Problems with Rcmdr via XQuartz on OSX Mavericks

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

------------------------------------------------
John Fox
McMaster University
Hamilton, Ontario, Canada
http://socserv.mcmaster.ca/jfox/

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

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 Sp?nola <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

-- 
Manuel Sp?nola, Ph.D. 
Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre 
Universidad Nacional 
Apartado 1350-3000 
Heredia 
COSTA RICA 
mspinola at una.ac.cr 
mspinola10 at gmail.com 
Tel?fono: (506) 2277-3598 
Fax: (506) 2237-7036 
Personal website: Lobito de r?o 
Institutional website: ICOMVIS

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.

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 Sp?nola <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

-- 
Manuel Sp?nola, Ph.D. 
Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre 
Universidad Nacional 
Apartado 1350-3000 
Heredia 
COSTA RICA 
mspinola at una.ac.cr 
mspinola10 at gmail.com 
Tel?fono: (506) 2277-3598 
Fax: (506) 2237-7036 
Personal website: Lobito de r?o 
Institutional website: ICOMVIS

Notes inlined below,

-pd


On 20 Nov 2013, at 18:19 , 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.

Affirmative. You can get similar behaviour from library(tcltk); demo(tkfaq) in R.app. It doesn?t seem to be happening with R in a Terminal window.

You can snap out of it temporarily by switching to the R console and back.

So a working hypothesis is that something is "backgrounding" the R process after a while, if it doesn?t have input focus. Since the tcltk event loop runs off the keyboard loop, we have the trouble. My take is that someone needs to take a look at how R.app handles keyboard input, in particular the timeout aspect. 

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.

Negative. I see the issue even with an older Rcmdr version without the Markdown stuff.

Please let me know what happens.

-- 
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

Thank you very much John.

How can I run R and Rcmdr in a terminal window?

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 Sp?nola <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

--
Manuel Sp?nola, Ph.D.
Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola at una.ac.cr
mspinola10 at gmail.com
Tel?fono: (506) 2277-3598
Fax: (506) 2237-7036
Personal website: Lobito de r?o
Institutional website: ICOMVIS

------------------------------------------------
John Fox
McMaster University
Hamilton, Ontario, Canada
http://socserv.mcmaster.ca/jfox/

-- 
*Manuel Sp?nola, Ph.D.*
Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola at una.ac.cr
mspinola10 at gmail.com
Tel?fono: (506) 2277-3598
Fax: (506) 2237-7036
Personal website: Lobito de r?o <https://sites.google.com/site/lobitoderio/>
Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>

	[[alternative HTML version deleted]]

On 20 Nov 2013, at 22:24 , Manuel Sp?nola <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 Sp?nola <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

--
Manuel Sp?nola, Ph.D.
Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola at una.ac.cr
mspinola10 at gmail.com
Tel?fono: (506) 2277-3598
Fax: (506) 2237-7036
Personal website: Lobito de r?o
Institutional website: ICOMVIS

------------------------------------------------
John Fox
McMaster University
Hamilton, Ontario, Canada
http://socserv.mcmaster.ca/jfox/

-- 
*Manuel Sp?nola, Ph.D.*
Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola at una.ac.cr
mspinola10 at gmail.com
Tel?fono: (506) 2277-3598
Fax: (506) 2237-7036
Personal website: Lobito de r?o <https://sites.google.com/site/lobitoderio/>
Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>

	[[alternative HTML version deleted]]

-- 
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

-----Original Message-----
From: John Fox [mailto:jfox at mcmaster.ca]
Sent: Wednesday, November 20, 2013 5:16 PM
To: peter dalgaard; Manuel Sp?nola
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 Sp?nola <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 Sp?nola

<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

--
Manuel Sp?nola, Ph.D.
Instituto Internacional en Conservaci?n y Manejo de Vida

Silvestre

Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola at una.ac.cr
mspinola10 at gmail.com
Tel?fono: (506) 2277-3598
Fax: (506) 2237-7036
Personal website: Lobito de r?o
Institutional website: ICOMVIS

------------------------------------------------
John Fox
McMaster University
Hamilton, Ontario, Canada
http://socserv.mcmaster.ca/jfox/

--
*Manuel Sp?nola, Ph.D.*
Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola at una.ac.cr
mspinola10 at gmail.com
Tel?fono: (506) 2277-3598
Fax: (506) 2237-7036
Personal website: Lobito de r?o

<https://sites.google.com/site/lobitoderio/>

Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>

	[[alternative HTML version deleted]]

--
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

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 Sp?nola <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

-- 
Manuel Sp?nola, Ph.D. 
Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre 
Universidad Nacional 
Apartado 1350-3000 
Heredia 
COSTA RICA 
mspinola at una.ac.cr 
mspinola10 at gmail.com 
Tel?fono: (506) 2277-3598 
Fax: (506) 2237-7036 
Personal website: Lobito de r?o 
Institutional website: ICOMVIS

	[[alternative HTML version deleted]]

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.

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]]

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.

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]]

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]]

-- 
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]]

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]]

-- 
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]]

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]]

-- 
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]]

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]]

-- 
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]]