[R-SIG-Mac] Problems with Rcmdr via XQuartz on OSX Mavericks
John Fox
jfox at mcmaster.ca
Fri Nov 29 16:47:02 CET 2013
Dear Simon,
> -----Original Message-----
> From: Simon Urbanek [mailto:simon.urbanek at r-project.org]
> Sent: Friday, November 29, 2013 10:35 AM
> To: John Fox
> Cc: peter dalgaard; R-SIG-Mac
> Subject: Re: [R-SIG-Mac] Problems with Rcmdr via XQuartz on OSX
> Mavericks
>
>
> On Nov 28, 2013, at 8:38 AM, John Fox <jfox at mcmaster.ca> wrote:
>
> > 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?)
>
> Yes, check for R_GUI_APP_VERSION env var.
>
> But let me say that what has been proposed is very heavy-handed to say
> it mildly - changing user's configuration files is not something that
> should be done without user's consent (if at all) - and AFAIK you're
> not allowed to do it if you plan to put this on CRAN. In addition, it's
> trying to swat the symptom with a hammer, it doesn't solve the problem
> (which is why doesn't tcltk wake up sleep with its activity).
>
Well, I was proposing to ask for the user's consent (I thought that was
clear from my message), but, as I said, it would be better to fix this in
either tcltk or R.app, depending upon the nature of the problem. So I think
that we're in agreement.
Also, I mentioned in a subsequent message that, for the time-being, I'll
simply put a note about NSAppSleepDisabled in the Rcmdr Mac OS X
installation notes.
Best,
John
>
> > Wouldn't it be better to handle this issue in R.app or even in tcltk,
> however?
> >
>
> Yes, it should be handled in either of the two - if this problem is
> tcltk-specific then tcltk should wake up the sleep, if it is something
> that affects other R code as well, then it may need to be handled in
> the R event loop.
>
> Cheers,
> Simon
>
>
> > 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
> >>>>>> R-SIG-Mac at r-project.org
> >>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>>>>>
> >>>>>>
> >>>>>
> >>>>>
> >>>
> >>> _______________________________________________
> >>> 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
> >>
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
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