Re: [R-SIG-Mac] R GUI very slow under mac OS 10.12.5 (Sierra)

[Jake Hosen]

This problem has continued to haunt me through more recent version of macos 
and R. My understanding from doing research is that this is something that 
Apple broke, but the problem is very disruptive when trying to debug longer 
scripts. Have you found any work-arounds other than the clear console 
solution?

I'd also be willing to contribute to a fix for this problem if there is a 
viable way forward.

On Saturday, June 17, 2017 at 6:36:46 AM UTC-4, Martin Batholdy via 
R-SIG-Mac wrote:
>
> Dear all,
>
> sorry for the late response.
>
> Here some more observations:
> It seems to really depend on the output length. As soon as I “clear 
> console” it is very fast again and slows down significantly the more lines 
> of code are printed.
>
> The strange error-message ("IMKInputSession 
> presentFunctionRowItemTextInputViewWithEndpoint:completionHandler …”) is 
> not unique to the RGui, but also appears in terminal occasionally (not sure 
> yet by what it is triggered exactly).
>
>
> I have installed:
> XQuartz 2.7.11
> XCode 8.1 (8B62) 
>
>
> And here is the output of sessionInfo():
>
> R version 3.4.0 (2017-04-21)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS Sierra 10.12.5
>
> Matrix products: default
> BLAS: 
> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] grid  graphics  grDevices utils datasets  stats methods  
> [8] base 
>
> other attached packages:
>  [1] markovchain_0.6.9.3 shape_1.4.2 fields_9.0 
>  [4] maps_3.2.0  spam_1.4-0  plotrix_3.6-5  
>  [7] plyr_1.8.4  GGally_1.3.1Hmisc_4.0-3
> [10] ggplot2_2.2.1   Formula_1.2-1   survival_2.41-3
> [13] lattice_0.20-35
>
> loaded via a namespace (and not attached):
>  [1] Rcpp_0.12.11compiler_3.4.0  RColorBrewer_1.1-2 
>  [4] base64enc_0.1-3 tools_3.4.0 rpart_4.1-11   
>  [7] digest_0.6.12   tibble_1.3.1gtable_0.2.0   
> [10] checkmate_1.8.2 htmlTable_1.9   rlang_0.1.1
> [13] igraph_1.0.1Matrix_1.2-9parallel_3.4.0 
> [16] expm_0.999-2gridExtra_2.2.1 stringr_1.2.0  
> [19] cluster_2.0.6   knitr_1.16  htmlwidgets_0.8
> [22] stats4_3.4.0nnet_7.3-12 reshape_0.8.6  
> [25] data.table_1.10.4   foreign_0.8-67  latticeExtra_0.6-28
> [28] matlab_1.0.2magrittr_1.5backports_1.1.0
> [31] scales_0.4.1htmltools_0.3.6 splines_3.4.0  
> [34] colorspace_1.3-2stringi_1.1.5   acepack_1.4.1  
> [37] RcppParallel_4.3.20 lazyeval_0.2.0  munsell_0.4.3  
>
> Hope that helps!
>
> > On 29. May 2017, at 22:44 , David Winsemius  > wrote:
> > 
> > 
> >> On May 27, 2017, at 3:44 AM, Martin Batholdy via R-SIG-Mac <
> r-si...@r-project.org > wrote:
> >> 
> >> Dear all,
> >> 
> >> I just switched to a new 2016 Macbook Pro and noticed that R is very 
> slow when used over the R app. Using R via the terminal is significantly 
> faster.
> >> Especially, drawing figures in quartz is really slow
> > 
> > Not sure what "drawing a figure" actually means. Can you present code?
> > 
> >> and sometimes the following error message is printed – but this might 
> be unrelated to the speed issue:
> >> 
> >> IMKInputSession 
> presentFunctionRowItemTextInputViewWithEndpoint:completionHandler: : [self 
> textInputContext]=0x0 *NO* NSRemoteViewController to client, NSError=Error 
> Domain=NSCocoaErrorDomain Code=4099 "The connection from pid 0 was 
> invalidated from this process." UserInfo={NSDebugDescription=The connection 
> from pid 0 was invalidated from this process.}, 
> com.apple.inputmethod.EmojiFunctionRowItem
> > 
> > This error in Sierra hosted apps has also been reported on other app 
> forums (as well as once before on this mailing list Mon, 19 Dec 2016 by 
> a.bec...@sheffield.ac.uk  but got no response):
> > 
> > https://discuss.atom.io/t/imkinputsession-error/36273
> > 
> > https://github.com/macvim-dev/macvim/issues/422
> > 
> > 
> https://stackoverflow.com/questions/41249603/tkinter-error-in-terminal-possibly-from-my-key-bind
> > 
> > 
> >> 
> >> Is this a known issue related to Sierra and/or the new Macbook Pros? 
> Are there any workarounds or fixes?
> > 
> > I surely don't know about workarounds but this does appear to be 
> specific to Sierra. My MacbookPro is too old to get an update to Sierra. I 
> do wonder if you have an updated (or any) XQuartz and XCode? Generally a 
> complete question will include your versions of all essential system and R 
> packages. 
> > 
> > What does sessionInfo() return?
> > 
> > Try clicking on the system taskbar XQuartz icon and  using 
> `XQuartz/About X11` and copying the version. I get:
> > 
> > 

Re: [R-SIG-Mac] R GUI very slow under mac OS 10.12.5 (Sierra)

[Martin Batholdy via R-SIG-Mac]

Dear all,

sorry for the late response.

Here some more observations:
It seems to really depend on the output length. As soon as I “clear console” it 
is very fast again and slows down significantly the more lines of code are 
printed.

The strange error-message ("IMKInputSession 
presentFunctionRowItemTextInputViewWithEndpoint:completionHandler …”) is not 
unique to the RGui, but also appears in terminal occasionally (not sure yet by 
what it is triggered exactly).


I have installed:
XQuartz 2.7.11
XCode 8.1 (8B62) 


And here is the output of sessionInfo():

R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.5

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid  graphics  grDevices utils datasets  stats methods  
[8] base 

other attached packages:
 [1] markovchain_0.6.9.3 shape_1.4.2 fields_9.0 
 [4] maps_3.2.0  spam_1.4-0  plotrix_3.6-5  
 [7] plyr_1.8.4  GGally_1.3.1Hmisc_4.0-3
[10] ggplot2_2.2.1   Formula_1.2-1   survival_2.41-3
[13] lattice_0.20-35

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11compiler_3.4.0  RColorBrewer_1.1-2 
 [4] base64enc_0.1-3 tools_3.4.0 rpart_4.1-11   
 [7] digest_0.6.12   tibble_1.3.1gtable_0.2.0   
[10] checkmate_1.8.2 htmlTable_1.9   rlang_0.1.1
[13] igraph_1.0.1Matrix_1.2-9parallel_3.4.0 
[16] expm_0.999-2gridExtra_2.2.1 stringr_1.2.0  
[19] cluster_2.0.6   knitr_1.16  htmlwidgets_0.8
[22] stats4_3.4.0nnet_7.3-12 reshape_0.8.6  
[25] data.table_1.10.4   foreign_0.8-67  latticeExtra_0.6-28
[28] matlab_1.0.2magrittr_1.5backports_1.1.0
[31] scales_0.4.1htmltools_0.3.6 splines_3.4.0  
[34] colorspace_1.3-2stringi_1.1.5   acepack_1.4.1  
[37] RcppParallel_4.3.20 lazyeval_0.2.0  munsell_0.4.3  



Hope that helps!



> On 29. May 2017, at 22:44 , David Winsemius  wrote:
> 
> 
>> On May 27, 2017, at 3:44 AM, Martin Batholdy via R-SIG-Mac 
>>  wrote:
>> 
>> Dear all,
>> 
>> I just switched to a new 2016 Macbook Pro and noticed that R is very slow 
>> when used over the R app. Using R via the terminal is significantly faster.
>> Especially, drawing figures in quartz is really slow
> 
> Not sure what "drawing a figure" actually means. Can you present code?
> 
>> and sometimes the following error message is printed – but this might be 
>> unrelated to the speed issue:
>> 
>> IMKInputSession 
>> presentFunctionRowItemTextInputViewWithEndpoint:completionHandler: : [self 
>> textInputContext]=0x0 *NO* NSRemoteViewController to client, NSError=Error 
>> Domain=NSCocoaErrorDomain Code=4099 "The connection from pid 0 was 
>> invalidated from this process." UserInfo={NSDebugDescription=The connection 
>> from pid 0 was invalidated from this process.}, 
>> com.apple.inputmethod.EmojiFunctionRowItem
> 
> This error in Sierra hosted apps has also been reported on other app forums 
> (as well as once before on this mailing list Mon, 19 Dec 2016 by 
> a.becker...@sheffield.ac.uk but got no response):
> 
> https://discuss.atom.io/t/imkinputsession-error/36273
> 
> https://github.com/macvim-dev/macvim/issues/422
> 
> https://stackoverflow.com/questions/41249603/tkinter-error-in-terminal-possibly-from-my-key-bind
> 
> 
>> 
>> Is this a known issue related to Sierra and/or the new Macbook Pros? Are 
>> there any workarounds or fixes?
> 
> I surely don't know about workarounds but this does appear to be specific to 
> Sierra. My MacbookPro is too old to get an update to Sierra. I do wonder if 
> you have an updated (or any) XQuartz and XCode? Generally a complete question 
> will include your versions of all essential system and R packages. 
> 
> What does sessionInfo() return?
> 
> Try clicking on the system taskbar XQuartz icon and  using `XQuartz/About 
> X11` and copying the version. I get:
> 
> XQuartz 2.7.11 (xorg-server 1.18.4)
> 
> My XCode version is: Version 8.2.1 (8C1002) but ISTR that Sierra needs a 
> later version.
> 
> And you should also probably indicate whether you have used either MacPorts 
> or homebrew.
> 
> The other system resource needed in the past was Tcl/Tk although I think that 
> now should get installed and attached by default with any current version of 
> R. The last link of the three above appeared related to the Tk interface 
> which is used by R.app and the tcltk package is part of the base 
> installation, so might be relevant, but this is written at the level of 
> speculation. My other hypothesis is that two different 

Re: [R-SIG-Mac] R GUI very slow under mac OS 10.12.5 (Sierra)

[Simon Urbanek]

> On May 27, 2017, at 6:44 AM, Martin Batholdy via R-SIG-Mac 
>  wrote:
> 
> Dear all,
> 
> I just switched to a new 2016 Macbook Pro and noticed that R is very slow 
> when used over the R app. Using R via the terminal is significantly faster.


Can you be more specific as of what is slow and how to reproduce it?

There was a report that the console UI gets slower in Sierra as the length of 
the output increases - you can clear the console to avoid that, but the cause 
is so far unknown, likely related to Xcode 8.3 an Sierra interaction since the 
problem has not appeared in Mavericks builds for R (try using R 3.3.3 to see if 
you see the same problem). 


> Especially, drawing figures in quartz is really slow and sometimes the 
> following error message is printed – but this might be unrelated to the speed 
> issue:
> 
> IMKInputSession 
> presentFunctionRowItemTextInputViewWithEndpoint:completionHandler: : [self 
> textInputContext]=0x0 *NO* NSRemoteViewController to client, NSError=Error 
> Domain=NSCocoaErrorDomain Code=4099 "The connection from pid 0 was 
> invalidated from this process." UserInfo={NSDebugDescription=The connection 
> from pid 0 was invalidated from this process.}, 
> com.apple.inputmethod.EmojiFunctionRowItem
> 
> 

I have not seen that error, is it reproducible?

Cheers,
Simon



> Is this a known issue related to Sierra and/or the new Macbook Pros? Are 
> there any workarounds or fixes?
> 
> 
> Thanks for any suggestions!
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

Re: [R-SIG-Mac] R GUI very slow under mac OS 10.12.5 (Sierra)

[David Winsemius]

> On May 27, 2017, at 3:44 AM, Martin Batholdy via R-SIG-Mac 
>  wrote:
> 
> Dear all,
> 
> I just switched to a new 2016 Macbook Pro and noticed that R is very slow 
> when used over the R app. Using R via the terminal is significantly faster.
> Especially, drawing figures in quartz is really slow

Not sure what "drawing a figure" actually means. Can you present code?

> and sometimes the following error message is printed – but this might be 
> unrelated to the speed issue:
> 
> IMKInputSession 
> presentFunctionRowItemTextInputViewWithEndpoint:completionHandler: : [self 
> textInputContext]=0x0 *NO* NSRemoteViewController to client, NSError=Error 
> Domain=NSCocoaErrorDomain Code=4099 "The connection from pid 0 was 
> invalidated from this process." UserInfo={NSDebugDescription=The connection 
> from pid 0 was invalidated from this process.}, 
> com.apple.inputmethod.EmojiFunctionRowItem

This error in Sierra hosted apps has also been reported on other app forums (as 
well as once before on this mailing list Mon, 19 Dec 2016 by 
a.becker...@sheffield.ac.uk but got no response):

https://discuss.atom.io/t/imkinputsession-error/36273

https://github.com/macvim-dev/macvim/issues/422

https://stackoverflow.com/questions/41249603/tkinter-error-in-terminal-possibly-from-my-key-bind


> 
> Is this a known issue related to Sierra and/or the new Macbook Pros? Are 
> there any workarounds or fixes?

I surely don't know about workarounds but this does appear to be specific to 
Sierra. My MacbookPro is too old to get an update to Sierra. I do wonder if you 
have an updated (or any) XQuartz and XCode? Generally a complete question will 
include your versions of all essential system and R packages. 

What does sessionInfo() return?

Try clicking on the system taskbar XQuartz icon and  using `XQuartz/About X11` 
and copying the version. I get:

XQuartz 2.7.11 (xorg-server 1.18.4)

My XCode version is: Version 8.2.1 (8C1002) but ISTR that Sierra needs a later 
version.

And you should also probably indicate whether you have used either MacPorts or 
homebrew.

The other system resource needed in the past was Tcl/Tk although I think that 
now should get installed and attached by default with any current version of R. 
The last link of the three above appeared related to the Tk interface which is 
used by R.app and the tcltk package is part of the base installation, so might 
be relevant, but this is written at the level of speculation. My other 
hypothesis is that two different installations of Tcl/Tk might give problems on 
one machine that were not encountered by others.

-- 
David.

> 
> 
> Thanks for any suggestions!
> 
> ___
> 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

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

[R-SIG-Mac] R GUI very slow under mac OS 10.12.5 (Sierra)

[Martin Batholdy via R-SIG-Mac]

Dear all,I just switched to a new 2016 Macbook Pro and noticed that R is very slow when used over the R app. Using R via the terminal is significantly faster.Especially, drawing figures in quartz is really slow and sometimes the following error message is printed – but this might be unrelated to the speed issue:IMKInputSession presentFunctionRowItemTextInputViewWithEndpoint:completionHandler: : [self textInputContext]=0x0 *NO* NSRemoteViewController to client, NSError=Error Domain=NSCocoaErrorDomain Code=4099 "The connection from pid 0 was invalidated from this process." UserInfo={NSDebugDescription=The connection from pid 0 was invalidated from this process.}, com.apple.inputmethod.EmojiFunctionRowItemIs this a known issue related to Sierra and/or the new Macbook Pros? Are there any workarounds or fixes?Thanks for any suggestions!
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac