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

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

2020-07-02 Thread Brandon Hurr

Simon,

I can happily report the same for me after opening over a dozen R scripts
with lots of functions in them. Code folding is working fine as well.

Thanks so much for sticking with us on this.

Cheers,
Brandon

On Thu, Jul 2, 2020 at 5:55 AM Carl Witthoft  wrote:

> Hi, I ran  7849 high sierra debug GUI,
>
> and am happy to report that I had zero crashes or hangs.
>
> I tried opening via the icon in the console window, from the File menu,
> and even by selecting a dozen "name.r" files in the Finder and hitting
> -O .  All files opened, no problems seen.
>
> On 7/2/20 1:27 AM, Simon Urbanek wrote:
> > Thanks to all, much appreciated. Please try the latest GUI revision 7849
> from https://mac.R-project.org
> > The issue I found so far seems to have to do with function folding in
> documents - which is why is actually depends on the document content - and
> a selector that is apparently missing in Catalina.
> >
> > Thanks,
> > Simon
> >
> >
> >> On 29/06/2020, at 11:22 AM, Brandon Hurr 
> wrote:
> >>
> >> Simon.
> >> Default changed, RGUI 7846 Debug downloaded and run on same scripts.
> >>
> >> Crash report here;
> >> https://gist.github.com/bhive01/fd844404ef3e1d295036e5abd127864b
> >>
> >> Let me know if you need more reports or to try something else.
> >>
> >> Brandon
> >>
> >> On Sun, Jun 28, 2020 at 4:00 PM Simon Urbanek <
> simon.urba...@r-project.org>
> >> wrote:
> >>
> >>> Brandon,
> >>>
> >>> Yes, this is of great help! It shows the the GUI spins in the segfault
> >>> handler (it segfaults while rendering text which calls the R segfault
> >>> handler which in turn tries to render more text etc. ...).
> >>> So first thing is to avoid the signal handler, run this command in
> >>> Terminal:
> >>>
> >>> defaults write org.R-project.R 'Disable R signal handlers' YES
> >>>
> >>> Then download the debug version of the R GUI from
> >>>
> >>> https://mac.R-project.org/
> >>>
> >>> where it says Mac OS X GUI ... high-sierra-Debug.dmg - pick the one
> >>> matching your R version (4.0 for release or 4.1 for R-devel). You don't
> >>> need to replace your regular one, you can run it simply from the image.
> >>> Note that it is signed, but not notarized, so right-click
> (=ctrl-click) on
> >>> it and select "Open".
> >>>
> >>> That will avoid the "hang" but will give a proper segfault with an
> Apple
> >>> report so won't help immediately but will make it easier to pinpoint.
> Also
> >>> it should include debug symbols with line numbers and all that. Please
> post
> >>> the crash report.
> >>>
> >>> Thank you for your help,
> >>> Simon
> >>>
> >>>
> >>>
>  On Jun 29, 2020, at 4:25 AM, Brandon Hurr 
> >>> wrote:
> 
>  Thanks Ben.
> 
>  I fired up R did a 20 second sample as I loaded files and it went
> into a
> >>> hang.
>  https://gist.github.com/bhive01/77ccd888da1ee74da12a5c91cfc3d727
> 
>  Seems to have the symbols you describe. Is that more helpful?
> 
>  Brandon
> >>>
> >>>
> >>
> >>  [[alternative HTML version deleted]]
> >>
> >> ___
> >> R-SIG-Mac mailing list
> >> R-SIG-Mac@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
>
> --
> Carl Witthoft
> c...@witthoft.com
> resume: https://app.box.com/file/498153801347
>

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

2020-07-02 Thread Carl Witthoft


Hi, I ran  7849 high sierra debug GUI,

and am happy to report that I had zero crashes or hangs.

I tried opening via the icon in the console window, from the File menu, 
and even by selecting a dozen "name.r" files in the Finder and hitting 
-O .  All files opened, no problems seen.


On 7/2/20 1:27 AM, Simon Urbanek wrote:

Thanks to all, much appreciated. Please try the latest GUI revision 7849 from 
https://mac.R-project.org
The issue I found so far seems to have to do with function folding in documents 
- which is why is actually depends on the document content - and a selector 
that is apparently missing in Catalina.

Thanks,
Simon



On 29/06/2020, at 11:22 AM, Brandon Hurr  wrote:

Simon.
Default changed, RGUI 7846 Debug downloaded and run on same scripts.

Crash report here;
https://gist.github.com/bhive01/fd844404ef3e1d295036e5abd127864b

Let me know if you need more reports or to try something else.

Brandon

On Sun, Jun 28, 2020 at 4:00 PM Simon Urbanek 
wrote:


Brandon,

Yes, this is of great help! It shows the the GUI spins in the segfault
handler (it segfaults while rendering text which calls the R segfault
handler which in turn tries to render more text etc. ...).
So first thing is to avoid the signal handler, run this command in
Terminal:

defaults write org.R-project.R 'Disable R signal handlers' YES

Then download the debug version of the R GUI from

https://mac.R-project.org/

where it says Mac OS X GUI ... high-sierra-Debug.dmg - pick the one
matching your R version (4.0 for release or 4.1 for R-devel). You don't
need to replace your regular one, you can run it simply from the image.
Note that it is signed, but not notarized, so right-click (=ctrl-click) on
it and select "Open".

That will avoid the "hang" but will give a proper segfault with an Apple
report so won't help immediately but will make it easier to pinpoint. Also
it should include debug symbols with line numbers and all that. Please post
the crash report.

Thank you for your help,
Simon




On Jun 29, 2020, at 4:25 AM, Brandon Hurr 

wrote:


Thanks Ben.

I fired up R did a 20 second sample as I loaded files and it went into a

hang.

https://gist.github.com/bhive01/77ccd888da1ee74da12a5c91cfc3d727

Seems to have the symbols you describe. Is that more helpful?

Brandon





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--
Carl Witthoft
c...@witthoft.com
resume: https://app.box.com/file/498153801347

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

2020-07-01 Thread Simon Urbanek

Thanks to all, much appreciated. Please try the latest GUI revision 7849 from 
https://mac.R-project.org
The issue I found so far seems to have to do with function folding in documents 
- which is why is actually depends on the document content - and a selector 
that is apparently missing in Catalina.

Thanks,
Simon


> On 29/06/2020, at 11:22 AM, Brandon Hurr  wrote:
> 
> Simon.
> Default changed, RGUI 7846 Debug downloaded and run on same scripts.
> 
> Crash report here;
> https://gist.github.com/bhive01/fd844404ef3e1d295036e5abd127864b
> 
> Let me know if you need more reports or to try something else.
> 
> Brandon
> 
> On Sun, Jun 28, 2020 at 4:00 PM Simon Urbanek 
> wrote:
> 
>> Brandon,
>> 
>> Yes, this is of great help! It shows the the GUI spins in the segfault
>> handler (it segfaults while rendering text which calls the R segfault
>> handler which in turn tries to render more text etc. ...).
>> So first thing is to avoid the signal handler, run this command in
>> Terminal:
>> 
>> defaults write org.R-project.R 'Disable R signal handlers' YES
>> 
>> Then download the debug version of the R GUI from
>> 
>> https://mac.R-project.org/
>> 
>> where it says Mac OS X GUI ... high-sierra-Debug.dmg - pick the one
>> matching your R version (4.0 for release or 4.1 for R-devel). You don't
>> need to replace your regular one, you can run it simply from the image.
>> Note that it is signed, but not notarized, so right-click (=ctrl-click) on
>> it and select "Open".
>> 
>> That will avoid the "hang" but will give a proper segfault with an Apple
>> report so won't help immediately but will make it easier to pinpoint. Also
>> it should include debug symbols with line numbers and all that. Please post
>> the crash report.
>> 
>> Thank you for your help,
>> Simon
>> 
>> 
>> 
>>> On Jun 29, 2020, at 4:25 AM, Brandon Hurr 
>> wrote:
>>> 
>>> Thanks Ben.
>>> 
>>> I fired up R did a 20 second sample as I loaded files and it went into a
>> hang.
>>> https://gist.github.com/bhive01/77ccd888da1ee74da12a5c91cfc3d727
>>> 
>>> Seems to have the symbols you describe. Is that more helpful?
>>> 
>>> Brandon
>> 
>> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01

2020-06-28 Thread Brandon Hurr

Simon.
Default changed, RGUI 7846 Debug downloaded and run on same scripts.

Crash report here;
https://gist.github.com/bhive01/fd844404ef3e1d295036e5abd127864b

Let me know if you need more reports or to try something else.

Brandon

On Sun, Jun 28, 2020 at 4:00 PM Simon Urbanek 
wrote:

> Brandon,
>
> Yes, this is of great help! It shows the the GUI spins in the segfault
> handler (it segfaults while rendering text which calls the R segfault
> handler which in turn tries to render more text etc. ...).
> So first thing is to avoid the signal handler, run this command in
> Terminal:
>
> defaults write org.R-project.R 'Disable R signal handlers' YES
>
> Then download the debug version of the R GUI from
>
> https://mac.R-project.org/
>
> where it says Mac OS X GUI ... high-sierra-Debug.dmg - pick the one
> matching your R version (4.0 for release or 4.1 for R-devel). You don't
> need to replace your regular one, you can run it simply from the image.
> Note that it is signed, but not notarized, so right-click (=ctrl-click) on
> it and select "Open".
>
> That will avoid the "hang" but will give a proper segfault with an Apple
> report so won't help immediately but will make it easier to pinpoint. Also
> it should include debug symbols with line numbers and all that. Please post
> the crash report.
>
> Thank you for your help,
> Simon
>
>
>
> > On Jun 29, 2020, at 4:25 AM, Brandon Hurr 
> wrote:
> >
> > Thanks Ben.
> >
> > I fired up R did a 20 second sample as I loaded files and it went into a
> hang.
> > https://gist.github.com/bhive01/77ccd888da1ee74da12a5c91cfc3d727
> >
> > Seems to have the symbols you describe. Is that more helpful?
> >
> > Brandon
>
>

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

2020-06-28 Thread Simon Urbanek

Brandon,

Yes, this is of great help! It shows the the GUI spins in the segfault handler 
(it segfaults while rendering text which calls the R segfault handler which in 
turn tries to render more text etc. ...).
So first thing is to avoid the signal handler, run this command in Terminal:

defaults write org.R-project.R 'Disable R signal handlers' YES

Then download the debug version of the R GUI from

https://mac.R-project.org/

where it says Mac OS X GUI ... high-sierra-Debug.dmg - pick the one matching 
your R version (4.0 for release or 4.1 for R-devel). You don't need to replace 
your regular one, you can run it simply from the image. Note that it is signed, 
but not notarized, so right-click (=ctrl-click) on it and select "Open".

That will avoid the "hang" but will give a proper segfault with an Apple report 
so won't help immediately but will make it easier to pinpoint. Also it should 
include debug symbols with line numbers and all that. Please post the crash 
report.

Thank you for your help,
Simon

> On Jun 29, 2020, at 4:25 AM, Brandon Hurr  wrote:
> 
> Thanks Ben. 
> 
> I fired up R did a 20 second sample as I loaded files and it went into a 
> hang. 
> https://gist.github.com/bhive01/77ccd888da1ee74da12a5c91cfc3d727
> 
> Seems to have the symbols you describe. Is that more helpful?
> 
> Brandon

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

2020-06-28 Thread Carl Witthoft


Hi, here's my sample R 10 dump:

Sampling process 16681 for 10 seconds with 1 millisecond of run time 
between samples

Sampling completed, processing symbols...
Sample analysis of process 16681 written to file 
/tmp/R_2020-06-28_170339_imcz.sample.txt


Analysis of sampling R (pid 16681) every 1 millisecond
Process: R [16681]
Path:/Applications/R.app/Contents/MacOS/R
Load Address:0x10e3dc000
Identifier:  org.R-project.R
Version: R for R 4.0.1 GUI 1.72 Catalina build (7845)
Code Type:   X86-64
Parent Process:  ??? [1]

Date/Time:   2020-06-28 17:03:39.436 -0400
Launch Time: 2020-06-28 17:02:38.458 -0400
OS Version:  Mac OS X 10.15.5 (19F101)
Report Version:  7
Analysis Tool:   /usr/bin/sample

Physical footprint: 190.6M
Physical footprint (peak):  233.4M


Call graph:
8617 Thread_2990078   DispatchQueue_1: com.apple.main-thread  (serial)
+ 8617 start  (in libdyld.dylib) + 1  [0x7fff735e3cc9]
+   8617 main  (in R) + 792  [0x10e3ddfa8]
+ 8617 -[REngine runREPL]  (in R) + 177  [0x10e3ee441]
+   8617 run_REngineRmainloop  (in R) + 263  [0x10e3f9837]
+ 8617 R_ReplDLLdo1  (in libR.dylib) + 148  [0x10e5ff1e4] 
main.c:371

+   8617 Re_ReadConsole  (in R) + 184  [0x10e3ebd38]
+ 8617 -[RController handleReadConsole:]  (in R) + 158 
[0x10e3e29be]
+   8617 -[RController doProcessEvents:]  (in R) + 190 
[0x10e3e836e]
+ 8617 -[NSApplication(NSEvent) 
_nextEventMatchingEventMask:untilDate:inMode:dequeue:]  (in AppKit) + 
1352  [0x7fff3685c070]
+   8617 _DPSNextEvent  (in AppKit) + 883 
[0x7fff3685d829]
+ 8617 
_BlockUntilNextEventMatchingListInModeWithFilter  (in HIToolbox) + 64 
[0x7fff38215579]
+   8617 ReceiveNextEventCommon  (in HIToolbox) 
+ 359  [0x7fff382156f4]
+ 8617 RunCurrentEventLoopInMode  (in 
HIToolbox) + 292  [0x7fff38215abd]
+   8617 CFRunLoopRunSpecific  (in 
CoreFoundation) + 462  [0x7fff395e6ece]
+ 8617 __CFRunLoopRun  (in 
CoreFoundation) + 874  [0x7fff395e7895]
+   8617 __CFRunLoopDoObservers  (in 
CoreFoundation) + 457  [0x7fff395e82f7]
+ 8617 
__CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__  (in 
CoreFoundation) + 23  [0x7fff395e83c5]
+   8617 
___NSRunLoopObserverCreateWithHandler_block_invoke  (in AppKit) + 41 
[0x7fff3711c850]
+ 8617 
__62+[CATransaction(NSCATransaction) 
NS_setFlushesWithDisplayLink]_block_invoke  (in AppKit) + 266 
[0x7fff369fd591]
+   8617 
CA::Transaction::commit()  (in QuartzCore) + 644  [0x7fff450ac0a0]
+ 8617 
CA::Context::commit_transaction(CA::Transaction*, double)  (in 
QuartzCore) + 334  [0x7fff450ad4b6]
+   8617 
CA::Layer::display_if_needed(CA::Transaction*)  (in QuartzCore) + 757 
[0x7fff450cf1fd]
+ 8617 
-[_NSViewBackingLayer display]  (in AppKit) + 800  [0x7fff36948977]
+   8617 
-[_NSBackingLayer display]  (in AppKit) + 537  [0x7fff369e6e8a]
+ 8617 -[CALayer 
_display]  (in QuartzCore) + 2103  [0x7fff450d0162]
+   8617 invocation 
function for block in CA::Layer::display_()  (in QuartzCore) + 53 
[0x7fff451307d9]
+ 8617 
CABackingStoreUpdate_  (in QuartzCore) + 595  [0x7fff450d0c5d]
+   8617 
-[NSView(NSLayerKitGlue) 
_drawViewBackingLayer:inContext:drawingHandler:]  (in AppKit) + 1271 
[0x7fff369e749a]
+ 8617 
-[NSView(NSInternal) 
_recursive:displayRectIgnoringOpacity:inContext:stopAtLayerBackedViews:] 
 (in AppKit) + 2170  [0x7fff369e809e]
+   8617 
_NSViewDrawRect  (in AppKit) + 139  [0x7fff369e8d8f]
+ 8617 
-[_NSRulerContentView drawRect:]  (in AppKit) + 157  [0x7fff36f6bd67]
+ 
8617 -[NSRulerView _drawContentRect:]  (in AppKit) + 233  [0x7fff36f6b02f]
+ 
8617 -[NoodleLineNumberView drawHashMarksAndLabelsInRect:]  (in R) + 345 
 [0x10e42e8e9]
+ 
8617 -[NSLayoutManager(NSPrivate) 
_glyphRangeForBoundingRect:inTextContainer:fast:okToFillHoles:]  (in 
UIFoundation) + 857  [0x7fff6a63611b]
+ 
  8617 -[NSLayoutManager(NSPrivate) 
_firstPassGlyphRangeForBoundingRect:inTextContainer:okToFillHoles:]  (in 
UIFoundation) + 1441  [0x7fff6a63765a]
+ 
8617 _NSF

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

2020-06-28 Thread Ben Haller via R-SIG-Mac

Well, I know nothing about the R GUI code, but it looks like the issue might be 
in either -[RScriptEditorTypeSetter actionForControlCharacterAtIndex:] or 
-[NoodleLineNumberView drawHashMarksAndLabelsInRect:].  The backtrace is a bit 
odd; I don’t know what sigactionSegv and -[RController handleReadConsole:] are 
doing in the middle of it.  Anyway, this looks like quite a useful backtrace to 
me!  :->

Cheers,
-B.


> On Jun 28, 2020, at 12:25 PM, Brandon Hurr  wrote:
> 
> Thanks Ben. 
> 
> I fired up R did a 20 second sample as I loaded files and it went into a 
> hang. 
> https://gist.github.com/bhive01/77ccd888da1ee74da12a5c91cfc3d727 
> 
> 
> Seems to have the symbols you describe. Is that more helpful?
> 
> Brandon


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

2020-06-28 Thread Brandon Hurr

Thanks Ben.

I fired up R did a 20 second sample as I loaded files and it went into a
hang.
https://gist.github.com/bhive01/77ccd888da1ee74da12a5c91cfc3d727

Seems to have the symbols you describe. Is that more helpful?

Brandon

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

2020-06-28 Thread Ben Haller via R-SIG-Mac

Hi all.  I’m not on 4.0.x yet, but have been reading this thread with interest.

It may be useful to know that you can sample a hung process on macOS with the 
“sample” command.  If the R GUI is hung, just go to Terminal and type “sample R 
10”.  After a short delay, you’ll get backtraces of all threads dumped into 
your Terminal.  My R 3.6.2 GUI, installed from CRAN not built from sources, 
appears to be symbolicated, so my backtraces have symbols in them even within 
the R GUI’s code.  If the 4.0.x R GUI is also symbolicated (which I think is a 
good idea for all shipping apps nowadays, since the size of app binaries is so 
irrelevant in this day and age), your backtraces from it should also have 
symbols.

Cheers,
-B.

Benjamin C. Haller
Messer Lab
Cornell University


> On Jun 27, 2020, at 1:17 AM, Simon Urbanek  
> wrote:
> 
> 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:
>>

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

2020-06-27 Thread Brandon Hurr

Simon,

I haven't added anything to the system other than what I said so it's a
good time to gather data.

I created a gist and it has 4 older scripts that seem to cause it
regularly, a spindump, and a sample of the process while it was hanging. I
could not get it to give me a "report" after a force-quit.
https://gist.github.com/bhive01/42a333ba189652e41df94407bdc94967

The line counts for the 4 files are as follows:

brandonhurr@Brandons-Air ~ % wc -l /Users/brandonhurr/Desktop/RGB2All.R
 134 /Users/brandonhurr/Desktop/RGB2All.R
brandonhurr@Brandons-Air ~ % wc -l /Users/brandonhurr/Desktop/HamiData.R
  15 /Users/brandonhurr/Desktop/HamiData.R
brandonhurr@Brandons-Air ~ % wc -l /Users/brandonhurr/Desktop/2014\ Melon.R
 210 /Users/brandonhurr/Desktop/2014 Melon.R
brandonhurr@Brandons-Air ~ % wc -l /Users/brandonhurr/Desktop/Drone\
Data\ Processing.r
  40 /Users/brandonhurr/Desktop/Drone Data Processing.r

These files are old and represent a different time for me programming-wise,
so don't judge too much. They are old and represent things that are safe to
send out.

RGB2All.R seems to be able to cause it more than most when loaded after any
of the other files. It has one main function in it that converts RGB to
other color coordinates. The only thing in common with the other files that
seem to cause this before I wiped my system is that it has a function
defined in it.

If you know of a way to get it to give me a report to send I will do it.

Thanks,

Brandon

On Fri, Jun 26, 2020 at 10:17 PM Simon Urbanek 
wrote:

> 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 <
> 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

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

2020-06-26 Thread 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

2020-06-26 Thread 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

2020-06-26 Thread 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

2020-06-26 Thread 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

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

2020-06-24 Thread Brandon Hurr

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
   - 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
   - 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. 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 R more intimately as Carl pointed
> > out.
> >
> > B
> >
> > On Sun, Jun 7, 2020 at 3:46 PM Simon Urbanek <
> simon.urba...@r-project.org>
> > wrote:
> >
> >> Thanks for the reports. Unfortunately, I still cannot reproduce it on
> >> Catalina - neither with 4.0.1 nor 4.0.0.
> >> Can someone post exactly how to replicate? (How do exactly you open the
> >> file? - the Open dialog works fine for me...)
> >>
> >> Note that the GUI is independent of R and compatible up to the patch
> >> version, i.e. the 4.0.0 GUI works with R 4.0.1 and vice-versa. You can
> also
> >> just download the GUI from
> >> https://mac.R-project.org
> >> and run it from the image, you don’t even have to install it.
> >>
> >> The only cha

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

2020-06-23 Thread Simon Urbanek

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. 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 R more intimately as Carl pointed
> out.
> 
> B
> 
> On Sun, Jun 7, 2020 at 3:46 PM Simon Urbanek 
> wrote:
> 
>> Thanks for the reports. Unfortunately, I still cannot reproduce it on
>> Catalina - neither with 4.0.1 nor 4.0.0.
>> Can someone post exactly how to replicate? (How do exactly you open the
>> file? - the Open dialog works fine for me...)
>> 
>> Note that the GUI is independent of R and compatible up to the patch
>> version, i.e. the 4.0.0 GUI works with R 4.0.1 and vice-versa. You can also
>> just download the GUI from
>> https://mac.R-project.org
>> and run it from the image, you don’t even have to install it.
>> 
>> The only changes in the GUI for 4.0.1 were in the colours for dark mode,
>> so file handling behaviour didn’t really change.
>> 
>> Some places to remove to try if it has any effect:
>> 
>> rm -rf ~/Library/Caches/org.R-project.R
>> rm ~/Library/Preferences/org.R-project.R.plist
>> 
>> Thanks,
>> Simon
>> 
>> 
>> 
>>> On Jun 8, 2020, at 10:22 AM, Brandon Hurr 
>> wrote:
>>> 
>>> This sounds exactly like the issue I am still having when I run to open
>>> more than one R script file in R-GUI’s editor. Perhaps it has got worse
>>> with the newer builds?
>>> 
>>> On Sun, Jun 7, 2020 at 15:16 Carl Witthoft  wrote:
>>> 
 I'm not sure what to look for in the Reports sections of Console.app,
 but I did find this report of R exceeding a diagnostic limit of CPU
 usage, which most likely is related to one of the hangs - R.app always
 goes full throttle on one CPU core.
 
 Date/Time:2020-06-05 18:58:36 -0400
 End time: 2020-06-05 19:00:16 -0400
 OS Version:   Mac OS X 10.15.5 (Build 19F101)
 Architecture: x86_64h
 Report Version:   29
 Incident Identifier: E3BE34D3-09C5-4AA9-A89D-A9E5F8F0EB6B
 
 Data Source:  Microstackshots
 Shared Cache: 0x3868000 57B2E2F3-10A7-3AAD-AC94-975B957DF535
 
 Command:  R
 Path: /Applications/R.app/Contents/MacOS/R
 Identifier:   org.R-project.R
 Version:  R 4.0.0 GUI 1.71 Catalina build (7827)
 PID:  21391
 
 Event:cpu usage
 Action taken: none
 CPU:  90 seconds cpu time over 100 seconds (90% cpu
 average), exceeding limit of 50% cpu over 180 seconds
 CPU limit:90s
 Limit duration:   180s
 CPU used: 90s
 CPU duration: 100s
 Duration: 10

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

2020-06-08 Thread Brandon Hurr

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 R more intimately as Carl pointed
out.

B

On Sun, Jun 7, 2020 at 3:46 PM Simon Urbanek 
wrote:

> Thanks for the reports. Unfortunately, I still cannot reproduce it on
> Catalina - neither with 4.0.1 nor 4.0.0.
> Can someone post exactly how to replicate? (How do exactly you open the
> file? - the Open dialog works fine for me...)
>
> Note that the GUI is independent of R and compatible up to the patch
> version, i.e. the 4.0.0 GUI works with R 4.0.1 and vice-versa. You can also
> just download the GUI from
> https://mac.R-project.org
> and run it from the image, you don’t even have to install it.
>
> The only changes in the GUI for 4.0.1 were in the colours for dark mode,
> so file handling behaviour didn’t really change.
>
> Some places to remove to try if it has any effect:
>
> rm -rf ~/Library/Caches/org.R-project.R
> rm ~/Library/Preferences/org.R-project.R.plist
>
> Thanks,
> Simon
>
>
>
> > On Jun 8, 2020, at 10:22 AM, Brandon Hurr 
> wrote:
> >
> > This sounds exactly like the issue I am still having when I run to open
> > more than one R script file in R-GUI’s editor. Perhaps it has got worse
> > with the newer builds?
> >
> > On Sun, Jun 7, 2020 at 15:16 Carl Witthoft  wrote:
> >
> >> I'm not sure what to look for in the Reports sections of Console.app,
> >> but I did find this report of R exceeding a diagnostic limit of CPU
> >> usage, which most likely is related to one of the hangs - R.app always
> >> goes full throttle on one CPU core.
> >>
> >> Date/Time:2020-06-05 18:58:36 -0400
> >> End time: 2020-06-05 19:00:16 -0400
> >> OS Version:   Mac OS X 10.15.5 (Build 19F101)
> >> Architecture: x86_64h
> >> Report Version:   29
> >> Incident Identifier: E3BE34D3-09C5-4AA9-A89D-A9E5F8F0EB6B
> >>
> >> Data Source:  Microstackshots
> >> Shared Cache: 0x3868000 57B2E2F3-10A7-3AAD-AC94-975B957DF535
> >>
> >> Command:  R
> >> Path: /Applications/R.app/Contents/MacOS/R
> >> Identifier:   org.R-project.R
> >> Version:  R 4.0.0 GUI 1.71 Catalina build (7827)
> >> PID:  21391
> >>
> >> Event:cpu usage
> >> Action taken: none
> >> CPU:  90 seconds cpu time over 100 seconds (90% cpu
> >> average), exceeding limit of 50% cpu over 180 seconds
> >> CPU limit:90s
> >> Limit duration:   180s
> >> CPU used: 90s
> >> CPU duration: 100s
> >> Duration: 100.35s
> >> Duration Sampled: 87.74s
> >> Steps:51
> >>
> >> Hardware model:   iMac19,2
> >> Active cpus:  4
> >>
> >> Fan speed:1200 rpm
> >>
> >> Heaviest stack for the target process:
> >>   51  start + 1 (libdyld.dylib + 109769) [0x7fff6a9b1cc9]
> >>   51  main + 720 (R + 8032) [0x105c66f60]
> >>   51  -[NSApplication finishLaunching] + 2601 (AppKit + 207160)
> >> [0x7fff2dc1c938]
> >>   51  -[NSApplication _postDidFinishNotification] + 312 (AppKit +
> >> 306403) [0x7fff2dc34ce3]
> >>   51  -[NSNotificationCenter postNotificationName:object:userInfo:] +
> >> 59 (Foundation + 38790) [0x7fff32ff6786]
> >>   51  _CFXNotificationPost + 1351 (CoreFoundation + 297529)
> >> [0x7fff3097ba39]
> >>   51  -[_CFXNotificationRegistrar find:object:observer:enumerator:] +
> >> 1554 (CoreFoundation + 300429) [0x7fff3097c58d]
> >>   51  ___CFXNotificationPost_block_invoke + 80 (CoreFoundation +
> >> 496660) [0x7fff309ac414]
> >>   51  _CFXRegistrationPost1 + 372 (CoreFoundation + 497576)
> >> [0x7fff309ac7a8]
> >>   51  ___CFXRegistrationPost1_block_invoke + 63 (CoreFoundation +
> >> 497715) [0x7fff309ac833]
> >>   51  __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 12
> >>

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

2020-06-08 Thread Dr Eberhard W Lisse

It sounds a little as if the R.app is somehow damaged. 

What do the commands

ls -ls $(which R)
ls -las $(which Rscript)

issued from a terminal show? 

Mine show (abbreviated)

[...] /usr/local/bin/R -> ../Cellar/r/4.0.0_1/bin/R
[...] /usr/local/bin/Rscript -> ../Cellar/r/4.0.0_1/bin/Rscript

I use homebrew and the plain (command line) R, ie not the App 
(installed as cask), with RStudio (installed as cask).

I have the following first line in most of my R scripts

#!/usr/bin/env Rscript

and they all run currently. 

I will wait for 4.0.1 to pitch up on homebrew and see that that does.

The editor scripts have nothing to do with this, they just reference 
the command line R (above). There are equally comfortable ones for 
TextMate2 and AlphaX, and others.

greetings, el

On 08/06/2020 14:13, Carl Witthoft wrote:
> In the meantime, there is a decent alternative.  I found some scripts
> for BBEdit which let you execute code or "source" code directly from
> BBEdit.  See http://bearak.org/code/text/index.html
> 
> On 6/7/20 11:39 PM, John Helly wrote:
>> Fails for me 100%.  If you want to zoom to look at it, I can arrange.
>> Hard to explain how to replicate since it happens right away as soon
>> as I try to do anything.  Running Catalina on a brand-new Mac Pro.
>>
>> J.
>>

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

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

2020-06-08 Thread Carl Witthoft

In the meantime, there is a decent alternative.  I found some scripts 
for BBEdit which let you execute code or "source" code directly from 
BBEdit.  See  http://bearak.org/code/text/index.html


On 6/7/20 11:39 PM, John Helly wrote:

Fails for me 100%.  If you want to zoom to look at it, I can arrange.
Hard to explain how to replicate since it happens right away as soon as
I try to do anything.  Running Catalina on a brand-new Mac Pro.

J.

On 6/7/20 15:46, Simon Urbanek wrote:

Thanks for the reports. Unfortunately, I still cannot reproduce it on Catalina 
- neither with 4.0.1 nor 4.0.0.
Can someone post exactly how to replicate? (How do exactly you open the file? - 
the Open dialog works fine for me...)

Note that the GUI is independent of R and compatible up to the patch version, 
i.e. the 4.0.0 GUI works with R 4.0.1 and vice-versa. You can also just 
download the GUI from
https://urldefense.com/v3/__https://mac.R-project.org__;!!Mih3wA!ReiXSbqAjm6U4nbE1g9kiDWBjuTDcKsZfnp69eK0Ey0VZg4-UB24sxHHdM6_uVk$
and run it from the image, you don’t even have to install it.

The only changes in the GUI for 4.0.1 were in the colours for dark mode, so 
file handling behaviour didn’t really change.

Some places to remove to try if it has any effect:

rm -rf ~/Library/Caches/org.R-project.R
rm ~/Library/Preferences/org.R-project.R.plist

Thanks,
Simon




On Jun 8, 2020, at 10:22 AM, Brandon Hurr  wrote:

This sounds exactly like the issue I am still having when I run to open
more than one R script file in R-GUI’s editor. Perhaps it has got worse
with the newer builds?

On Sun, Jun 7, 2020 at 15:16 Carl Witthoft  wrote:


I'm not sure what to look for in the Reports sections of Console.app,
but I did find this report of R exceeding a diagnostic limit of CPU
usage, which most likely is related to one of the hangs - R.app always
goes full throttle on one CPU core.

Date/Time:2020-06-05 18:58:36 -0400
End time: 2020-06-05 19:00:16 -0400
OS Version:   Mac OS X 10.15.5 (Build 19F101)
Architecture: x86_64h
Report Version:   29
Incident Identifier: E3BE34D3-09C5-4AA9-A89D-A9E5F8F0EB6B

Data Source:  Microstackshots
Shared Cache: 0x3868000 57B2E2F3-10A7-3AAD-AC94-975B957DF535

Command:  R
Path: /Applications/R.app/Contents/MacOS/R
Identifier:   org.R-project.R
Version:  R 4.0.0 GUI 1.71 Catalina build (7827)
PID:  21391

Event:cpu usage
Action taken: none
CPU:  90 seconds cpu time over 100 seconds (90% cpu
average), exceeding limit of 50% cpu over 180 seconds
CPU limit:90s
Limit duration:   180s
CPU used: 90s
CPU duration: 100s
Duration: 100.35s
Duration Sampled: 87.74s
Steps:51

Hardware model:   iMac19,2
Active cpus:  4

Fan speed:1200 rpm

Heaviest stack for the target process:
   51  start + 1 (libdyld.dylib + 109769) [0x7fff6a9b1cc9]
   51  main + 720 (R + 8032) [0x105c66f60]
   51  -[NSApplication finishLaunching] + 2601 (AppKit + 207160)
[0x7fff2dc1c938]
   51  -[NSApplication _postDidFinishNotification] + 312 (AppKit +
306403) [0x7fff2dc34ce3]
   51  -[NSNotificationCenter postNotificationName:object:userInfo:] +
59 (Foundation + 38790) [0x7fff32ff6786]
   51  _CFXNotificationPost + 1351 (CoreFoundation + 297529)
[0x7fff3097ba39]
   51  -[_CFXNotificationRegistrar find:object:observer:enumerator:] +
1554 (CoreFoundation + 300429) [0x7fff3097c58d]
   51  ___CFXNotificationPost_block_invoke + 80 (CoreFoundation +
496660) [0x7fff309ac414]
   51  _CFXRegistrationPost1 + 372 (CoreFoundation + 497576)
[0x7fff309ac7a8]
   51  ___CFXRegistrationPost1_block_invoke + 63 (CoreFoundation +
497715) [0x7fff309ac833]
   51  __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 12
(CoreFoundation + 497823) [0x7fff309ac89f]
   51  -[RController applicationDidFinishLaunching:] + 1176 (R + 15960)
[0x105c68e58]
   51  -[REngine executeString:] + 286 (R + 76926) [0x105c77c7e]
   51  -[NSRunLoop(NSRunLoop) runMode:beforeDate:] + 212 (Foundation +
393672) [0x7fff3304d1c8]
   51  CFRunLoopRunSpecific + 462 (CoreFoundation + 532174)
[0x7fff309b4ece]
   51  __CFRunLoopRun + 874 (CoreFoundation + 534677) [0x7fff309b5895]
   51  __CFRunLoopDoObservers + 457 (CoreFoundation + 537335)
[0x7fff309b62f7]
   51  __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ +
23 (CoreFoundation + 537541) [0x7fff309b63c5]
   51  ___NSRunLoopObserverCreateWithHandler_block_invoke + 41 (AppKit +
9439312) [0x7fff2e4ea850]
   51  __62+[CATransaction(NSCATransaction)
NS_setFlushesWithDisplayLink]_block_invoke + 266 (AppKit + 1971601)
[0x7fff2ddcb591]
   51  CA::Transaction::commit() + 644 (QuartzCore + 8352) [0x7fff3c47a0a0]
   51  CA::Context::commit_transaction(CA::Transaction*, double) + 334
(QuartzCore + 13494) [0x7fff3c47b4b6]
   51  CA::Layer::display_if_needed(CA::Transaction*) + 757 (QuartzCore
+ 152061) [0x7fff3c49d1fd]
   51  -[_NSViewBackingLayer display] + 800 (AppKit + 1231223)
[0x7fff2dd1

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

2020-06-07 Thread John Helly via R-SIG-Mac

Fails for me 100%.  If you want to zoom to look at it, I can arrange. 
Hard to explain how to replicate since it happens right away as soon as
I try to do anything.  Running Catalina on a brand-new Mac Pro.

J.

On 6/7/20 15:46, Simon Urbanek wrote:
> Thanks for the reports. Unfortunately, I still cannot reproduce it on 
> Catalina - neither with 4.0.1 nor 4.0.0.
> Can someone post exactly how to replicate? (How do exactly you open the file? 
> - the Open dialog works fine for me...)
>
> Note that the GUI is independent of R and compatible up to the patch version, 
> i.e. the 4.0.0 GUI works with R 4.0.1 and vice-versa. You can also just 
> download the GUI from
> https://urldefense.com/v3/__https://mac.R-project.org__;!!Mih3wA!ReiXSbqAjm6U4nbE1g9kiDWBjuTDcKsZfnp69eK0Ey0VZg4-UB24sxHHdM6_uVk$
>  
> and run it from the image, you don’t even have to install it.
>
> The only changes in the GUI for 4.0.1 were in the colours for dark mode, so 
> file handling behaviour didn’t really change.
>
> Some places to remove to try if it has any effect:
>
> rm -rf ~/Library/Caches/org.R-project.R
> rm ~/Library/Preferences/org.R-project.R.plist 
>
> Thanks,
> Simon
>
>
>
>> On Jun 8, 2020, at 10:22 AM, Brandon Hurr  wrote:
>>
>> This sounds exactly like the issue I am still having when I run to open
>> more than one R script file in R-GUI’s editor. Perhaps it has got worse
>> with the newer builds?
>>
>> On Sun, Jun 7, 2020 at 15:16 Carl Witthoft  wrote:
>>
>>> I'm not sure what to look for in the Reports sections of Console.app,
>>> but I did find this report of R exceeding a diagnostic limit of CPU
>>> usage, which most likely is related to one of the hangs - R.app always
>>> goes full throttle on one CPU core.
>>>
>>> Date/Time:2020-06-05 18:58:36 -0400
>>> End time: 2020-06-05 19:00:16 -0400
>>> OS Version:   Mac OS X 10.15.5 (Build 19F101)
>>> Architecture: x86_64h
>>> Report Version:   29
>>> Incident Identifier: E3BE34D3-09C5-4AA9-A89D-A9E5F8F0EB6B
>>>
>>> Data Source:  Microstackshots
>>> Shared Cache: 0x3868000 57B2E2F3-10A7-3AAD-AC94-975B957DF535
>>>
>>> Command:  R
>>> Path: /Applications/R.app/Contents/MacOS/R
>>> Identifier:   org.R-project.R
>>> Version:  R 4.0.0 GUI 1.71 Catalina build (7827)
>>> PID:  21391
>>>
>>> Event:cpu usage
>>> Action taken: none
>>> CPU:  90 seconds cpu time over 100 seconds (90% cpu
>>> average), exceeding limit of 50% cpu over 180 seconds
>>> CPU limit:90s
>>> Limit duration:   180s
>>> CPU used: 90s
>>> CPU duration: 100s
>>> Duration: 100.35s
>>> Duration Sampled: 87.74s
>>> Steps:51
>>>
>>> Hardware model:   iMac19,2
>>> Active cpus:  4
>>>
>>> Fan speed:1200 rpm
>>>
>>> Heaviest stack for the target process:
>>>   51  start + 1 (libdyld.dylib + 109769) [0x7fff6a9b1cc9]
>>>   51  main + 720 (R + 8032) [0x105c66f60]
>>>   51  -[NSApplication finishLaunching] + 2601 (AppKit + 207160)
>>> [0x7fff2dc1c938]
>>>   51  -[NSApplication _postDidFinishNotification] + 312 (AppKit +
>>> 306403) [0x7fff2dc34ce3]
>>>   51  -[NSNotificationCenter postNotificationName:object:userInfo:] +
>>> 59 (Foundation + 38790) [0x7fff32ff6786]
>>>   51  _CFXNotificationPost + 1351 (CoreFoundation + 297529)
>>> [0x7fff3097ba39]
>>>   51  -[_CFXNotificationRegistrar find:object:observer:enumerator:] +
>>> 1554 (CoreFoundation + 300429) [0x7fff3097c58d]
>>>   51  ___CFXNotificationPost_block_invoke + 80 (CoreFoundation +
>>> 496660) [0x7fff309ac414]
>>>   51  _CFXRegistrationPost1 + 372 (CoreFoundation + 497576)
>>> [0x7fff309ac7a8]
>>>   51  ___CFXRegistrationPost1_block_invoke + 63 (CoreFoundation +
>>> 497715) [0x7fff309ac833]
>>>   51  __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 12
>>> (CoreFoundation + 497823) [0x7fff309ac89f]
>>>   51  -[RController applicationDidFinishLaunching:] + 1176 (R + 15960)
>>> [0x105c68e58]
>>>   51  -[REngine executeString:] + 286 (R + 76926) [0x105c77c7e]
>>>   51  -[NSRunLoop(NSRunLoop) runMode:beforeDate:] + 212 (Foundation +
>>> 393672) [0x7fff3304d1c8]
>>>   51  CFRunLoopRunSpecific + 462 (CoreFoundation + 532174)
>>> [0x7fff309b4ece]
>>>   51  __CFRunLoopRun + 874 (CoreFoundation + 534677) [0x7fff309b5895]
>>>   51  __CFRunLoopDoObservers + 457 (CoreFoundation + 537335)
>>> [0x7fff309b62f7]
>>>   51  __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ +
>>> 23 (CoreFoundation + 537541) [0x7fff309b63c5]
>>>   51  ___NSRunLoopObserverCreateWithHandler_block_invoke + 41 (AppKit +
>>> 9439312) [0x7fff2e4ea850]
>>>   51  __62+[CATransaction(NSCATransaction)
>>> NS_setFlushesWithDisplayLink]_block_invoke + 266 (AppKit + 1971601)
>>> [0x7fff2ddcb591]
>>>   51  CA::Transaction::commit() + 644 (QuartzCore + 8352) [0x7fff3c47a0a0]
>>>   51  CA::Context::commit_transaction(CA::Transaction*, double) + 334
>>> (QuartzCore + 13494) [0x7fff3c47b4b6]
>>>   51  CA::Layer::display_if_needed(CA::Transaction*)

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

2020-06-07 Thread Carl Witthoft


I tried removing those Pref and Cache items. No help
It doesn't matter how I try to open a file: double-click the file, 
drag&drop,  from the Rgui File menu or the icon in the header of the 
console window.  They all hang the same way.  I tried turning off 
DefaultFolder and QuickSilver; no help.
I'm happy to try other experiments -- about the only other "unusual" 
thing in my setup is  USBOverdrive.


Just in case:  10.15.5, 3.6 GHz quadcore i3, 16GB Apple-installed RAM , 
APFS, SATA hard drive (not SSD)


On 6/7/20 6:46 PM, Simon Urbanek wrote:

Thanks for the reports. Unfortunately, I still cannot reproduce it on Catalina 
- neither with 4.0.1 nor 4.0.0.
Can someone post exactly how to replicate? (How do exactly you open the file? - 
the Open dialog works fine for me...)

Note that the GUI is independent of R and compatible up to the patch version, 
i.e. the 4.0.0 GUI works with R 4.0.1 and vice-versa. You can also just 
download the GUI from
https://mac.R-project.org
and run it from the image, you don’t even have to install it.

The only changes in the GUI for 4.0.1 were in the colours for dark mode, so 
file handling behaviour didn’t really change.

Some places to remove to try if it has any effect:

rm -rf ~/Library/Caches/org.R-project.R
rm ~/Library/Preferences/org.R-project.R.plist

Thanks,
Simon




On Jun 8, 2020, at 10:22 AM, Brandon Hurr  wrote:

This sounds exactly like the issue I am still having when I run to open
more than one R script file in R-GUI’s editor. Perhaps it has got worse
with the newer builds?

On Sun, Jun 7, 2020 at 15:16 Carl Witthoft  wrote:


I'm not sure what to look for in the Reports sections of Console.app,
but I did find this report of R exceeding a diagnostic limit of CPU
usage, which most likely is related to one of the hangs - R.app always
goes full throttle on one CPU core.

Date/Time:2020-06-05 18:58:36 -0400
End time: 2020-06-05 19:00:16 -0400
OS Version:   Mac OS X 10.15.5 (Build 19F101)
Architecture: x86_64h
Report Version:   29
Incident Identifier: E3BE34D3-09C5-4AA9-A89D-A9E5F8F0EB6B

Data Source:  Microstackshots
Shared Cache: 0x3868000 57B2E2F3-10A7-3AAD-AC94-975B957DF535

Command:  R
Path: /Applications/R.app/Contents/MacOS/R
Identifier:   org.R-project.R
Version:  R 4.0.0 GUI 1.71 Catalina build (7827)
PID:  21391

Event:cpu usage
Action taken: none
CPU:  90 seconds cpu time over 100 seconds (90% cpu
average), exceeding limit of 50% cpu over 180 seconds
CPU limit:90s
Limit duration:   180s
CPU used: 90s
CPU duration: 100s
Duration: 100.35s
Duration Sampled: 87.74s
Steps:51

Hardware model:   iMac19,2
Active cpus:  4

Fan speed:1200 rpm

Heaviest stack for the target process:
   51  start + 1 (libdyld.dylib + 109769) [0x7fff6a9b1cc9]
   51  main + 720 (R + 8032) [0x105c66f60]
   51  -[NSApplication finishLaunching] + 2601 (AppKit + 207160)
[0x7fff2dc1c938]
   51  -[NSApplication _postDidFinishNotification] + 312 (AppKit +
306403) [0x7fff2dc34ce3]
   51  -[NSNotificationCenter postNotificationName:object:userInfo:] +
59 (Foundation + 38790) [0x7fff32ff6786]
   51  _CFXNotificationPost + 1351 (CoreFoundation + 297529)
[0x7fff3097ba39]
   51  -[_CFXNotificationRegistrar find:object:observer:enumerator:] +
1554 (CoreFoundation + 300429) [0x7fff3097c58d]
   51  ___CFXNotificationPost_block_invoke + 80 (CoreFoundation +
496660) [0x7fff309ac414]
   51  _CFXRegistrationPost1 + 372 (CoreFoundation + 497576)
[0x7fff309ac7a8]
   51  ___CFXRegistrationPost1_block_invoke + 63 (CoreFoundation +
497715) [0x7fff309ac833]
   51  __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 12
(CoreFoundation + 497823) [0x7fff309ac89f]
   51  -[RController applicationDidFinishLaunching:] + 1176 (R + 15960)
[0x105c68e58]
   51  -[REngine executeString:] + 286 (R + 76926) [0x105c77c7e]
   51  -[NSRunLoop(NSRunLoop) runMode:beforeDate:] + 212 (Foundation +
393672) [0x7fff3304d1c8]
   51  CFRunLoopRunSpecific + 462 (CoreFoundation + 532174)
[0x7fff309b4ece]
   51  __CFRunLoopRun + 874 (CoreFoundation + 534677) [0x7fff309b5895]
   51  __CFRunLoopDoObservers + 457 (CoreFoundation + 537335)
[0x7fff309b62f7]
   51  __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ +
23 (CoreFoundation + 537541) [0x7fff309b63c5]
   51  ___NSRunLoopObserverCreateWithHandler_block_invoke + 41 (AppKit +
9439312) [0x7fff2e4ea850]
   51  __62+[CATransaction(NSCATransaction)
NS_setFlushesWithDisplayLink]_block_invoke + 266 (AppKit + 1971601)
[0x7fff2ddcb591]
   51  CA::Transaction::commit() + 644 (QuartzCore + 8352) [0x7fff3c47a0a0]
   51  CA::Context::commit_transaction(CA::Transaction*, double) + 334
(QuartzCore + 13494) [0x7fff3c47b4b6]
   51  CA::Layer::display_if_needed(CA::Transaction*) + 757 (QuartzCore
+ 152061) [0x7fff3c49d1fd]
   51  -[_NSViewBackingLayer display] + 800 (AppKit + 1231223)
[0x7fff2dd16977]
   51  -[_NSBackingLayer dis

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

2020-06-07 Thread Simon Urbanek

Thanks for the reports. Unfortunately, I still cannot reproduce it on Catalina 
- neither with 4.0.1 nor 4.0.0.
Can someone post exactly how to replicate? (How do exactly you open the file? - 
the Open dialog works fine for me...)

Note that the GUI is independent of R and compatible up to the patch version, 
i.e. the 4.0.0 GUI works with R 4.0.1 and vice-versa. You can also just 
download the GUI from
https://mac.R-project.org
and run it from the image, you don’t even have to install it.

The only changes in the GUI for 4.0.1 were in the colours for dark mode, so 
file handling behaviour didn’t really change.

Some places to remove to try if it has any effect:

rm -rf ~/Library/Caches/org.R-project.R
rm ~/Library/Preferences/org.R-project.R.plist 

Thanks,
Simon



> On Jun 8, 2020, at 10:22 AM, Brandon Hurr  wrote:
> 
> This sounds exactly like the issue I am still having when I run to open
> more than one R script file in R-GUI’s editor. Perhaps it has got worse
> with the newer builds?
> 
> On Sun, Jun 7, 2020 at 15:16 Carl Witthoft  wrote:
> 
>> I'm not sure what to look for in the Reports sections of Console.app,
>> but I did find this report of R exceeding a diagnostic limit of CPU
>> usage, which most likely is related to one of the hangs - R.app always
>> goes full throttle on one CPU core.
>> 
>> Date/Time:2020-06-05 18:58:36 -0400
>> End time: 2020-06-05 19:00:16 -0400
>> OS Version:   Mac OS X 10.15.5 (Build 19F101)
>> Architecture: x86_64h
>> Report Version:   29
>> Incident Identifier: E3BE34D3-09C5-4AA9-A89D-A9E5F8F0EB6B
>> 
>> Data Source:  Microstackshots
>> Shared Cache: 0x3868000 57B2E2F3-10A7-3AAD-AC94-975B957DF535
>> 
>> Command:  R
>> Path: /Applications/R.app/Contents/MacOS/R
>> Identifier:   org.R-project.R
>> Version:  R 4.0.0 GUI 1.71 Catalina build (7827)
>> PID:  21391
>> 
>> Event:cpu usage
>> Action taken: none
>> CPU:  90 seconds cpu time over 100 seconds (90% cpu
>> average), exceeding limit of 50% cpu over 180 seconds
>> CPU limit:90s
>> Limit duration:   180s
>> CPU used: 90s
>> CPU duration: 100s
>> Duration: 100.35s
>> Duration Sampled: 87.74s
>> Steps:51
>> 
>> Hardware model:   iMac19,2
>> Active cpus:  4
>> 
>> Fan speed:1200 rpm
>> 
>> Heaviest stack for the target process:
>>   51  start + 1 (libdyld.dylib + 109769) [0x7fff6a9b1cc9]
>>   51  main + 720 (R + 8032) [0x105c66f60]
>>   51  -[NSApplication finishLaunching] + 2601 (AppKit + 207160)
>> [0x7fff2dc1c938]
>>   51  -[NSApplication _postDidFinishNotification] + 312 (AppKit +
>> 306403) [0x7fff2dc34ce3]
>>   51  -[NSNotificationCenter postNotificationName:object:userInfo:] +
>> 59 (Foundation + 38790) [0x7fff32ff6786]
>>   51  _CFXNotificationPost + 1351 (CoreFoundation + 297529)
>> [0x7fff3097ba39]
>>   51  -[_CFXNotificationRegistrar find:object:observer:enumerator:] +
>> 1554 (CoreFoundation + 300429) [0x7fff3097c58d]
>>   51  ___CFXNotificationPost_block_invoke + 80 (CoreFoundation +
>> 496660) [0x7fff309ac414]
>>   51  _CFXRegistrationPost1 + 372 (CoreFoundation + 497576)
>> [0x7fff309ac7a8]
>>   51  ___CFXRegistrationPost1_block_invoke + 63 (CoreFoundation +
>> 497715) [0x7fff309ac833]
>>   51  __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 12
>> (CoreFoundation + 497823) [0x7fff309ac89f]
>>   51  -[RController applicationDidFinishLaunching:] + 1176 (R + 15960)
>> [0x105c68e58]
>>   51  -[REngine executeString:] + 286 (R + 76926) [0x105c77c7e]
>>   51  -[NSRunLoop(NSRunLoop) runMode:beforeDate:] + 212 (Foundation +
>> 393672) [0x7fff3304d1c8]
>>   51  CFRunLoopRunSpecific + 462 (CoreFoundation + 532174)
>> [0x7fff309b4ece]
>>   51  __CFRunLoopRun + 874 (CoreFoundation + 534677) [0x7fff309b5895]
>>   51  __CFRunLoopDoObservers + 457 (CoreFoundation + 537335)
>> [0x7fff309b62f7]
>>   51  __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ +
>> 23 (CoreFoundation + 537541) [0x7fff309b63c5]
>>   51  ___NSRunLoopObserverCreateWithHandler_block_invoke + 41 (AppKit +
>> 9439312) [0x7fff2e4ea850]
>>   51  __62+[CATransaction(NSCATransaction)
>> NS_setFlushesWithDisplayLink]_block_invoke + 266 (AppKit + 1971601)
>> [0x7fff2ddcb591]
>>   51  CA::Transaction::commit() + 644 (QuartzCore + 8352) [0x7fff3c47a0a0]
>>   51  CA::Context::commit_transaction(CA::Transaction*, double) + 334
>> (QuartzCore + 13494) [0x7fff3c47b4b6]
>>   51  CA::Layer::display_if_needed(CA::Transaction*) + 757 (QuartzCore
>> + 152061) [0x7fff3c49d1fd]
>>   51  -[_NSViewBackingLayer display] + 800 (AppKit + 1231223)
>> [0x7fff2dd16977]
>>   51  -[_NSBackingLayer display] + 537 (AppKit + 1879690) [0x7fff2ddb4e8a]
>>   51  -[CALayer _display] + 2103 (QuartzCore + 156002) [0x7fff3c49e162]
>>   51  invocation function for block in CA::Layer::display_() + 53
>> (QuartzCore + 550873) [0x7fff3c4fe7d9]
>>   51  CABackingStoreUpdate_ + 595 (QuartzCore + 158813) [0x7fff3c49ec5d]
>>

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

2020-06-07 Thread Brandon Hurr

This sounds exactly like the issue I am still having when I run to open
more than one R script file in R-GUI’s editor. Perhaps it has got worse
with the newer builds?

On Sun, Jun 7, 2020 at 15:16 Carl Witthoft  wrote:

> I'm not sure what to look for in the Reports sections of Console.app,
> but I did find this report of R exceeding a diagnostic limit of CPU
> usage, which most likely is related to one of the hangs - R.app always
> goes full throttle on one CPU core.
>
> Date/Time:2020-06-05 18:58:36 -0400
> End time: 2020-06-05 19:00:16 -0400
> OS Version:   Mac OS X 10.15.5 (Build 19F101)
> Architecture: x86_64h
> Report Version:   29
> Incident Identifier: E3BE34D3-09C5-4AA9-A89D-A9E5F8F0EB6B
>
> Data Source:  Microstackshots
> Shared Cache: 0x3868000 57B2E2F3-10A7-3AAD-AC94-975B957DF535
>
> Command:  R
> Path: /Applications/R.app/Contents/MacOS/R
> Identifier:   org.R-project.R
> Version:  R 4.0.0 GUI 1.71 Catalina build (7827)
> PID:  21391
>
> Event:cpu usage
> Action taken: none
> CPU:  90 seconds cpu time over 100 seconds (90% cpu
> average), exceeding limit of 50% cpu over 180 seconds
> CPU limit:90s
> Limit duration:   180s
> CPU used: 90s
> CPU duration: 100s
> Duration: 100.35s
> Duration Sampled: 87.74s
> Steps:51
>
> Hardware model:   iMac19,2
> Active cpus:  4
>
> Fan speed:1200 rpm
>
> Heaviest stack for the target process:
>51  start + 1 (libdyld.dylib + 109769) [0x7fff6a9b1cc9]
>51  main + 720 (R + 8032) [0x105c66f60]
>51  -[NSApplication finishLaunching] + 2601 (AppKit + 207160)
> [0x7fff2dc1c938]
>51  -[NSApplication _postDidFinishNotification] + 312 (AppKit +
> 306403) [0x7fff2dc34ce3]
>51  -[NSNotificationCenter postNotificationName:object:userInfo:] +
> 59 (Foundation + 38790) [0x7fff32ff6786]
>51  _CFXNotificationPost + 1351 (CoreFoundation + 297529)
> [0x7fff3097ba39]
>51  -[_CFXNotificationRegistrar find:object:observer:enumerator:] +
> 1554 (CoreFoundation + 300429) [0x7fff3097c58d]
>51  ___CFXNotificationPost_block_invoke + 80 (CoreFoundation +
> 496660) [0x7fff309ac414]
>51  _CFXRegistrationPost1 + 372 (CoreFoundation + 497576)
> [0x7fff309ac7a8]
>51  ___CFXRegistrationPost1_block_invoke + 63 (CoreFoundation +
> 497715) [0x7fff309ac833]
>51  __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 12
> (CoreFoundation + 497823) [0x7fff309ac89f]
>51  -[RController applicationDidFinishLaunching:] + 1176 (R + 15960)
> [0x105c68e58]
>51  -[REngine executeString:] + 286 (R + 76926) [0x105c77c7e]
>51  -[NSRunLoop(NSRunLoop) runMode:beforeDate:] + 212 (Foundation +
> 393672) [0x7fff3304d1c8]
>51  CFRunLoopRunSpecific + 462 (CoreFoundation + 532174)
> [0x7fff309b4ece]
>51  __CFRunLoopRun + 874 (CoreFoundation + 534677) [0x7fff309b5895]
>51  __CFRunLoopDoObservers + 457 (CoreFoundation + 537335)
> [0x7fff309b62f7]
>51  __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ +
> 23 (CoreFoundation + 537541) [0x7fff309b63c5]
>51  ___NSRunLoopObserverCreateWithHandler_block_invoke + 41 (AppKit +
> 9439312) [0x7fff2e4ea850]
>51  __62+[CATransaction(NSCATransaction)
> NS_setFlushesWithDisplayLink]_block_invoke + 266 (AppKit + 1971601)
> [0x7fff2ddcb591]
>51  CA::Transaction::commit() + 644 (QuartzCore + 8352) [0x7fff3c47a0a0]
>51  CA::Context::commit_transaction(CA::Transaction*, double) + 334
> (QuartzCore + 13494) [0x7fff3c47b4b6]
>51  CA::Layer::display_if_needed(CA::Transaction*) + 757 (QuartzCore
> + 152061) [0x7fff3c49d1fd]
>51  -[_NSViewBackingLayer display] + 800 (AppKit + 1231223)
> [0x7fff2dd16977]
>51  -[_NSBackingLayer display] + 537 (AppKit + 1879690) [0x7fff2ddb4e8a]
>51  -[CALayer _display] + 2103 (QuartzCore + 156002) [0x7fff3c49e162]
>51  invocation function for block in CA::Layer::display_() + 53
> (QuartzCore + 550873) [0x7fff3c4fe7d9]
>51  CABackingStoreUpdate_ + 595 (QuartzCore + 158813) [0x7fff3c49ec5d]
>51  -[NSView(NSLayerKitGlue)
> _drawViewBackingLayer:inContext:drawingHandler:] + 1271 (AppKit +
> 1881242) [0x7fff2ddb549a]
>51  -[NSView(NSInternal)
> _recursive:displayRectIgnoringOpacity:inContext:stopAtLayerBackedViews:]
> + 2170 (AppKit + 1884318) [0x7fff2ddb609e]
>51  _NSViewDrawRect + 139 (AppKit + 1887631) [0x7fff2ddb6d8f]
>51  -[_NSRulerContentView drawRect:] + 157 (AppKit + 7667047)
> [0x7fff2e339d67]
>51  -[NSRulerView _drawContentRect:] + 233 (AppKit + 7663663)
> [0x7fff2e33902f]
>51  -[NoodleLineNumberView drawHashMarksAndLabelsInRect:] + 345 (R +
> 338153) [0x105cb78e9]
>51  -[NSLayoutManager(NSPrivate)
> _glyphRangeForBoundingRect:inTextContainer:fast:okToFillHoles:] + 857
> (UIFoundation + 336155) [0x7fff61a0411b]
>51  -[NSLayoutManager(NSPrivate)
> _firstPassGlyphRangeForBoundingRect:inTextContainer:okToFillHoles:] +
> 1441 (UIFoundation + 341594) [0x

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

2020-06-07 Thread Carl Witthoft

I'm not sure what to look for in the Reports sections of Console.app, 
but I did find this report of R exceeding a diagnostic limit of CPU 
usage, which most likely is related to one of the hangs - R.app always 
goes full throttle on one CPU core.


Date/Time:2020-06-05 18:58:36 -0400
End time: 2020-06-05 19:00:16 -0400
OS Version:   Mac OS X 10.15.5 (Build 19F101)
Architecture: x86_64h
Report Version:   29
Incident Identifier: E3BE34D3-09C5-4AA9-A89D-A9E5F8F0EB6B

Data Source:  Microstackshots
Shared Cache: 0x3868000 57B2E2F3-10A7-3AAD-AC94-975B957DF535

Command:  R
Path: /Applications/R.app/Contents/MacOS/R
Identifier:   org.R-project.R
Version:  R 4.0.0 GUI 1.71 Catalina build (7827)
PID:  21391

Event:cpu usage
Action taken: none
CPU:  90 seconds cpu time over 100 seconds (90% cpu 
average), exceeding limit of 50% cpu over 180 seconds

CPU limit:90s
Limit duration:   180s
CPU used: 90s
CPU duration: 100s
Duration: 100.35s
Duration Sampled: 87.74s
Steps:51

Hardware model:   iMac19,2
Active cpus:  4

Fan speed:1200 rpm

Heaviest stack for the target process:
  51  start + 1 (libdyld.dylib + 109769) [0x7fff6a9b1cc9]
  51  main + 720 (R + 8032) [0x105c66f60]
  51  -[NSApplication finishLaunching] + 2601 (AppKit + 207160) 
[0x7fff2dc1c938]
  51  -[NSApplication _postDidFinishNotification] + 312 (AppKit + 
306403) [0x7fff2dc34ce3]
  51  -[NSNotificationCenter postNotificationName:object:userInfo:] + 
59 (Foundation + 38790) [0x7fff32ff6786]
  51  _CFXNotificationPost + 1351 (CoreFoundation + 297529) 
[0x7fff3097ba39]
  51  -[_CFXNotificationRegistrar find:object:observer:enumerator:] + 
1554 (CoreFoundation + 300429) [0x7fff3097c58d]
  51  ___CFXNotificationPost_block_invoke + 80 (CoreFoundation + 
496660) [0x7fff309ac414]
  51  _CFXRegistrationPost1 + 372 (CoreFoundation + 497576) 
[0x7fff309ac7a8]
  51  ___CFXRegistrationPost1_block_invoke + 63 (CoreFoundation + 
497715) [0x7fff309ac833]
  51  __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 12 
(CoreFoundation + 497823) [0x7fff309ac89f]
  51  -[RController applicationDidFinishLaunching:] + 1176 (R + 15960) 
[0x105c68e58]

  51  -[REngine executeString:] + 286 (R + 76926) [0x105c77c7e]
  51  -[NSRunLoop(NSRunLoop) runMode:beforeDate:] + 212 (Foundation + 
393672) [0x7fff3304d1c8]

  51  CFRunLoopRunSpecific + 462 (CoreFoundation + 532174) [0x7fff309b4ece]
  51  __CFRunLoopRun + 874 (CoreFoundation + 534677) [0x7fff309b5895]
  51  __CFRunLoopDoObservers + 457 (CoreFoundation + 537335) 
[0x7fff309b62f7]
  51  __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ + 
23 (CoreFoundation + 537541) [0x7fff309b63c5]
  51  ___NSRunLoopObserverCreateWithHandler_block_invoke + 41 (AppKit + 
9439312) [0x7fff2e4ea850]
  51  __62+[CATransaction(NSCATransaction) 
NS_setFlushesWithDisplayLink]_block_invoke + 266 (AppKit + 1971601) 
[0x7fff2ddcb591]

  51  CA::Transaction::commit() + 644 (QuartzCore + 8352) [0x7fff3c47a0a0]
  51  CA::Context::commit_transaction(CA::Transaction*, double) + 334 
(QuartzCore + 13494) [0x7fff3c47b4b6]
  51  CA::Layer::display_if_needed(CA::Transaction*) + 757 (QuartzCore 
+ 152061) [0x7fff3c49d1fd]
  51  -[_NSViewBackingLayer display] + 800 (AppKit + 1231223) 
[0x7fff2dd16977]

  51  -[_NSBackingLayer display] + 537 (AppKit + 1879690) [0x7fff2ddb4e8a]
  51  -[CALayer _display] + 2103 (QuartzCore + 156002) [0x7fff3c49e162]
  51  invocation function for block in CA::Layer::display_() + 53 
(QuartzCore + 550873) [0x7fff3c4fe7d9]

  51  CABackingStoreUpdate_ + 595 (QuartzCore + 158813) [0x7fff3c49ec5d]
  51  -[NSView(NSLayerKitGlue) 
_drawViewBackingLayer:inContext:drawingHandler:] + 1271 (AppKit + 
1881242) [0x7fff2ddb549a]
  51  -[NSView(NSInternal) 
_recursive:displayRectIgnoringOpacity:inContext:stopAtLayerBackedViews:] 
+ 2170 (AppKit + 1884318) [0x7fff2ddb609e]

  51  _NSViewDrawRect + 139 (AppKit + 1887631) [0x7fff2ddb6d8f]
  51  -[_NSRulerContentView drawRect:] + 157 (AppKit + 7667047) 
[0x7fff2e339d67]
  51  -[NSRulerView _drawContentRect:] + 233 (AppKit + 7663663) 
[0x7fff2e33902f]
  51  -[NoodleLineNumberView drawHashMarksAndLabelsInRect:] + 345 (R + 
338153) [0x105cb78e9]
  51  -[NSLayoutManager(NSPrivate) 
_glyphRangeForBoundingRect:inTextContainer:fast:okToFillHoles:] + 857 
(UIFoundation + 336155) [0x7fff61a0411b]
  51  -[NSLayoutManager(NSPrivate) 
_firstPassGlyphRangeForBoundingRect:inTextContainer:okToFillHoles:] + 
1441 (UIFoundation + 341594) [0x7fff61a0565a]
  51  _NSFastFillAllLayoutHolesForGlyphRange + 1863 (UIFoundation + 
202864) [0x7fff619e3870]
  51  _resizeTextViewsIfNeeded + 284 (UIFoundation + 427013) 
[0x7fff61a1a405]
  51  -[NSLayoutManager(NSPrivate) _resizeTextViewForTextContainer:] + 
1103 (UIFoundation + 144184) [0x7fff619d5338]
  51  -[NSTextView setConstrainedFrameSize:] + 591 (AppKit + 1539771) 
[0x7fff2dd61ebb]

  51  -[NSTextView setFram

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

2020-06-07 Thread Bob Rudis

Are there any entries in Console.app that might help triage?

Have you tried creating a new user on your Mac and seeing if that account has 
issues performing the same tasks your user account is having?

Having said that, I just grabbed "Mac OS X GUI rev. 7843 for R 4.0.x" from 
mac.r-project.org (I never use R.app nor do I keep it installed unless testing 
something) and am running R 4.0.1 on latest Catalina beta — 10.15.6 Beta 
(19G36e) — and it crashes every time I try to open a .R file (crashlog 
https://paste.sr.ht/~hrbrmstr/9899f3a7f3c1724cc952b935c3fc39a47cac88ac)

> On Jun 7, 2020, at 16:22, Carl Witthoft  wrote:
> 
> 
> 
> 
> Hi,
> 2 weeks ago I installed R 4.0 on my new Catalina machine. Things seemed to be 
> working fine.
> Today I installed R 4.01, and now I can't open any FILE.r - no matter what 
> way I try, i.e. double-click the file, drag/drop, or open from the R GUI 
> menu,  R hangs with the beachball.
> I tried giving R full disk access and other privileges via Security settings; 
> no help.
> 
> So I deleted R 4.01 and reinstalled R 4.0, and dang if I no longer can open 
> files any more!  I've tried all the suggestions in the previous thread in 
> this mailing group; no help.
> 
> What else can I do, or delete, or uninstall, to at least get back to where I 
> was? Right now I'm basically DIW.
> -- 
> Carl Witthoft
> c...@witthoft.com
> resume: https://app.box.com/file/498153801347
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

2020-06-07 Thread Carl Witthoft






Hi,
2 weeks ago I installed R 4.0 on my new Catalina machine. Things seemed 
to be working fine.
Today I installed R 4.01, and now I can't open any FILE.r - no matter 
what way I try, i.e. double-click the file, drag/drop, or open from the 
R GUI menu,  R hangs with the beachball.
I tried giving R full disk access and other privileges via Security 
settings; no help.


So I deleted R 4.01 and reinstalled R 4.0, and dang if I no longer can 
open files any more!  I've tried all the suggestions in the previous 
thread in this mailing group; no help.


What else can I do, or delete, or uninstall, to at least get back to 
where I was? Right now I'm basically DIW.

--
Carl Witthoft
c...@witthoft.com
resume: https://app.box.com/file/498153801347

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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