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

John Fox jfox at mcmaster.ca
Thu Nov 21 02:21:10 CET 2013


Dear all,

I've added the following to the Rcmdr installation notes:

---------------- snip -------------

Under Mac OS X 10.9 ("Mavericks"), the R Commander may slow down or
occasionally hesitate to display a menu as your session progresses. This
behaviour appears to be due to a problem general to the tcltk package
running in R.app under Mac OS X 10.9. You can avoid the problem by running R
in a terminal window rather than using R.app:

o Open the Utilities subfolder inside the Applications folder on your Mac.
Click on Terminal.app to open a terminal window.

o At the Unix command prompt in the terminal window, type R and press the
enter (or return) key. On my Mac, the Unix command prompt looks like this:
john-fox-mbp:~ jfox$

o Once R starts up, you'll see the usual initial messages, followed by the R
command prompt, >

o As usual type library(Rcmdr) at the R prompt and press the enter key.

o After you exit from the R Commander, you can safely close the terminal
window, whether or not you have exited from R.

There really is no reason to prefer running the R Commander in R.app, so
using R from a terminal should be perfectly fine.

---------------- snip -------------

And, in the "Mac OS X Trouble-shooting" section:

---------------- snip -------------

If you are using Mac OS X 10.9 ("Mavericks") and the R Commander becomes
slow or unresponsive, you can run R and the R Commander in a terminal window
on your Mac rather than from R.app. See the installation notes above.

---------------- snip -------------

I hope that this helps, at least for the time-being. If and when the
tcltk/R.app problem is solved, I'll remove these instructions.

Best,
John

> -----Original Message-----
> From: John Fox [mailto:jfox at mcmaster.ca]
> Sent: Wednesday, November 20, 2013 5:16 PM
> To: peter dalgaard; Manuel Spínola
> Cc: John Fox; r-sig-mac at r-project.org; urbanek at research.att.com;
> Jonathan Chapman
> Subject: Re: [R-SIG-Mac] Problems with Rcmdr via XQuartz on OSX
> Mavericks
> 
> Dear Peter,
> 
> Thank you for fielding this question.
> 
> For the time-being, and pending a more general resolution in R.app,
> I'll add a note to this effect in the Rcmdr installation notes.
> 
> Best,
>  John
> 
> On Wed, 20 Nov 2013 22:53:11 +0100
>  peter dalgaard <pdalgd at gmail.com> wrote:
> >
> > On 20 Nov 2013, at 22:24 , Manuel Spínola <mspinola10 at gmail.com>
> wrote:
> >
> > > Thank you very much John.
> > >
> > > How can I run R and Rcmdr in a terminal window?
> > >
> >
> > [Kids these days...]
> >
> > Just open the Terminal application (it’s in the Utilities subfolder
> of the Applications folder) and type R at its prompt. Then
> library(Rcmdr) at the R prompt.
> >
> > -pd
> >
> > > Best,
> > >
> > > Manuel
> > >
> > >
> > > 2013/11/20 John Fox <jfox at mcmaster.ca>
> > >
> > >> Dear all,
> > >>
> > >> I was able to reproduce the problem on my Macbook and believe I
> have a
> > >> solution, which is to run R and the Rcmdr in a terminal window.
> When I did
> > >> this, the Rcmdr behaved normally. I'll investigate further and
> report my
> > >> findings back to the list.
> > >>
> > >> I'm copying this message to Simon Urbanek who maintains R.app in
> case he
> > >> has insight into the problem.
> > >>
> > >> I'm also interested whether running R from a terminal window
> solves the
> > >> problem for others who experienced it.
> > >>
> > >> Best,
> > >> John
> > >>
> > >> On Wed, 20 Nov 2013 12:19:04 -0500
> > >> "John Fox" <jfox at mcmaster.ca> wrote:
> > >>> Dear Jonathan et al,
> > >>>
> > >>> First, thank you to all who responded. As I said, I haven't
> noticed this
> > >> problem myself, but I'll try again on my Mac later today when I
> have some
> > >> time and see whether I can reproduce it. I suspect that this is a
> > >> tcltk-related issue, not specific to the Rcmdr, but I don't know
> that for
> > >> sure.
> > >>>
> > >>> In the meantime, here are two things to try:
> > >>>
> > >>> (1) Reijo Sund suggested trying to run R and the Rcmdr from the
> command
> > >> line (i.e., in a terminal window), to see whether the problem
> manifests
> > >> itself there. The Rcmdr doesn't need R.app.
> > >>>
> > >>> (2) It's possible that the slowdown is caused by the way that the
> Rcmdr
> > >> handles R Markdown documents. The overhead gets greater as the
> session
> > >> proceeds. To test this possibility, you could suppress the R
> Markdown tab
> > >> (via the Rcmdr Tools -> Options menu, Output tab -- uncheck the
> box for R
> > >> Markdown) and see whether the problem disappears.
> > >>>
> > >>> Please let me know what happens.
> > >>>
> > >>> Best,
> > >>> John
> > >>>
> > >>>
> > >>> On Wed, 20 Nov 2013 10:41:28 -0600
> > >>> Jonathan Chapman <petsrme2 at icloud.com> wrote:
> > >>>> I upgraded to XQuartz 2.7.5, but it still lags.
> > >>>>
> > >>>> Jonathan M. Chapman, DVM
> > >>>> 312-813-1166
> > >>>> petsrme2 at icloud.com
> > >>>>
> > >>>>> On Nov 20, 2013, at 10:05 AM, Manuel Spínola
> <mspinola10 at gmail.com>
> > >> wrote:
> > >>>>>
> > >>>>> I also have the same experience (like Jonathan) with Rcmdr in
> Mac
> > >> with Mavericks.  After few minutes Rcmdr starts to have time lags.
> I
> > >> updated to XQuartz 2.7.5 but the behavior is the same.
> > >>>>>
> > >>>>> Best,
> > >>>>>
> > >>>>> Manuel
> > >>>>>
> > >>>>>
> > >>>>> 2013/11/20 Reijo Sund <reijo.sund at helsinki.fi>
> > >>>>>> So far I have not had problems with XQuartz, but similar slow-
> down
> > >> occasionally happens while using tcltk-applications with the Aqua
> version
> > >> of Tcl/Tk (ActiveTcl 8.6.x binary distribution). Unfortunately I
> have not
> > >> been able to create a reproducible example.
> > >>>>>>
> > >>>>>> Anyhow, if XQuartz update won’t help, maybe it is worth
> checking if
> > >> there is any difference while using R.app or command-line R.
> > >>>>>>
> > >>>>>> - - -
> > >>>>>>
> > >>>>>> Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
> > >>>>>>> Just checking: which version of XQuartz?
> > >>>>>>>
> > >>>>>>> Although I have not experienced any problems, people
> recommended
> > >> updating to 2.7.5 and I got prompted to do that yesterday (it was
> released
> > >> last week).
> > >>>>>>>
> > >>>>>>> On 20/11/2013 11:52, John Fox wrote:
> > >>>>>>>> Dear Jonathan,
> > >>>>>>>>
> > >>>>>>>> I'm afraid that I don't know why you're experiencing this
> > >> problem. I upgraded my own Mac to Mavericks and the Rcmdr still
> appears to
> > >> work fine. Also, no one else has reported this problem to me,
> which of
> > >> course doesn't mean that no one else has experienced it.
> > >>>>>>>>
> > >>>>>>>> I don't doubt that something is wrong on your system but I
> don't
> > >> know what it might be. You've already reinstalled all of the
> relevant
> > >> software, which is what I would have suggested.
> > >>>>>>>>
> > >>>>>>>> I'm copying this response to the R Mac OS X email list in
> case
> > >> someone who reads the list has a suggestion or, perhaps, has also
> > >> experienced the problem.
> > >>>>>>>>
> > >>>>>>>> I'm sorry that I can't be of more help at this time.
> > >>>>>>>>
> > >>>>>>>> John
> > >>>>>>>>
> > >>>>>>>> On Wed, 20 Nov 2013 00:19:54 -0600
> > >>>>>>>> Jonathan Chapman <petsrme2 at icloud.com> wrote:
> > >>>>>>>>> Dr. Fox,
> > >>>>>>>>>
> > >>>>>>>>> I am an MPH student at the University of Minnesota.  I was
> > >> referred to you by Dr. Ann Brearley because I am having issues
> running
> > >> Rcmdr in XQuartz since upgrading to OSX Mavericks.  Rcmdr runs
> slowly,
> > >> more-so as a lag, after an initial 1-2 minutes of use.  Prior to
> that 1-2
> > >> minutes of use and the subsequent lag in performance, Rcmdr runs
> perfectly
> > >> fine via XQuartz.  Once closing out XQuartz and restarting it,
> Rcmdr runs
> > >> fine until after 1-2 minutes of use when the lag sets in again.
> > >>>>>>>>> I’ve tried to remedy the situation prior to contacting you.
> > >> First, I reinstalled XQuartz.  When that failed to solve the
> problem, I
> > >> reinstalled XQuartz along with R and Rcmdr.  That attempt also
> failed.  I
> > >> do not know what else to do or who/where else to turn.
> > >>>>>>>>> Do you have any incite?  Have you heard of anyone else
> > >> encountering this problem?
> > >>>>>>>>>
> > >>>>>>>>> Jonathan M. Chapman, DVM
> > >>>>>>>>> 312-813-1166
> > >>>>>>>>> petsrme2 at icloud.com
> > >>>>>>>>>
> > >>>>>>
> > >>>>>> _______________________________________________
> > >>>>>> R-SIG-Mac mailing list
> > >>>>>> R-SIG-Mac at r-project.org
> > >>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>> --
> > >>>>> Manuel Spínola, Ph.D.
> > >>>>> Instituto Internacional en Conservación y Manejo de Vida
> Silvestre
> > >>>>> Universidad Nacional
> > >>>>> Apartado 1350-3000
> > >>>>> Heredia
> > >>>>> COSTA RICA
> > >>>>> mspinola at una.ac.cr
> > >>>>> mspinola10 at gmail.com
> > >>>>> Teléfono: (506) 2277-3598
> > >>>>> Fax: (506) 2237-7036
> > >>>>> Personal website: Lobito de río
> > >>>>> Institutional website: ICOMVIS
> > >>
> > >> ------------------------------------------------
> > >> John Fox
> > >> McMaster University
> > >> Hamilton, Ontario, Canada
> > >> http://socserv.mcmaster.ca/jfox/
> > >>
> > >>
> > >>
> > >
> > >
> > > --
> > > *Manuel Spínola, Ph.D.*
> > > Instituto Internacional en Conservación y Manejo de Vida Silvestre
> > > Universidad Nacional
> > > Apartado 1350-3000
> > > Heredia
> > > COSTA RICA
> > > mspinola at una.ac.cr
> > > mspinola10 at gmail.com
> > > Teléfono: (506) 2277-3598
> > > Fax: (506) 2237-7036
> > > Personal website: Lobito de río
> <https://sites.google.com/site/lobitoderio/>
> > > Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
> > >
> > > 	[[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
> >



More information about the R-SIG-Mac mailing list