[R-SIG-Mac] Problems with Rcmdr via XQuartz on OSX Mavericks

peter dalgaard pdalgd at gmail.com
Thu Nov 28 12:00:31 CET 2013


On 28 Nov 2013, at 01:46 , John Fox <jfox at mcmaster.ca> wrote:

> Hi Rob,
> 
> I had some time today and so I started to implement this solution in the
> Rcmdr. I first tested whether setting
> 
>  system("defaults write org.R-project.R NSAppSleepDisabled -bool yes")
> 
> fixes the problem; I verified via 
> 
>  system("defaults read org.R-project.R NSAppSleepDisabled")
> 
> that the key was in fact set properly. 
> 
> I'm afraid that even with NSAppSleepDisabled set, the Rcmdr still freezes
> periodically. Whatever is going on is probably more complicated than
> power-saving.
> 

Hmm. The tkfaq issue seems to have gone away for me. You did remember to restart R.app after setting the key?

-pd

> Best,
> John
> 
>> -----Original Message-----
>> From: Robert J Goedman [mailto:goedman at icloud.com]
>> Sent: Sunday, November 24, 2013 11:50 AM
>> To: John Fox
>> Cc: r-sig-mac at r-project.org
>> Subject: Re: [R-SIG-Mac] Problems with Rcmdr via XQuartz on OSX
>> Mavericks
>> 
>> Hi John,
>> 
>> If it's not too much work, I would implement it in Rcmdr because I
>> don't know if there are other consequences of App Nap, so until the
>> dust settles using the defaults system might be ok.
>> 
>> Regards,
>> Rob J. Goedman
>> goedman at icloud.com
>> 
>> 
>> 
>> 
>> On Nov 24, 2013, at 8:30 AM, John Fox <jfox at mcmaster.ca> wrote:
>> 
>>> Hi Rob,
>>> 
>>> You've just answered my next question! I was holding off to give you
>> a
>>> chance to address the issue directly in R.app.
>>> 
>>> Is there any reason for me, at least for the time-being, not to do
>> this from
>>> the Rcmdr via system()? I just tried, and that seems to work. If
>> necessary,
>>> I could check for the existence and (if it exists) the current state
>> of this
>>> key, and restore that when the Commander() exits. Of course, if you
>> plan to
>>> address the issue directly soon, it doesn't make sense for me to do
>> so.
>>> 
>>> Thanks again for your help.
>>> 
>>> John
>>> 
>>>> -----Original Message-----
>>>> From: Robert J Goedman [mailto:goedman at icloud.com]
>>>> Sent: Sunday, November 24, 2013 10:32 AM
>>>> To: John Fox
>>>> Cc: r-sig-mac at r-project.org
>>>> Subject: Re: [R-SIG-Mac] Problems with Rcmdr via XQuartz on OSX
>>>> Mavericks
>>>> 
>>>> Hi John,
>>>> 
>>>> If you want to play around with NSAppSleepDisabled yourself, you
>> can,
>>>> in a Terminal:
>>>> 
>>>> defaults write org.R-project.R NSAppSleepDisabled -bool yes
>>>> 
>>>> to check the setting:
>>>> 
>>>> defaults read org.R-project.R NSAppSleepDisabled
>>>> 
>>>> or to re-enable AppNap:
>>>> 
>>>> defaults write org.R-project.R NSAppSleepDisabled -bool no
>>>> 
>>>> or just delete the key:
>>>> 
>>>> defaults delete org.R-project.R NSAppSleepDisabled
>>>> 
>>>> Regards,
>>>> Rob J. Goedman
>>>> goedman at icloud.com
>>>> 
>>>> 
>>>> 
>>>> 
>>>> On Nov 23, 2013, at 10:31 PM, Robert J Goedman <goedman at icloud.com>
>>>> wrote:
>>>> 
>>>> 
>>>> 	Hi John,
>>>> 
>>>> 	I'm just starting, but it look likes 'defaults write ...' can be
>>>> used to manage the setting. Not elegant, but maybe temporarily ok
>> for
>>>> tcltk users.
>>>> 
>>>> 	Someone from TexShop (Richard Koch) reported that if R.app is
>>>> compiled against the 10.9 APIs, the 'Prevent App Nap' check box will
>>>> not appear. The ultimate solution is for R.app to know when App Nap
>>>> should not kick in, there is a new API for that.
>>>> 
>>>> 	So, some more homework...
>>>> 
>>>> 	Regards,
>>>> 	Rob J. Goedman
>>>> 	goedman at icloud.com
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 	On Nov 23, 2013, at 9:06 PM, John Fox <jfox at mcmaster.ca> wrote:
>>>> 
>>>> 
>>>> 
>>>> 		Hi Rob,
>>>> 
>>>> 		Thanks for the explanation -- that makes sense of the
>>> current
>>>> behaviour. I think that you know that I'm not very knowledgeable
>> about
>>>> OS X. A couple of follow-up questions:
>>>> 
>>>> 		If you make this change to R.app, will the default be to
>>>> disable App Nap or just to provide the check box?
>>>> 
>>>> 		If App Nap isn't disable by R.app by default, would it be
>>>> possible to disable it under program control, e.g., when the Rcmdr
>>>> package is loaded?
>>>> 
>>>> 		Best,
>>>> 		John
>>>> 
>>>> 		On Sat, 23 Nov 2013 18:59:12 -0800
>>>> 		Robert J Goedman <goedman at icloud.com> wrote:
>>>> 
>>>> 
>>>> 			Hi John,
>>>> 
>>>> 			Looking at Activity Monitor on my system, R will
>>> always
>>>> take up say 2.5% CPU time while R.app will almost go away if it is
>> not
>>>> active. This might be because in a terminal the process might not be
>>>> treated as a pure application but maybe more as a traditional Unix
>>>> process. But that's just a guess from my side.
>>>> 
>>>> 			What surprised me a bit is that we couldn't switch
>>> off
>>>> App Nap, as is possible with several other apps (go to the Info
>> panel
>>>> of an app and it should show a 'Prevent App Nap' box, e.g. Dropbox).
>>>> R.app did not show that box, probably a consequence of an older
>>>> build/project creation?
>>>> 
>>>> 			Anyway, on my system I added that property in the
>>>> info.plist and disabled the App Nap behavior. It seems to be working
>>>> fine now. I'll do some more testing to see if I can get the check
>> box
>>>> on the Info screen show up and check with Simon if it's ok to commit
>>>> the change. Of course, in that case R.app will also always consume
>> 2.5%
>>>> CPU. Under the energy tab of the Activity Monitor you can see which
>>>> apps allow App Nap.
>>>> 
>>>> 			Rob J. Goedman
>>>> 			goedman at icloud.com
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 			On Nov 23, 2013, at 5:43 AM, John Fox
>>> <jfox at mcmaster.ca>
>>>> wrote:
>>>> 
>>>> 
>>>> 
>>>> 				Dear Rob et al.,
>>>> 
>>>> 				I'm glad that there's progress in
>>> understanding
>>>> the source of the problem, but I wonder why the problem doesn't
>>>> manifest itself -- at least in my experience -- when R runs in a
>>>> terminal window.
>>>> 
>>>> 				Best,
>>>> 				John
>>>> 
>>>> 				On Fri, 22 Nov 2013 14:42:00 -0800
>>>> 				Robert J Goedman <goedman at icloud.com> wrote:
>>>> 
>>>> 
>>>> 					Thansk Peter,
>>>> 
>>>> 					Now I can reproduce it!
>>>> 
>>>> 					Rob J. Goedman
>>>> 					goedman at icloud.com
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 					On Nov 22, 2013, at 1:00 PM, peter
>>> dalgaard
>>>> <pdalgd at gmail.com> wrote:
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 						On 22 Nov 2013, at 16:42 ,
>>> Robert J
>>>> Goedman <goedman at icloud.com> wrote:
>>>> 
>>>> 
>>>> 
>>>> 							Not sure how long it
>>> takes to see
>>>> the lagging (a few minutes someone reported), but I've not been able
>> to
>>>> reproduce this problem.
>>>> 
>>>> 
>>>> 
>>>> 						For me, library(tcltk);
>>> demo(tkfaq),
>>>> click to focus, then use Fn-Down (i.e. PgDown) to go to the bottom
>> of
>>>> the file, Fn-Up to the top, etc. Less than two iteration for me
>> before
>>>> the effect kicks in.
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 							Which makes me
>>> wonder if anyone
>>>> has seen this behavior after rebuilding R.app on Mavericks (from the
>>>> R.app sources).
>>>> 
>>>> 							Regards,
>>>> 							Rob J. Goedman
>>>> 							goedman at icloud.com
>>>> 
>>>> 
>>>> 							On Nov 22, 2013, at
>>> 7:29 AM, Simon
>>>> Urbanek <simon.urbanek at r-project.org> wrote:
>>>> 
>>>> 
>>>> 
>>>> 								On Nov 20,
>>> 2013, at 11:41 AM,
>>>> Jonathan Chapman <petsrme2 at icloud.com> wrote:
>>>> 
>>>> 
>>>> 
>>>> 									I
>>> upgraded to XQuartz
>>>> 2.7.5, but it still lags.
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 								Please read
>>> Peter's response
>>>> - it has nothing to do with XQuartz versions
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 							[[alternative HTML
>>> version
>>>> deleted]]
>>>> 
>>>> 
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>>>> 
>>>> 
>>>> 						--
>>>> 						Peter Dalgaard, Professor,
>>>> 						Center for Statistics,
>>> Copenhagen
>>>> Business School
>>>> 						Solbjerg Plads 3, 2000
>>> Frederiksberg,
>>>> Denmark
>>>> 						Phone: (+45)38153501
>>>> 						Email: pd.mes at cbs.dk  Priv:
>>>> PDalgd at gmail.com
>>>> 
>>>> 
>>>> 
>>>> 
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>>>> 
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>>>> 
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>>> 
>>> 
> 
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-- 
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com



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