[R-SIG-Mac] Using XQuartz - any known issues?

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[R-SIG-Mac] Using XQuartz - any known issues?

ANDERSON Niall

Dear all,

 

I’m relatively new to MacOS and have only recently started trying to use XQuartz to enable me to run Rcmdr. Are there any common issues/ tips for getting good performance out of it (or should it usually run well with default settings)?

 

On first installation, I found there was a very long lag in menus being populated (i.e. the menu shape was generated, but no usable options were added), to the extent that Rcmdr was then effectively useless (not Rcmdr’s fault, I don’t think). One of my students suggested reducing Output Colors option from the default “Millions” setting. That seems to deal with the problem, thankfully.

 

Is that typical of XQuartz, and is there anything else I should be doing to get the best performance from it?

 

Thanks,

 

Niall Anderson

 

 

________________________________

 

Dr Niall H. Anderson | Senior Lecturer in Medical Statistics/ Programme Co-director, MPH (on campus)

Room G113B, Doorway 1

Usher Institute, University of Edinburgh

Old Medical School, Teviot Place, Edinburgh, EH8 9AG

 

[hidden email]  | +44 (0)131 650 3212 Skype = live:niall.h.anderson

 

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Re: [R-SIG-Mac] Using XQuartz - any known issues?

Dr Eberhard W Lisse
Take Rstudio.

el

— 
Sent from Dr Lisse’s iPad Mini 5
On 20 Apr 2020, 21:42 +0200, ANDERSON Niall <[hidden email]>, wrote:

Dear all,

 

I’m relatively new to MacOS and have only recently started trying to use XQuartz to enable me to run Rcmdr. Are there any common issues/ tips for getting good performance out of it (or should it usually run well with default settings)?

 

On first installation, I found there was a very long lag in menus being populated (i.e. the menu shape was generated, but no usable options were added), to the extent that Rcmdr was then effectively useless (not Rcmdr’s fault, I don’t think). One of my students suggested reducing Output Colors option from the default “Millions” setting. That seems to deal with the problem, thankfully.

 

Is that typical of XQuartz, and is there anything else I should be doing to get the best performance from it?

 

Thanks,

 

Niall Anderson

 

 

________________________________

 

Dr Niall H. Anderson | Senior Lecturer in Medical Statistics/ Programme Co-director, MPH (on campus)

Room G113B, Doorway 1

Usher Institute, University of Edinburgh

Old Medical School, Teviot Place, Edinburgh, EH8 9AG

 

[hidden email]  | +44 (0)131 650 3212 Skype = live:niall.h.anderson

 

Responses to emails are only expected during your working hours

<image001.png>

www.ed.ac.uk/usher | @EdinUniUsher

 

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Re: [R-SIG-Mac] Using XQuartz - any known issues?

Fox, John
In reply to this post by ANDERSON Niall
Dear Niall,

> On Apr 20, 2020, at 3:42 PM, ANDERSON Niall <[hidden email]> wrote:
>
> Dear all,
>  
> I’m relatively new to MacOS and have only recently started trying to use XQuartz to enable me to run Rcmdr. Are there any common issues/ tips for getting good performance out of it (or should it usually run well with default settings)?
>  
> On first installation, I found there was a very long lag in menus being populated (i.e. the menu shape was generated, but no usable options were added), to the extent that Rcmdr was then effectively useless (not Rcmdr’s fault, I don’t think). One of my students suggested reducing Output Colors option from the default “Millions” setting. That seems to deal with the problem, thankfully.
>  
> Is that typical of XQuartz, and is there anything else I should be doing to get the best performance from it?

I haven't observed the problem you describe on my Mac, which is a three- or four-year-old MacBook Pro (that is, the Rcmdr dialogs display reasonably crisply for me), and I haven't done anything special to configure XQuartz. Here are the specs for my Mac:

 Model Name: MacBook Pro
  Model Identifier: MacBookPro13,2
  Processor Name: Dual-Core Intel Core i7
  Processor Speed: 3.3 GHz
  Number of Processors: 1
  Total Number of Cores: 2
  L2 Cache (per Core): 256 KB
  L3 Cache: 4 MB
  Hyper-Threading Technology: Enabled
  Memory: 8 GB
 
It might help to have some more information. I assume that you're using the most recent versions of R, the Rcmdr package, and other packages, and a recent version of macOS. What Mac do you have, and did you reboot it after installing XQuartz? If you updated R, did you reinstall XQuartz?

Best,
 John

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

>  
> Thanks,
>  
> Niall Anderson
>  
>  
> ________________________________
>  
> Dr Niall H. Anderson | Senior Lecturer in Medical Statistics/ Programme Co-director, MPH (on campus)
>
> Room G113B, Doorway 1
> Usher Institute, University of Edinburgh
> Old Medical School, Teviot Place, Edinburgh, EH8 9AG
>  
> [hidden email]  | +44 (0)131 650 3212 | Skype = live:niall.h.anderson
>  
> Responses to emails are only expected during your working hours
> <image001.png>
> www.ed.ac.uk/usher | @EdinUniUsher
>  
> <image002.png>
>  
>  
> The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. _______________________________________________
> R-SIG-Mac mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac




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Re: [R-SIG-Mac] Using XQuartz - any known issues?

ANDERSON Niall
Eberhard, Thanks - I'm also  an RStudio user, but am trying to use Rcmdr as a gentle introduction to R for a course (building up to RStudio use later).

John, thanks also for responding (not at all an Rcmdr issue, I think - that's just what happened to show the problem). Tech details:

MacBook Pro 15 (bought 2019)
Catalina 10.15.4
2.6 GHz 6-core Intel Core i7
16 GB 2400 MHz DDR4 memory
Radeon Pro 555X 4GB & Intel UHD Graphics 360 1536MB graphics.

R 3.6.3, new download of Rcmdr etc (reinstalled everything from scratch before realising X11 was the reason Rcmdr wasn't working and downloading XQuartz). I'm almost certain I would have rebooted before trying to run this - I saw that warning somewhere (CRAN FAQ maybe?). I certainly have since, but perhaps that's why it is now appearing to function correctly? I should say that 2-3 students have reported the same problem over the last 3-4 days, so it isn't just me.

Thanks again for input. Best wishes to all on the list.

Niall

________________________________
 
Dr Niall H. Anderson | Senior Lecturer in Medical Statistics/ Programme Co-director, MPH (on campus)
Room G113B, Doorway 1
Usher Institute, University of Edinburgh
Old Medical School, Teviot Place, Edinburgh, EH8 9AG
 
[hidden email]  | +44 (0)131 650 3212 | Skype = live:niall.h.anderson
 
Responses to emails are only expected during your working hours

www.ed.ac.uk/usher <http://www.ed.ac.uk/usher> | @EdinUniUsher <https://twitter.com/edinuniusher>
 

 
 

On 21/04/2020, 04:55, "Fox, John" <[hidden email]> wrote:

    Dear Niall,
   
    > On Apr 20, 2020, at 3:42 PM, ANDERSON Niall <[hidden email]> wrote:
    >
    > Dear all,
    >  
    > I’m relatively new to MacOS and have only recently started trying to use XQuartz to enable me to run Rcmdr. Are there any common issues/ tips for getting good performance out of it (or should it usually run well with default settings)?
    >  
    > On first installation, I found there was a very long lag in menus being populated (i.e. the menu shape was generated, but no usable options were added), to the extent that Rcmdr was then effectively useless (not Rcmdr’s fault, I don’t think). One of my students suggested reducing Output Colors option from the default “Millions” setting. That seems to deal with the problem, thankfully.
    >  
    > Is that typical of XQuartz, and is there anything else I should be doing to get the best performance from it?
   
    I haven't observed the problem you describe on my Mac, which is a three- or four-year-old MacBook Pro (that is, the Rcmdr dialogs display reasonably crisply for me), and I haven't done anything special to configure XQuartz. Here are the specs for my Mac:
   
     Model Name: MacBook Pro
      Model Identifier: MacBookPro13,2
      Processor Name: Dual-Core Intel Core i7
      Processor Speed: 3.3 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
     
    It might help to have some more information. I assume that you're using the most recent versions of R, the Rcmdr package, and other packages, and a recent version of macOS. What Mac do you have, and did you reboot it after installing XQuartz? If you updated R, did you reinstall XQuartz?
   
    Best,
     John
   
      -----------------------------
      John Fox, Professor Emeritus
      McMaster University
      Hamilton, Ontario, Canada
      Web: http::/socserv.mcmaster.ca/jfox
   
    >  
    > Thanks,
    >  
    > Niall Anderson
    >  
    >  
    > ________________________________
    >  
    > Dr Niall H. Anderson | Senior Lecturer in Medical Statistics/ Programme Co-director, MPH (on campus)
    >
    > Room G113B, Doorway 1
    > Usher Institute, University of Edinburgh
    > Old Medical School, Teviot Place, Edinburgh, EH8 9AG
    >  
    > [hidden email]  | +44 (0)131 650 3212 | Skype = live:niall.h.anderson
    >  
    > Responses to emails are only expected during your working hours
    > <image001.png>
    > www.ed.ac.uk/usher | @EdinUniUsher
    >  
    > <image002.png>
    >  
    >  
    > The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. _______________________________________________
    > R-SIG-Mac mailing list
    > [hidden email]
    > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
   
   
   
   
   

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[R-SIG-Mac] Using XQuartz - any known issues?

Fox, John
In reply to this post by ANDERSON Niall
I neglected to include the list in my reply, which appears below..

John

Begin forwarded message:

From: John Fox <[hidden email]>
Subject: Re: [R-SIG-Mac] Using XQuartz - any known issues?
Date: April 21, 2020 at 10:43:33 AM EDT
To: ANDERSON Niall <[hidden email]>

Dear Niall,

On Apr 21, 2020, at 4:41 AM, ANDERSON Niall <[hidden email]> wrote:

Eberhard, Thanks - I'm also  an RStudio user, but am trying to use Rcmdr as a gentle introduction to R for a course (building up to RStudio use later).

John, thanks also for responding (not at all an Rcmdr issue, I think - that's just what happened to show the problem).

I of course have an interest in getting the Rcmdr to work well on all platforms. Most problems are on macOS. It's hard, however, to address an issue that I can't observe, and I've never seen this one.

Tech details:

MacBook Pro 15 (bought 2019)
Catalina 10.15.4
2.6 GHz 6-core Intel Core i7
16 GB 2400 MHz DDR4 memory
Radeon Pro 555X 4GB & Intel UHD Graphics 360 1536MB graphics.

As I would have guessed, your new Mac has more horsepower than my relatively old one, so other things equal it should probably display dialogs more crisply.


R 3.6.3, new download of Rcmdr etc (reinstalled everything from scratch before realising X11 was the reason Rcmdr wasn't working and downloading XQuartz). I'm almost certain I would have rebooted before trying to run this - I saw that warning somewhere (CRAN FAQ maybe?). I certainly have since, but perhaps that's why it is now appearing to function correctly?

I wish I knew, but it's rather strange that the problem went away by itself.

I should say that 2-3 students have reported the same problem over the last 3-4 days, so it isn't just me.

To be clear, I never thought that you were hallucinating. It would be nice to know why the problem occurs so that, depending on the nature of the explanation, I could potentially advise users to avoid it. In particular, did you ask your students to reboot their Macs and try again?

Best,
John


Thanks again for input. Best wishes to all on the list.
Niall

________________________________

Dr Niall H. Anderson | Senior Lecturer in Medical Statistics/ Programme Co-director, MPH (on campus)
Room G113B, Doorway 1
Usher Institute, University of Edinburgh
Old Medical School, Teviot Place, Edinburgh, EH8 9AG

[hidden email]  | +44 (0)131 650 3212 | Skype = live:niall.h.anderson

Responses to emails are only expected during your working hours

www.ed.ac.uk/usher <http://www.ed.ac.uk/usher> | @EdinUniUsher <https://twitter.com/edinuniusher>





On 21/04/2020, 04:55, "Fox, John" <[hidden email]> wrote:

  Dear Niall,

On Apr 20, 2020, at 3:42 PM, ANDERSON Niall <[hidden email]> wrote:

Dear all,

I’m relatively new to MacOS and have only recently started trying to use XQuartz to enable me to run Rcmdr. Are there any common issues/ tips for getting good performance out of it (or should it usually run well with default settings)?

On first installation, I found there was a very long lag in menus being populated (i.e. the menu shape was generated, but no usable options were added), to the extent that Rcmdr was then effectively useless (not Rcmdr’s fault, I don’t think). One of my students suggested reducing Output Colors option from the default “Millions” setting. That seems to deal with the problem, thankfully.

Is that typical of XQuartz, and is there anything else I should be doing to get the best performance from it?

  I haven't observed the problem you describe on my Mac, which is a three- or four-year-old MacBook Pro (that is, the Rcmdr dialogs display reasonably crisply for me), and I haven't done anything special to configure XQuartz. Here are the specs for my Mac:

   Model Name: MacBook Pro
    Model Identifier: MacBookPro13,2
    Processor Name: Dual-Core Intel Core i7
    Processor Speed: 3.3 GHz
    Number of Processors: 1
    Total Number of Cores: 2
    L2 Cache (per Core): 256 KB
    L3 Cache: 4 MB
    Hyper-Threading Technology: Enabled
    Memory: 8 GB

  It might help to have some more information. I assume that you're using the most recent versions of R, the Rcmdr package, and other packages, and a recent version of macOS. What Mac do you have, and did you reboot it after installing XQuartz? If you updated R, did you reinstall XQuartz?

  Best,
   John

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


Thanks,

Niall Anderson


________________________________

Dr Niall H. Anderson | Senior Lecturer in Medical Statistics/ Programme Co-director, MPH (on campus)

Room G113B, Doorway 1
Usher Institute, University of Edinburgh
Old Medical School, Teviot Place, Edinburgh, EH8 9AG

[hidden email]  | +44 (0)131 650 3212 | Skype = live:niall.h.anderson

Responses to emails are only expected during your working hours
<image001.png>
www.ed.ac.uk/usher | @EdinUniUsher

<image002.png>


The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. _______________________________________________
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Re: [R-SIG-Mac] Using XQuartz - any known issues?

Simon Urbanek
In reply to this post by ANDERSON Niall
Just a quick note in the hopes that is may be helpful: X11 (fontconfig, really) creates a font cache the first time is it started which can take substantial time depending on hardware (HDD vs SSD...) during which XQuartz doesn't respond. So I wouldn't be surprised if that was actually happening, unrelated to any setttings. If you start XQuartz later after the cache has been built, it will work fine immediately. So if that is what it was, the issue should not re-occur if you were patient enough the first time.

Cheers,
Simon



> On 21/04/2020, at 8:41 PM, ANDERSON Niall <[hidden email]> wrote:
>
> Eberhard, Thanks - I'm also  an RStudio user, but am trying to use Rcmdr as a gentle introduction to R for a course (building up to RStudio use later).
>
> John, thanks also for responding (not at all an Rcmdr issue, I think - that's just what happened to show the problem). Tech details:
>
> MacBook Pro 15 (bought 2019)
> Catalina 10.15.4
> 2.6 GHz 6-core Intel Core i7
> 16 GB 2400 MHz DDR4 memory
> Radeon Pro 555X 4GB & Intel UHD Graphics 360 1536MB graphics.
>
> R 3.6.3, new download of Rcmdr etc (reinstalled everything from scratch before realising X11 was the reason Rcmdr wasn't working and downloading XQuartz). I'm almost certain I would have rebooted before trying to run this - I saw that warning somewhere (CRAN FAQ maybe?). I certainly have since, but perhaps that's why it is now appearing to function correctly? I should say that 2-3 students have reported the same problem over the last 3-4 days, so it isn't just me.
>
> Thanks again for input. Best wishes to all on the list.
>
> Niall
>
> ________________________________
>
> Dr Niall H. Anderson | Senior Lecturer in Medical Statistics/ Programme Co-director, MPH (on campus)
> Room G113B, Doorway 1
> Usher Institute, University of Edinburgh
> Old Medical School, Teviot Place, Edinburgh, EH8 9AG
>
> [hidden email]  | +44 (0)131 650 3212 | Skype = live:niall.h.anderson
>
> Responses to emails are only expected during your working hours
>
> www.ed.ac.uk/usher <http://www.ed.ac.uk/usher> | @EdinUniUsher <https://twitter.com/edinuniusher>
>
>
>
>
>
> On 21/04/2020, 04:55, "Fox, John" <[hidden email]> wrote:
>
>    Dear Niall,
>
>> On Apr 20, 2020, at 3:42 PM, ANDERSON Niall <[hidden email]> wrote:
>>
>> Dear all,
>>
>> I’m relatively new to MacOS and have only recently started trying to use XQuartz to enable me to run Rcmdr. Are there any common issues/ tips for getting good performance out of it (or should it usually run well with default settings)?
>>
>> On first installation, I found there was a very long lag in menus being populated (i.e. the menu shape was generated, but no usable options were added), to the extent that Rcmdr was then effectively useless (not Rcmdr’s fault, I don’t think). One of my students suggested reducing Output Colors option from the default “Millions” setting. That seems to deal with the problem, thankfully.
>>
>> Is that typical of XQuartz, and is there anything else I should be doing to get the best performance from it?
>
>    I haven't observed the problem you describe on my Mac, which is a three- or four-year-old MacBook Pro (that is, the Rcmdr dialogs display reasonably crisply for me), and I haven't done anything special to configure XQuartz. Here are the specs for my Mac:
>
>     Model Name: MacBook Pro
>      Model Identifier: MacBookPro13,2
>      Processor Name: Dual-Core Intel Core i7
>      Processor Speed: 3.3 GHz
>      Number of Processors: 1
>      Total Number of Cores: 2
>      L2 Cache (per Core): 256 KB
>      L3 Cache: 4 MB
>      Hyper-Threading Technology: Enabled
>      Memory: 8 GB
>
>    It might help to have some more information. I assume that you're using the most recent versions of R, the Rcmdr package, and other packages, and a recent version of macOS. What Mac do you have, and did you reboot it after installing XQuartz? If you updated R, did you reinstall XQuartz?
>
>    Best,
>     John
>
>      -----------------------------
>      John Fox, Professor Emeritus
>      McMaster University
>      Hamilton, Ontario, Canada
>      Web: http::/socserv.mcmaster.ca/jfox
>
>>
>> Thanks,
>>
>> Niall Anderson
>>
>>
>> ________________________________
>>
>> Dr Niall H. Anderson | Senior Lecturer in Medical Statistics/ Programme Co-director, MPH (on campus)
>>
>> Room G113B, Doorway 1
>> Usher Institute, University of Edinburgh
>> Old Medical School, Teviot Place, Edinburgh, EH8 9AG
>>
>> [hidden email]  | +44 (0)131 650 3212 | Skype = live:niall.h.anderson
>>
>> Responses to emails are only expected during your working hours
>> <image001.png>
>> www.ed.ac.uk/usher | @EdinUniUsher
>>
>> <image002.png>
>>
>>
>> The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. _______________________________________________
>> R-SIG-Mac mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
>
>
>
>
>
> _______________________________________________
> R-SIG-Mac mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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Re: [R-SIG-Mac] Using XQuartz - any known issues?

R-SIG-Mac mailing list
In reply to this post by ANDERSON Niall
Hello,

Regarding R with XQuartz on Mac--I found one reference claiming that
after upgrading to MacOS 10.15 Catalina, users may be required to
re-install XQuartz. The MacOS Catalina installer moves/quarantines
prior XQuartz installations to a folder called "Relocated Items",
which may disrupt programs linking to XQuartz and expecting to find it
in the old location:

"Installing or Reinstalling XQuartz if Upgrade to macOS 10.15 Catalina
Causes Issues"
https://www.harrisgeospatial.com/Support/Self-Help-Tools/Help-Articles/Help-Articles-Detail/ArtMID/10220/ArticleID/23855/default

HTH, Bill.

W. Michels, Ph.D.



On Tue, Apr 21, 2020 at 4:25 PM <[hidden email]> wrote:
>
> Send R-SIG-Mac mailing list submissions to
>         [hidden email]

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Re: [R-SIG-Mac] Using XQuartz - any known issues?

Simon Urbanek
Bill,

that has been always the case. You have to re-install XQuartz with every macOS upgrade. There are many issues with Catalina, but at least this one is not new ;).

Cheers,
Simon


> On 22/04/2020, at 4:37 PM, William Michels via R-SIG-Mac <[hidden email]> wrote:
>
> Hello,
>
> Regarding R with XQuartz on Mac--I found one reference claiming that
> after upgrading to MacOS 10.15 Catalina, users may be required to
> re-install XQuartz. The MacOS Catalina installer moves/quarantines
> prior XQuartz installations to a folder called "Relocated Items",
> which may disrupt programs linking to XQuartz and expecting to find it
> in the old location:
>
> "Installing or Reinstalling XQuartz if Upgrade to macOS 10.15 Catalina
> Causes Issues"
> https://www.harrisgeospatial.com/Support/Self-Help-Tools/Help-Articles/Help-Articles-Detail/ArtMID/10220/ArticleID/23855/default
>
> HTH, Bill.
>
> W. Michels, Ph.D.
>
>
>
> On Tue, Apr 21, 2020 at 4:25 PM <[hidden email]> wrote:
>>
>> Send R-SIG-Mac mailing list submissions to
>>        [hidden email]
>
> _______________________________________________
> R-SIG-Mac mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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Re: [R-SIG-Mac] Using XQuartz - any known issues?

ANDERSON Niall
In reply to this post by Simon Urbanek
Thanks to everyone who has responded.

The consensus view seems to be that the reboot after initial installation is vital and I/ we probably missed that! Also that very first use may involve more system preparation to generate the font cache, so it may run more slowly until that is complete. I'm inclined to think one or both of these explanations underlay the issues and that we can mark this as User Error, but Resolved!

Best wishes to all.

Niall


________________________________
 
Dr Niall H. Anderson | Senior Lecturer in Medical Statistics/ Programme Co-director, MPH (on campus)
Room G113B, Doorway 1
Usher Institute, University of Edinburgh
Old Medical School, Teviot Place, Edinburgh, EH8 9AG
 
[hidden email]  | +44 (0)131 650 3212 | Skype = live:niall.h.anderson
 
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On 22/04/2020, 00:24, "Simon Urbanek" <[hidden email]> wrote:

    Just a quick note in the hopes that is may be helpful: X11 (fontconfig, really) creates a font cache the first time is it started which can take substantial time depending on hardware (HDD vs SSD...) during which XQuartz doesn't respond. So I wouldn't be surprised if that was actually happening, unrelated to any setttings. If you start XQuartz later after the cache has been built, it will work fine immediately. So if that is what it was, the issue should not re-occur if you were patient enough the first time.
   
    Cheers,
    Simon
   
   
   
    > On 21/04/2020, at 8:41 PM, ANDERSON Niall <[hidden email]> wrote:
    >
    > Eberhard, Thanks - I'm also  an RStudio user, but am trying to use Rcmdr as a gentle introduction to R for a course (building up to RStudio use later).
    >
    > John, thanks also for responding (not at all an Rcmdr issue, I think - that's just what happened to show the problem). Tech details:
    >
    > MacBook Pro 15 (bought 2019)
    > Catalina 10.15.4
    > 2.6 GHz 6-core Intel Core i7
    > 16 GB 2400 MHz DDR4 memory
    > Radeon Pro 555X 4GB & Intel UHD Graphics 360 1536MB graphics.
    >
    > R 3.6.3, new download of Rcmdr etc (reinstalled everything from scratch before realising X11 was the reason Rcmdr wasn't working and downloading XQuartz). I'm almost certain I would have rebooted before trying to run this - I saw that warning somewhere (CRAN FAQ maybe?). I certainly have since, but perhaps that's why it is now appearing to function correctly? I should say that 2-3 students have reported the same problem over the last 3-4 days, so it isn't just me.
    >
    > Thanks again for input. Best wishes to all on the list.
    >
    > Niall
    >
    > ________________________________
    >
    > Dr Niall H. Anderson | Senior Lecturer in Medical Statistics/ Programme Co-director, MPH (on campus)
    > Room G113B, Doorway 1
    > Usher Institute, University of Edinburgh
    > Old Medical School, Teviot Place, Edinburgh, EH8 9AG
    >
    > [hidden email]  | +44 (0)131 650 3212 | Skype = live:niall.h.anderson
    >
    > Responses to emails are only expected during your working hours
    >
    > www.ed.ac.uk/usher <http://www.ed.ac.uk/usher> | @EdinUniUsher <https://twitter.com/edinuniusher>
    >
    >
    >
    >
    >
    > On 21/04/2020, 04:55, "Fox, John" <[hidden email]> wrote:
    >
    >    Dear Niall,
    >
    >> On Apr 20, 2020, at 3:42 PM, ANDERSON Niall <[hidden email]> wrote:
    >>
    >> Dear all,
    >>
    >> I’m relatively new to MacOS and have only recently started trying to use XQuartz to enable me to run Rcmdr. Are there any common issues/ tips for getting good performance out of it (or should it usually run well with default settings)?
    >>
    >> On first installation, I found there was a very long lag in menus being populated (i.e. the menu shape was generated, but no usable options were added), to the extent that Rcmdr was then effectively useless (not Rcmdr’s fault, I don’t think). One of my students suggested reducing Output Colors option from the default “Millions” setting. That seems to deal with the problem, thankfully.
    >>
    >> Is that typical of XQuartz, and is there anything else I should be doing to get the best performance from it?
    >
    >    I haven't observed the problem you describe on my Mac, which is a three- or four-year-old MacBook Pro (that is, the Rcmdr dialogs display reasonably crisply for me), and I haven't done anything special to configure XQuartz. Here are the specs for my Mac:
    >
    >     Model Name: MacBook Pro
    >      Model Identifier: MacBookPro13,2
    >      Processor Name: Dual-Core Intel Core i7
    >      Processor Speed: 3.3 GHz
    >      Number of Processors: 1
    >      Total Number of Cores: 2
    >      L2 Cache (per Core): 256 KB
    >      L3 Cache: 4 MB
    >      Hyper-Threading Technology: Enabled
    >      Memory: 8 GB
    >
    >    It might help to have some more information. I assume that you're using the most recent versions of R, the Rcmdr package, and other packages, and a recent version of macOS. What Mac do you have, and did you reboot it after installing XQuartz? If you updated R, did you reinstall XQuartz?
    >
    >    Best,
    >     John
    >
    >      -----------------------------
    >      John Fox, Professor Emeritus
    >      McMaster University
    >      Hamilton, Ontario, Canada
    >      Web: http::/socserv.mcmaster.ca/jfox
    >
    >>
    >> Thanks,
    >>
    >> Niall Anderson
    >>
    >>
    >> ________________________________
    >>
    >> Dr Niall H. Anderson | Senior Lecturer in Medical Statistics/ Programme Co-director, MPH (on campus)
    >>
    >> Room G113B, Doorway 1
    >> Usher Institute, University of Edinburgh
    >> Old Medical School, Teviot Place, Edinburgh, EH8 9AG
    >>
    >> [hidden email]  | +44 (0)131 650 3212 | Skype = live:niall.h.anderson
    >>
    >> Responses to emails are only expected during your working hours
    >> <image001.png>
    >> www.ed.ac.uk/usher | @EdinUniUsher
    >>
    >> <image002.png>
    >>
    >>
    >> The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. _______________________________________________
    >> R-SIG-Mac mailing list
    >> [hidden email]
    >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
    >
    >
    >
    >
    >
    >
    > _______________________________________________
    > R-SIG-Mac mailing list
    > [hidden email]
    > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
   
   

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Re: [R-SIG-Mac] Using XQuartz - any known issues?

Fox, John
In reply to this post by ANDERSON Niall
Dear Simon,

Thanks for the explanation -- it makes sense of what Niall and some of his students observed and why I haven't seen this problem, because XQuartz was first installed on my Mac years ago.

Best,
 John

> On Apr 21, 2020, at 7:24 PM, Simon Urbanek <[hidden email]> wrote:
>
> Just a quick note in the hopes that is may be helpful: X11 (fontconfig, really) creates a font cache the first time is it started which can take substantial time depending on hardware (HDD vs SSD...) during which XQuartz doesn't respond. So I wouldn't be surprised if that was actually happening, unrelated to any setttings. If you start XQuartz later after the cache has been built, it will work fine immediately. So if that is what it was, the issue should not re-occur if you were patient enough the first time.
>
> Cheers,
> Simon
>
>
>
>> On 21/04/2020, at 8:41 PM, ANDERSON Niall <[hidden email]> wrote:
>>
>> Eberhard, Thanks - I'm also  an RStudio user, but am trying to use Rcmdr as a gentle introduction to R for a course (building up to RStudio use later).
>>
>> John, thanks also for responding (not at all an Rcmdr issue, I think - that's just what happened to show the problem). Tech details:
>>
>> MacBook Pro 15 (bought 2019)
>> Catalina 10.15.4
>> 2.6 GHz 6-core Intel Core i7
>> 16 GB 2400 MHz DDR4 memory
>> Radeon Pro 555X 4GB & Intel UHD Graphics 360 1536MB graphics.
>>
>> R 3.6.3, new download of Rcmdr etc (reinstalled everything from scratch before realising X11 was the reason Rcmdr wasn't working and downloading XQuartz). I'm almost certain I would have rebooted before trying to run this - I saw that warning somewhere (CRAN FAQ maybe?). I certainly have since, but perhaps that's why it is now appearing to function correctly? I should say that 2-3 students have reported the same problem over the last 3-4 days, so it isn't just me.
>>
>> Thanks again for input. Best wishes to all on the list.
>>
>> Niall
>>
>> ________________________________
>>
>> Dr Niall H. Anderson | Senior Lecturer in Medical Statistics/ Programme Co-director, MPH (on campus)
>> Room G113B, Doorway 1
>> Usher Institute, University of Edinburgh
>> Old Medical School, Teviot Place, Edinburgh, EH8 9AG
>>
>> [hidden email]  | +44 (0)131 650 3212 | Skype = live:niall.h.anderson
>>
>> Responses to emails are only expected during your working hours
>>
>> www.ed.ac.uk/usher <http://www.ed.ac.uk/usher> | @EdinUniUsher <https://twitter.com/edinuniusher>
>>
>>
>>
>>
>>
>> On 21/04/2020, 04:55, "Fox, John" <[hidden email]> wrote:
>>
>>   Dear Niall,
>>
>>> On Apr 20, 2020, at 3:42 PM, ANDERSON Niall <[hidden email]> wrote:
>>>
>>> Dear all,
>>>
>>> I’m relatively new to MacOS and have only recently started trying to use XQuartz to enable me to run Rcmdr. Are there any common issues/ tips for getting good performance out of it (or should it usually run well with default settings)?
>>>
>>> On first installation, I found there was a very long lag in menus being populated (i.e. the menu shape was generated, but no usable options were added), to the extent that Rcmdr was then effectively useless (not Rcmdr’s fault, I don’t think). One of my students suggested reducing Output Colors option from the default “Millions” setting. That seems to deal with the problem, thankfully.
>>>
>>> Is that typical of XQuartz, and is there anything else I should be doing to get the best performance from it?
>>
>>   I haven't observed the problem you describe on my Mac, which is a three- or four-year-old MacBook Pro (that is, the Rcmdr dialogs display reasonably crisply for me), and I haven't done anything special to configure XQuartz. Here are the specs for my Mac:
>>
>>    Model Name: MacBook Pro
>>     Model Identifier: MacBookPro13,2
>>     Processor Name: Dual-Core Intel Core i7
>>     Processor Speed: 3.3 GHz
>>     Number of Processors: 1
>>     Total Number of Cores: 2
>>     L2 Cache (per Core): 256 KB
>>     L3 Cache: 4 MB
>>     Hyper-Threading Technology: Enabled
>>     Memory: 8 GB
>>
>>   It might help to have some more information. I assume that you're using the most recent versions of R, the Rcmdr package, and other packages, and a recent version of macOS. What Mac do you have, and did you reboot it after installing XQuartz? If you updated R, did you reinstall XQuartz?
>>
>>   Best,
>>    John
>>
>>     -----------------------------
>>     John Fox, Professor Emeritus
>>     McMaster University
>>     Hamilton, Ontario, Canada
>>     Web: http::/socserv.mcmaster.ca/jfox
>>
>>>
>>> Thanks,
>>>
>>> Niall Anderson
>>>
>>>
>>> ________________________________
>>>
>>> Dr Niall H. Anderson | Senior Lecturer in Medical Statistics/ Programme Co-director, MPH (on campus)
>>>
>>> Room G113B, Doorway 1
>>> Usher Institute, University of Edinburgh
>>> Old Medical School, Teviot Place, Edinburgh, EH8 9AG
>>>
>>> [hidden email]  | +44 (0)131 650 3212 | Skype = live:niall.h.anderson
>>>
>>> Responses to emails are only expected during your working hours
>>> <image001.png>
>>> www.ed.ac.uk/usher | @EdinUniUsher
>>>
>>> <image002.png>
>>>
>>>
>>> The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. _______________________________________________
>>> R-SIG-Mac mailing list
>>> [hidden email]
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> _______________________________________________
> R-SIG-Mac mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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Re: [R-SIG-Mac] Using XQuartz - any known issues?

Fox, John
In reply to this post by Simon Urbanek
Dear Niall,

I'll update the Rcmdr macOS installation notes to reflect Simon's information about XQuartz causing a font cache to be built on first installation.

I'm glad that the Rcmdr is now working normally for you and your students. I wouldn't code this as "user error," but as a previously unnoticed (by me) consequence of installing XQuartz for the first time.

Best,
 John

> On Apr 22, 2020, at 5:06 AM, ANDERSON Niall <[hidden email]> wrote:
>
> Thanks to everyone who has responded.
>
> The consensus view seems to be that the reboot after initial installation is vital and I/ we probably missed that! Also that very first use may involve more system preparation to generate the font cache, so it may run more slowly until that is complete. I'm inclined to think one or both of these explanations underlay the issues and that we can mark this as User Error, but Resolved!
>
> Best wishes to all.
>
> Niall
>
>
> ________________________________
>
> Dr Niall H. Anderson | Senior Lecturer in Medical Statistics/ Programme Co-director, MPH (on campus)
> Room G113B, Doorway 1
> Usher Institute, University of Edinburgh
> Old Medical School, Teviot Place, Edinburgh, EH8 9AG
>
> [hidden email]  | +44 (0)131 650 3212 | Skype = live:niall.h.anderson
>
> Responses to emails are only expected during your working hours
>
> www.ed.ac.uk/usher <http://www.ed.ac.uk/usher> | @EdinUniUsher <https://twitter.com/edinuniusher>
>
>
>
>
>
> On 22/04/2020, 00:24, "Simon Urbanek" <[hidden email]> wrote:
>
>    Just a quick note in the hopes that is may be helpful: X11 (fontconfig, really) creates a font cache the first time is it started which can take substantial time depending on hardware (HDD vs SSD...) during which XQuartz doesn't respond. So I wouldn't be surprised if that was actually happening, unrelated to any setttings. If you start XQuartz later after the cache has been built, it will work fine immediately. So if that is what it was, the issue should not re-occur if you were patient enough the first time.
>
>    Cheers,
>    Simon
>
>
>
>> On 21/04/2020, at 8:41 PM, ANDERSON Niall <[hidden email]> wrote:
>>
>> Eberhard, Thanks - I'm also  an RStudio user, but am trying to use Rcmdr as a gentle introduction to R for a course (building up to RStudio use later).
>>
>> John, thanks also for responding (not at all an Rcmdr issue, I think - that's just what happened to show the problem). Tech details:
>>
>> MacBook Pro 15 (bought 2019)
>> Catalina 10.15.4
>> 2.6 GHz 6-core Intel Core i7
>> 16 GB 2400 MHz DDR4 memory
>> Radeon Pro 555X 4GB & Intel UHD Graphics 360 1536MB graphics.
>>
>> R 3.6.3, new download of Rcmdr etc (reinstalled everything from scratch before realising X11 was the reason Rcmdr wasn't working and downloading XQuartz). I'm almost certain I would have rebooted before trying to run this - I saw that warning somewhere (CRAN FAQ maybe?). I certainly have since, but perhaps that's why it is now appearing to function correctly? I should say that 2-3 students have reported the same problem over the last 3-4 days, so it isn't just me.
>>
>> Thanks again for input. Best wishes to all on the list.
>>
>> Niall
>>
>> ________________________________
>>
>> Dr Niall H. Anderson | Senior Lecturer in Medical Statistics/ Programme Co-director, MPH (on campus)
>> Room G113B, Doorway 1
>> Usher Institute, University of Edinburgh
>> Old Medical School, Teviot Place, Edinburgh, EH8 9AG
>>
>> [hidden email]  | +44 (0)131 650 3212 | Skype = live:niall.h.anderson
>>
>> Responses to emails are only expected during your working hours
>>
>> www.ed.ac.uk/usher <http://www.ed.ac.uk/usher> | @EdinUniUsher <https://twitter.com/edinuniusher>
>>
>>
>>
>>
>>
>> On 21/04/2020, 04:55, "Fox, John" <[hidden email]> wrote:
>>
>>   Dear Niall,
>>
>>> On Apr 20, 2020, at 3:42 PM, ANDERSON Niall <[hidden email]> wrote:
>>>
>>> Dear all,
>>>
>>> I’m relatively new to MacOS and have only recently started trying to use XQuartz to enable me to run Rcmdr. Are there any common issues/ tips for getting good performance out of it (or should it usually run well with default settings)?
>>>
>>> On first installation, I found there was a very long lag in menus being populated (i.e. the menu shape was generated, but no usable options were added), to the extent that Rcmdr was then effectively useless (not Rcmdr’s fault, I don’t think). One of my students suggested reducing Output Colors option from the default “Millions” setting. That seems to deal with the problem, thankfully.
>>>
>>> Is that typical of XQuartz, and is there anything else I should be doing to get the best performance from it?
>>
>>   I haven't observed the problem you describe on my Mac, which is a three- or four-year-old MacBook Pro (that is, the Rcmdr dialogs display reasonably crisply for me), and I haven't done anything special to configure XQuartz. Here are the specs for my Mac:
>>
>>    Model Name: MacBook Pro
>>     Model Identifier: MacBookPro13,2
>>     Processor Name: Dual-Core Intel Core i7
>>     Processor Speed: 3.3 GHz
>>     Number of Processors: 1
>>     Total Number of Cores: 2
>>     L2 Cache (per Core): 256 KB
>>     L3 Cache: 4 MB
>>     Hyper-Threading Technology: Enabled
>>     Memory: 8 GB
>>
>>   It might help to have some more information. I assume that you're using the most recent versions of R, the Rcmdr package, and other packages, and a recent version of macOS. What Mac do you have, and did you reboot it after installing XQuartz? If you updated R, did you reinstall XQuartz?
>>
>>   Best,
>>    John
>>
>>     -----------------------------
>>     John Fox, Professor Emeritus
>>     McMaster University
>>     Hamilton, Ontario, Canada
>>     Web: http::/socserv.mcmaster.ca/jfox
>>
>>>
>>> Thanks,
>>>
>>> Niall Anderson
>>>
>>>
>>> ________________________________
>>>
>>> Dr Niall H. Anderson | Senior Lecturer in Medical Statistics/ Programme Co-director, MPH (on campus)
>>>
>>> Room G113B, Doorway 1
>>> Usher Institute, University of Edinburgh
>>> Old Medical School, Teviot Place, Edinburgh, EH8 9AG
>>>
>>> [hidden email]  | +44 (0)131 650 3212 | Skype = live:niall.h.anderson
>>>
>>> Responses to emails are only expected during your working hours
>>> <image001.png>
>>> www.ed.ac.uk/usher | @EdinUniUsher
>>>
>>> <image002.png>
>>>
>>>
>>> The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. _______________________________________________
>>> R-SIG-Mac mailing list
>>> [hidden email]
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
>
>
> _______________________________________________
> R-SIG-Mac mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

_______________________________________________
R-SIG-Mac mailing list
[hidden email]
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