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

Wed Nov 20 22:53:11 CET 2013

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/>
> 
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