0 for R 4.1
>>  o Installed via untar
>> The only system extensions I see in my Sys Preferences are Google Drive, 
>> Dropbox, One Drive, and OneNote. I haven't ever used the OneNote one and 
>> rarely One Drive. Google Drive and Dropbox are installed and regularly 
>> syncing a few folders. R seems to crash when opening a second file 
>> regardless of where it is located (e.g. synced folder, non-synced folder, 
>> external drive, system drive, etc.). I exited all of these programs and 
>> tried again and it still happened.
>> Anything else I should try or more information I could supply to narrow this 
>> down?
>> Thanks,
>> Brandon
>> On Tue, Jun 23, 2020 at 5:02 PM Simon Urbanek > > wrote:
>>Brandon,
>>Thanks for your reports. I tested all Catalinas 10.15.3 through
>>10.15.5 and, frustratingly, I cannot replicate the issue. I tried
>>opening documents of different sizes, multiple documents, even
>>changing the "close windows when quitting the app" global setting
>>and still no crash.
>>There are a few posts that suggest the a crash on Open is not
>>entirely uncommon on Catalina. There is no definite answer, but
>>there are pointers to unnotarized parts/libraries loaded into a
>>process. So one theory would be that users experiencing such issues
>>have some 3rd part libraries or tools on the machine which are not
>>notarized and cause the issue. So two comments from that:
>>1) do you have any 3rd party software that is not notarized? (like
>>Homebrew, Haxxies, UI-plugins or similar) If so try to remove them
>>(or rename their directories).
>>2) try using the unnotarized version of R to see if the problem
>>persists - see R for Mac FAQ 10.17:
>>
>> https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#I-cannot-attach-debugger-to-R
>>Thanks,
>>Simon
>> > On Jun 9, 2020, at 2:39 AM, Brandon Hurr >> wrote:
>> >
>> > Simon,
>> >
>> > When I removed these two I did get a slightly different behavior
>>on my MBA.
>> > In the past I would get the pinwheel of death and R would peg at
>>100%, but
>> > now when I try and load a second file it simply crashes R
>>immediately.
>> > Debug Console log here:
>> > https://gist.github.com/bhive01/1421f464ce5d345644878cd41309f647
>> > Separately I loaded up R from my applications folder and then
>>clicked on a
>> > file to load it and it did the same thing:
>> > https://gist.github.com/bhive01/d7791d0070a43d73de2489f6cab9211f
>> > The same crashing behavior if you load it from the Open Recents
>>in the menu:
>> > https://gist.github.com/bhive01/1bae74d6cbcbb8c014415d47ac9fe456
>> >
>> > In the first instance I double clicked the file from Finder and
>>it would
>> > open with R-GUI/R

Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01

[Simon Urbanek]

If you say longer scripts, can you clarify? Number of lines, size ... Is it a 
particular script that triggers it?

Thanks,
Simon


> On Jun 27, 2020, at 4:32 AM, Brandon Hurr  wrote:
> 
> Simon,
> 
> I installed Big Sur Beta out of desperation and it was exhibiting the same
> exact behavior there. So, this morning I wiped my 2019 MBA and reinstalled
> Catalina.
> 
>   - I installed command line tools.
>   - Then installed the gfortran tools linked in the "tools" section.
>   - Then installed 4.0.2 signed package.
>  - I did not install any packages other than base. I didn't change any
>  colors or anything.
> 
> I loaded 3 scripts randomly from my folders. These are longer scripts, but
> nothing ridiculous. I have not run any code in any of them. Just loaded
> them.
> 
> I got the pinwheel of death and 1 core pegged at 100%. Image here:
> https://imgur.com/a/PQA1QJ6
> 
> This system literally has nothing on it otherwise. Fresh install via
> internet recovery on a wiped drive.
> 
> Seriously at a loss over here. I guess most folks don't use the GUI, but I
> do and I like it. RStudio is nice but feature bloated and I can't exit vim
> (mostly joking).
> 
> Let me know if there's something I can do while my system is in this state.
> I will be looking to install more stuff very soon so I can use it to do my
> work again.
> 
> Thanks,
> Brandon
> 
> 
> 
> On Fri, Jun 26, 2020 at 9:16 AM Carl Witthoft  wrote:
> 
>> Well, dang me if today I wasn't able to open a file in R. -- but only
>> once or twice, and then I get the 100% CPU hang.  Same result if I
>> double-clike the file in Finder or use the R-menu "Open" dialog.
>> 
>> R- version 4.01, and to my knowledge I didn't change anything of import
>> in my Mac's system or set of applications.
>> 
>> If you can suggest a logfile or other tool I can pull info from to show
>> what happened, please do so.
>> 
>> thanks
>> Carl
>> 
>> On 6/24/20 5:32 PM, Brandon Hurr wrote:
>>> Simon,
>>> 
>>> 1) Yes, I use homebrew for installing python/openCV and GIS stuff. I
>>> don't recognize the others mentioned and I have a few system extensions
>>> installed (discussed below).
>>> 2) I have been using Bob's Rswitch app recently and downloading the
>>> bundle rather than using the installer. The behavior is unchanged for me
>>> on two separate macs whether it's installed this way or not.
>>> 
>>> Related to #1, I have two separate macs where this is happening and both
>>> more or less have the same software bundle from homebrew (and most other
>>> apps).
>>> brew list returns
>>> gdbm openssl@1.1 python sqlite
>>> jhead pandoc readline xz
>>> 
>>> I just wiped my homebrew install, rebooted, loaded an Rscript by double
>>> clicking into R-gui and its editor, then tried to load another script
>>> and it crashed R like before.
>>> The behavior is the same with
>>> 
>>>  * R 4.0.2 & R.app GUI 1.72 (7846) x86_64-apple-darwin17.0 for R 4.0
>>>  o Installed via PKG
>>>  * R 4.1.0 (2020-06-21 r78727) & R.app GUI 1.72 (7846)
>>>x86_64-apple-darwin17.0 for R 4.1
>>>  o Installed via untar
>>> 
>>> The only system extensions I see in my Sys Preferences are Google Drive,
>>> Dropbox, One Drive, and OneNote. I haven't ever used the OneNote one and
>>> rarely One Drive. Google Drive and Dropbox are installed and regularly
>>> syncing a few folders. R seems to crash when opening a second file
>>> regardless of where it is located (e.g. synced folder, non-synced
>>> folder, external drive, system drive, etc.). I exited all of these
>>> programs and tried again and it still happened.
>>> 
>>> Anything else I should try or more information I could supply to narrow
>>> this down?
>>> 
>>> Thanks,
>>> Brandon
>>> 
>>> On Tue, Jun 23, 2020 at 5:02 PM Simon Urbanek
>>> mailto:simon.urba...@r-project.org>>
>> wrote:
>>> 
>>>Brandon,
>>> 
>>>Thanks for your reports. I tested all Catalinas 10.15.3 through
>>>10.15.5 and, frustratingly, I cannot replicate the issue. I tried
>>>opening documents of different sizes, multiple documents, even
>>>changing the "close windows when quitting the app" global setting
>>>and still no crash.
>>> 
>>>There are a few posts that suggest the a crash on Open is not
>>>entirely uncommon on Catalina. There is no definite answer, but
>>>there are pointers to unnotarized parts/libraries loaded into a
>>>process. So one theory would be that users experiencing such issues
>>>have some 3rd part libraries or tools on the machine which are not
>>>notarized and cause the issue. So two comments from that:
>>> 
>>>1) do you have any 3rd party software that is not notarized? (like
>>>Homebrew, Haxxies, UI-plugins or similar) If so try to remove them
>>>(or rename their directories).
>>> 
>>>2) try using the unnotarized version of R to see if the problem
>>>persists - see R for Mac FAQ 10.17:
>>> 
>> https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#I-cannot-attach-debugger-to-R
>>> 
>>>T

Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01

[Brandon Hurr]

Simon,

I installed Big Sur Beta out of desperation and it was exhibiting the same
exact behavior there. So, this morning I wiped my 2019 MBA and reinstalled
Catalina.

   - I installed command line tools.
   - Then installed the gfortran tools linked in the "tools" section.
   - Then installed 4.0.2 signed package.
  - I did not install any packages other than base. I didn't change any
  colors or anything.

I loaded 3 scripts randomly from my folders. These are longer scripts, but
nothing ridiculous. I have not run any code in any of them. Just loaded
them.

I got the pinwheel of death and 1 core pegged at 100%. Image here:
https://imgur.com/a/PQA1QJ6

This system literally has nothing on it otherwise. Fresh install via
internet recovery on a wiped drive.

Seriously at a loss over here. I guess most folks don't use the GUI, but I
do and I like it. RStudio is nice but feature bloated and I can't exit vim
(mostly joking).

Let me know if there's something I can do while my system is in this state.
I will be looking to install more stuff very soon so I can use it to do my
work again.

Thanks,
Brandon



On Fri, Jun 26, 2020 at 9:16 AM Carl Witthoft  wrote:

> Well, dang me if today I wasn't able to open a file in R. -- but only
> once or twice, and then I get the 100% CPU hang.  Same result if I
> double-clike the file in Finder or use the R-menu "Open" dialog.
>
> R- version 4.01, and to my knowledge I didn't change anything of import
> in my Mac's system or set of applications.
>
> If you can suggest a logfile or other tool I can pull info from to show
> what happened, please do so.
>
> thanks
> Carl
>
> On 6/24/20 5:32 PM, Brandon Hurr wrote:
> > Simon,
> >
> > 1) Yes, I use homebrew for installing python/openCV and GIS stuff. I
> > don't recognize the others mentioned and I have a few system extensions
> > installed (discussed below).
> > 2) I have been using Bob's Rswitch app recently and downloading the
> > bundle rather than using the installer. The behavior is unchanged for me
> > on two separate macs whether it's installed this way or not.
> >
> > Related to #1, I have two separate macs where this is happening and both
> > more or less have the same software bundle from homebrew (and most other
> > apps).
> > brew list returns
> > gdbm openssl@1.1 python sqlite
> > jhead pandoc readline xz
> >
> > I just wiped my homebrew install, rebooted, loaded an Rscript by double
> > clicking into R-gui and its editor, then tried to load another script
> > and it crashed R like before.
> > The behavior is the same with
> >
> >   * R 4.0.2 & R.app GUI 1.72 (7846) x86_64-apple-darwin17.0 for R 4.0
> >   o Installed via PKG
> >   * R 4.1.0 (2020-06-21 r78727) & R.app GUI 1.72 (7846)
> > x86_64-apple-darwin17.0 for R 4.1
> >   o Installed via untar
> >
> > The only system extensions I see in my Sys Preferences are Google Drive,
> > Dropbox, One Drive, and OneNote. I haven't ever used the OneNote one and
> > rarely One Drive. Google Drive and Dropbox are installed and regularly
> > syncing a few folders. R seems to crash when opening a second file
> > regardless of where it is located (e.g. synced folder, non-synced
> > folder, external drive, system drive, etc.). I exited all of these
> > programs and tried again and it still happened.
> >
> > Anything else I should try or more information I could supply to narrow
> > this down?
> >
> > Thanks,
> > Brandon
> >
> > On Tue, Jun 23, 2020 at 5:02 PM Simon Urbanek
> > mailto:simon.urba...@r-project.org>>
> wrote:
> >
> > Brandon,
> >
> > Thanks for your reports. I tested all Catalinas 10.15.3 through
> > 10.15.5 and, frustratingly, I cannot replicate the issue. I tried
> > opening documents of different sizes, multiple documents, even
> > changing the "close windows when quitting the app" global setting
> > and still no crash.
> >
> > There are a few posts that suggest the a crash on Open is not
> > entirely uncommon on Catalina. There is no definite answer, but
> > there are pointers to unnotarized parts/libraries loaded into a
> > process. So one theory would be that users experiencing such issues
> > have some 3rd part libraries or tools on the machine which are not
> > notarized and cause the issue. So two comments from that:
> >
> > 1) do you have any 3rd party software that is not notarized? (like
> > Homebrew, Haxxies, UI-plugins or similar) If so try to remove them
> > (or rename their directories).
> >
> > 2) try using the unnotarized version of R to see if the problem
> > persists - see R for Mac FAQ 10.17:
> >
> https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#I-cannot-attach-debugger-to-R
> >
> > Thanks,
> > Simon
> >
> >
> >
> >  > On Jun 9, 2020, at 2:39 AM, Brandon Hurr  > > wrote:
> >  >
> >  > Simon,
> >  >
> >  > When I removed these two I did get a slightly different behavior
> > on my MBA.
>

Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01

[Carl Witthoft]

Well, dang me if today I wasn't able to open a file in R. -- but only 
once or twice, and then I get the 100% CPU hang.  Same result if I 
double-clike the file in Finder or use the R-menu "Open" dialog.


R- version 4.01, and to my knowledge I didn't change anything of import 
in my Mac's system or set of applications.


If you can suggest a logfile or other tool I can pull info from to show 
what happened, please do so.


thanks
Carl

On 6/24/20 5:32 PM, Brandon Hurr wrote:

Simon,

1) Yes, I use homebrew for installing python/openCV and GIS stuff. I 
don't recognize the others mentioned and I have a few system extensions 
installed (discussed below).
2) I have been using Bob's Rswitch app recently and downloading the 
bundle rather than using the installer. The behavior is unchanged for me 
on two separate macs whether it's installed this way or not.


Related to #1, I have two separate macs where this is happening and both 
more or less have the same software bundle from homebrew (and most other 
apps).

brew list returns
gdbm openssl@1.1 python sqlite
jhead pandoc readline xz

I just wiped my homebrew install, rebooted, loaded an Rscript by double 
clicking into R-gui and its editor, then tried to load another script 
and it crashed R like before.

The behavior is the same with

  * R 4.0.2 & R.app GUI 1.72 (7846) x86_64-apple-darwin17.0 for R 4.0
  o Installed via PKG
  * R 4.1.0 (2020-06-21 r78727) & R.app GUI 1.72 (7846)
x86_64-apple-darwin17.0 for R 4.1
  o Installed via untar

The only system extensions I see in my Sys Preferences are Google Drive, 
Dropbox, One Drive, and OneNote. I haven't ever used the OneNote one and 
rarely One Drive. Google Drive and Dropbox are installed and regularly 
syncing a few folders. R seems to crash when opening a second file 
regardless of where it is located (e.g. synced folder, non-synced 
folder, external drive, system drive, etc.). I exited all of these 
programs and tried again and it still happened.


Anything else I should try or more information I could supply to narrow 
this down?


Thanks,
Brandon

On Tue, Jun 23, 2020 at 5:02 PM Simon Urbanek 
mailto:simon.urba...@r-project.org>> wrote:


Brandon,

Thanks for your reports. I tested all Catalinas 10.15.3 through
10.15.5 and, frustratingly, I cannot replicate the issue. I tried
opening documents of different sizes, multiple documents, even
changing the "close windows when quitting the app" global setting
and still no crash.

There are a few posts that suggest the a crash on Open is not
entirely uncommon on Catalina. There is no definite answer, but
there are pointers to unnotarized parts/libraries loaded into a
process. So one theory would be that users experiencing such issues
have some 3rd part libraries or tools on the machine which are not
notarized and cause the issue. So two comments from that:

1) do you have any 3rd party software that is not notarized? (like
Homebrew, Haxxies, UI-plugins or similar) If so try to remove them
(or rename their directories).

2) try using the unnotarized version of R to see if the problem
persists - see R for Mac FAQ 10.17:

https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#I-cannot-attach-debugger-to-R

Thanks,
Simon



 > On Jun 9, 2020, at 2:39 AM, Brandon Hurr mailto:brandon.h...@gmail.com>> wrote:
 >
 > Simon,
 >
 > When I removed these two I did get a slightly different behavior
on my MBA.
 > In the past I would get the pinwheel of death and R would peg at
100%, but
 > now when I try and load a second file it simply crashes R
immediately.
 > Debug Console log here:
 > https://gist.github.com/bhive01/1421f464ce5d345644878cd41309f647
 > Separately I loaded up R from my applications folder and then
clicked on a
 > file to load it and it did the same thing:
 > https://gist.github.com/bhive01/d7791d0070a43d73de2489f6cab9211f
 > The same crashing behavior if you load it from the Open Recents
in the menu:
 > https://gist.github.com/bhive01/1bae74d6cbcbb8c014415d47ac9fe456
 >
 > In the first instance I double clicked the file from Finder and
it would
 > open with R-GUI/R. But a second file would not, once R was loaded.
 >
 > I don't know if that gets us any closer, but apparently there is some
 > difference in that it crashes immediately rather than a pinwheel
of death.
 > The only thing I can think of is that I did have my own custom color
 > palette and you reference changing the color scheme. Seems
unlikely, but
 > perhaps there's a connection there?
 > As Carl says, I'm happy to try other things if you have
suggestions or have
 > ideas on more information. I've been using BBEdit to open other
scripts,
 > but often forget and end up with a crash because I double-click
on a file.
 > I might try to get BBEdit to work with