[R-SIG-Mac] Problems with Rcmdr via XQuartz on OSX Mavericks
John Fox
jfox at mcmaster.ca
Thu Nov 28 14:38:55 CET 2013
Dear Peter,
On Thu, 28 Nov 2013 12:00:31 +0100
peter dalgaard <pdalgd at gmail.com> wrote:
>
> 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?
>
I didn't "remember" to restart R.app because I didn't know that it was necessary to do so. In fact, the code that I wrote, but didn't commit, for the Rcmdr carefully resets the key to its previous state or deletes it if it didn't previously exist when the Commander is closed.
I think that you've almost surely identified my problem, but the solution also raises a question about what to do. I'm reluctant to have the Rcmdr make a permanent change to users' OS settings. I guess that I could detect whether the NSAppSleepDisabled key is set and pop up a dialog box if it isn't, offering to make the change, and suggesting that the user restart R.app. (BTW, is there an easy way to check whether R is running in R.app or a terminal?) Wouldn't it be better to handle this issue in R.app or even in tcltk, however?
If restarting R.app after setting the NSAppSleepDisabled key doesn't work for me, I'll then pursue Rob's suggestions.
Thanks for this,
John
> -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]]
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> R-SIG-Mac mailing
> >>> list
> >>>>
> >>> R-SIG-Mac at r-project.org
> >>>>
> >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> 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
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> [[alternative HTML version deleted]]
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> R-SIG-Mac mailing list
> >>>> R-SIG-Mac at r-project.org
> >>>>
> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-
> >>>> mac
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> R-SIG-Mac mailing list
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> >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>>>
> >>>>
> >>>
> >>>
> >
> > _______________________________________________
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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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