Re: [R-SIG-Mac] Graphic problem Rcmdr

[Fox, John]

Dear JB,

> On Apr 29, 2020, at 1:44 PM, jean benoit TANIS  wrote:
> 
> This actually works well on the terminal session !! Very strange that the App 
> GUI does not work well. I do not know if it is a general Mac problem or due 
> to my computer settings…. 

I don't think that it could be a general Mac problem, because R.app works with 
the Rcmdr for me and others. At least you now have a couple of solutions.

Best,
 John

> 
> JB
> 
>> On 29 Apr 2020, at 18:18, Fox, John  wrote:
>> 
>> Dear JB,
>> 
>> If you use the Rcmdr with RStudio, by default it will direct output to the 
>> RStudio console. You can change that, if you wish -- look at the Rcmdr 
>> options in ?Commander.
>> 
>> Also, have you tried running R and the Rcmdr in a Terminal window, as I 
>> suggested? If the problem is with R.app, then that might work too.
>> 
>> Peter: Thanks for chiming in.
>> 
>> Best,
>> John
>> 
>>> -----Original Message-
>>> From: jean benoit TANIS 
>>> Sent: Wednesday, April 29, 2020 1:04 PM
>>> To: peter dalgaard 
>>> Cc: Fox, John ; R-Sig-Mac 
>>> Subject: Re: [R-SIG-Mac] Graphic problem Rcmdr
>>> 
>>> I have just tried with R studio and it works … I do not know why it does
>>> not work with Rapp but at least I can use it now.
>>> 
>>> Thank you very much for your precious help !!
>>> 
>>> JB
>>> 
>>>> On 29 Apr 2020, at 16:14, peter dalgaard  wrote:
>>>> 
>>>> Also not seen by me on Mojave (admittedly 4.0.0 beta, which I can't be
>>> bothered to upgrade at this point). Works both from R.app and Terminal,
>>> and even from RStudio.
>>>> 
>>>> One thought is a missing font, but same font is used elsewhere is it
>>> not?
>>>> 
>>>> You could try playing with generic Tcl/Tk via the tcltk package and
>>>> see if you can reproduce the problem in a simpler setting (perhaps try
>>>> the package demos?)
>>>> 
>>>> -pd
>>>> 
>>>>> On 29 Apr 2020, at 15:07 , Fox, John  wrote:
>>>>> 
>>>>> Dear JB,
>>>>> 
>>>>> We corresponded privately about this problem, and I suggested that you
>>> post a message to the R-SIG-Mac list when I was unable to help you solve
>>> it. I don't experience the problem on a Mac similar to yours, but running
>>> macOS Catalina, and no one else to my knowledge has reported a similar
>>> problem (with blank menus).
>>>>> 
>>>>> I do have one additional suggestion: I assume that you're running the
>>> Rcmdr under the standard R.app GUI. Try running R in a Terminal session.
>>> That is open the Mac Terminal, type R  at the % command prompt and then
>>> library(Rcmdr) at the R > prompt.
>>>>> 
>>>>> Perhaps others will think of additional suggestions.
>>>>> 
>>>>> Best,
>>>>> John
>>>>> 
>>>>>> On Apr 29, 2020, at 2:18 AM, jean benoit TANIS 
>>> wrote:
>>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I recently downloaded 4.0.0 and the Rcmdr package with dependencies (I
>>> used to work on R2.6 on Windows).
>>>>>> 
>>>>>> When I load the Rcmdr package, this is what I obtain - see picture
>>>>>> (the drop down menu does not display). 
>>>>>> 
>>>>>> I manage to have access to the drop-down menu only once despite 20 or
>>> so attempts of closing and reopening R.
>>>>>> 
>>>>>> I have tried to:
>>>>>> - turn-off nap-app => same issue
>>>>>> - uninstall R and rebook and start again => same issue
>>>>>> - uninstall XQuartz and reboot and start again => same issue
>>>>>> 
>>>>>> For more information about my system, please find the pictures below
>>>>>> 
>>>>>> <7D8214F7-97BD-45F0-A21F-9A5333AF2C94.tiff>
>>>>>> <28E41AFC-0091-4F73-8A48-D9B8D33D341D.tiff>
>>>>>> 
>>>>>> Did you encounter this problem before ? Is there any way you could
>>> help me solving it ?
>>>>>> 
>>>>>> 
>>>>>> Thank you very much for your help,
>>>>>> 
>>>>>> Best wishes,
>>>>>> 
>>>>>> 
>>>>>> JB
>>>>>> 
>>>>>> 
>>>>>> ___
>>>>>> R-SIG-Mac mailing list
>>>>>> R-SIG-Mac@r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>> 
>>>>> ___
>>>>> R-SIG-Mac mailing list
>>>>> R-SIG-Mac@r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>> 
>>>> --
>>>> Peter Dalgaard, Professor,
>>>> Center for Statistics, Copenhagen Business School Solbjerg Plads 3,
>>>> 2000 Frederiksberg, Denmark
>>>> Phone: (+45)38153501
>>>> Office: A 4.23
>>>> Email: pd@cbs.dk  Priv: pda...@gmail.com
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>> 
> 

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Re: [R-SIG-Mac] Graphic problem Rcmdr

[Fox, John]

Dear JB,

If you use the Rcmdr with RStudio, by default it will direct output to the 
RStudio console. You can change that, if you wish -- look at the Rcmdr options 
in ?Commander.

Also, have you tried running R and the Rcmdr in a Terminal window, as I 
suggested? If the problem is with R.app, then that might work too.

Peter: Thanks for chiming in.

Best,
 John

> -Original Message-
> From: jean benoit TANIS 
> Sent: Wednesday, April 29, 2020 1:04 PM
> To: peter dalgaard 
> Cc: Fox, John ; R-Sig-Mac 
> Subject: Re: [R-SIG-Mac] Graphic problem Rcmdr
> 
> I have just tried with R studio and it works … I do not know why it does
> not work with Rapp but at least I can use it now.
> 
> Thank you very much for your precious help !!
> 
> JB
> 
> > On 29 Apr 2020, at 16:14, peter dalgaard  wrote:
> >
> > Also not seen by me on Mojave (admittedly 4.0.0 beta, which I can't be
> bothered to upgrade at this point). Works both from R.app and Terminal,
> and even from RStudio.
> >
> > One thought is a missing font, but same font is used elsewhere is it
> not?
> >
> > You could try playing with generic Tcl/Tk via the tcltk package and
> > see if you can reproduce the problem in a simpler setting (perhaps try
> > the package demos?)
> >
> > -pd
> >
> >> On 29 Apr 2020, at 15:07 , Fox, John  wrote:
> >>
> >> Dear JB,
> >>
> >> We corresponded privately about this problem, and I suggested that you
> post a message to the R-SIG-Mac list when I was unable to help you solve
> it. I don't experience the problem on a Mac similar to yours, but running
> macOS Catalina, and no one else to my knowledge has reported a similar
> problem (with blank menus).
> >>
> >> I do have one additional suggestion: I assume that you're running the
> Rcmdr under the standard R.app GUI. Try running R in a Terminal session.
> That is open the Mac Terminal, type R  at the % command prompt and then
> library(Rcmdr) at the R > prompt.
> >>
> >> Perhaps others will think of additional suggestions.
> >>
> >> Best,
> >> John
> >>
> >>> On Apr 29, 2020, at 2:18 AM, jean benoit TANIS 
> wrote:
> >>>
> >>> Hi,
> >>>
> >>> I recently downloaded 4.0.0 and the Rcmdr package with dependencies (I
> used to work on R2.6 on Windows).
> >>>
> >>> When I load the Rcmdr package, this is what I obtain - see picture
> >>> (the drop down menu does not display). 
> >>>
> >>> I manage to have access to the drop-down menu only once despite 20 or
> so attempts of closing and reopening R.
> >>>
> >>> I have tried to:
> >>> - turn-off nap-app => same issue
> >>> - uninstall R and rebook and start again => same issue
> >>> - uninstall XQuartz and reboot and start again => same issue
> >>>
> >>> For more information about my system, please find the pictures below
> >>>
> >>> <7D8214F7-97BD-45F0-A21F-9A5333AF2C94.tiff>
> >>> <28E41AFC-0091-4F73-8A48-D9B8D33D341D.tiff>
> >>>
> >>> Did you encounter this problem before ? Is there any way you could
> help me solving it ?
> >>>
> >>>
> >>> Thank you very much for your help,
> >>>
> >>> Best wishes,
> >>>
> >>>
> >>> JB
> >>>
> >>>
> >>> ___
> >>> R-SIG-Mac mailing list
> >>> R-SIG-Mac@r-project.org
> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>
> >> ___
> >> R-SIG-Mac mailing list
> >> R-SIG-Mac@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
> > --
> > Peter Dalgaard, Professor,
> > Center for Statistics, Copenhagen Business School Solbjerg Plads 3,
> > 2000 Frederiksberg, Denmark
> > Phone: (+45)38153501
> > Office: A 4.23
> > Email: pd@cbs.dk  Priv: pda...@gmail.com
> >
> >
> >
> >
> >
> >
> >
> >
> >

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Re: [R-SIG-Mac] Graphic problem Rcmdr

[Fox, John]

Dear JB,

We corresponded privately about this problem, and I suggested that you post a 
message to the R-SIG-Mac list when I was unable to help you solve it. I don't 
experience the problem on a Mac similar to yours, but running macOS Catalina, 
and no one else to my knowledge has reported a similar problem (with blank 
menus).

I do have one additional suggestion: I assume that you're running the Rcmdr 
under the standard R.app GUI. Try running R in a Terminal session. That is open 
the Mac Terminal, type R  at the % command prompt and then library(Rcmdr) at 
the R > prompt.

Perhaps others will think of additional suggestions.

Best,
 John

> On Apr 29, 2020, at 2:18 AM, jean benoit TANIS  wrote:
> 
> Hi,
> 
> I recently downloaded 4.0.0 and the Rcmdr package with dependencies (I used 
> to work on R2.6 on Windows). 
> 
> When I load the Rcmdr package, this is what I obtain - see picture (the drop 
> down menu does not display). 
> 
> I manage to have access to the drop-down menu only once despite 20 or so 
> attempts of closing and reopening R. 
> 
> I have tried to:
> - turn-off nap-app => same issue 
> - uninstall R and rebook and start again => same issue 
> - uninstall XQuartz and reboot and start again => same issue 
> 
> For more information about my system, please find the pictures below 
> 
> <7D8214F7-97BD-45F0-A21F-9A5333AF2C94.tiff>
> <28E41AFC-0091-4F73-8A48-D9B8D33D341D.tiff>
> 
> Did you encounter this problem before ? Is there any way you could help me 
> solving it ? 
> 
> 
> Thank you very much for your help,
> 
> Best wishes,
> 
> 
> JB 
> 
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

[Fox, John]

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  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
> 
> niall.ander...@ed.ac.uk  | +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"  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  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
>> 
>> niall.ander...@ed.ac.uk  | +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"  wrote:
>> 
>>   Dear Niall,
>> 
>>> On Apr 20, 2020, at 3:42 PM, ANDERSON Niall  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 Rc

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

[Fox, John]

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  
> 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  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
>> 
>> niall.ander...@ed.ac.uk  | +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"  wrote:
>> 
>>   Dear Niall,
>> 
>>> On Apr 20, 2020, at 3:42 PM, ANDERSON Niall  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 

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

[Fox, John]

I neglected to include the list in my reply, which appears below..


John



Begin forwarded message:


From:
John Fox <j...@mcmaster.ca>


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


Date:
April 21, 2020 at 10:43:33 AM EDT


To:
ANDERSON Niall <niall.ander...@ed.ac.uk>



Dear Niall,

On Apr 21, 2020, at 4:41 AM, ANDERSON Niall <niall.ander...@ed.ac.uk> 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

niall.ander...@ed.ac.uk  | +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" <j...@mcmaster.ca> wrote:

  Dear Niall,

On Apr 20, 2020, at 3:42 PM, ANDERSON Niall <niall.ander...@ed.ac.uk> 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 Edinbur

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

[Fox, John]

Dear Niall,

> On Apr 20, 2020, at 3:42 PM, ANDERSON Niall  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
>  
> niall.ander...@ed.ac.uk  | +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 | @EdinUniUsher
>  
> 
>  
>  
> The University of Edinburgh is a charitable body, registered in Scotland, 
> with registration number SC005336. 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac




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Re: [R-SIG-Mac] Error when fitting a brms model, maybe associated with Catalina MacOS

[Fox, John]

Dear Manuel,

As far as I can tell, a lot of people are experiencing problems with rstan 
under Catalina -- I don't use brms but rather rstan directly, and I thrashed 
around quite a bit to get it work reliably (at least so far!).

The final bit of the puzzle for me was to modify Makevars in the .R 
subdirectory of my home directory according to the instructions at 
. Maybe that 
will work for you too. If this is in fact a generally satisfactory solution, 
one would hope that it could be made more convenient for macOS rstan users.

I hope this helps,
 John

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

> On Dec 14, 2019, at 6:28 PM, Manuel Spínola  wrote:
> 
> Dear list members,
> 
> I updated everything, Catalina, Xcode, CLT, R 3.6.2, rstan from source, and
> installed the r-macos-rtools, but I still have problems.
> 
> library(brms)
> group <- rep(c("treat", "placebo"), each = 30)
> symptom_post <- c(rnorm(30, mean = 1, sd = 2), rnorm(30, mean = 0, sd = 1))
> dat1 <- data.frame(group, symptom_post)
> 
> fit1 <- brm(bf(symptom_post ~ group, sigma ~ group),
>data = dat1, family = gaussian())
> 
> Chain 4: Iteration:1 / 2000 [  0%]  (Warmup)
> [1] "Error in sampler$call_sampler(args_list[[i]]) : "
> [2] "  c++ exception (unknown reason)"
> error occurred during calling the sampler; sampling not done
> 
> 
> 
> 
> 
> 
> El jue., 12 dic. 2019 a las 12:51, Balamuta, James Joseph (<
> balam...@illinois.edu>) escribió:
> 
>> Greetings and Salutations All,
>> 
>> Great to see the `r-macos-rtools` installer popping up! As the author of
>> it, please note that it's an unofficial (non-CRAN backed) installer that
>> seeks to automatically establish the CRAN toolchain in a friendly GUI
>> installer. We developed it to help out students in STAT 385 @ UIUC [
>> http://stat385.com/ ]  setup the correct developer environment in a
>> uniform manner as there wasn't really any prior installer packages made
>> available at the time. We're grateful for the financial support that was
>> given by Timothy Bates to sign the installer.
>> 
>> With this being said, each step the installer takes is documented across a
>> README file, installer splash screen, and by a post.
>> 
>> README Overview:
>> https://github.com/rmacoslib/r-macos-rtools#what-does-the-installer-do
>> Installer Splash:
>> https://raw.githubusercontent.com/rmacoslib/r-macos-rtools/master/readme_img/lock_icon.png
>> Post:
>> https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/
>> 
>> That said, there is also Appendix C.3 macOS of R Installation and
>> Administration [
>> https://cran.r-project.org/doc/manuals/r-release/R-admin.html#macOS ]
>> that goes over the details in greater depth.
>> 
>> For those who are worried about security, please note that we've taken
>> steps to ensure secure downloads by verifying the installer hashes prior to
>> installing per prior remarks by Simon regarding earlier versions of the
>> installer [ see the prior discussion and my response here:
>> https://stat.ethz.ch/pipermail/r-sig-mac/2018-May/012745.html ].
>> 
>> Lastly, and perhaps more critically, please note that just using Xcode CLI
>> is not sufficient as it does not match the prescribed compilation toolchain
>> (clang7 with OpenMP enabled and gfortran).
>> 
>> Best,
>> 
>> JJB
>> 
>> On 12/11/19, 7:25 PM, "R-SIG-Mac on behalf of Manuel Spínola" <
>> r-sig-mac-boun...@r-project.org on behalf of mspinol...@gmail.com> wrote:
>> 
>>An update.
>> 
>>Before doing the suggested installation, I updated Catalina to 10.5.2,
>>Xtools to 11.3 and the Command Line Tools and it works.
>> 
>>Manuel
>> 
>>El mié., 11 dic. 2019 a las 16:05, Ken Beath ()
>>escribió:
>> 
>>> No, it only downloads and installs the right compilers and updates
>>> Makevars and REnvirons. These are what Stan and RCpp require so you
>> could
>>> do these manually.
>>> 
>>> What it does is described at
>> https://github.com/rmacoslib/r-macos-rtools
>>> 
>>> Ken
>>> 
 On 12 Dec 2019, at 1:14 am, Manuel Spínola 
>> wrote:
 
 Thank you very much to all.
 
 Does Installing the macos-rtools could affect R in other ways?
 
 Manuel
 
 El mié., 11 dic. 2019 a las 6:56, Ken Beath ()
>>> escribió:
 What worked for me was installing the tools using
>>> https://github.com/rmacoslib/r-macos-rtools/releases
 
 and then installing rstan from source ie
>>> install.packages(“rstan”,type=“source) as suggested on one of the
>> stan
>>> forums
 
 Ken
 
> On 11 Dec 2019, at 11:09 am, Manuel Spínola <
>> mspinol...@gmail.com>
>>> wrote:
> 
> Dear list members,
> 
> When trying to fit this example from the CRAN repository fro
>> brms, I
>>> got
> the following error message after the 4th chain.  I am using R
>> 

Re: [R-SIG-Mac] Error message reading files in R Commander

[Fox, John]

Dear José,

As a general matter and an ideal, users should *never* see errors in the Rcmdr 
code -- the Rcmdr should ideally intercept all errors.

I'm now able to reproduce the error you reported. I believe that I've fixed it 
in the development version 2.7-0 of the Rcmdr package on R-Forge. I should test 
the fix some more, but if it holds up, I'll also apply it to Rcmdr 2.6-2 when 
and if that's submitted to CRAN.

If you want to try Rcmdr 2.7-0, you can download the source tree for the 
package from R-Forge via svn and build and install it yourself.

Also see some comments below:

> On Nov 25, 2019, at 2:25 PM, Jose G Conde Santiago  
> wrote:
> 
> Dear John.
> 
> My apologies, and thanks for your patience. This is what I did today:
> 
> 1. I read the data set using the R Commander menu “Data”  -> “Load dataset”.  
> When I am working with an R workspace, I load the workspace with the “Data”  
> ->  “Load dataset” menu, and then read the specific data set in the work 
> space with the “Data set” button.

Once again, the "Data set" button doesn't read a data set, it just makes a data 
frame in your R workspace the active data set in the Rcmdr. It also closes and 
reopens the data set viewer for the data set if such a window is open. The 
source of the error was that the Rcmdr didn't detect that you had closed the 
viewer window for the data set.

> 
> 2. Viewed the data set using R Commander’s “View data set button”.
> 
> 3. Closed the “View data set” window. 
> 
> 4. Try to read the same data set using R Commander’s “Data set” button.

Please see my preceding remark.

> 
> Then I get the error message.
> 
> After I found the problem with my files,

These aren't files but data frames residing in memory. 

I apologize if these distinctions seem pedantic, but the failure to make them 
made it hard for me to understand your original report of the problem.

Thank you for the bug report.

John

> I tested with a few data sets from the packages in R available thorough the 
> “Data”  ->  “Data in packages” menu and had the same results. The files are: 
> CO2, airquality  and ChickWeight included in the “datasets” package, and 
> ethanol from the “lattice” package.
> 
> José
> 
> José G. Conde, MD, MPH
> Catedrático
> Escuela de Medicina
> Recinto de Ciencias Médicas
> Universidad de Puerto Rico
> 
> Tel  (787) 763-9401  Fax (787) 758-5206
> 
> Correo electrónico: jose.con...@upr.edu
> 
>> On Nov 25, 2019, at 11:42 AM, Fox, John  wrote:
>> 
>> Dear José,
>> 
>>> On Nov 25, 2019, at 10:17 AM, Jose G Conde Santiago  
>>> wrote:
>>> 
>>> Dear John,
>>> 
>>> To keep the session as simple as possible, this time I did not configure R 
>>> Commander to send the output to the R console.
>>> 
>>> This is what I did.
>>> 
>>> 1.  Load the file/workspace using R Commander.
>> 
>> What does this mean? What is a "file/workspace"? How did you "load" it with 
>> the R Commander? Can you share the "file/workspace" so that I can replicate 
>> what you did?
>> 
>>> 
>>> 2. Read the data set using R Commander’s “Data set” button. 
>> 
>> As I said in my earlier response, the R Commander's "Data set" button 
>> doesn't "read" a data set -- it chooses from among data frames currently in 
>> the user's R workspace.
>> 
>>> 
>>> 3. View the data set using R Commander’s “View data set button”.
>>> 
>>> 4. Close the “View data set” window. 
>>> 
>>> 5. Try to read the same data set using R Commander’s “Data set” button.
>>> 
>>> This is the error message I got today. It was displayed in the R Console, 
>>> not in the R Commander output window .
>>> 
>>>> Error in structure(.External(.C_dotTcl, ...), class = "tclObj") : 
>>>> [tcl] bad window path name ".3".
>>> 
>>> 
>>> 
>>> Additional information:
>>> 
>>> I tried to “Refresh the active data set” from the “Data”  ->  “Active Data 
>>> set” menu, and got the same error message, but with a different number at 
>>> the end.
>>> 
>>>> Error in structure(.External(.C_dotTcl, ...), class = "tclObj") : 
>>>> [tcl] bad window path name ".6".
>>> 
>>> 
>>> I saved the file with a different name, but when I tried to read the file 
>>> with the new name I got a similar error message.
>> 
>> Do you really mean a *file* -- that is stored on your computer's file system 
>> -- or a data frame in the R workspac

Re: [R-SIG-Mac] Error message reading files in R Commander

[Fox, John]

Dear José,

As a general matter and an ideal, users should *never* see errors in the Rcmdr 
code -- the Rcmdr should ideally intercept all errors.

I'm now able to reproduce the error you reported. I believe that I've fixed it 
in the development version 2.7-0 of the Rcmdr package on R-Forge. I should test 
the fix some more, but if it holds up, I'll also apply it to Rcmdr 2.6-2 when 
and if that's submitted to CRAN.

If you want to try Rcmdr 2.7-0, you can download the source tree for the 
package from R-Forge via svn and build and install it yourself.

Also see some comments below:

> On Nov 25, 2019, at 2:25 PM, Jose G Conde Santiago  
> wrote:
> 
> Dear John.
> 
> My apologies, and thanks for your patience. This is what I did today:
> 
> 1. I read the data set using the R Commander menu “Data”  -> “Load dataset”.  
> When I am working with an R workspace, I load the workspace with the “Data”  
> ->  “Load dataset” menu, and then read the specific data set in the work 
> space with the “Data set” button.

Once again, the "Data set" button doesn't read a data set, it just makes a data 
frame in your R workspace the active data set in the Rcmdr. It also closes and 
reopens the data set viewer for the data set if such a window is open. The 
source of the error was that the Rcmdr didn't detect that you had closed the 
viewer window for the data set.

> 
> 2. Viewed the data set using R Commander’s “View data set button”.
> 
> 3. Closed the “View data set” window. 
> 
> 4. Try to read the same data set using R Commander’s “Data set” button.

Please see my preceding remark.

> 
> Then I get the error message.
> 
> After I found the problem with my files,

These aren't files but data frames residing in memory. 

I apologize if these distinctions seem pedantic, but the failure to make them 
made it hard for me to understand your original report of the problem.

Thank you for the bug report.

John

> I tested with a few data sets from the packages in R available thorough the 
> “Data”  ->  “Data in packages” menu and had the same results. The files are: 
> CO2, airquality  and ChickWeight included in the “datasets” package, and 
> ethanol from the “lattice” package.
> 
> José
> 
> José G. Conde, MD, MPH
> Catedrático
> Escuela de Medicina
> Recinto de Ciencias Médicas
> Universidad de Puerto Rico
> 
> Tel  (787) 763-9401  Fax (787) 758-5206
> 
> Correo electrónico: jose.con...@upr.edu
> 
>> On Nov 25, 2019, at 11:42 AM, Fox, John  wrote:
>> 
>> Dear José,
>> 
>>> On Nov 25, 2019, at 10:17 AM, Jose G Conde Santiago  
>>> wrote:
>>> 
>>> Dear John,
>>> 
>>> To keep the session as simple as possible, this time I did not configure R 
>>> Commander to send the output to the R console.
>>> 
>>> This is what I did.
>>> 
>>> 1.  Load the file/workspace using R Commander.
>> 
>> What does this mean? What is a "file/workspace"? How did you "load" it with 
>> the R Commander? Can you share the "file/workspace" so that I can replicate 
>> what you did?
>> 
>>> 
>>> 2. Read the data set using R Commander’s “Data set” button. 
>> 
>> As I said in my earlier response, the R Commander's "Data set" button 
>> doesn't "read" a data set -- it chooses from among data frames currently in 
>> the user's R workspace.
>> 
>>> 
>>> 3. View the data set using R Commander’s “View data set button”.
>>> 
>>> 4. Close the “View data set” window. 
>>> 
>>> 5. Try to read the same data set using R Commander’s “Data set” button.
>>> 
>>> This is the error message I got today. It was displayed in the R Console, 
>>> not in the R Commander output window .
>>> 
>>>> Error in structure(.External(.C_dotTcl, ...), class = "tclObj") : 
>>>> [tcl] bad window path name ".3".
>>> 
>>> 
>>> 
>>> Additional information:
>>> 
>>> I tried to “Refresh the active data set” from the “Data”  ->  “Active Data 
>>> set” menu, and got the same error message, but with a different number at 
>>> the end.
>>> 
>>>> Error in structure(.External(.C_dotTcl, ...), class = "tclObj") : 
>>>> [tcl] bad window path name ".6".
>>> 
>>> 
>>> I saved the file with a different name, but when I tried to read the file 
>>> with the new name I got a similar error message.
>> 
>> Do you really mean a *file* -- that is stored on your computer's file system 
>> -- or a data frame in the R workspac

Re: [R-SIG-Mac] Error message reading files in R Commander

[Fox, John]

Dear José,

> On Nov 25, 2019, at 10:17 AM, Jose G Conde Santiago  
> wrote:
> 
> Dear John,
> 
> To keep the session as simple as possible, this time I did not configure R 
> Commander to send the output to the R console.
> 
> This is what I did.
> 
> 1.  Load the file/workspace using R Commander.

What does this mean? What is a "file/workspace"? How did you "load" it with the 
R Commander? Can you share the "file/workspace" so that I can replicate what 
you did?

> 
> 2. Read the data set using R Commander’s “Data set” button. 

As I said in my earlier response, the R Commander's "Data set" button doesn't 
"read" a data set -- it chooses from among data frames currently in the user's 
R workspace.

> 
> 3. View the data set using R Commander’s “View data set button”.
> 
> 4. Close the “View data set” window. 
> 
> 5. Try to read the same data set using R Commander’s “Data set” button.
> 
> This is the error message I got today. It was displayed in the R Console, not 
> in the R Commander output window .
> 
>> Error in structure(.External(.C_dotTcl, ...), class = "tclObj") : 
>>  [tcl] bad window path name ".3".
> 
> 
> 
> Additional information:
> 
> I tried to “Refresh the active data set” from the “Data”  ->  “Active Data 
> set” menu, and got the same error message, but with a different number at the 
> end.
> 
>> Error in structure(.External(.C_dotTcl, ...), class = "tclObj") : 
>>  [tcl] bad window path name ".6".
> 
> 
> I saved the file with a different name, but when I tried to read the file 
> with the new name I got a similar error message.

Do you really mean a *file* -- that is stored on your computer's file system -- 
or a data frame in the R workspace? 

In either case, if you can share the file or data frame, creating a 
reproducible example, I'd be much more likely to be able to figure out what's 
happening.

Best,
 John

> 
>> Error in structure(.External(.C_dotTcl, ...), class = "tclObj") : 
>>  [tcl] bad window path name ".6".
> 
> 
> Thanks for your time.
> 
> José
> 
> 
> José G. Conde, MD, MPH
> Catedrático
> Escuela de Medicina
> Recinto de Ciencias Médicas
> Universidad de Puerto Rico
> 
> Tel  (787) 763-9401  Fax (787) 758-5206
> 
> Correo electrónico: jose.con...@upr.edu
> 
>> On Nov 23, 2019, at 2:44 PM, Fox, John  wrote:
>> 
>> Dear José,
>> 
>> Please keep the discussion on the r-sig-mac list rather than replying only 
>> to me, so that other potentially interested individuals can follow it. I'm 
>> therefore cc'ing this response to the list.
>> 
>>> On Nov 22, 2019, at 9:43 PM, Jose G Conde Santiago  
>>> wrote:
>>> 
>>> Thanks for your prompt reply, John.
>>> 
>>> I clicked on the "Data set" button to read an R dataset. Then I clicked on 
>>> the "View data set" button to view it, and closed the view window. I tried 
>>> to read the same file again, and that is where I get the error message.
>> 
>> That's different from what I understood. When you use the "Data set" button 
>> in the Rcmdr toolbar you can choose among data sets that have *already* been 
>> read into the workspace, assuming that there are more than one.
>> 
>> I still can't duplicate the problem that you report. I can repeatedly select 
>> a data set using the button, and each time it becomes the active data set 
>> and the data viewer window is refreshed.
>> 
>>> I had the same issue when I tested with R Commander and R, without RStudio.
>> 
>> Yes, I saw that and I can't duplicate the problem in either context.
>> 
>> Best,
>> John
>> 
>>> 
>>> I will check again on Monday with the file you used.
>>> 
>>> Best,
>>> 
>>> José
>>> 
>>> On Fri, Nov 22, 2019, 6:04 PM Fox, John  wrote:
>>> Dear Jose,
>>> 
>>> I'm afraid that I can't duplicate this problem. I tried with the current 
>>> CRAN version of the Rcmdr under RStudio, reading a text file repeatedly 
>>> into the same data set. My session info is 
>>> 
>>> - snip -
>>> 
>>>> sessionInfo()
>>> R version 3.6.1 (2019-07-05)
>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>> Running under: macOS Catalina 10.15.1
>>> 
>>> Matrix products: default
>>> BLAS:   
>>> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLA

Re: [R-SIG-Mac] Error message reading files in R Commander

[Fox, John]

Dear José,

Please keep the discussion on the r-sig-mac list rather than replying only to 
me, so that other potentially interested individuals can follow it. I'm 
therefore cc'ing this response to the list.

> On Nov 22, 2019, at 9:43 PM, Jose G Conde Santiago  
> wrote:
> 
> Thanks for your prompt reply, John.
> 
> I clicked on the "Data set" button to read an R dataset. Then I clicked on 
> the "View data set" button to view it, and closed the view window. I tried to 
> read the same file again, and that is where I get the error message.

That's different from what I understood. When you use the "Data set" button in 
the Rcmdr toolbar you can choose among data sets that have *already* been read 
into the workspace, assuming that there are more than one.

I still can't duplicate the problem that you report. I can repeatedly select a 
data set using the button, and each time it becomes the active data set and the 
data viewer window is refreshed.

> I had the same issue when I tested with R Commander and R, without RStudio.

Yes, I saw that and I can't duplicate the problem in either context.

Best,
 John

> 
> I will check again on Monday with the file you used.
> 
> Best,
> 
> José
> 
> On Fri, Nov 22, 2019, 6:04 PM Fox, John  wrote:
> Dear Jose,
> 
> I'm afraid that I can't duplicate this problem. I tried with the current CRAN 
> version of the Rcmdr under RStudio, reading a text file repeatedly into the 
> same data set. My session info is 
> 
> - snip -
> 
> > sessionInfo()
> R version 3.6.1 (2019-07-05)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS Catalina 10.15.1
> 
> Matrix products: default
> BLAS:   
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
> 
> locale:
> [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
> 
> attached base packages:
> [1] splines   stats graphics  grDevices utils datasets  methods  
> [8] base 
> 
> other attached packages:
> [1] Rcmdr_2.6-1 effects_4.1-4   RcmdrMisc_2.5-1 sandwich_2.5-1 
> [5] car_3.0-5   carData_3.0-3  
> 
> loaded via a namespace (and not attached):
>  [1] Formula_1.2-3   assertthat_0.2.1latticeExtra_0.6-28
>  [4] cellranger_1.1.0pillar_1.4.2backports_1.1.5
>  [7] lattice_0.20-38 glue_1.3.1  digest_0.6.22  
> [10] RColorBrewer_1.1-2  checkmate_1.9.4 minqa_1.2.4
> [13] colorspace_1.4-1htmltools_0.4.0 Matrix_1.2-17  
> [16] survey_3.36 pkgconfig_2.0.3 haven_2.2.0
> [19] purrr_0.3.3 scales_1.0.0openxlsx_4.1.3 
> [22] rio_0.5.16  lme4_1.1-21 htmlTable_1.13.2   
> [25] tibble_2.1.3relimp_1.0-5ggplot2_3.2.1  
> [28] nnet_7.3-12 lazyeval_0.2.2  survival_3.1-7
> [31] magrittr_1.5crayon_1.3.4readxl_1.3.1   
> [34] nlme_3.1-142MASS_7.3-51.4   forcats_0.4.0  
> [37] foreign_0.8-72  class_7.3-15tools_3.6.1
> [40] data.table_1.12.6   hms_0.5.2   mitools_2.4
> [43] tcltk2_1.2-11   stringr_1.4.0   munsell_0.5.0  
> [46] cluster_2.1.0   zip_2.0.4   compiler_3.6.1 
> [49] e1071_1.7-2 rlang_0.4.1 grid_3.6.1 
> [52] nloptr_1.2.1rstudioapi_0.10 htmlwidgets_1.5.1  
> [55] tcltk_3.6.1 base64enc_0.1-3 boot_1.3-23
> [58] gtable_0.3.0abind_1.4-5 DBI_1.0.0  
> [61] curl_4.2R6_2.4.0gridExtra_2.3  
> [64] zoo_1.8-6   knitr_1.25  dplyr_0.8.3
> [67] zeallot_0.1.0   nortest_1.0-4   Hmisc_4.3-0
> [70] stringi_1.4.3   Rcpp_1.0.3  vctrs_0.2.0
> [73] rpart_4.1-15acepack_1.4.1   tidyselect_0.2.5  
> [76] xfun_0.10 
> 
> - snip -
> 
> The output that the Rcmdr generates each time in the RStudio console is
> 
> Rcmdr>  Duncan <- 
> Rcmdr+
> read.table("/Users/johnfox/Documents/Courses/2017-2018/ICPSR/Lectures/Duncan.txt",
> Rcmdr+ header=TRUE, sep="", na.strings="NA", dec=".", strip.white=TRUE)
> RcmdrMsg: [3] NOTE: The dataset Duncan has 45 rows and 4 columns.
> 
> Of course, there's a warning each time that Duncan will be overwritten, and 
> the dataset in the viewer is automatically refreshed. That is, AFAICS 
> everything works as it should.
> 
> You can find the data file I used at 
> <https://socialsciences.mcmaster.ca/jfox/Books/RCommander/Duncan.txt

Re: [R-SIG-Mac] Error message reading files in R Commander

[Fox, John]

Dear Jose,

I'm afraid that I can't duplicate this problem. I tried with the current CRAN 
version of the Rcmdr under RStudio, reading a text file repeatedly into the 
same data set. My session info is 

- snip -

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.1

Matrix products: default
BLAS:   
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] splines   stats graphics  grDevices utils datasets  methods  
[8] base 

other attached packages:
[1] Rcmdr_2.6-1 effects_4.1-4   RcmdrMisc_2.5-1 sandwich_2.5-1 
[5] car_3.0-5   carData_3.0-3  

loaded via a namespace (and not attached):
 [1] Formula_1.2-3   assertthat_0.2.1latticeExtra_0.6-28
 [4] cellranger_1.1.0pillar_1.4.2backports_1.1.5
 [7] lattice_0.20-38 glue_1.3.1  digest_0.6.22  
[10] RColorBrewer_1.1-2  checkmate_1.9.4 minqa_1.2.4
[13] colorspace_1.4-1htmltools_0.4.0 Matrix_1.2-17  
[16] survey_3.36 pkgconfig_2.0.3 haven_2.2.0
[19] purrr_0.3.3 scales_1.0.0openxlsx_4.1.3 
[22] rio_0.5.16  lme4_1.1-21 htmlTable_1.13.2   
[25] tibble_2.1.3relimp_1.0-5ggplot2_3.2.1  
[28] nnet_7.3-12 lazyeval_0.2.2  survival_3.1-7
[31] magrittr_1.5crayon_1.3.4readxl_1.3.1   
[34] nlme_3.1-142MASS_7.3-51.4   forcats_0.4.0  
[37] foreign_0.8-72  class_7.3-15tools_3.6.1
[40] data.table_1.12.6   hms_0.5.2   mitools_2.4
[43] tcltk2_1.2-11   stringr_1.4.0   munsell_0.5.0  
[46] cluster_2.1.0   zip_2.0.4   compiler_3.6.1 
[49] e1071_1.7-2 rlang_0.4.1 grid_3.6.1 
[52] nloptr_1.2.1rstudioapi_0.10 htmlwidgets_1.5.1  
[55] tcltk_3.6.1 base64enc_0.1-3 boot_1.3-23
[58] gtable_0.3.0abind_1.4-5 DBI_1.0.0  
[61] curl_4.2R6_2.4.0gridExtra_2.3  
[64] zoo_1.8-6   knitr_1.25  dplyr_0.8.3
[67] zeallot_0.1.0   nortest_1.0-4   Hmisc_4.3-0
[70] stringi_1.4.3   Rcpp_1.0.3  vctrs_0.2.0
[73] rpart_4.1-15acepack_1.4.1   tidyselect_0.2.5  
[76] xfun_0.10 

- snip -

The output that the Rcmdr generates each time in the RStudio console is

Rcmdr>  Duncan <- 
Rcmdr+
read.table("/Users/johnfox/Documents/Courses/2017-2018/ICPSR/Lectures/Duncan.txt",
Rcmdr+ header=TRUE, sep="", na.strings="NA", dec=".", strip.white=TRUE)
RcmdrMsg: [3] NOTE: The dataset Duncan has 45 rows and 4 columns.

Of course, there's a warning each time that Duncan will be overwritten, and the 
dataset in the viewer is automatically refreshed. That is, AFAICS everything 
works as it should.

You can find the data file I used at 
.

Can you elaborate what you did and ideally create a reproducible example of the 
problem?

Best,
 John

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

> On Nov 22, 2019, at 2:23 PM, Jose G Conde Santiago via R-SIG-Mac 
>  wrote:
> 
> Hi,
> 
> I am using R Commander in combination with RStudio. I configured RStudio to 
> display the output on the RStudio console.
> 
> If I open a file in R Commander, then view the data file in R Commander and 
> then try to read the same file again using R Commander, the following error 
> message is displayed in the console and I cannot read the file with R 
> Commander:
> 
>> Error in structure(.External(.C_dotTcl, ...), class = "tclObj") : 
>>  [tcl] bad window path name “.29”.
> 
> The message is always the same, except that the number at the end changes. 
> Here are a few more examples:
> 
>> Error in structure(.External(.C_dotTcl, ...), class = "tclObj") : 
>>  [tcl] bad window path name ".35".
> 
>> Error in structure(.External(.C_dotTcl, ...), class = "tclObj") : 
>>  [tcl] bad window path name ".51".
> 
>> Error in structure(.External(.C_dotTcl, ...), class = "tclObj") : 
>>  [tcl] bad window path name ".56".
> 
> 
> Initially, I thought there could be a problem between R Commander and 
> RStudio, but I got the same error message under the same conditions when I 
> tested using R Commander with R alone (without RStudio).
> 
> The files seem to be fine, since I can access them directly with R or with 
> RStudio.
> 
> My computer is  an iMac (27-inch, late 2012)
> MacOS High Sierra version 10.13.6.  
> R version 3.6.1
> RStudio version 1.2.5001
> R Commander version 2.6-0
> XQuartz 2.7.11

Re: [R-SIG-Mac] Problem with R commander installation under MAC OX 10.10

[Fox, John]

Dear Fran,

Please include the R-SIG-Mac list in a discussion started on the list.

> On Nov 24, 2018, at 3:16 PM, FRANCISCO JOSE OTERO FERRER 
>  wrote:
> 
> Dear John,
> 
> thanks again. I had tried “R CMD INSTALL”:
> 
> MacBook-Pro-de-Francisco-2:~ franciscooteroferrer$ R CMD INSTALL 
> Rcmdr_2.2-5.tar.gz
> Warning: invalid package ‘Rcmdr_2.2-5.tar.gz’
> Error: ERROR: no packages specified
> 
> but again did not work…

You may have picked the wrong version of the Rcmdr package for your R version, 
the file may have been corrupted, or may be in the wrong directory.

> I will probably update my MAC OS version and install the last R Commander. It 
> would be better.

Yes, that’s a much better idea, and it’s generally a good idea to keep software 
up to date.

Best,
 John

> 
> Thank you for your time and sorry to disturb you,
> 
> All the Best 
> 
> Fran
> Francisco Otero Ferrer, PhD
> University Institute of Sustainable Aquaculture and Marine Ecosystems (IU 
> ECOAQUA)
> Scientific and Technological Marine Park
> University of Las Palmas de Gran Canaria
> 35200 Telde (Las Palmas - España)
> +34 928 454910
> 
> 
> 
> 
> 
> 
> 
> 
> 
>> El 24/11/2018, a las 20:10, Fox, John  escribió:
>> 
>> Dear Fran,
>> 
>>> On Nov 24, 2018, at 2:40 PM, FRANCISCO JOSE OTERO FERRER 
>>>  wrote:
>>> 
>>> Dear Professor Fox,
>>> 
>>> thank you very much for your advices.
>>> 
>>> I have tried to install old Rcmdr version through MAC OS Terminal window 
>>> putting “R CMD INSTALL Rcmdr_2.2-5.tar.gz” and downloading previously the 
>>> file Rcmdr_2.2-5.tar.gz from 
>>> <https://cran.r-project.org/src/contrib/Archive/Rcmdr/>.
>>> 
>>> MacBook-Pro-de-Francisco-2:~ franciscooteroferrer$ INSTALL 
>>> Rcmdr_2.2-5.tar.gz
>> 
>> The command is R CMD INSTALL *not* INSTALL
>> 
>> Also, the command assumes that the downloaded file is in the current 
>> directory — your home directory in your failed attempt.
>> 
>> Finally, as I said initially, I’d anticipate problems installing some of the 
>> other packages on which the Rcmdr depends.
>> 
>> Best,
>> John
>> 
>>> usage: install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode]
>>>   [-o owner] file1 file2
>>>   install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode]
>>>   [-o owner] file1 ... fileN directory
>>>   install -d [-v] [-g group] [-m mode] [-o owner] directory …
>>> 
>>> Then I have tried to open in R following the standard procedure:
>>> install.packages(“Rcmdr")
>>> 
>>> Then
>>> --- Please select a CRAN mirror for use in this session ---
>>> Warning message:
>>> package ‘Rcmdr’ is not available (for R version 3.3.3)
>>> 
>>> but again there is some problems to install Rcommander.
>>> Sorry to disturb you again, it is my first contact with R… not really 
>>> successful.
>>> 
>>> Thank you for your time,
>>> 
>>> Best wishes,
>>> 
>>> Fran
>>> 
>>> Francisco Otero Ferrer, PhD
>>> University Institute of Sustainable Aquaculture and Marine Ecosystems (IU 
>>> ECOAQUA)
>>> Scientific and Technological Marine Park
>>> University of Las Palmas de Gran Canaria
>>> 35200 Telde (Las Palmas - España)
>>> +34 928 454910
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> El 24/11/2018, a las 15:55, Fox, John  escribió:
>>>> 
>>>> Dear Fran,
>>>> 
>>>> To elaborate slightly, old sources for the Rcmdr package (and all other 
>>>> CRAN packages) are available on CRAN. The old-package archive for the 
>>>> Rcmdr is at <https://cran.r-project.org/src/contrib/Archive/Rcmdr/>.
>>>> 
>>>> You can download the source package for an older version of the Rcmdr and 
>>>> install it in a macOS terminal window from the directory where you put the 
>>>> file, via the command R CMD INSTALL Rcmdr_x.y-z.tar.gz (where x, y, z 
>>>> correspond to the version that you downloaded).
>>>> 
>>>> This should work because the Rcmdr package includes no compiled code but 
>>>> you may encounter problems: The Rcmdr package depends on many other 
>>>> packages and some of these may also be unavailable in their current 
>>>> versions for your version of macOS or may be inco

Re: [R-SIG-Mac] Problem with R commander installation under MAC OX 10.10

[Fox, John]

Dear Fran,

To elaborate slightly, old sources for the Rcmdr package (and all other CRAN 
packages) are available on CRAN. The old-package archive for the Rcmdr is at 
. 

You can download the source package for an older version of the Rcmdr and 
install it in a macOS terminal window from the directory where you put the 
file, via the command R CMD INSTALL Rcmdr_x.y-z.tar.gz (where x, y, z 
correspond to the version that you downloaded). 

This should work because the Rcmdr package includes no compiled code but you 
may encounter problems: The Rcmdr package depends on many other packages and 
some of these may also be unavailable in their current versions for your 
version of macOS or may be incompatible with the older version of the Rcmdr 
that you install.

I hope this helps,
 John

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


> -Original Message-
> From: R-SIG-Mac [mailto:r-sig-mac-boun...@r-project.org] On Behalf Of
> Mario
> Sent: Saturday, November 24, 2018 8:11 AM
> To: FRANCISCO JOSE OTERO FERRER 
> Cc: r-sig-mac@r-project.org
> Subject: Re: [R-SIG-Mac] Problem with R commander installation under MAC
> OX 10.10
> 
> Old sources:  Rcmdr archive
> 
> ---
> Mario
> 
> > El 24 nov 2018, a las 9:43, FRANCISCO JOSE OTERO FERRER
>  escribió:
> >
> > Dear users,
> >
> > I am quite new with R, so apologizes for my ignorance. I have MAC OX 10.10
> (Yosemite) and I would like to install  Rcommander, however apparently it is
> not possible:
> >
> >> install.packages("Rcmdr")
> > --- Please select a CRAN mirror for use in this session --- Warning
> > message:
> > package ‘Rcmdr’ is not available (for R version 3.3.3)
> >>
> >
> > As I have other softwares that it could have problems with OX update, I am
> just wondering if there is any manner to install R commander without update
> my OX version.
> >
> > Thank you very much,
> >
> > Fran
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > Antes de imprimir este correo electrónico, piense bien si es necesario
> hacerlo: el medio ambiente es una cuestión de todos.
> >
> > Please consider the environment before printing this email.
> >
> >[[alternative HTML version deleted]]
> >
> > ___
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
>   [[alternative HTML version deleted]]
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
___
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Re: [R-SIG-Mac] bug on Rcmdr Mac OS X

[Fox, John]

Dear Frédéric Pamoukdjian,

This problem results from the failure of the RcmdrMisc package to load, 
produced by an incompatibility with version 4.1-0 of the Hmisc package, which 
was briefly on CRAN, but then withdrawn and reverted to version 4.0-3. The 
macOS binary of the Hmisc package is still at version 4.1-0, however, producing 
the problem.

You have the following options:

(1) If you have the necessary tools, install Hmisc from the sources on CRAN, 
e.g., via the command install.packages("Hmisc", type="source") .

(2) Wait until the macOS binary for Hmisc on CRAN catches up with the source 
package and then install the binary, install.packages("Hmisc").

(3) Be even more patient, and wait until an updated version of Hmisc (either 
version 4.1-0 resubmitted or 4.1-1) appears on CRAN, and install it along with 
what will be the compatible version 1.0-7 of the RcmdrMisc package, which I've 
already submitted to CRAN, to be released when the new Hmisc appears.

I hope that this helps,
 John

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



> -Original Message-
> From: R-SIG-Mac [mailto:r-sig-mac-boun...@r-project.org] On Behalf Of
> frederic pamoukdjian
> Sent: Friday, December 29, 2017 3:26 PM
> To: r-sig-mac@r-project.org
> Subject: [R-SIG-Mac] bug on Rcmdr Mac OS X
> 
> Dear friends,
> 
> I’m working on Max OSX 10.13.2 with the latest version of R and the latest
> version of X quartz
> 
> When i launch R then Rcmdr, i have a bug for the first time in Mac that i use 
> to
> have
> 
> This is the message from R:
> > library(Rcmdr)
> Le chargement a nécessité le package : splines Le chargement a nécessité le
> package : RcmdrMisc Le chargement a nécessité le package : car Le
> chargement a nécessité le package : sandwich
> Error: package or namespace load failed for ‘RcmdrMisc’:
>  l'objet ‘print.rcorr’ n'est pas exporté par 'namespace:Hmisc'
> Erreur : le package ‘RcmdrMisc’ ne peut être chargé
> 
> I’m sure that RcmdrMisc is download from cran binaries and Hmisc too
> 
> I don’t understand what’s happened
> 
> Please help me !!!
> 
> Best regards
> 
> Frédéric Pamoukdjian
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
___
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Re: [R-SIG-Mac] Rcmdr start-up issue

[Fox, John]

Dear Robert,

If I understand you correctly, you had to agree to the Xcode license in order 
to get the tcltk and Rcmdr packages to work. That wasn't my experience. Is it 
possible that you did something else, like rebooting your computer after 
installing XQuartz?

The reason I ask is that I want to understand what went wrong in case someone 
else has a similar problem in future.

Best,
 John

> -Original Message-
> From: Robert Baer [mailto:rb...@atsu.edu]
> Sent: Wednesday, October 4, 2017 10:09 AM
> To: Fox, John <j...@mcmaster.ca>
> Cc: r-sig-mac@r-project.org
> Subject: Re: [R-SIG-Mac] Rcmdr start-up issue
> 
> Thanks so much for taking the time to respond.   I followed the Xcode
> instructions in your first paragraph and  instructions and everything is 
> working
> now as expected.  Not sure what happened before.  As of last year, more that
> half my students now live in the Mac world, so it seems I need to up my skill
> level.
> 
> Enjoyed the little tcltk exercise/test you supplied.    Thanks again.
> 
> Sincerely,
> 
> Rob
> 
> 
> On 10/3/2017 7:35 PM, Fox, John wrote:
> > Dear Robert,
> >
> > As a brief addendum to my previous message, I’ve now installed the
> > newest version of Xcode, and I still have no trouble using the Rcmdr 
> > package.
> >
> > I did get the following message when I initially loaded the Rcmdr package:
> > “Agreeing to the Xcode/iOS license requires admin privileges, please
> > run “sudo xcodebuild -license” and then retry this command.” But the
> > Rcmdr loaded properly both before *and* after I followed the
> > instruction in the message.
> >
> > Best,
> >   John
> >
> > -
> > John Fox, Professor Emeritus
> > McMaster University
> > Hamilton, Ontario, Canada
> > Web: http://socserv.mcmaster.ca/jfox/
> >
> >
> >
> >
> > On 2017-10-03, 1:03 PM, "R-SIG-Mac on behalf of Fox, John"
> > <r-sig-mac-boun...@r-project.org on behalf of j...@mcmaster.ca> wrote:
> >
> >> Dear Robert,
> >>
> >> The most common Rcmdr problem on macOS is failure to install XQuartz,
> >> which is required by the tcltk package. If you haven't installed
> >> XQuartz, then start there, and remember to reboot after the XQuartz
> installation:
> >> <https://www.xquartz.org/>. For more details, please see the Rcmdr
> >> installation notes for macOS at
> >> <http://socserv.socsci.mcmaster.ca/jfox/Misc/Rcmdr/installation-notes
> >> .html
> >>> . You should be able to use the Rcmdr from R.app, a terminal window,
> >>> or RStudio.
> >> On the other hand, if you *have* installed XQuartz and rebooted, and
> >> the problem still occurs, then see whether you can load and use the
> >> tcltk package directly, without the Rcmdr; try, e.g. (from
> >> ?TkWidgets),
> >>
> >>library(tcltk)
> >>tt <- tktoplevel()
> >>label.widget <- tklabel(tt, text = "Hello, World!")
> >>button.widget <- tkbutton(tt, text = "Push",command =
> >> function()cat("OW!\n"))
> >>tkpack(label.widget, button.widget)
> >>
> >> Finally, your setup is very similar to mine -- that is, I haven't yet
> >> upgraded my Mac to R 3.4.2 (which I don't think is built yet for
> >> macOS) but all my R packages are up-to-date. An exception is that I
> >> haven't yet installed the latest version of Xcode, which I'll do now
> >> to see what happens. It's unclear to me from your message whether the
> >> Rcmdr package worked before you installed the newest Xcode.
> >>
> >> I hope this helps,
> >> John
> >>
> >> --
> >> John Fox, Professor Emeritus
> >> McMaster University
> >> Hamilton, Ontario, Canada
> >> Web: socserv.mcmaster.ca/jfox
> >>
> >>
> >>
> >>> -Original Message-
> >>> From: R-SIG-Mac [mailto:r-sig-mac-boun...@r-project.org] On Behalf
> >>> Of Robert Baer
> >>> Sent: Saturday, September 23, 2017 10:25 AM
> >>> To: r-sig-mac@r-project.org
> >>> Subject: [R-SIG-Mac] Rcmdr start-up issue
> >>>
> >>> I seem to be having a problem starting Rcmdr:
> >>>
> >>>> library(Rcmdr)
> >>> Loading required package: splines
> >>> Loading required package: RcmdrMisc
> >>> Loading required package: car
> >>> Loading requi

Re: [R-SIG-Mac] Rcmdr start-up issue

[Fox, John]

Dear Robert,

As a brief addendum to my previous message, I’ve now installed the newest
version of Xcode, and I still have no trouble using the Rcmdr package.

I did get the following message when I initially loaded the Rcmdr package:
“Agreeing to the Xcode/iOS license requires admin privileges, please run
“sudo xcodebuild -license” and then retry this command.” But the Rcmdr
loaded properly both before *and* after I followed the instruction in the
message.

Best,
 John

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




On 2017-10-03, 1:03 PM, "R-SIG-Mac on behalf of Fox, John"
<r-sig-mac-boun...@r-project.org on behalf of j...@mcmaster.ca> wrote:

>Dear Robert,
>
>The most common Rcmdr problem on macOS is failure to install XQuartz,
>which is required by the tcltk package. If you haven't installed XQuartz,
>then start there, and remember to reboot after the XQuartz installation:
><https://www.xquartz.org/>. For more details, please see the Rcmdr
>installation notes for macOS at
><http://socserv.socsci.mcmaster.ca/jfox/Misc/Rcmdr/installation-notes.html
>>. You should be able to use the Rcmdr from R.app, a terminal window, or
>>RStudio.
>
>On the other hand, if you *have* installed XQuartz and rebooted, and the
>problem still occurs, then see whether you can load and use the tcltk
>package directly, without the Rcmdr; try, e.g. (from ?TkWidgets),
>
>   library(tcltk)
>   tt <- tktoplevel()
>   label.widget <- tklabel(tt, text = "Hello, World!")
>   button.widget <- tkbutton(tt, text = "Push",command =
>function()cat("OW!\n"))
>   tkpack(label.widget, button.widget)
>
>Finally, your setup is very similar to mine -- that is, I haven't yet
>upgraded my Mac to R 3.4.2 (which I don't think is built yet for macOS)
>but all my R packages are up-to-date. An exception is that I haven't yet
>installed the latest version of Xcode, which I'll do now to see what
>happens. It's unclear to me from your message whether the Rcmdr package
>worked before you installed the newest Xcode.
>
>I hope this helps,
> John
>
>--
>John Fox, Professor Emeritus
>McMaster University
>Hamilton, Ontario, Canada
>Web: socserv.mcmaster.ca/jfox
>
>
>
>> -Original Message-
>> From: R-SIG-Mac [mailto:r-sig-mac-boun...@r-project.org] On Behalf Of
>> Robert Baer
>> Sent: Saturday, September 23, 2017 10:25 AM
>> To: r-sig-mac@r-project.org
>> Subject: [R-SIG-Mac] Rcmdr start-up issue
>> 
>> I seem to be having a problem starting Rcmdr:
>> 
>> > library(Rcmdr)
>> Loading required package: splines
>> Loading required package: RcmdrMisc
>> Loading required package: car
>> Loading required package: sandwich
>> Loading required package: effects
>> Loading required package: carData
>> 
>> Attaching package: ‘carData’
>> 
>> The following objects are masked from ‘package:car’:
>> 
>> Guyer, UN, Vocab
>> 
>> lattice theme set by effectsTheme()
>> See ?effectsTheme for details.
>> Error: package or namespace load failed for ‘Rcmdr’:
>>  package ‘tcltk’ does not have a namespace
>> >
>> 
>> I tried first from within RStudio, then from R itself. Same outcome.
>> Reinstalling Rcmdr, tcltk or tcltk2 package did not seem to help.
>> 
>> I’m brand new to mac, so I may be missing something basic.  On the other
>> hand I should confess to just having just “updated” Xcode.
>> 
>> > R.Version()
>> $platform
>> [1] "x86_64-apple-darwin15.6.0"
>> 
>> $arch
>> [1] "x86_64"
>> 
>> $os
>> [1] "darwin15.6.0"
>> 
>> $system
>> [1] "x86_64, darwin15.6.0"
>> 
>> $status
>> [1] ""
>> 
>> $major
>> [1] "3"
>> 
>> $minor
>> [1] "4.1"
>> 
>> $year
>> [1] "2017"
>> 
>> $month
>> [1] "06"
>> 
>> $day
>> [1] "30"
>> 
>> $`svn rev`
>> [1] "72865"
>> 
>> $language
>> [1] "R"
>> 
>> $version.string
>> [1] "R version 3.4.1 (2017-06-30)"
>> 
>> $nickname
>> [1] "Single Candle"
>> 
>> 
>>  [[alternative HTML version deleted]]
>> 
>> ___
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Re: [R-SIG-Mac] Rcmdr start-up issue

[Fox, John]

Dear Robert,

The most common Rcmdr problem on macOS is failure to install XQuartz, which is 
required by the tcltk package. If you haven't installed XQuartz, then start 
there, and remember to reboot after the XQuartz installation: 
. For more details, please see the Rcmdr installation 
notes for macOS at 
. 
You should be able to use the Rcmdr from R.app, a terminal window, or RStudio.

On the other hand, if you *have* installed XQuartz and rebooted, and the 
problem still occurs, then see whether you can load and use the tcltk package 
directly, without the Rcmdr; try, e.g. (from ?TkWidgets),

library(tcltk)
tt <- tktoplevel()
label.widget <- tklabel(tt, text = "Hello, World!")
button.widget <- tkbutton(tt, text = "Push",command = 
function()cat("OW!\n"))
tkpack(label.widget, button.widget)

Finally, your setup is very similar to mine -- that is, I haven't yet upgraded 
my Mac to R 3.4.2 (which I don't think is built yet for macOS) but all my R 
packages are up-to-date. An exception is that I haven't yet installed the 
latest version of Xcode, which I'll do now to see what happens. It's unclear to 
me from your message whether the Rcmdr package worked before you installed the 
newest Xcode.

I hope this helps,
 John

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



> -Original Message-
> From: R-SIG-Mac [mailto:r-sig-mac-boun...@r-project.org] On Behalf Of
> Robert Baer
> Sent: Saturday, September 23, 2017 10:25 AM
> To: r-sig-mac@r-project.org
> Subject: [R-SIG-Mac] Rcmdr start-up issue
> 
> I seem to be having a problem starting Rcmdr:
> 
> > library(Rcmdr)
> Loading required package: splines
> Loading required package: RcmdrMisc
> Loading required package: car
> Loading required package: sandwich
> Loading required package: effects
> Loading required package: carData
> 
> Attaching package: ‘carData’
> 
> The following objects are masked from ‘package:car’:
> 
> Guyer, UN, Vocab
> 
> lattice theme set by effectsTheme()
> See ?effectsTheme for details.
> Error: package or namespace load failed for ‘Rcmdr’:
>  package ‘tcltk’ does not have a namespace
> >
> 
> I tried first from within RStudio, then from R itself. Same outcome.
> Reinstalling Rcmdr, tcltk or tcltk2 package did not seem to help.
> 
> I’m brand new to mac, so I may be missing something basic.  On the other
> hand I should confess to just having just “updated” Xcode.
> 
> > R.Version()
> $platform
> [1] "x86_64-apple-darwin15.6.0"
> 
> $arch
> [1] "x86_64"
> 
> $os
> [1] "darwin15.6.0"
> 
> $system
> [1] "x86_64, darwin15.6.0"
> 
> $status
> [1] ""
> 
> $major
> [1] "3"
> 
> $minor
> [1] "4.1"
> 
> $year
> [1] "2017"
> 
> $month
> [1] "06"
> 
> $day
> [1] "30"
> 
> $`svn rev`
> [1] "72865"
> 
> $language
> [1] "R"
> 
> $version.string
> [1] "R version 3.4.1 (2017-06-30)"
> 
> $nickname
> [1] "Single Candle"
> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] Rcmdr¡

[Fox, John]

Dear Dr. German,

I'll respond to your message in English, which is the language of this email 
list (and my written Spanish is poor anyway).

It's not clear from your email what problem or problems you're experiencing. 
You say that you can't install "them" (R, the Rcmdr package, other packages?) 
for "security factors" (what security factors?). 

If your aim is to install and use the R Commander-- you mention the Rcmdr in 
the subject of your message but not in the message itself -- then the 
installation notes at < 
http://socserv.socsci.mcmaster.ca/jfox/Misc/Rcmdr/installation-notes.html> 
might help, but they don't address security issues.

You might also consult the posting guide for the R email lists at < 
https://www.r-project.org/posting-guide.html>, which has useful information 
about how to ask a question.

I hope this helps,
 John

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

 
> -Original Message-
> From: R-SIG-Mac [mailto:r-sig-mac-boun...@r-project.org] On Behalf Of
> GERMAN GIACOMAN VALLEJOS
> Sent: Tuesday, June 6, 2017 1:10 AM
> To: r-sig-mac@r-project.org
> Subject: [R-SIG-Mac] Rcmdr¡
> 
> Quien me puede apoyar en la instalaci�n de R.app y otros paquetes para que
> puede usar en mi maquina MacBook Pro y poder usar diversos paquetes de R
> y su manejo en gr�ficos , al cual ya actualice a MacOs Sierra versi�n 10.12.5
> 
> MacBook Pro (15-inch, Mid 2012) Procesador 2.3 GHz Intel Core i7 memoria 4
> GB 1600 MHz DDR3 gr�ficos NVIDIA GeForce GT 650M 512 MB
> 
> Intel HD Graphics 4000 1536 MB.
> 
> He intentado instalarlos, pero no me deja por factores de seguridad.
> 
> Saludos
> 
> 
> Dr. Gi�coman
> 
>   [[alternative HTML version deleted]]

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Re: [R-SIG-Mac] R commander fonts on R 3.4.0

[Fox, John]

Dear Peter,

First, thank you very much for persisting with this. I greatly appreciate it.

> -Original Message-
> From: Peter Dalgaard [mailto:pda...@gmail.com]
> Sent: Wednesday, May 17, 2017 2:52 PM
> To: Simon Urbanek <simon.urba...@r-project.org>
> Cc: Fox, John <j...@mcmaster.ca>; r-sig-mac@r-project.org
> Subject: Re: [R-SIG-Mac] R commander fonts on R 3.4.0
> 
> A few more data points:
> 
> I tried building Tcl/Tk 8.6.6 from the sources from sourceforge.
> Contrary to what it says on the package, it insists on building Tcl and
> Tk as frameworks, which in turn requires that R's configure needs
> special instructions. This works reasonably well for simple tcltk stuff
> (demos, the CRAN selection menu), but unfortunately, library(Rcmdr)
> causes an "Abort trap: 6" almost immediately. (I get a sense of deja vu
> about this... Did Brian try something similar years ago?)

I believe that Brian mentioned to me years ago that he was able to get R (and 
the Rcmdr package) to work fine with a native version of Tcl/Tk for Macs. 
Beyond that, I don't recall.

> 
> It does actually seem to work to build R against the system-supplied
> v.8.5 frameworks. However, this is Aqua-based, and the fonts are a bit
> weird (smooth, but way too small) and the Rcmdr menus get moved to the
> top bar.

Moving the menus to the top bar is desirable, in my opinion, because it's what 
Mac users expect. If the problem is simply with the font sizes, I should be 
able to adjust that automatically, as I do now.

> 
> I am pretty sure by now that all this stuff is a generic tcltk build
> problem and way out of John's domain. (Thanks for posting the font code,
> John. I hope I can get around to having a closer look at it at some
> point. Those .Tcl(paste()) constructs make me cringe a bit, but not all
> are easily eliminated.)

If you see a better way to do this, of course I'd appreciate that. It took a 
fair amount of work to adjust the fonts so that they look right on Windows, 
macOS, and Linux systems.

Best,
 John

> 
> -pd
> 
> > On 16 May 2017, at 23:52 , peter dalgaard <pda...@gmail.com> wrote:
> >
> >
> >> On 16 May 2017, at 21:03 , peter dalgaard <pda...@gmail.com> wrote:
> >>
> >> I don't think the config flags for R matter in this regard. The
> behaviour is completely paralleled by wish8.6:
> >
> > Hmmm, not sure the wish ::tk::pkgconfig thing proves anything, after I
> tried some of the ActiveState installs and a source build. This stuff is
> making my head spin!
> >
> > However, I discovered that it is possible to install R-3.4.0.pkg as
> usual, and then a customized install of (say) R-3.3-branch-
> mavericks.pkg, omitting everything except the Tcl/Tk stuff. That gives
> you R 3.4.0 and Rcmdr with antialiased fonts.
> >
> > --
> > Peter Dalgaard, Professor,
> > Center for Statistics, Copenhagen Business School Solbjerg Plads 3,
> > 2000 Frederiksberg, Denmark
> > Phone: (+45)38153501
> > Office: A 4.23
> > Email: pd@cbs.dk  Priv: pda...@gmail.com
> >
> >
> >
> >
> >
> >
> >
> >
> >
> 
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000
> Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd@cbs.dk  Priv: pda...@gmail.com
> 
> 
> 
> 
> 
> 
> 
> 

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Re: [R-SIG-Mac] R commander fonts on R 3.4.0

[Fox, John]

Dear Peter and Simon,

I don't fully understand the issues either and, again, haven't observed a 
problem, but I'm grateful that both of you are taking a look at it.

For what it's worth, here's what the Rcmdr package does with fonts. This code 
is from the development version of the Rcmdr, where the code is refactored for 
clarity, but the current CRAN version does the same things.

-- snip 

setupFonts <- function(){
current <- getOption("Rcmdr")
# set up Rcmdr default and text (log) fonts, Tk scaling factor
default.font.family.val <- tclvalue(.Tcl("font actual TkDefaultFont 
-family"))
default.font.family.val <- gsub("\\{", "", gsub("\\}", "", 
default.font.family.val))
default.font.family <- setOption("default.font.family", 
default.font.family.val)
if (!("RcmdrDefaultFont" %in% as.character(.Tcl("font names"{
.Tcl(paste("font create RcmdrDefaultFont", 
tclvalue(tkfont.actual("TkDefaultFont"
.Tcl("option add *font RcmdrDefaultFont")
}

.Tcl(paste("font configure RcmdrDefaultFont -family {", 
default.font.family, "}", sep=""))

if (!("RcmdrTitleFont" %in% as.character(.Tcl("font names"{
.Tcl(paste("font create RcmdrTitleFont", 
tclvalue(tkfont.actual("TkDefaultFont"
}
.Tcl(paste("font configure RcmdrTitleFont -family {", default.font.family, 
"}", sep=""))
if (!("RcmdrOutputMessagesFont" %in% as.character(.Tcl("font names"{
.Tcl(paste("font create RcmdrOutputMessagesFont", 
tclvalue(tkfont.actual("RcmdrTitleFont"
}
.Tcl(paste("font configure RcmdrTitleFont -family {", default.font.family, 
"}", sep=""))
.Tcl(paste("font configure RcmdrOutputMessagesFont -family {", 
default.font.family, "}", sep=""))

.Tcl(paste("font configure TkDefaultFont -family {",  default.font.family, 
"}", sep=""))
log.font.family.val <- tclvalue(.Tcl("font actual TkFixedFont -family"))
log.font.family.val <- gsub("\\{", "", gsub("\\}", "", log.font.family.val))
log.font.family <- setOption("log.font.family", log.font.family.val)
if (!("RcmdrLogFont" %in% as.character(.Tcl("font names"{
.Tcl(paste("font create RcmdrLogFont", 
tclvalue(tkfont.actual("TkFixedFont"
}
.Tcl(paste("font configure RcmdrLogFont -family {", log.font.family, "}", 
sep=""))
.Tcl(paste("font configure TkFixedFont -family {",  log.font.family, "}", 
sep=""))
putRcmdr("logFont", "RcmdrLogFont")
scale.factor <- current$scale.factor

if (!is.null(scale.factor)) .Tcl(paste("tk scaling ", scale.factor, sep=""))
# set various font sizes 
if (WindowsP()){
default.font.size.val <- abs(as.numeric(.Tcl("font actual TkDefaultFont 
-size")))
if (is.na(default.font.size.val)) default.font.size.val <- 10
}
else default.font.size.val <- 10
default.font.size <- setOption("default.font.size", default.font.size.val)
tkfont.configure("RcmdrDefaultFont", size=default.font.size)
tkfont.configure("RcmdrTitleFont", size=default.font.size)
tkfont.configure("RcmdrOutputMessagesFont", size=default.font.size)
tkfont.configure("TkDefaultFont", size=default.font.size)
tkfont.configure("TkTextFont", size=default.font.size)
tkfont.configure("TkCaptionFont", size=default.font.size)
log.font.size <- setOption("log.font.size", 10)
tkfont.configure("RcmdrLogFont", size=log.font.size)
tkfont.configure("TkFixedFont", size=log.font.size)

.Tcl("ttk::style configure TButton -font RcmdrDefaultFont")
.Tcl("ttk::style configure TLabel -font RcmdrDefaultFont")
.Tcl("ttk::style configure TCheckbutton -font RcmdrDefaultFont")
.Tcl("ttk::style configure TRadiobutton -font RcmdrDefaultFont")

standard.title.color <- as.character(.Tcl("ttk::style lookup 
TLabelframe.Label -foreground"))
title.color <- setOption("title.color", standard.title.color) 
if (tolower(title.color) == "black" || title.color == "#00"){
tkfont.configure("RcmdrTitleFont", weight="bold")
}
else tkfont.configure("RcmdrTitleFont", weight="normal")
}

---

Re: [R-SIG-Mac] R commander fonts on R 3.4.0

[Fox, John]

Dear Jose,

It's a bit difficult to respond to your latest messages because you sent so 
many of them.

I'm not entirely sure what's producing your font problems -- perhaps Simon will 
have some additional ideas -- but you should be aware that you can't load the 
Rcmdr package -- or, more generally, the tcltk package -- without XQuartz (or 
another X11 system). Normally, XQuartz should start automatically when the 
Rcmdr (or tcltk) package is loaded. That is, you should not have to start it 
separately.

It may help to know that the Rcmdr package selects its default dialog font by 
querying the default Tk font, via the command

tclvalue(.Tcl("font actual TkDefaultFont -family"))

and sets the font for commands and output by querying the default Tk 
fixed-width font:

tclvalue(.Tcl("font actual TkFixedFont -family"))

On my Macs, these are respectively the helvetica and courier fonts.

In any event, I'm glad that you seem to have solved your problem.

John

> -Original Message-
> From: Jose G Conde Santiago [mailto:jose.con...@upr.edu]
> Sent: Monday, May 15, 2017 3:18 PM
> To: Simon Urbanek <simon.urba...@r-project.org>; Fox, John
> <j...@mcmaster.ca>; r-sig-mac@r-project.org
> Subject: Re: [R-SIG-Mac] R commander fonts on R 3.4.0
> 
> When I run R without XQuartz, the text from the help screen renders
> well. I think the problem seems to be related to XQuartz.
> 
> José
> 
> 
> José G. Conde, MD, MPH
> Professor, School of Medicine
> Director, CentIT2
> UPR Medical Sciences Campus
> 
> Tel  (787) 763-9401 Fax (787) 758-5206
> 
> Email: jose.con...@upr.edu
> 
> URL: http://rcmi.rcm.upr.edu
> 
> > On May 15, 2017, at 2:16 PM, Jose G Conde Santiago
> <jose.con...@upr.edu> wrote:
> >
> > … and the same I get the same issue with R “help” screens in my iMac.
> I cannot reproduce this in the macBook.
> >
> > José
> >
> >
> >
> >
> > 
> >
> >
> >
> >
> > José G. Conde, MD, MPH
> > Catedrático, Escuela de Medicina
> > Director, CentIT2
> > Recinto de Ciencias Médicas, UPR
> >
> > Tel  (787) 763-9401  Fax (787) 758-5206
> >
> > Correo electrónico: jose.con...@upr.edu
> >
> > URL: http://rcmi.rcm.upr.edu
> >
> >> On May 15, 2017, at 2:14 PM, Jose G Conde Santiago
> <jose.con...@upr.edu> wrote:
> >>
> >> This is the actual resolutions.
> >>
> >> José
> >>
> >> 
> >> José G. Conde, MD, MPH
> >> Professor, School of Medicine
> >> Director, CentIT2
> >> UPR Medical Sciences Campus
> >>
> >> Tel  (787) 763-9401 Fax (787) 758-5206
> >>
> >> Email: jose.con...@upr.edu
> >>
> >> URL: http://rcmi.rcm.upr.edu
> >>
> >>> On May 15, 2017, at 12:31 PM, Jose G Conde Santiago
> <jose.con...@upr.edu> wrote:
> >>>
> >>> 
> >>
> >

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Re: [R-SIG-Mac] R commander fonts on R 3.4.0

[Fox, John]

Dear David,


Jose and I corresponded earlier today, and I can’t duplicate his problem
on two MacBook Pros, both with apparently the same setup as Jose’s: macOS
Sierra, R 3.4.0, Rcmdr 2.3-2, and XQuartz 2.7.11 (i.e., all current
versions). 

If the problem were with availability of X11 fonts, why would the fonts
appear properly for him with R 3.3.3 but not R 3.4.0?

I thought that someone more familiar with Macs than I am might spot the
cause of the problem from Jose’s screenshot, and so I suggested that he
write to the R-SIG-Mac list.

Best,
 John

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



On 2017-05-09, 6:45 PM, "R-SIG-Mac on behalf of David Winsemius"

wrote:

>
>> On May 9, 2017, at 3:08 PM, Jose G Conde Santiago via R-SIG-Mac
>> wrote:
>> 
>> Hello,
>> 
>> I recently upgraded to R 3.4.0, but now I get very poor fonts from
>>Rcmdr 2.3-2 as shown below:
>> 
>> 
>
>I'm not an Rcmdr user but I tried bringing a current version up. (I
>included a request to install Rcmdr with all dependencies but X11
>complained that aplpack was missing and that needed to be installed as
>well.)  Seems you don't like teh proportionally space serif font you are
>seeing which was different than what I saw. Think you might want to show
>what this returns for you
>
>names(X11Fonts())
>[1] "serif""sans" "mono" "Times"
>"Helvetica"   
>[6] "CyrTimes" "CyrHelvetica" "Arial""Mincho"
>
>> X11Fonts()$serif
>[1] "-*-times-%s-%s-*-*-%d-*-*-*-*-*-*-*"
>
>I'm running R 3.4.0, El Cap, XQuartz 2.7.11 (xorg-server 1.18.4)  and
>that won't change since my box is "end of life" per Apple's inflexible OS
>support.
>
>I tried running your test code and it seemed to lock up my X11 session as
>well as my R console (Perhaps this is due to running Rcmder in the R.app
>GUI?) 
>
>Best;
>David.
>
>
> 
>> I reloaded the older version of R (3.3.3), ran Rcmdr and the problem
>>disappeared. I downloaded R 3.4.0 again and the problem with Rcmdr
>>reappeared.
>
>> 
>> I read a previous post on the list regarding an issue with Rcmdr and
>>followed your suggestions to that posting:
>> 
>> 1. The following test went well with R 3.4.0:
>> 
>>> > library (tcltk)
>>> > tk_messageBox(message="test")
>>> [1] "ok"
>>> > 
>> 
>> 2. Ran R 3.4.0 from the terminal, and then ran R Commander. The problem
>>persists.
>> 
>> I am running XQuartz 2.7.11. My machine is an iMac (27-inch, Late
>>2012); Processor 3.4 GHz Intel Core i7, with 32 GB RAM. Graphics: NVIDIA
>>GeForce GTX 675MX 1024 MB. OS X Sierra 10.12.4.
>> 
>> I will appreciate any suggestions.
>> 
>> Thanks in advance.
>> 
>> José
>> 
>> José G. Conde, MD, MPH
>> Professor, School of Medicine
>> Director, CentIT2
>> UPR Medical Sciences Campus
>> 
>> Tel  (787) 763-9401 Fax (787) 758-5206
>> 
>> Email: jose.con...@upr.edu
>> 
>> URL: http://rcmi.rcm.upr.edu
>> 
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>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
>David Winsemius
>Alameda, CA, USA
>
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Re: [R-SIG-Mac] Rcmdr and macOS Sierra

[Fox, John]

Dear Eric,

I'm also running Mac OS Sierra with the current Mac version of R 3.3.2, the 
current version of XQuartz, and all R packages up-to-date. The Rcmdr works 
perfectly fine for me. 

Here are my session and system info:

 snip ---

> Sys.info()
sysname 
"Darwin" 
release 
"16.1.0" 
version
"Darwin Kernel Version 16.1.0: Thu Oct 13 21:26:57 PDT 2016; 
root:xnu-3789.21.3~60/RELEASE_X86_64" 
nodename 
"Johns-MBP" 
machine 
"x86_64" 
login 
"johnfox" 
user 
"johnfox" 
effective_user 
"johnfox" 

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS Sierra 10.12.1

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] splines   stats graphics  grDevices utils datasets  methods   base  
   

other attached packages:
[1] Rcmdr_2.3-1 RcmdrMisc_1.0-5 sandwich_2.3-4  car_2.1-4  

loaded via a namespace (and not attached):
 [1] zoo_1.7-13  lattice_0.20-34 tcltk_3.3.2 
colorspace_1.3-2   
 [5] htmltools_0.3.5 mgcv_1.8-16 relimp_1.0-5
survival_2.40-1
 [9] e1071_1.6-7 nloptr_1.0.4foreign_0.8-67  
RColorBrewer_1.1-2 
[13] readxl_0.1.1plyr_1.8.4  stringr_1.1.0   
MatrixModels_0.4-1 
[17] munsell_0.4.3   gtable_0.2.0latticeExtra_0.6-28 knitr_1.15.1   

[21] SparseM_1.74quantreg_5.29   pbkrtest_0.4-6  parallel_3.3.2 

[25] class_7.3-14htmlTable_1.7   Rcpp_0.12.8 acepack_1.4.1  

[29] openssl_0.9.5   scales_0.4.1tcltk2_1.2-11   base64_2.0 

[33] Hmisc_4.0-1 abind_1.4-5 lme4_1.1-12 
gridExtra_2.2.1
[37] ggplot2_2.2.0   digest_0.6.10   stringi_1.1.2   grid_3.3.2 

[41] tools_3.3.2 magrittr_1.5lazyeval_0.2.0  tibble_1.2 

[45] Formula_1.2-1   cluster_2.0.5   MASS_7.3-45 Matrix_1.2-7.1 

[49] data.table_1.10.0   assertthat_0.1  minqa_1.2.4 rpart_4.1-10   

[53] nnet_7.3-12 nlme_3.1-128   

 snip --


And here's a guess: Perhaps you didn't restart your Mac (or alternatively log 
out of and back into your account) before starting R.app.

I hope this helps,
 John

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



> -Original Message-
> From: R-SIG-Mac [mailto:r-sig-mac-boun...@r-project.org] On Behalf Of
> Eric Leroy
> Sent: Thursday, December 15, 2016 3:30 AM
> To: r-sig-mac@r-project.org
> Subject: [R-SIG-Mac] Rcmdr and macOS Sierra
> 
> Hi,
> Since I installed the last version of R.app and macOS sierra, I am not
> able to launch R Commander. I type library(Rcmdr), I see some messages
> and the window of R commander never appears. It is the same with
> Rstudio. The only way I was able to launch Rcmdr is from XQuartz from
> xterm via R and then library(Rcmdr).
> Do you have the same problem and an idea to fix it?
> Best regards,
> 
> --
> 
> 
> Eric Leroy
> 
> Responsable de la plateforme microscopie électronique
> 
> ICMPE - UMR 7182 - CNRS - UPEC
> 
> 2/8, rue Henri Dunant
> 
> 94320 Thiais
> 
> Tél : 01.49.78.12.09
> 
> Fax : 01.49.78.12.03
> 
> courriel : eric.le...@icmpe.cnrs.fr 
> 
> Page Web : : http://www.icmpe.cnrs.fr

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Re: [R-SIG-Mac] R commander installation problem (Mac OSX Capitan)

[Fox, John]

Dear Candice,

I'm glad that you were able to get everything to work. The message offering to 
install additional packages on initial Rcmdr start-up is expected, as is 
mentioned in the R Commander installation notes.

My guess is that you didn't log out or reboot after installing XQuartz, 
something that the R Commander Mac installation notes tell you to do.

It's a good idea to keep the R-SIG-Mac list in the loop so that others who 
experience a similar problem will see the solution, so I've cc'ed the list.

Best,
 John

> -Original Message-
> From: Candice Chan [mailto:aurorasea...@hotmail.com]
> Sent: Wednesday, June 1, 2016 11:17 AM
> To: Fox, John <j...@mcmaster.ca>
> Subject: RE: [R-SIG-Mac] R commander installation problem (Mac OSX
> Capitan)
> 
> Hi John,
> 
> Thank you very much for your detailed explanation. I have already
> checked out that webpage before posting but did not solve my problem.
> Tried the tcltk check and it was not working. So I rebooted the system,
> restarted R, tried to run Rcmdr and it now tells me to install some
> missing softwares. Now, Rcmdr is finally working and thank you very
> much!
> 
> C
> 
> 
> > From: j...@mcmaster.ca
> > To: aurorasea...@hotmail.com
> > CC: r-sig-mac@r-project.org
> > Subject: RE: [R-SIG-Mac] R commander installation problem (Mac OSX
> > Capitan)
> > Date: Wed, 1 Jun 2016 12:41:51 +
> >
> > Dear Candice,
> >
> > Your message is a bit hard to read -- R-SIG-Mac list doesn't accept
> HTML email and reformatted the message. Also, although you don't say so,
> I assume that you're using the current versions of R and the Rcmdr
> package. If you haven't already done so, please read the R Commander
> installation notes at
> <http://socserv.socsci.mcmaster.ca/jfox/Misc/Rcmdr/installation-
> notes.html>.
> >
> > I don't know the source of your problem but it may help to try to
> isolate it. First, see whether the tcltk package -- a standard part of R
> -- is working. In a fresh session, type the command library(tcltk) at
> the > R command prompt and then the command
> tk_messageBox(message="test") . If that doesn't work, as is likely,
> you'll know that the problem isn't peculiar to the Rcmdr package.
> >
> > Second, if you haven't already done so, log out of your account and
> then back in -- or just reboot your Mac -- and try again. You have to
> log out after installing XQuartz.
> >
> > Next, try running R in a Mac terminal window (just type R at the
> terminal command prompt) rather than using R.app. See whether the tcltk
> and Rcmdr packages work when you bypass R.app.
> >
> > Finally, try reinstalling everything -- R, the Rcmdr package, and
> XQuartz. Reboot and try again.
> >
> > Let us know what happens.
> >
> > I hope this helps,
> > John
> >
> > -
> > John Fox, Professor
> > McMaster University
> > Hamilton, Ontario
> > Canada L8S 4M4
> > Web: socserv.mcmaster.ca/jfox
> >
> >
> >
> > > -Original Message-
> > > From: R-SIG-Mac [mailto:r-sig-mac-boun...@r-project.org] On Behalf
> > > Of Candice Chan
> > > Sent: June 1, 2016 7:31 AM
> > > To: r-sig-mac@r-project.org
> > > Subject: [R-SIG-Mac] R commander installation problem (Mac OSX
> > > Capitan)
> > >
> > >
> > >
> > >
> > > Hello, I am completely new to using R and I'm trying to install it
> > > onto my laptop (Mac Capitan 10.11.5). I have downloaded R commander,
> > > and also ensured I installed the latest X Quartz. I then run
> > > "library(Rcmdr)", but received the following message: Loading
> > > required package: splinesLoading required
> > > package: RcmdrMiscLoading required package: carLoading required
> package:
> > > sandwichError : .onLoad failed in loadNamespace() for 'Rcmdr',
> details: call:
> > > structure(.External(.C_dotTclObjv, objv), class = "tclObj") error:
> > > [tcl] invalid command name "tk_messageBox".Error: package or
> > > namespace load failed for  Rcmdr I searched for help and some
> > > previous posts suggested running X quartz in the background and
> > > restarting R, and try again. However that failed to solve the
> problem. I would really appreciate your help and advice on this.
> > > Thank you very much Candice NUS Student
> > >
> > > [[alternative HTML version deleted]]
> >

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Re: [R-SIG-Mac] R commander installation problem (Mac OSX Capitan)

[Fox, John]

Dear Candice,

Your message is a bit hard to read -- R-SIG-Mac list doesn't accept HTML email 
and reformatted the message. Also, although you don't say so, I assume that 
you're using the current versions of R and the Rcmdr package. If you haven't 
already done so, please read the R Commander installation notes at 
.

I don't know the source of your problem but it may help to try to isolate it. 
First, see whether the tcltk package -- a standard part of R -- is working. In 
a fresh session, type the command library(tcltk) at the > R command prompt and 
then the command tk_messageBox(message="test") . If that doesn't work, as is 
likely, you'll know that the problem isn't peculiar to the Rcmdr package.

Second, if you haven't already done so, log out of your account and then back 
in -- or just reboot your Mac -- and try again. You have to log out after 
installing XQuartz.

Next, try running R in a Mac terminal window (just type R at the terminal 
command prompt) rather than using R.app. See whether the tcltk and Rcmdr 
packages work when you bypass R.app.

Finally, try reinstalling everything -- R, the Rcmdr package, and XQuartz. 
Reboot and try again.

Let us know what happens.

I hope this helps,
 John

-
John Fox, Professor
McMaster University
Hamilton, Ontario
Canada L8S 4M4
Web: socserv.mcmaster.ca/jfox



> -Original Message-
> From: R-SIG-Mac [mailto:r-sig-mac-boun...@r-project.org] On Behalf Of
> Candice Chan
> Sent: June 1, 2016 7:31 AM
> To: r-sig-mac@r-project.org
> Subject: [R-SIG-Mac] R commander installation problem (Mac OSX Capitan)
> 
> 
> 
> 
> Hello, I am completely new to using R and I'm trying to install it onto my 
> laptop
> (Mac Capitan 10.11.5). I have downloaded R commander, and also ensured I
> installed the latest X Quartz. I then run "library(Rcmdr)", but received the
> following message: Loading required package: splinesLoading required
> package: RcmdrMiscLoading required package: carLoading required package:
> sandwichError : .onLoad failed in loadNamespace() for 'Rcmdr', details:  call:
> structure(.External(.C_dotTclObjv, objv), class = "tclObj")  error: [tcl] 
> invalid
> command name "tk_messageBox".Error: package or namespace load failed for
> �Rcmdr�I searched for help and some previous posts suggested running X
> quartz in the background and restarting R, and try again. However that failed
> to solve the problem. I would really appreciate your help and advice on this.
> Thank you very much Candice NUS Student
> 
>   [[alternative HTML version deleted]]

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Re: [R-SIG-Mac] rgl crashes R.app in El Capitan

[Fox, John]

Hi Duncan,

Thanks again for taking care of this.

John

> -Original Message-
> From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
> Sent: Thursday, October 15, 2015 2:46 PM
> To: Fox, John; r-sig-mac@r-project.org
> Cc: jose.con...@upr.edu
> Subject: Re: rgl crashes R.app in El Capitan
> 
> On 15/10/2015 2:21 PM, Fox, John wrote:
> > Hi Duncan,
> >
> > Thanks for looking into this. Please see below:
> >
> > > -Original Message-
> > > From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
> > > Sent: Thursday, October 15, 2015 12:29 PM
> > > To: Fox, John; r-sig-mac@r-project.org
> > > Cc: jose.con...@upr.edu
> > > Subject: Re: rgl crashes R.app in El Capitan
> > >
> > > One of my students has El Capitan, so I got to see this.  It appears
> > > it's the old aglrgl.so problem.  I should just give up on native
> > > support, since I don't really know how to debug it.
> > >
> > > The "simple" fix is to delete the aglrgl.so file.  This means R.app
> will
> > > use the X11 driver, the same as the terminal version or RStudio
> would
> > > use.  Some users will have problems with this:
> > >
> > >  - It means they need Xquartz installed.
> > >  - You need admin privileges to delete aglrgl.so, and you need to
> know
> > > how to find it.  To find it, in R you can run
> > >
> > > system.file("libs/aglrgl.so", package="rgl")
> > >
> > > in R; I see
> > >
> > >
> "/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rgl/libs
> > > /aglrgl.so"
> > >
> > > but others may see it elsewhere.  I don't know if there is a way to
> > > delete it from R; I'd expect
> > >
> > > unlink(system.file("libs/aglrgl.so", package="rgl"))
> > >
> > > to fail because of permission problems, but I'm not sure of that.
> >
> > Actually, that works for me and fixes the problem.
> >
> > >
> > > I'm not going to attempt to describe Xquartz installation, but
> Google
> > > should be able to help.
> >
> > Jose encountered this problem using the Rcmdr package, which already
> requires XQuartz due to Tcl/Tk, but more generally the car package
> doesn't need XQuartz. XQuartz installation is simple in any event.
> >
> > One thing is unclear to me, however. Will you simply remove aglrgl.so
> from the next version of rgl? If so, you should be able to test for the
> presence of XQuartz and print a warning message in its absence.
> 
> Yes, I'll be dropping aglrgl.so.  rgl can run without any display (using
> options(rgl.useNULL = TRUE) and writing WebGL or some other kinds of
> output to a file), so I'm not sure whether a warning will be needed;
> I'll have to think about use cases.
> 
> Duncan Murdoch
> 
> >
> > Best,
> >   John
> >
> > >
> > > Duncan Murdoch
> > >
> > >
> > >
> > > On 13/10/2015 4:05 PM, Fox, John wrote:
> > > > Dear Duncan,
> > > >
> > > >> -Original Message-
> > > >> From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
> > > >> Sent: Tuesday, October 13, 2015 3:34 PM
> > > >> To: Fox, John; r-sig-mac@r-project.org
> > > >> Cc: jose.con...@upr.edu
> > > >> Subject: Re: rgl crashes R.app in El Capitan
> > > >>
> > > >> On 13/10/2015 3:03 PM, Fox, John wrote:
> > > >>> Dear r-sig-mac list members,
> > > >>>
> > > >>> I can reliably crash R.app in R 3.2.2 under El Capitan with
> > > >>>
> > > >>>   library(rgl)
> > > >>>   demo("rgl")  # a few returns
> > > >>>
> > > >>> My session info:
> > > >>>
> > > >>>> sessionInfo()
> > > >>> R version 3.2.2 (2015-08-14)
> > > >>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> > > >>> Running under: OS X 10.11 (El Capitan)
> > > >>>
> > > >>> locale:
> > > >>> [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-
> 8
> > > >>>
> > > >>> attached base packages:
> > > >>> [1] stats graphics  grDevices utils datasets  methods
> base
> > > >>>
> > > >>> other attached packages:
> > > >>> [1] rgl_0.95.1367
>

Re: [R-SIG-Mac] rgl crashes R.app in El Capitan

[Fox, John]

Hi Duncan,

Thanks for looking into this. Please see below:

> -Original Message-
> From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
> Sent: Thursday, October 15, 2015 12:29 PM
> To: Fox, John; r-sig-mac@r-project.org
> Cc: jose.con...@upr.edu
> Subject: Re: rgl crashes R.app in El Capitan
> 
> One of my students has El Capitan, so I got to see this.  It appears
> it's the old aglrgl.so problem.  I should just give up on native
> support, since I don't really know how to debug it.
> 
> The "simple" fix is to delete the aglrgl.so file.  This means R.app will
> use the X11 driver, the same as the terminal version or RStudio would
> use.  Some users will have problems with this:
> 
>  - It means they need Xquartz installed.
>  - You need admin privileges to delete aglrgl.so, and you need to know
> how to find it.  To find it, in R you can run
> 
> system.file("libs/aglrgl.so", package="rgl")
> 
> in R; I see
> 
> "/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rgl/libs
> /aglrgl.so"
> 
> but others may see it elsewhere.  I don't know if there is a way to
> delete it from R; I'd expect
> 
> unlink(system.file("libs/aglrgl.so", package="rgl"))
> 
> to fail because of permission problems, but I'm not sure of that.

Actually, that works for me and fixes the problem.

> 
> I'm not going to attempt to describe Xquartz installation, but Google
> should be able to help.

Jose encountered this problem using the Rcmdr package, which already requires 
XQuartz due to Tcl/Tk, but more generally the car package doesn't need XQuartz. 
XQuartz installation is simple in any event.

One thing is unclear to me, however. Will you simply remove aglrgl.so from the 
next version of rgl? If so, you should be able to test for the presence of 
XQuartz and print a warning message in its absence.

Best,
 John

> 
> Duncan Murdoch
> 
> 
> 
> On 13/10/2015 4:05 PM, Fox, John wrote:
> > Dear Duncan,
> >
> >> -Original Message-
> >> From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
> >> Sent: Tuesday, October 13, 2015 3:34 PM
> >> To: Fox, John; r-sig-mac@r-project.org
> >> Cc: jose.con...@upr.edu
> >> Subject: Re: rgl crashes R.app in El Capitan
> >>
> >> On 13/10/2015 3:03 PM, Fox, John wrote:
> >>> Dear r-sig-mac list members,
> >>>
> >>> I can reliably crash R.app in R 3.2.2 under El Capitan with
> >>>
> >>>   library(rgl)
> >>>   demo("rgl")  # a few returns
> >>>
> >>> My session info:
> >>>
> >>>> sessionInfo()
> >>> R version 3.2.2 (2015-08-14)
> >>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> >>> Running under: OS X 10.11 (El Capitan)
> >>>
> >>> locale:
> >>> [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
> >>>
> >>> attached base packages:
> >>> [1] stats graphics  grDevices utils datasets  methods   base
> >>>
> >>> other attached packages:
> >>> [1] rgl_0.95.1367
> >>>
> >>> I see this problem only in R.app, not when R is run in a terminal or
> >> in RStudio.
> >>>
> >>> This problem was original brought to my attention by Jose Conde (to
> >> whom I'm cc'ing this message), who encountered the problem using the
> >> scatter3d() function in the car package via the Rcmdr, but the
> problem
> >> isn't unique to either scatter3d() or the Rcmdr. In the case of
> >> scatter3d() the command
> >>>
> >>> scatter3d(prestige ~ income + education, data=Prestige)
> >>>
> >>> which draws a regression surface, reliably crashes R.app, but
> >>>
> >>> scatter3d(prestige ~ income + education, data=Prestige,
> >> surface=FALSE)
> >>>
> >>> which plots only points (as spheres) doesn't.
> >>>
> >>> I hope that this provides enough clues to diagnose the problem.
> >>>
> >>>
> >>
> >> I don't have El Capitan, I'm still running under OS X 10.9.5
> >> (Mavericks), and it doesn't crash.
> >
> > That was my experience as well -- I didn't experience this problem
> under either Mavericks or Yosemite. BTW, I reinstalled R 3.2.2 and
> XQuartz after upgrading to El Capitan. I usually upgrade fairly early to
> see whether there are any problems.
> >
> >>
> >> Since you're using the latest rgl, you must have built it yourself --
> >> CRAN doesn't distribute binaries for it (at least for Mavericks).
> Did
> >> you get any errors or warnings during compilation?
> >
> > Right again. I ran update.packages() to make sure that the error
> wasn't fixed and compiled packages that didn't yet have Mac binaries.
> AFAICS, there were no errors in compiling the rgl package.
> >
> > BTW, my apologies for posting my message twice -- my mailer complained
> about the address in the first message and I thought it wasn't sent.
> >
> > Thanks for looking into this,
> >  John
> >
> >>
> >> Duncan Murdoch

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[R-SIG-Mac] rgl crashes R.app in El Capitan

[Fox, John]

Dear r-sig-mac list members,

I can reliably crash R.app in R 3.2.2 under El Capitan with

  library(rgl)
  demo("rgl")  # a few returns

My session info:

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11 (El Capitan)

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base 

other attached packages:
[1] rgl_0.95.1367

I see this problem only in R.app, not when R is run in a terminal or in RStudio.

This problem was original brought to my attention by Jose Conde (to whom I'm 
cc'ing this message), who encountered the problem using the scatter3d() 
function in the car package via the Rcmdr, but the problem isn't unique to 
either scatter3d() or the Rcmdr. In the case of scatter3d() the command

scatter3d(prestige ~ income + education, data=Prestige)

which draws a regression surface, reliably crashes R.app, but

scatter3d(prestige ~ income + education, data=Prestige, surface=FALSE)

which plots only points (as spheres) doesn't.

I hope that this provides enough clues to diagnose the problem.

John

-
John Fox, Professor
McMaster University
Hamilton, Ontario
Canada L8S 4M4
web: socserv.mcmaster.ca/jfox


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Re: [R-SIG-Mac] rgl crashes R.app in El Capitan

[Fox, John]

Dear Duncan,

> -Original Message-
> From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
> Sent: Tuesday, October 13, 2015 3:34 PM
> To: Fox, John; r-sig-mac@r-project.org
> Cc: jose.con...@upr.edu
> Subject: Re: rgl crashes R.app in El Capitan
> 
> On 13/10/2015 3:03 PM, Fox, John wrote:
> > Dear r-sig-mac list members,
> >
> > I can reliably crash R.app in R 3.2.2 under El Capitan with
> >
> >   library(rgl)
> >   demo("rgl")  # a few returns
> >
> > My session info:
> >
> >> sessionInfo()
> > R version 3.2.2 (2015-08-14)
> > Platform: x86_64-apple-darwin13.4.0 (64-bit)
> > Running under: OS X 10.11 (El Capitan)
> >
> > locale:
> > [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
> >
> > attached base packages:
> > [1] stats graphics  grDevices utils datasets  methods   base
> >
> > other attached packages:
> > [1] rgl_0.95.1367
> >
> > I see this problem only in R.app, not when R is run in a terminal or
> in RStudio.
> >
> > This problem was original brought to my attention by Jose Conde (to
> whom I'm cc'ing this message), who encountered the problem using the
> scatter3d() function in the car package via the Rcmdr, but the problem
> isn't unique to either scatter3d() or the Rcmdr. In the case of
> scatter3d() the command
> >
> > scatter3d(prestige ~ income + education, data=Prestige)
> >
> > which draws a regression surface, reliably crashes R.app, but
> >
> > scatter3d(prestige ~ income + education, data=Prestige,
> surface=FALSE)
> >
> > which plots only points (as spheres) doesn't.
> >
> > I hope that this provides enough clues to diagnose the problem.
> >
> >
> 
> I don't have El Capitan, I'm still running under OS X 10.9.5
> (Mavericks), and it doesn't crash.

That was my experience as well -- I didn't experience this problem under either 
Mavericks or Yosemite. BTW, I reinstalled R 3.2.2 and XQuartz after upgrading 
to El Capitan. I usually upgrade fairly early to see whether there are any 
problems.

> 
> Since you're using the latest rgl, you must have built it yourself --
> CRAN doesn't distribute binaries for it (at least for Mavericks).  Did
> you get any errors or warnings during compilation?

Right again. I ran update.packages() to make sure that the error wasn't fixed 
and compiled packages that didn't yet have Mac binaries. AFAICS, there were no 
errors in compiling the rgl package.

BTW, my apologies for posting my message twice -- my mailer complained about 
the address in the first message and I thought it wasn't sent.

Thanks for looking into this,
 John

> 
> Duncan Murdoch

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[R-SIG-Mac] rgl crashes R.app under El Capitan

[Fox, John]

Dear r-sig-mac list members,

The following reliably crashes R.app for R 3.2.2 under El Capitan (at least for 
me):

library(rgl)
demo("rgl") # press return a few times

My session info:

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11 (El Capitan)

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base 

other attached packages:
[1] rgl_0.95.1367

As far as I can tell, this problem occurs only in R.app, not when R is run from 
a terminal, nor in RStudio.

The problem was brought to my attention by José Conde (whom I've cc'd this 
message), who encountered the problem using the scatter3d() function from the 
car package through the Rcmdr GUI -- but the problem apparently isn't specific 
either to the Rcmdr or to scatter3d().

In the case of scatter3d(), the problem occurs only when displaying a 
regression surface, as in

scatter3d(prestige ~ income + education, data=Prestige)

but not in

scatter3d(prestige ~ income + education, data=Prestige, surface=FALSE)

I hope that this provides enough clues to resolve the problem.

Best,
 John
-
John Fox, Professor
McMaster University
Hamilton, Ontario
Canada L8S 4M4
web: socserv.mcmaster.ca/jfox

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