Re: [R-SIG-Mac] R Console (R.app) crashes - on Mac OS - caught segfault * address 0x18, cause 'memory not mapped'

[Christoph Napierala]

On 30.12.16 19:59, David Winsemius wrote:

On Dec 30, 2016, at 8:44 AM, Christoph Napierala  wrote:

Dear All

macOS Sierra - V 10.12.2
R 3.3.2 GUI 1.68 Mavericks build (7288)

I encountered an issue with the R console crashing after having saved the image. Normally 
I work with R-Studio which still runs "perfectly".
The following report was generated after having deleted R and R-Studio and 
cleaned libraries. The following message was generated:


Blockquote

*** caught segfault ***
address 0x18, cause 'memory not mapped'

   Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

2016-12-30 14:57:47.245 R[1475:47927] -[_CUIInternalLinkRendition 
setRuleThickness:]: unrecognized selector sent to instance 0x7ffeb66745d0

2016-12-30 14:57:47.247 R[1475:47927] *** RController: caught ObjC exception 
while processing system events. Update to the latest GUI version and consider 
reporting this properly (see FAQ) if it persists and is not known.

The latest GUI version at http://r.research.att.com/ is:

R-GUI-7299-3.3-mavericks-Debug.dmg

I tried but while installing I definitely do not get the current version?




*** reason: -[_CUIInternalLinkRendition setRuleThickness:]: unrecognized 
selector sent to instance 0x7ffeb66745d0

*** name: NSInvalidArgumentException, info: (null)

*** Version: R 3.3.2 (71607) R.app R 3.3.2 GUI 1.68 Mavericks build
Consider saving your work soon in case this develops into a problem.

You should probably reinstall the whole bundle since your version of R is not 
uptodate either:

R-3.3-branch
3.3.2 Patched
(2016/12/28, r71859)

The installer bundles at either of these sites should be the same:

http://r.research.att.com/mavericks/R-3.3-branch/R-3.3-branch-mavericks.pkg
https://cloud.r-project.org/bin/macosx/R-3.3.2.pkg


I tried but while installing I definitely do not get the current version?
AND I do get German as language in the R I have downloaded and 
re-installed? Something is really odd.



And then I am offered to select one of the above options and the crash 
reproduces.

Thanks for any support.

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David Winsemius
Alameda, CA, USA




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Re: [R-SIG-Mac] R Console (R.app) crashes - on Mac OS - caught segfault * address 0x18, cause 'memory not mapped'

[David Winsemius]

> On Dec 30, 2016, at 8:44 AM, Christoph Napierala  wrote:
> 
> Dear All
> 
> macOS Sierra - V 10.12.2
> R 3.3.2 GUI 1.68 Mavericks build (7288)
> 
> I encountered an issue with the R console crashing after having saved the 
> image. Normally I work with R-Studio which still runs "perfectly".
> The following report was generated after having deleted R and R-Studio and 
> cleaned libraries. The following message was generated:
> 
>> Blockquote
> *** caught segfault ***
> address 0x18, cause 'memory not mapped'
> 
>   Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> 
> 2016-12-30 14:57:47.245 R[1475:47927] -[_CUIInternalLinkRendition 
> setRuleThickness:]: unrecognized selector sent to instance 0x7ffeb66745d0
> 
> 2016-12-30 14:57:47.247 R[1475:47927] *** RController: caught ObjC exception 
> while processing system events. Update to the latest GUI version and consider 
> reporting this properly (see FAQ) if it persists and is not known.

The latest GUI version at http://r.research.att.com/ is:

R-GUI-7299-3.3-mavericks-Debug.dmg


> 
> *** reason: -[_CUIInternalLinkRendition setRuleThickness:]: unrecognized 
> selector sent to instance 0x7ffeb66745d0
> 
> *** name: NSInvalidArgumentException, info: (null)
> 
> *** Version: R 3.3.2 (71607) R.app R 3.3.2 GUI 1.68 Mavericks build
> Consider saving your work soon in case this develops into a problem.

You should probably reinstall the whole bundle since your version of R is not 
uptodate either:

R-3.3-branch
3.3.2 Patched
(2016/12/28, r71859)

The installer bundles at either of these sites should be the same:

http://r.research.att.com/mavericks/R-3.3-branch/R-3.3-branch-mavericks.pkg
https://cloud.r-project.org/bin/macosx/R-3.3.2.pkg



> 
> And then I am offered to select one of the above options and the crash 
> reproduces.
> 
> Thanks for any support.
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

David Winsemius
Alameda, CA, USA

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[R-SIG-Mac] R Console (R.app) crashes - on Mac OS - caught segfault * address 0x18, cause 'memory not mapped'

[Christoph Napierala]

Dear All

macOS Sierra - V 10.12.2
R 3.3.2 GUI 1.68 Mavericks build (7288)

I encountered an issue with the R console crashing after having saved 
the image. Normally I work with R-Studio which still runs "perfectly".
The following report was generated after having deleted R and R-Studio 
and cleaned libraries. The following message was generated:



Blockquote

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

   Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

2016-12-30 14:57:47.245 R[1475:47927] -[_CUIInternalLinkRendition 
setRuleThickness:]: unrecognized selector sent to instance 0x7ffeb66745d0


2016-12-30 14:57:47.247 R[1475:47927] *** RController: caught ObjC 
exception while processing system events. Update to the latest GUI 
version and consider reporting this properly (see FAQ) if it persists 
and is not known.


*** reason: -[_CUIInternalLinkRendition setRuleThickness:]: unrecognized 
selector sent to instance 0x7ffeb66745d0


*** name: NSInvalidArgumentException, info: (null)

*** Version: R 3.3.2 (71607) R.app R 3.3.2 GUI 1.68 Mavericks build
Consider saving your work soon in case this develops into a problem.

And then I am offered to select one of the above options and the crash 
reproduces.


Thanks for any support.

___
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R-SIG-Mac@r-project.org
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Re: [R-SIG-Mac] Totally frozen Gui and Forced Quit ... resolved.

[Joseph Kunkel]

Bryan,   aha!  … Exactly what I was fishing for in my turmoil … "an R.app 
plist”.  I look forward to that option since the “Open Recent” button is nice 
when it works but cursed when it does not.  Such a plist, I can see, has many 
ramifications to get right.  Thanks again for reviving my productivity.  I love 
the terminal mode for its independence and capacity but the GUI is essential 
for script development and fast turnaround.

Joe

> On Dec 30, 2016, at 7:41 AM, Bryan Hanson  wrote:
> 
> Excellent Joe.  If you have further problems, there have also been 
> discussions here in the past two months about the recent files list and an 
> R.app plist which can be removed manually, forcing the app to write a fresh 
> copy.  Bryan
> 
>> On Dec 29, 2016, at 11:10 PM, Joseph Kunkel  wrote:
>> 
>> Bryan,  Following the directions in section 10.11 I removed every .RData and 
>> .Rhistory in my entire tree with no satisfaction.
>> 
>> Finally, after removing every .Rapp.history ... R failed again but I was 
>> able to exit R ungracefully using option 1. 
>> 
>> On rebooting, R-gui reopened with all the 3 prior R-scripts also opened but 
>> the R-console was not frozen and after closing the R-scripts I q() R and on 
>> reopening I had a normal R-gui and no R-scripts opened.
>> 
>> I had known about the .Rhistory and .Rdata files but they were not the 
>> problem.  The .Rapp.history was the culprit but trying to be logical and 
>> just removing it from the most obvious directories did not work.  I had to 
>> remove every single one.  
>> 
>> Perhaps a clue?  I was unable to remove two of the  ‘.Rapp.history' files 
>> using their file paths in a rm statement.  Looking closely at the path there 
>> was a gramatically-poor directory in both failed removes.
>> One failure had ‘/text file/‘ which had an illegal space in the directory 
>> name and the other failure had another illegal character in a path component 
>> /1&2/.   After I removed those two  ‘.Rapp.history’ files I was able to 
>> break the loop.
>> 
>> Thanks for the URL with directions that included the solution!
>> 
>> In addition I will redouble my conscious use of good unix path names!  OS X 
>> allows navigating through paths that may be easier to read but are traps for 
>> unix command syntax.
>> 
>> Joe
>> 
>> 
>>> On Dec 29, 2016, at 7:56 PM, Bryan Hanson  wrote:
>>> 
>>> Take a look at section 10.3 and 10.11 in 
>>> https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#Miscellaneous-questions
>>> 
>>> I also remove .Rhistory routinely (in addition to the files listed in 
>>> 10.11) when having trouble.
>>> 
>>> If you need assistance finding these files throughout your system using 
>>> terminal, let us know.
>>> 
>>> Another alternative is to get R devel at http://r.research.att.com/ That 
>>> version of the GUI appears to have some fixes.
>>> 
>>> Bryan
>>> 
 On Dec 29, 2016, at 7:46 PM, Joseph Kunkel  wrote:
 
 Dear R-Sig-Mac,
 
 I have not received any response to my request for help in unlocking my 
 R-gui from its infinite loop.
 
 To restate it simply.
 
 1) I was running the newest version of R as of Dec 19th including the 
 latest R-gui.
 2) I needed to force-quit R with three R-scripts open.
 3) On rebooting the R-gui the three scripts are reopened and the R-console 
 is in its active mode without me being able to get its attention or close 
 it without another force quit.
 This is an infinite loop that I have not been able to break.
 
 I can run R from a terminal window without the conveniences of the gui but 
 as I have proceded from Dec 19 I have discovered that some of the 
 conveniences of the R-gui are truly valuable and I would like to get back 
 to a state where I can use the R-gui.
 
 Is there anyone back from the Holidays yet who can tell me the minimum I 
 need to do to break the infinite loop?
 
 Re installing R from CRAN did not work.  There is some log that I need to 
 erase to stop the system from recreating the problem each time I reboot R.
 
 Joe
 
> On Dec 19, 2016, at 9:29 AM, Joseph Kunkel  wrote:
> 
> Using the R Gui a ’new' unsolvable situation has arisen.  I have been 
> using R almost daily since 2002 acording to my records.  This is the 
> first time I have not been able to rectify an R crash. 
> 
> I am running R version 3.3.2 (2016-10-31) — “Sincere Pumpkin Patch”  on 
> Mac Os Sierra Ver 10.12.1 MacBook Pro early 2013 2.7 GHh Intel Core i7, 
> 16 GB 1600 MHz DDR3
> 
> With three R-scripts in their editor windows and one R-script actually 
> invoked I needed to force a quit using the Activity Monitor.
> 
> Then, when the R Gui was re-invoked all the previous Gui windows opened 
> (as with previous experiences),  but this time R was still in 

Re: [R-SIG-Mac] Totally frozen Gui and Forced Quit does not resolve.

[Bryan Hanson]

Excellent Joe.  If you have further problems, there have also been discussions 
here in the past two months about the recent files list and an R.app plist 
which can be removed manually, forcing the app to write a fresh copy.  Bryan

> On Dec 29, 2016, at 11:10 PM, Joseph Kunkel  wrote:
> 
> Bryan,  Following the directions in section 10.11 I removed every .RData and 
> .Rhistory in my entire tree with no satisfaction.
> 
> Finally, after removing every .Rapp.history ... R failed again but I was able 
> to exit R ungracefully using option 1. 
> 
> On rebooting, R-gui reopened with all the 3 prior R-scripts also opened but 
> the R-console was not frozen and after closing the R-scripts I q() R and on 
> reopening I had a normal R-gui and no R-scripts opened.
> 
> I had known about the .Rhistory and .Rdata files but they were not the 
> problem.  The .Rapp.history was the culprit but trying to be logical and just 
> removing it from the most obvious directories did not work.  I had to remove 
> every single one.  
> 
> Perhaps a clue?  I was unable to remove two of the  ‘.Rapp.history' files 
> using their file paths in a rm statement.  Looking closely at the path there 
> was a gramatically-poor directory in both failed removes.
> One failure had ‘/text file/‘ which had an illegal space in the directory 
> name and the other failure had another illegal character in a path component 
> /1&2/.   After I removed those two  ‘.Rapp.history’ files I was able to break 
> the loop.
> 
> Thanks for the URL with directions that included the solution!
> 
> In addition I will redouble my conscious use of good unix path names!  OS X 
> allows navigating through paths that may be easier to read but are traps for 
> unix command syntax.
> 
> Joe
> 
> 
>> On Dec 29, 2016, at 7:56 PM, Bryan Hanson  wrote:
>> 
>> Take a look at section 10.3 and 10.11 in 
>> https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#Miscellaneous-questions
>> 
>> I also remove .Rhistory routinely (in addition to the files listed in 10.11) 
>> when having trouble.
>> 
>> If you need assistance finding these files throughout your system using 
>> terminal, let us know.
>> 
>> Another alternative is to get R devel at http://r.research.att.com/ That 
>> version of the GUI appears to have some fixes.
>> 
>> Bryan
>> 
>>> On Dec 29, 2016, at 7:46 PM, Joseph Kunkel  wrote:
>>> 
>>> Dear R-Sig-Mac,
>>> 
>>> I have not received any response to my request for help in unlocking my 
>>> R-gui from its infinite loop.
>>> 
>>> To restate it simply.
>>> 
>>> 1) I was running the newest version of R as of Dec 19th including the 
>>> latest R-gui.
>>> 2) I needed to force-quit R with three R-scripts open.
>>> 3) On rebooting the R-gui the three scripts are reopened and the R-console 
>>> is in its active mode without me being able to get its attention or close 
>>> it without another force quit.
>>> This is an infinite loop that I have not been able to break.
>>> 
>>> I can run R from a terminal window without the conveniences of the gui but 
>>> as I have proceded from Dec 19 I have discovered that some of the 
>>> conveniences of the R-gui are truly valuable and I would like to get back 
>>> to a state where I can use the R-gui.
>>> 
>>> Is there anyone back from the Holidays yet who can tell me the minimum I 
>>> need to do to break the infinite loop?
>>> 
>>> Re installing R from CRAN did not work.  There is some log that I need to 
>>> erase to stop the system from recreating the problem each time I reboot R.
>>> 
>>> Joe
>>> 
 On Dec 19, 2016, at 9:29 AM, Joseph Kunkel  wrote:
 
 Using the R Gui a ’new' unsolvable situation has arisen.  I have been 
 using R almost daily since 2002 acording to my records.  This is the first 
 time I have not been able to rectify an R crash. 
 
 I am running R version 3.3.2 (2016-10-31) — “Sincere Pumpkin Patch”  on 
 Mac Os Sierra Ver 10.12.1 MacBook Pro early 2013 2.7 GHh Intel Core i7, 16 
 GB 1600 MHz DDR3
 
 With three R-scripts in their editor windows and one R-script actually 
 invoked I needed to force a quit using the Activity Monitor.
 
 Then, when the R Gui was re-invoked all the previous Gui windows opened 
 (as with previous experiences),  but this time R was still in process with 
 activity monitor showing R as non-responsive and rainbow wheel spinning 
 whenever a Gui window is hovered.
 
 'Activity monitor' or ‘Dock' force quit does not resolve the above issue.  
 Each time R Gui is reinvoked all windows are restored to the R (Non 
 Responding) state.  Activity monitor shows 2/3 of a core CPU devoted to R 
 with ~125 Mb of memory devoted to R.
 
 Previously the R Gui R-script windows could be closed and when R was 
 closed and reopened ‘normal’ R-Gui opening could be invoked.
 
 *** I have deleted R.app from the Applications