Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Re: [External] Please test R 4.0.4 RC

2021-02-13 Thread Peter West
Hi Duncan,

When you say ‘fix,’ did that include running the compiled rgl successfully 
against your R installation?

Peter
—
p...@ehealth.id.au
Moved with pity, he stretched out his hand and touched him and said to him, “I 
will; be clean.”



> On 14 Feb 2021, at 11:42 am, Duncan Murdoch  wrote:
> 
> This worked for me to apparently fix my system:
> 
> Start with a newly rebooted system.
> 
> Uninstall XQuartz by dragging it to the trash.
> 
> Look in /Library/LaunchAgents/ for filenames related to xquartz.  I had two:  
> a five year old one called org.macosforge.xquartz.startx.plist, and one from 
> around the time I installed the XQuartz beta named org.xquartz.startx.plist.  
> I deleted the latter.
> 
> Look in /Library/LaunchDaemons/ for similar files.  I deleted one with the 
> same name, i.e. org.xquartz.startx.plist, and left an older one.
> 
> Reboot the system again, and install XQuartz 2.7.11.  Relogin, and things 
> seem fine.
> 
> Duncan Murdoch
> 


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Re: [R-SIG-Mac] Unable to change some members of a vector

2021-02-13 Thread Peter West
Just incidentally, \xCA in MacRoman encoding is an NBSP – non-breaking space, 
which is the only one that looks sane. In Unicode, it’s Latin capital letter E 
with circumflex, as it is in ISO 8859-1.

Peter
—
p...@ehealth.id.au
Moved with pity, he stretched out his hand and touched him and said to him, “I 
will; be clean.”



> On 14 Feb 2021, at 2:34 pm, Ken Beath  wrote:
…
> There is an option in the read.table command of stringsAsFactors. You can set 
> it to FALSE to obtain character strings. You can also convert the factor to 
> character using as.character().
> 
…
> Ken
> 
>> On 14 Feb 2021, at 9:54 am, Parkhurst, David F.  wrote:
>> 
>> I have a problem I don’t know how to deal with.  I’ve used read.table to 
>> create the data frame called msPdf.  It contains three vectors:  month, 
>> site, conc.  Some of the site values look like this:  MLH\xca.  

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Re: [R-SIG-Mac] Unable to change some members of a vector

2021-02-13 Thread Ken Beath
This question is not related to Macs, but here is the answer anyway.

First up, anyone who uses R should understand what a factor is. Find an 
introductory text on R and read the section on factors. Even better, read the 
whole book.  It seems that it has been decided that R will not automatically 
add a factor level, which is probably a good idea.

There is an option in the read.table command of stringsAsFactors. You can set 
it to FALSE to obtain character strings. You can also convert the factor to 
character using as.character().

If Excel decides to put strange characters into your data file then that is 
Excel’s problem. I suggest looking at the file with a text editor. The free 
version of BBEdit will work fine. You can read Excel files directly using teh 
readxl package.

Ken

> On 14 Feb 2021, at 9:54 am, Parkhurst, David F.  wrote:
> 
> I have a problem I don’t know how to deal with.  I’ve used read.table to 
> create the data frame called msPdf.  It contains three vectors:  month, site, 
> conc.  Some of the site values look like this:  MLH\xca.  I was able to 
> change that with this command: msPdf$site[13]="MLH”.  That seems to have been 
> allowed because some of the other sites are simply MLH.  But the system won’t 
> let me make the same kind of change in another case:
> msPdf$site[29]="MUH”.  When I ask for that, I get 
> Warning message:
> In `[<-.factor`(`*tmp*`, 29, value = c(5L, 2L, 1L, 11L, 5L, 12L,  :
>   invalid factor level, NA generated
>> #13  May MLH\xca 0.007
> Then if I enter msPdf$site[29], I get this response:
> [1] 
> Levels: CrCr LMO MCE MCH MFSC MLE MLH MLH\xca MUE MUH\xca NFSC SFSC
> 
> In other words, although other sites that were just plain MLH, there were not 
> other sites that were just plain MUH.
> How can I fix this problem?  I have no idea why excel added those \xca bits 
> to a few of the site values.
> 
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Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Re: [External] Please test R 4.0.4 RC

2021-02-13 Thread Richard M. Heiberger
Thank you.  dragging the org.xquartz.startx.* to Trash and reinstalling 2.7.11 
restored my system to sanity.


From: Duncan Murdoch 
Sent: Saturday, February 13, 2021 8:42 PM
To: Richard M. Heiberger; R-SIG-Mac
Subject: Re: [External] Re: [R-SIG-Mac] [External] Re: [External] Re: 
[External] Please test R 4.0.4 RC

This worked for me to apparently fix my system:

Start with a newly rebooted system.

Uninstall XQuartz by dragging it to the trash.

Look in /Library/LaunchAgents/ for filenames related to xquartz.  I had
two:  a five year old one called org.macosforge.xquartz.startx.plist,
and one from around the time I installed the XQuartz beta named
org.xquartz.startx.plist.  I deleted the latter.

Look in /Library/LaunchDaemons/ for similar files.  I deleted one with
the same name, i.e. org.xquartz.startx.plist, and left an older one.

Reboot the system again, and install XQuartz 2.7.11.  Relogin, and
things seem fine.

Duncan Murdoch



On 13/02/2021 7:22 p.m., Richard M. Heiberger wrote:
> It is looking for:
>   missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
>
> This is the entirety of
>/Library/Developer/CommandLineTools/usr/share/
>
>/Library/Developer/CommandLineTools/usr/share/man:
>total used in directory 40 available 1.3 TiB
>drwxr-xr-x  3 root  wheel 96 Feb 11 12:34 .
>drwxr-xr-x  3 root  wheel 96 Feb 11 12:34 ..
>-rw-r--r--  1 root  wheel  20198 Jan 27 16:11 whatis
>
> So I will again try
> sudo xcode-select --install
>
> It took a few minutes, and now from a new R session
>> X11()
> Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  :
>unable to start device X11
> In addition: Warning message:
> In X11() : unable to open connection to X11 display ''
>> Sys.getenv("DISPLAY")
> [1] "/private/tmp/com.apple.launchd.l0xAmiv83n/org.xquartz:0"
>> Sys.setenv(DISPLAY=":0.0")
>> Sys.getenv("DISPLAY")
> [1] ":0.0"
>> X11()
> Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  :
>unable to start device X11
> In addition: Warning message:
> In X11() : unable to open connection to X11 display ''
>>
>
>
>
> the xcrun is still not on the machine, and specifically not in 
> /Library/Developer/CommandLineTools/
> 
> From: Dr Eberhard W Lisse 
> Sent: Saturday, February 13, 2021 6:50 PM
> To: Duncan Murdoch; R-SIG-Mac; Richard M. Heiberger
> Cc: e...@lisse.na
> Subject: Re: [External] Re: [R-SIG-Mac] [External] Re: [External] Re: 
> [External] Please test R 4.0.4 RC
>
> Remove the directory where xcrun says it is supposed to live and re-install 
> the command line tools?
>
> el
>
> —
> Sent from Dr Lisse’s iPhone
> On 14 Feb 2021, 01:41 +0200, Richard M. Heiberger , wrote:
> I reported on installing xcode tools in my email
> Sat 2/13/2021 3:59 PM
> It didn't help.
>
> I did all this R_4.0.4 RC testing after updating to Big Sur 11.2.1.
>
> 
> From: Dr Eberhard W Lisse 
> Sent: Saturday, February 13, 2021 4:44 PM
> To: Duncan Murdoch; R-SIG-Mac; Richard M. Heiberger
> Cc: e...@lisse.na
> Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Re: [External] 
> Please test R 4.0.4 RC
>
> the Xcode Command line tools are missing. Install them and see what happens.
>
> Did you recently upgrade MacOS?
>
> el
>
> —
> Sent from Dr Lisse’s iPhone
> On 13 Feb 2021, 23:21 +0200, Richard M. Heiberger , wrote:
> That is next. Again a fresh session.
>
>
> setwd('/Users/rmh/Rwd/')
> Sys.setenv(DISPLAY=":0.0")
> X11()
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, :
> unable to start device X11
> In addition: Warning messages:
> 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
> running command ''otool' -L 
> '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
> 2: In X11() : unable to open connection to X11 display ''
>
>
>
> and the R session is still alive.
>
>
> This rasies for me a different question. Why should I want X11()?
>
> When X11 was working it was very slow, and didn't allow paging back through
> previous images.
>
> In favor of X11, I think it uses the display space better. X11() has better 
> size and spacing for xlab, ylab, and main than quartz(). But that isn't a 
> strong enough
> reason to use it while develkoping a graph. When I want it to look good,
> I go directly to pdf() and get the spacing that I think looks better.
>
> 
> From: Duncan Murdoch 
> Sent: Saturday, February 13, 2021 4:05 PM
> To: Richard M. Heiberger; R-SIG-Mac
> Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R 
> 4.0.4 RC
>
> Have you tried the change to DISPLAY, i.e.
>
> Sys.setenv(DISPLAY=":0.0")
>
> before running X11()?
>
> 

Re: [R-SIG-Mac] Please test R 4.0.4 RC

2021-02-13 Thread Michael Hall



> On Feb 13, 2021, at 8:30 PM, Simon Urbanek  
> wrote:
> 
> Michael,
> Thanks, but please don't post 3rd party links that are just one-liners with 
> extra advertising, especially when they have been already mentioned.
> Cheers,
> Simon

I think my link expanded some on the original answer which it didn’t sound like 
worked.
‘
It included additionally…

sudo xcode-select —reset

and…

If even that fails, go to the Apple developer download section and download 
Xcode manually.

But I did just google it and have no personal experience with the error. Often 
though just google will find you someone else who has dealt with the issue.

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Re: [R-SIG-Mac] Please test R 4.0.4 RC

2021-02-13 Thread Simon Urbanek
Michael,
Thanks, but please don't post 3rd party links that are just one-liners with 
extra advertising, especially when they have been already mentioned.
Cheers,
Simon


> On Feb 14, 2021, at 15:00, Michael Hall  wrote:
> 
> 
> 
>> On Feb 13, 2021, at 5:41 PM, r-sig-mac-requ...@r-project.org wrote:
>> 
>> xcrun: error: invalid active developer path 
>> (/Library/Developer/CommandLineTools), missing xcrun at: 
>> /Library/Developer/CommandLineTools/usr/bin/xcrun
> 
> https://ma.ttias.be/mac-os-xcrun-error-invalid-active-developer-path-missing-xcrun/
> 
> 
>   [[alternative HTML version deleted]]
> 
> ___
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> 

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Re: [R-SIG-Mac] Please test R 4.0.4 RC

2021-02-13 Thread Michael Hall



> On Feb 13, 2021, at 5:41 PM, r-sig-mac-requ...@r-project.org wrote:
> 
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun

https://ma.ttias.be/mac-os-xcrun-error-invalid-active-developer-path-missing-xcrun/


[[alternative HTML version deleted]]

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Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Re: [External] Please test R 4.0.4 RC

2021-02-13 Thread Duncan Murdoch

This worked for me to apparently fix my system:

Start with a newly rebooted system.

Uninstall XQuartz by dragging it to the trash.

Look in /Library/LaunchAgents/ for filenames related to xquartz.  I had 
two:  a five year old one called org.macosforge.xquartz.startx.plist, 
and one from around the time I installed the XQuartz beta named 
org.xquartz.startx.plist.  I deleted the latter.


Look in /Library/LaunchDaemons/ for similar files.  I deleted one with 
the same name, i.e. org.xquartz.startx.plist, and left an older one.


Reboot the system again, and install XQuartz 2.7.11.  Relogin, and 
things seem fine.


Duncan Murdoch



On 13/02/2021 7:22 p.m., Richard M. Heiberger wrote:

It is looking for:
  missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

This is the entirety of
   /Library/Developer/CommandLineTools/usr/share/

   /Library/Developer/CommandLineTools/usr/share/man:
   total used in directory 40 available 1.3 TiB
   drwxr-xr-x  3 root  wheel 96 Feb 11 12:34 .
   drwxr-xr-x  3 root  wheel 96 Feb 11 12:34 ..
   -rw-r--r--  1 root  wheel  20198 Jan 27 16:11 whatis

So I will again try
sudo xcode-select --install

It took a few minutes, and now from a new R session

X11()

Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  :
   unable to start device X11
In addition: Warning message:
In X11() : unable to open connection to X11 display ''

Sys.getenv("DISPLAY")

[1] "/private/tmp/com.apple.launchd.l0xAmiv83n/org.xquartz:0"

Sys.setenv(DISPLAY=":0.0")
Sys.getenv("DISPLAY")

[1] ":0.0"

X11()

Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  :
   unable to start device X11
In addition: Warning message:
In X11() : unable to open connection to X11 display ''






the xcrun is still not on the machine, and specifically not in 
/Library/Developer/CommandLineTools/

From: Dr Eberhard W Lisse 
Sent: Saturday, February 13, 2021 6:50 PM
To: Duncan Murdoch; R-SIG-Mac; Richard M. Heiberger
Cc: e...@lisse.na
Subject: Re: [External] Re: [R-SIG-Mac] [External] Re: [External] Re: 
[External] Please test R 4.0.4 RC

Remove the directory where xcrun says it is supposed to live and re-install the 
command line tools?

el

—
Sent from Dr Lisse’s iPhone
On 14 Feb 2021, 01:41 +0200, Richard M. Heiberger , wrote:
I reported on installing xcode tools in my email
Sat 2/13/2021 3:59 PM
It didn't help.

I did all this R_4.0.4 RC testing after updating to Big Sur 11.2.1.


From: Dr Eberhard W Lisse 
Sent: Saturday, February 13, 2021 4:44 PM
To: Duncan Murdoch; R-SIG-Mac; Richard M. Heiberger
Cc: e...@lisse.na
Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Re: [External] 
Please test R 4.0.4 RC

the Xcode Command line tools are missing. Install them and see what happens.

Did you recently upgrade MacOS?

el

—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 23:21 +0200, Richard M. Heiberger , wrote:
That is next. Again a fresh session.


setwd('/Users/rmh/Rwd/')
Sys.setenv(DISPLAY=":0.0")
X11()
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun
Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, :
unable to start device X11
In addition: Warning messages:
1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
running command ''otool' -L 
'/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
2: In X11() : unable to open connection to X11 display ''



and the R session is still alive.


This rasies for me a different question. Why should I want X11()?

When X11 was working it was very slow, and didn't allow paging back through
previous images.

In favor of X11, I think it uses the display space better. X11() has better 
size and spacing for xlab, ylab, and main than quartz(). But that isn't a 
strong enough
reason to use it while develkoping a graph. When I want it to look good,
I go directly to pdf() and get the spacing that I think looks better.


From: Duncan Murdoch 
Sent: Saturday, February 13, 2021 4:05 PM
To: Richard M. Heiberger; R-SIG-Mac
Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R 
4.0.4 RC

Have you tried the change to DISPLAY, i.e.

Sys.setenv(DISPLAY=":0.0")

before running X11()?

Duncan Murdoch

On 13/02/2021 3:50 p.m., Richard M. Heiberger wrote:
I tried this. It made no difference. Both before and after running
sudo xcode-select —install
I ran (in both cases, in a brand new *R* sessio n)

X11()
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun


My prior was that the xcode call was irrelevant is that X11() using XQuart 
8.0.3beta
worked with intel R_4.0.3 on the Mac M1.


From: Dr Eberhard 

Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Re: [External] Please test R 4.0.4 RC

2021-02-13 Thread Richard M. Heiberger
It is looking for:
 missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

This is the entirety of
  /Library/Developer/CommandLineTools/usr/share/

  /Library/Developer/CommandLineTools/usr/share/man:
  total used in directory 40 available 1.3 TiB
  drwxr-xr-x  3 root  wheel 96 Feb 11 12:34 .
  drwxr-xr-x  3 root  wheel 96 Feb 11 12:34 ..
  -rw-r--r--  1 root  wheel  20198 Jan 27 16:11 whatis

So I will again try
sudo xcode-select --install

It took a few minutes, and now from a new R session
> X11()
Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  : 
  unable to start device X11
In addition: Warning message:
In X11() : unable to open connection to X11 display ''
> Sys.getenv("DISPLAY")
[1] "/private/tmp/com.apple.launchd.l0xAmiv83n/org.xquartz:0"
> Sys.setenv(DISPLAY=":0.0")
> Sys.getenv("DISPLAY")
[1] ":0.0"
> X11()
Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  : 
  unable to start device X11
In addition: Warning message:
In X11() : unable to open connection to X11 display ''
> 



the xcrun is still not on the machine, and specifically not in 
/Library/Developer/CommandLineTools/

From: Dr Eberhard W Lisse 
Sent: Saturday, February 13, 2021 6:50 PM
To: Duncan Murdoch; R-SIG-Mac; Richard M. Heiberger
Cc: e...@lisse.na
Subject: Re: [External] Re: [R-SIG-Mac] [External] Re: [External] Re: 
[External] Please test R 4.0.4 RC

Remove the directory where xcrun says it is supposed to live and re-install the 
command line tools?

el

—
Sent from Dr Lisse’s iPhone
On 14 Feb 2021, 01:41 +0200, Richard M. Heiberger , wrote:
I reported on installing xcode tools in my email
Sat 2/13/2021 3:59 PM
It didn't help.

I did all this R_4.0.4 RC testing after updating to Big Sur 11.2.1.


From: Dr Eberhard W Lisse 
Sent: Saturday, February 13, 2021 4:44 PM
To: Duncan Murdoch; R-SIG-Mac; Richard M. Heiberger
Cc: e...@lisse.na
Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Re: [External] 
Please test R 4.0.4 RC

the Xcode Command line tools are missing. Install them and see what happens.

Did you recently upgrade MacOS?

el

—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 23:21 +0200, Richard M. Heiberger , wrote:
That is next. Again a fresh session.


setwd('/Users/rmh/Rwd/')
Sys.setenv(DISPLAY=":0.0")
X11()
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun
Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, :
unable to start device X11
In addition: Warning messages:
1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
running command ''otool' -L 
'/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
2: In X11() : unable to open connection to X11 display ''



and the R session is still alive.


This rasies for me a different question. Why should I want X11()?

When X11 was working it was very slow, and didn't allow paging back through
previous images.

In favor of X11, I think it uses the display space better. X11() has better 
size and spacing for xlab, ylab, and main than quartz(). But that isn't a 
strong enough
reason to use it while develkoping a graph. When I want it to look good,
I go directly to pdf() and get the spacing that I think looks better.


From: Duncan Murdoch 
Sent: Saturday, February 13, 2021 4:05 PM
To: Richard M. Heiberger; R-SIG-Mac
Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R 
4.0.4 RC

Have you tried the change to DISPLAY, i.e.

Sys.setenv(DISPLAY=":0.0")

before running X11()?

Duncan Murdoch

On 13/02/2021 3:50 p.m., Richard M. Heiberger wrote:
I tried this. It made no difference. Both before and after running
sudo xcode-select —install
I ran (in both cases, in a brand new *R* sessio n)

X11()
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun


My prior was that the xcode call was irrelevant is that X11() using XQuart 
8.0.3beta
worked with intel R_4.0.3 on the Mac M1.


From: Dr Eberhard W Lisse 
Sent: Saturday, February 13, 2021 3:33 AM
To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
Cc: e...@lisse.na
Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC

that has nothing to do with Xquartz but means you need to install the Command 
line tools

sudo xcode-select —install

—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
Using the intel R_4.0.4RC on the Mac M1.

Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
8.0.3beta.
X11() now does not work at all.

X11()
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 

Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Re: [External] Please test R 4.0.4 RC

2021-02-13 Thread Dr Eberhard W Lisse
Remove the directory where xcrun says it is supposed to live and re-install the 
command line tools?

el

—
Sent from Dr Lisse’s iPhone
On 14 Feb 2021, 01:41 +0200, Richard M. Heiberger , wrote:
> I reported on installing xcode tools in my email
> Sat 2/13/2021 3:59 PM
> It didn't help.
>
> I did all this R_4.0.4 RC testing after updating to Big Sur 11.2.1.
>
> 
> From: Dr Eberhard W Lisse 
> Sent: Saturday, February 13, 2021 4:44 PM
> To: Duncan Murdoch; R-SIG-Mac; Richard M. Heiberger
> Cc: e...@lisse.na
> Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Re: [External] 
> Please test R 4.0.4 RC
>
> the Xcode Command line tools are missing. Install them and see what happens.
>
> Did you recently upgrade MacOS?
>
> el
>
> —
> Sent from Dr Lisse’s iPhone
> On 13 Feb 2021, 23:21 +0200, Richard M. Heiberger , wrote:
> That is next. Again a fresh session.
>
>
> setwd('/Users/rmh/Rwd/')
> Sys.setenv(DISPLAY=":0.0")
> X11()
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, :
> unable to start device X11
> In addition: Warning messages:
> 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
> running command ''otool' -L 
> '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
> 2: In X11() : unable to open connection to X11 display ''
>
>
>
> and the R session is still alive.
>
>
> This rasies for me a different question. Why should I want X11()?
>
> When X11 was working it was very slow, and didn't allow paging back through
> previous images.
>
> In favor of X11, I think it uses the display space better. X11() has better 
> size and spacing for xlab, ylab, and main than quartz(). But that isn't a 
> strong enough
> reason to use it while develkoping a graph. When I want it to look good,
> I go directly to pdf() and get the spacing that I think looks better.
>
> 
> From: Duncan Murdoch 
> Sent: Saturday, February 13, 2021 4:05 PM
> To: Richard M. Heiberger; R-SIG-Mac
> Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R 
> 4.0.4 RC
>
> Have you tried the change to DISPLAY, i.e.
>
> Sys.setenv(DISPLAY=":0.0")
>
> before running X11()?
>
> Duncan Murdoch
>
> On 13/02/2021 3:50 p.m., Richard M. Heiberger wrote:
> I tried this. It made no difference. Both before and after running
> sudo xcode-select —install
> I ran (in both cases, in a brand new *R* sessio n)
>
> X11()
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
>
>
> My prior was that the xcode call was irrelevant is that X11() using XQuart 
> 8.0.3beta
> worked with intel R_4.0.3 on the Mac M1.
>
> 
> From: Dr Eberhard W Lisse 
> Sent: Saturday, February 13, 2021 3:33 AM
> To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
> Cc: e...@lisse.na
> Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC
>
> that has nothing to do with Xquartz but means you need to install the Command 
> line tools
>
> sudo xcode-select —install
>
> —
> Sent from Dr Lisse’s iPhone
> On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
> Using the intel R_4.0.4RC on the Mac M1.
>
> Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
> 8.0.3beta.
> X11() now does not work at all.
>
> X11()
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> C-c C-c C-c C-c
>
> Force-Killing XQuartz from the Activity Monitor doesn't help.
> I have to Force-kill the R process.
>
> 
> From: R-SIG-Mac  on behalf of Simon Urbanek 
> 
> Sent: Friday, February 12, 2021 6:50 PM
> To: R-SIG-Mac
> Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC
>
> Dear macOS useRs,
>
> please test the latest R 4.0.4 RC builds from
>
> https://mac.r-project.org/
>
> especially if you are running macOS Big Sur. The known issues introduced by 
> Big Sur have been fixed, but I cannot replicate nor test the spurious 
> touchbar warning.
>
> Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - 
> they are betas for a reason (=unstable) and break things.
>
> Cheers,
> Simon
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> ___
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>
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> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
>
> 

Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Re: [External] Please test R 4.0.4 RC

2021-02-13 Thread Richard M. Heiberger
I reported on installing xcode tools in my email
 Sat 2/13/2021 3:59 PM
It didn't help.

I did all this R_4.0.4 RC testing after updating to Big Sur 11.2.1.


From: Dr Eberhard W Lisse 
Sent: Saturday, February 13, 2021 4:44 PM
To: Duncan Murdoch; R-SIG-Mac; Richard M. Heiberger
Cc: e...@lisse.na
Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Re: [External] 
Please test R 4.0.4 RC

the Xcode Command line tools are missing. Install them and see what happens.

Did you recently upgrade MacOS?

el

—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 23:21 +0200, Richard M. Heiberger , wrote:
That is next. Again a fresh session.


setwd('/Users/rmh/Rwd/')
Sys.setenv(DISPLAY=":0.0")
X11()
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun
Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, :
unable to start device X11
In addition: Warning messages:
1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
running command ''otool' -L 
'/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
2: In X11() : unable to open connection to X11 display ''



and the R session is still alive.


This rasies for me a different question. Why should I want X11()?

When X11 was working it was very slow, and didn't allow paging back through
previous images.

In favor of X11, I think it uses the display space better. X11() has better 
size and spacing for xlab, ylab, and main than quartz(). But that isn't a 
strong enough
reason to use it while develkoping a graph. When I want it to look good,
I go directly to pdf() and get the spacing that I think looks better.


From: Duncan Murdoch 
Sent: Saturday, February 13, 2021 4:05 PM
To: Richard M. Heiberger; R-SIG-Mac
Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R 
4.0.4 RC

Have you tried the change to DISPLAY, i.e.

Sys.setenv(DISPLAY=":0.0")

before running X11()?

Duncan Murdoch

On 13/02/2021 3:50 p.m., Richard M. Heiberger wrote:
I tried this. It made no difference. Both before and after running
sudo xcode-select —install
I ran (in both cases, in a brand new *R* sessio n)

X11()
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun


My prior was that the xcode call was irrelevant is that X11() using XQuart 
8.0.3beta
worked with intel R_4.0.3 on the Mac M1.


From: Dr Eberhard W Lisse 
Sent: Saturday, February 13, 2021 3:33 AM
To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
Cc: e...@lisse.na
Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC

that has nothing to do with Xquartz but means you need to install the Command 
line tools

sudo xcode-select —install

—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
Using the intel R_4.0.4RC on the Mac M1.

Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
8.0.3beta.
X11() now does not work at all.

X11()
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun
C-c C-c C-c C-c

Force-Killing XQuartz from the Activity Monitor doesn't help.
I have to Force-kill the R process.


From: R-SIG-Mac  on behalf of Simon Urbanek 

Sent: Friday, February 12, 2021 6:50 PM
To: R-SIG-Mac
Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC

Dear macOS useRs,

please test the latest R 4.0.4 RC builds from

https://mac.r-project.org/

especially if you are running macOS Big Sur. The known issues introduced by Big 
Sur have been fixed, but I cannot replicate nor test the spurious touchbar 
warning.

Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - 
they are betas for a reason (=unstable) and break things.

Cheers,
Simon

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Re: [R-SIG-Mac] [External] Re: [External] Please test R 4.0.4 RC

2021-02-13 Thread Richard M. Heiberger
Well, my original report didn't give full information because R locked up too 
early.

>From here I am following instructions and reporting back:

R version 4.0.4 RC (2021-02-12 r79998) -- "Lost Library Book"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> setwd('/Users/rmh/Rwd/')
> system("Applications/Xquartz")
sh: Applications/Xquartz: No such file or directory
Warning message:
In system("Applications/Xquartz") : error in running command
> system("/Applications/Xquartz")
sh: /Applications/Xquartz: No such file or directory
Warning message:
In system("/Applications/Xquartz") : error in running command
> system("/Applications/Utilities/Xquartz")
sh: /Applications/Utilities/Xquartz: No such file or directory
Warning message:
In system("/Applications/Utilities/Xquartz") : error in running command
> system("/Applications/Utilities/Xquartz.app")
sh: /Applications/Utilities/Xquartz.app: is a directory
> system("/Applications/Utilities/Xquartz.app/Contents/MacOS/X11")
> X11()
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun
Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  :
  unable to start device X11
In addition: Warning messages:
1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
  running command ''otool' -L 
'/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
2: In X11() : unable to open connection to X11 display ''
> system("/Applications/Utilities/Xquartz.app/Contents/MacOS/X11")
> ## from the Cmd-Tab I opened Xquartz, and from its Applications I opened 
> xterm, and then ran an ls in xterm. it works.
> X11()
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun
Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  :
  unable to start device X11
In addition: Warning messages:
1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
  running command ''otool' -L 
'/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
2: In X11() : unable to open connection to X11 display ''
> Sys.getenv("DISPLAY")
[1] "/private/tmp/com.apple.launchd.l0xAmiv83n/org.xquartz:0"
> unlink(Sys.getenv("DISPLAY"))
>Sys.setenv(DISPLAY=":0.0")
> X11()
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun
Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  :
  unable to start device X11
In addition: Warning messages:
1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
  running command ''otool' -L 
'/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
2: In X11() : unable to open connection to X11 display ''
>


From: Simon Urbanek 
Sent: Saturday, February 13, 2021 5:35 PM
To: Richard M. Heiberger
Cc: Dr Eberhard W Lisse; R-SIG-Mac
Subject: Re: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC

Richard,

thanks - finally a more complete output to go on. This is exactly the reminder 
why it is so important to post the _full_output - the actual facts were 
completely missing from your previous report.

Firstly, the xcrun output is just a warning which indicates that R can't find 
out whether you have XQuartz installed or not. It also shows that your 
Xcode/command line tools are broken. That in itself is not a problem as long as 
you don't intend to compile packages - but probably you should look into it.

But more importantly your XQuartz doesn't work - or at least is not running at 
the time you are trying to run X11() in R. Make sure you start XQuartz first 
(from Applications -> Utilities) and it works. If in doubt, you can wipe it (it 
lives in /opt/X11) and re-install.

Either way, neither seems to be an R issue per se.

Cheers,
Simon


`
> On Feb 14, 2021, at 11:00 AM, Richard M. Heiberger  wrote:
>
> another fresh R session
>
>> X11(":0")
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  :
>  unable to start device X11
> In addition: Warning messages:
> 1: In 

[R-SIG-Mac] Unable to change some members of a vector

2021-02-13 Thread Parkhurst, David F.
I have a problem I don’t know how to deal with.  I’ve used read.table to create 
the data frame called msPdf.  It contains three vectors:  month, site, conc.  
Some of the site values look like this:  MLH\xca.  I was able to change that 
with this command: msPdf$site[13]="MLH”.  That seems to have been allowed 
because some of the other sites are simply MLH.  But the system won’t let me 
make the same kind of change in another case:
 msPdf$site[29]="MUH”.  When I ask for that, I get 
Warning message:
In `[<-.factor`(`*tmp*`, 29, value = c(5L, 2L, 1L, 11L, 5L, 12L,  :
  invalid factor level, NA generated
> #13  May MLH\xca 0.007
Then if I enter msPdf$site[29], I get this response:
[1] 
Levels: CrCr LMO MCE MCH MFSC MLE MLH MLH\xca MUE MUH\xca NFSC SFSC

In other words, although other sites that were just plain MLH, there were not 
other sites that were just plain MUH.
How can I fix this problem?  I have no idea why excel added those \xca bits to 
a few of the site values.

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Re: [R-SIG-Mac] [External] Re: [External] Please test R 4.0.4 RC

2021-02-13 Thread Duncan Murdoch

On 13/02/2021 5:43 p.m., Simon Urbanek wrote:

Duncan,

not really - this is why the XQuartz betas are such a disaster - they replace 
libraries with incompatible versions (under same file name) - and even remove 
some libraries, thus breaking anything that was compiled against either 
version. If you downgrade, you have to re-compile anything you compiled against 
the beta. That is probably one of the lesser evils since you can't expect 
anything to be forwards-compatible.

In theory, you could detect the version using otool - that's what X11() is 
doing to find whether XQuartz is present, but it only works for users that have 
dev tools installed, so not a good idea in general.


Okay, thanks.  I already have a no-X11 workaround; I'll just change the 
error message if the dyn.load() fails.


Duncan



Cheers,
Simon




On Feb 14, 2021, at 11:32 AM, Duncan Murdoch  wrote:

On 13/02/2021 4:54 p.m., Simon Urbanek wrote:

As mentioned earlier, the issue is likely that your X11-auto-launch is not working. You 
can start X11 (=XQuartz) yourself and set DISPLAY=:0 as you would on any unix system or 
start X11 with X11(":0")
[personally, I hate that auto-launch "feature" since it tries to start XQuartz 
even if you don't want it].


Thanks.  Here's another datum:  I did my last build of rgl with the beta 
XQuartz installed.  I'm now back to 2.7.11 and I get this when I try to start 
rgl:


library(rgl)

Error in dyn.load(dynlib) :
  unable to load shared object 
'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgl/libs/rgl.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgl/libs/rgl.so,
 6): Library not loaded: /opt/X11/lib/libX11.6.dylib
  Referenced from: 
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgl/libs/rgl.so
  Reason: Incompatible library version: rgl.so requires version 11.0.0 or 
later, but libX11.6.dylib provides version 10.0.0
Error: package or namespace load failed for ‘rgl’:
.onLoad failed in loadNamespace() for 'rgl', details:
  call: NULL
  error:Loading rgl's DLL failed.
This build of rgl depends on XQuartz, which you can download from 
xquartz.org.

So it appears they updated the version of libX11.6.dylib, and rgl is asking for 
the wrong one.

Is there some way for me to request a particular version during my build, or at 
least detect that the wrong version is installed?

Duncan Murdoch


Cheers,
Simon

On Feb 14, 2021, at 9:50 AM, Richard M. Heiberger  wrote:

I tried this.  It made no difference.  Both before and after running
sudo xcode-select —install
I ran (in both cases, in a brand new *R* sessio n)


X11()

xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun


My prior was that the xcode call was irrelevant is that X11() using XQuart 
8.0.3beta
worked with intel R_4.0.3 on the Mac M1.


From: Dr Eberhard W Lisse 
Sent: Saturday, February 13, 2021 3:33 AM
To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
Cc: e...@lisse.na
Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC

that has nothing to do with Xquartz but means you need to install the Command 
line tools

sudo xcode-select —install

—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
Using the intel R_4.0.4RC on the Mac M1.

Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
8.0.3beta.
X11() now does not work at all.

X11()
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun
C-c C-c C-c C-c

Force-Killing XQuartz from the Activity Monitor doesn't help.
I have to Force-kill the R process.


From: R-SIG-Mac  on behalf of Simon Urbanek 

Sent: Friday, February 12, 2021 6:50 PM
To: R-SIG-Mac
Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC

Dear macOS useRs,

please test the latest R 4.0.4 RC builds from

https://mac.r-project.org/

especially if you are running macOS Big Sur. The known issues introduced by Big 
Sur have been fixed, but I cannot replicate nor test the spurious touchbar 
warning.

Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - 
they are betas for a reason (=unstable) and break things.

Cheers,
Simon

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Re: [R-SIG-Mac] [External] Re: [External] Please test R 4.0.4 RC

2021-02-13 Thread Simon Urbanek
Duncan,

not really - this is why the XQuartz betas are such a disaster - they replace 
libraries with incompatible versions (under same file name) - and even remove 
some libraries, thus breaking anything that was compiled against either 
version. If you downgrade, you have to re-compile anything you compiled against 
the beta. That is probably one of the lesser evils since you can't expect 
anything to be forwards-compatible.

In theory, you could detect the version using otool - that's what X11() is 
doing to find whether XQuartz is present, but it only works for users that have 
dev tools installed, so not a good idea in general.

Cheers,
Simon



> On Feb 14, 2021, at 11:32 AM, Duncan Murdoch  wrote:
> 
> On 13/02/2021 4:54 p.m., Simon Urbanek wrote:
>> As mentioned earlier, the issue is likely that your X11-auto-launch is not 
>> working. You can start X11 (=XQuartz) yourself and set DISPLAY=:0 as you 
>> would on any unix system or start X11 with X11(":0")
>> [personally, I hate that auto-launch "feature" since it tries to start 
>> XQuartz even if you don't want it].
> 
> Thanks.  Here's another datum:  I did my last build of rgl with the beta 
> XQuartz installed.  I'm now back to 2.7.11 and I get this when I try to start 
> rgl:
> 
> > library(rgl)
> Error in dyn.load(dynlib) :
>  unable to load shared object 
> '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgl/libs/rgl.so':
> dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgl/libs/rgl.so,
>  6): Library not loaded: /opt/X11/lib/libX11.6.dylib
>  Referenced from: 
> /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgl/libs/rgl.so
>  Reason: Incompatible library version: rgl.so requires version 11.0.0 or 
> later, but libX11.6.dylib provides version 10.0.0
> Error: package or namespace load failed for ‘rgl’:
> .onLoad failed in loadNamespace() for 'rgl', details:
>  call: NULL
>  error:   Loading rgl's DLL failed.
>   This build of rgl depends on XQuartz, which you can download from 
> xquartz.org.
> 
> So it appears they updated the version of libX11.6.dylib, and rgl is asking 
> for the wrong one.
> 
> Is there some way for me to request a particular version during my build, or 
> at least detect that the wrong version is installed?
> 
> Duncan Murdoch
> 
>> Cheers,
>> Simon
>>> On Feb 14, 2021, at 9:50 AM, Richard M. Heiberger  wrote:
>>> 
>>> I tried this.  It made no difference.  Both before and after running
>>> sudo xcode-select —install
>>> I ran (in both cases, in a brand new *R* sessio n)
>>> 
 X11()
>>> xcrun: error: invalid active developer path 
>>> (/Library/Developer/CommandLineTools), missing xcrun at: 
>>> /Library/Developer/CommandLineTools/usr/bin/xcrun
>>> 
>>> 
>>> My prior was that the xcode call was irrelevant is that X11() using XQuart 
>>> 8.0.3beta
>>> worked with intel R_4.0.3 on the Mac M1.
>>> 
>>> 
>>> From: Dr Eberhard W Lisse 
>>> Sent: Saturday, February 13, 2021 3:33 AM
>>> To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
>>> Cc: e...@lisse.na
>>> Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC
>>> 
>>> that has nothing to do with Xquartz but means you need to install the 
>>> Command line tools
>>> 
>>> sudo xcode-select —install
>>> 
>>> —
>>> Sent from Dr Lisse’s iPhone
>>> On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
>>> Using the intel R_4.0.4RC on the Mac M1.
>>> 
>>> Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
>>> 8.0.3beta.
>>> X11() now does not work at all.
>>> 
>>> X11()
>>> xcrun: error: invalid active developer path 
>>> (/Library/Developer/CommandLineTools), missing xcrun at: 
>>> /Library/Developer/CommandLineTools/usr/bin/xcrun
>>> C-c C-c C-c C-c
>>> 
>>> Force-Killing XQuartz from the Activity Monitor doesn't help.
>>> I have to Force-kill the R process.
>>> 
>>> 
>>> From: R-SIG-Mac  on behalf of Simon 
>>> Urbanek 
>>> Sent: Friday, February 12, 2021 6:50 PM
>>> To: R-SIG-Mac
>>> Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC
>>> 
>>> Dear macOS useRs,
>>> 
>>> please test the latest R 4.0.4 RC builds from
>>> 
>>> https://mac.r-project.org/
>>> 
>>> especially if you are running macOS Big Sur. The known issues introduced by 
>>> Big Sur have been fixed, but I cannot replicate nor test the spurious 
>>> touchbar warning.
>>> 
>>> Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - 
>>> they are betas for a reason (=unstable) and break things.
>>> 
>>> Cheers,
>>> Simon
>>> 
>>> ___
>>> 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
>>> 
>> ___
>> 

Re: [R-SIG-Mac] [External] Re: [External] Please test R 4.0.4 RC

2021-02-13 Thread Simon Urbanek
Richard,

thanks - finally a more complete output to go on. This is exactly the reminder 
why it is so important to post the _full_output - the actual facts were 
completely missing from your previous report.

Firstly, the xcrun output is just a warning which indicates that R can't find 
out whether you have XQuartz installed or not. It also shows that your 
Xcode/command line tools are broken. That in itself is not a problem as long as 
you don't intend to compile packages - but probably you should look into it.

But more importantly your XQuartz doesn't work - or at least is not running at 
the time you are trying to run X11() in R. Make sure you start XQuartz first 
(from Applications -> Utilities) and it works. If in doubt, you can wipe it (it 
lives in /opt/X11) and re-install.

Either way, neither seems to be an R issue per se.

Cheers,
Simon


`
> On Feb 14, 2021, at 11:00 AM, Richard M. Heiberger  wrote:
> 
> another fresh R session
> 
>> X11(":0")
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  :
>  unable to start device X11
> In addition: Warning messages:
> 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
>  running command ''otool' -L 
> '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
> 2: In X11(":0") : unable to open connection to X11 display ':0'
>> 
> 
> 
> From: Simon Urbanek 
> Sent: Saturday, February 13, 2021 4:54 PM
> To: Richard M. Heiberger
> Cc: Dr Eberhard W Lisse; R-SIG-Mac
> Subject: Re: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC
> 
> As mentioned earlier, the issue is likely that your X11-auto-launch is not 
> working. You can start X11 (=XQuartz) yourself and set DISPLAY=:0 as you 
> would on any unix system or start X11 with X11(":0")
> [personally, I hate that auto-launch "feature" since it tries to start 
> XQuartz even if you don't want it].
> 
> Cheers,
> Simon
> 
> 
>> On Feb 14, 2021, at 9:50 AM, Richard M. Heiberger  wrote:
>> 
>> I tried this.  It made no difference.  Both before and after running
>> sudo xcode-select —install
>> I ran (in both cases, in a brand new *R* sessio n)
>> 
>>> X11()
>> xcrun: error: invalid active developer path 
>> (/Library/Developer/CommandLineTools), missing xcrun at: 
>> /Library/Developer/CommandLineTools/usr/bin/xcrun
>> 
>> 
>> My prior was that the xcode call was irrelevant is that X11() using XQuart 
>> 8.0.3beta
>> worked with intel R_4.0.3 on the Mac M1.
>> 
>> 
>> From: Dr Eberhard W Lisse 
>> Sent: Saturday, February 13, 2021 3:33 AM
>> To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
>> Cc: e...@lisse.na
>> Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC
>> 
>> that has nothing to do with Xquartz but means you need to install the 
>> Command line tools
>> 
>> sudo xcode-select —install
>> 
>> —
>> Sent from Dr Lisse’s iPhone
>> On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
>> Using the intel R_4.0.4RC on the Mac M1.
>> 
>> Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
>> 8.0.3beta.
>> X11() now does not work at all.
>> 
>> X11()
>> xcrun: error: invalid active developer path 
>> (/Library/Developer/CommandLineTools), missing xcrun at: 
>> /Library/Developer/CommandLineTools/usr/bin/xcrun
>> C-c C-c C-c C-c
>> 
>> Force-Killing XQuartz from the Activity Monitor doesn't help.
>> I have to Force-kill the R process.
>> 
>> 
>> From: R-SIG-Mac  on behalf of Simon Urbanek 
>> 
>> Sent: Friday, February 12, 2021 6:50 PM
>> To: R-SIG-Mac
>> Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC
>> 
>> Dear macOS useRs,
>> 
>> please test the latest R 4.0.4 RC builds from
>> 
>> https://mac.r-project.org/
>> 
>> especially if you are running macOS Big Sur. The known issues introduced by 
>> Big Sur have been fixed, but I cannot replicate nor test the spurious 
>> touchbar warning.
>> 
>> Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - 
>> they are betas for a reason (=unstable) and break things.
>> 
>> Cheers,
>> Simon
>> 
>> ___
>> 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
>> 
> 

___
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Re: [R-SIG-Mac] [External] Re: [External] Please test R 4.0.4 RC

2021-02-13 Thread Duncan Murdoch

On 13/02/2021 4:54 p.m., Simon Urbanek wrote:

As mentioned earlier, the issue is likely that your X11-auto-launch is not working. You 
can start X11 (=XQuartz) yourself and set DISPLAY=:0 as you would on any unix system or 
start X11 with X11(":0")
[personally, I hate that auto-launch "feature" since it tries to start XQuartz 
even if you don't want it].


Thanks.  Here's another datum:  I did my last build of rgl with the beta 
XQuartz installed.  I'm now back to 2.7.11 and I get this when I try to 
start rgl:


> library(rgl)
Error in dyn.load(dynlib) :
  unable to load shared object 
'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgl/libs/rgl.so':


dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgl/libs/rgl.so, 
6): Library not loaded: /opt/X11/lib/libX11.6.dylib
  Referenced from: 
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rgl/libs/rgl.so
  Reason: Incompatible library version: rgl.so requires version 11.0.0 
or later, but libX11.6.dylib provides version 10.0.0

Error: package or namespace load failed for ‘rgl’:
 .onLoad failed in loadNamespace() for 'rgl', details:
  call: NULL
  error:Loading rgl's DLL failed.
	This build of rgl depends on XQuartz, which you can download from 
xquartz.org.


So it appears they updated the version of libX11.6.dylib, and rgl is 
asking for the wrong one.


Is there some way for me to request a particular version during my 
build, or at least detect that the wrong version is installed?


Duncan Murdoch



Cheers,
Simon



On Feb 14, 2021, at 9:50 AM, Richard M. Heiberger  wrote:

I tried this.  It made no difference.  Both before and after running
sudo xcode-select —install
I ran (in both cases, in a brand new *R* sessio n)


X11()

xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun


My prior was that the xcode call was irrelevant is that X11() using XQuart 
8.0.3beta
worked with intel R_4.0.3 on the Mac M1.


From: Dr Eberhard W Lisse 
Sent: Saturday, February 13, 2021 3:33 AM
To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
Cc: e...@lisse.na
Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC

that has nothing to do with Xquartz but means you need to install the Command 
line tools

sudo xcode-select —install

—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
Using the intel R_4.0.4RC on the Mac M1.

Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
8.0.3beta.
X11() now does not work at all.

X11()
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun
C-c C-c C-c C-c

Force-Killing XQuartz from the Activity Monitor doesn't help.
I have to Force-kill the R process.


From: R-SIG-Mac  on behalf of Simon Urbanek 

Sent: Friday, February 12, 2021 6:50 PM
To: R-SIG-Mac
Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC

Dear macOS useRs,

please test the latest R 4.0.4 RC builds from

https://mac.r-project.org/

especially if you are running macOS Big Sur. The known issues introduced by Big 
Sur have been fixed, but I cannot replicate nor test the spurious touchbar 
warning.

Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - 
they are betas for a reason (=unstable) and break things.

Cheers,
Simon

___
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___
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https://stat.ethz.ch/mailman/listinfo/r-sig-mac



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Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Please test R 4.0.4 RC

2021-02-13 Thread Richard M. Heiberger
another new session


> setwd('/Users/rmh/Rwd/')
> Sys.getenv("DISPLAY")
[1] "/private/tmp/com.apple.launchd.l0xAmiv83n/org.xquartz:0"
> unlink(Sys.getenv("DISPLAY"))
>Sys.setenv(DISPLAY=":0.0")
> X11()
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun
Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  :
  unable to start device X11
In addition: Warning messages:
1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
  running command ''otool' -L 
'/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
2: In X11() : unable to open connection to X11 display ''
> Sys.getenv("DISPLAY")
[1] ":0.0"
>


I didn't make any more changes to the Xquartz.  I previously had the beta and 
replaced it with 2.7.11, so I just continued from there.


From: Duncan Murdoch 
Sent: Saturday, February 13, 2021 4:55 PM
To: Richard M. Heiberger; R-SIG-Mac
Subject: Re: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R 
4.0.4 RC

Thanks for your detailed descriptions!  I can now reproduce this, and I
have an ugly workaround.  I should be able to get a better workaround soon.

To reproduce:

Install the beta.  (I did this when it was pushed to me.)  It worked
fine for me.

Install the previous version, 2.7.11.  Reboot the system.

Now running x11() in R causes the spinning beach ball.

The workaround:

Start R.  The DISPLAY environment variable will show the name something like

[1] "/private/tmp/com.apple.launchd.RuLLnvteCn/org.xquartz:0"

This is a socket, not a regular file.

Delete this, and set DISPLAY to ":0.0":

   unlink(Sys.getenv("DISPLAY"))
   Sys.setenv(DISPLAY=":0.0")

Now x11() is fine.

This is only a workaround.  The unlink() is permanent, but setting the
environment variable only lasts for the length of the R session.  You'll
need to enter Sys.setenv(DISPLAY=":0.0") again in future sessions, and I
would guess the socket will be recreated the next time you restart the
system (or maybe on login).

Duncan Murdoch








On 13/02/2021 4:21 p.m., Richard M. Heiberger wrote:
> That is next.  Again a fresh session.
>
>
>> setwd('/Users/rmh/Rwd/')
>> Sys.setenv(DISPLAY=":0.0")
>> X11()
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  :
>unable to start device X11
> In addition: Warning messages:
> 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
>running command ''otool' -L 
> '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
> 2: In X11() : unable to open connection to X11 display ''
>>
>
>
> and the R session is still alive.
>
>
> This rasies for me a different question.  Why should I want X11()?
>
> When X11 was working it was very slow, and didn't allow paging back through
> previous images.
>
> In favor of X11, I think it uses the display space better.  X11() has better 
> size and spacing for xlab, ylab, and main than quartz().  But that isn't a 
> strong enough
> reason to use it while develkoping a graph.  When I want it to look good,
> I go directly to pdf() and get the spacing that I  think looks better.
>
> 
> From: Duncan Murdoch 
> Sent: Saturday, February 13, 2021 4:05 PM
> To: Richard M. Heiberger; R-SIG-Mac
> Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R 
> 4.0.4 RC
>
> Have you tried the change to DISPLAY, i.e.
>
> Sys.setenv(DISPLAY=":0.0")
>
> before running X11()?
>
> Duncan Murdoch
>
> On 13/02/2021 3:50 p.m., Richard M. Heiberger wrote:
>> I tried this.  It made no difference.  Both before and after running
>> sudo xcode-select —install
>> I ran (in both cases, in a brand new *R* sessio n)
>>
>>> X11()
>> xcrun: error: invalid active developer path 
>> (/Library/Developer/CommandLineTools), missing xcrun at: 
>> /Library/Developer/CommandLineTools/usr/bin/xcrun
>>
>>
>> My prior was that the xcode call was irrelevant is that X11() using XQuart 
>> 8.0.3beta
>> worked with intel R_4.0.3 on the Mac M1.
>>
>> 
>> From: Dr Eberhard W Lisse 
>> Sent: Saturday, February 13, 2021 3:33 AM
>> To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
>> Cc: e...@lisse.na
>> Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC
>>
>> that has nothing to do with Xquartz but means you need to install the 
>> Command line tools
>>
>> sudo xcode-select —install
>>
>> —
>> Sent from Dr Lisse’s iPhone
>> On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
>> Using the intel R_4.0.4RC on the Mac M1.
>>
>> Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
>> 8.0.3beta.
>> X11() now does not work at all.
>>
>> X11()
>> xcrun: error: invalid 

Re: [R-SIG-Mac] [External] Re: [External] Please test R 4.0.4 RC

2021-02-13 Thread Richard M. Heiberger
another fresh R session

> X11(":0")
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun
Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  :
  unable to start device X11
In addition: Warning messages:
1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
  running command ''otool' -L 
'/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
2: In X11(":0") : unable to open connection to X11 display ':0'
>


From: Simon Urbanek 
Sent: Saturday, February 13, 2021 4:54 PM
To: Richard M. Heiberger
Cc: Dr Eberhard W Lisse; R-SIG-Mac
Subject: Re: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC

As mentioned earlier, the issue is likely that your X11-auto-launch is not 
working. You can start X11 (=XQuartz) yourself and set DISPLAY=:0 as you would 
on any unix system or start X11 with X11(":0")
[personally, I hate that auto-launch "feature" since it tries to start XQuartz 
even if you don't want it].

Cheers,
Simon


> On Feb 14, 2021, at 9:50 AM, Richard M. Heiberger  wrote:
>
> I tried this.  It made no difference.  Both before and after running
> sudo xcode-select —install
> I ran (in both cases, in a brand new *R* sessio n)
>
>> X11()
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
>
>
> My prior was that the xcode call was irrelevant is that X11() using XQuart 
> 8.0.3beta
> worked with intel R_4.0.3 on the Mac M1.
>
> 
> From: Dr Eberhard W Lisse 
> Sent: Saturday, February 13, 2021 3:33 AM
> To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
> Cc: e...@lisse.na
> Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC
>
> that has nothing to do with Xquartz but means you need to install the Command 
> line tools
>
> sudo xcode-select —install
>
> —
> Sent from Dr Lisse’s iPhone
> On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
> Using the intel R_4.0.4RC on the Mac M1.
>
> Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
> 8.0.3beta.
> X11() now does not work at all.
>
> X11()
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> C-c C-c C-c C-c
>
> Force-Killing XQuartz from the Activity Monitor doesn't help.
> I have to Force-kill the R process.
>
> 
> From: R-SIG-Mac  on behalf of Simon Urbanek 
> 
> Sent: Friday, February 12, 2021 6:50 PM
> To: R-SIG-Mac
> Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC
>
> Dear macOS useRs,
>
> please test the latest R 4.0.4 RC builds from
>
> https://mac.r-project.org/
>
> especially if you are running macOS Big Sur. The known issues introduced by 
> Big Sur have been fixed, but I cannot replicate nor test the spurious 
> touchbar warning.
>
> Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - 
> they are betas for a reason (=unstable) and break things.
>
> Cheers,
> Simon
>
> ___
> 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
>

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac


Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Please test R 4.0.4 RC

2021-02-13 Thread Duncan Murdoch
Thanks for your detailed descriptions!  I can now reproduce this, and I 
have an ugly workaround.  I should be able to get a better workaround soon.


To reproduce:

Install the beta.  (I did this when it was pushed to me.)  It worked 
fine for me.


Install the previous version, 2.7.11.  Reboot the system.

Now running x11() in R causes the spinning beach ball.

The workaround:

Start R.  The DISPLAY environment variable will show the name something like

[1] "/private/tmp/com.apple.launchd.RuLLnvteCn/org.xquartz:0"

This is a socket, not a regular file.

Delete this, and set DISPLAY to ":0.0":

  unlink(Sys.getenv("DISPLAY"))
  Sys.setenv(DISPLAY=":0.0")

Now x11() is fine.

This is only a workaround.  The unlink() is permanent, but setting the 
environment variable only lasts for the length of the R session.  You'll 
need to enter Sys.setenv(DISPLAY=":0.0") again in future sessions, and I 
would guess the socket will be recreated the next time you restart the 
system (or maybe on login).


Duncan Murdoch








On 13/02/2021 4:21 p.m., Richard M. Heiberger wrote:

That is next.  Again a fresh session.



setwd('/Users/rmh/Rwd/')
Sys.setenv(DISPLAY=":0.0")
X11()

xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun
Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  :
   unable to start device X11
In addition: Warning messages:
1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
   running command ''otool' -L 
'/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
2: In X11() : unable to open connection to X11 display ''





and the R session is still alive.


This rasies for me a different question.  Why should I want X11()?

When X11 was working it was very slow, and didn't allow paging back through
previous images.

In favor of X11, I think it uses the display space better.  X11() has better 
size and spacing for xlab, ylab, and main than quartz().  But that isn't a 
strong enough
reason to use it while develkoping a graph.  When I want it to look good,
I go directly to pdf() and get the spacing that I  think looks better.


From: Duncan Murdoch 
Sent: Saturday, February 13, 2021 4:05 PM
To: Richard M. Heiberger; R-SIG-Mac
Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R 
4.0.4 RC

Have you tried the change to DISPLAY, i.e.

Sys.setenv(DISPLAY=":0.0")

before running X11()?

Duncan Murdoch

On 13/02/2021 3:50 p.m., Richard M. Heiberger wrote:

I tried this.  It made no difference.  Both before and after running
sudo xcode-select —install
I ran (in both cases, in a brand new *R* sessio n)


X11()

xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun


My prior was that the xcode call was irrelevant is that X11() using XQuart 
8.0.3beta
worked with intel R_4.0.3 on the Mac M1.


From: Dr Eberhard W Lisse 
Sent: Saturday, February 13, 2021 3:33 AM
To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
Cc: e...@lisse.na
Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC

that has nothing to do with Xquartz but means you need to install the Command 
line tools

sudo xcode-select —install

—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
Using the intel R_4.0.4RC on the Mac M1.

Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
8.0.3beta.
X11() now does not work at all.

X11()
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun
C-c C-c C-c C-c

Force-Killing XQuartz from the Activity Monitor doesn't help.
I have to Force-kill the R process.


From: R-SIG-Mac  on behalf of Simon Urbanek 

Sent: Friday, February 12, 2021 6:50 PM
To: R-SIG-Mac
Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC

Dear macOS useRs,

please test the latest R 4.0.4 RC builds from

https://mac.r-project.org/

especially if you are running macOS Big Sur. The known issues introduced by Big 
Sur have been fixed, but I cannot replicate nor test the spurious touchbar 
warning.

Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - 
they are betas for a reason (=unstable) and break things.

Cheers,
Simon

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Re: [R-SIG-Mac] [External] Re: [External] Please test R 4.0.4 RC

2021-02-13 Thread Simon Urbanek
As mentioned earlier, the issue is likely that your X11-auto-launch is not 
working. You can start X11 (=XQuartz) yourself and set DISPLAY=:0 as you would 
on any unix system or start X11 with X11(":0")
[personally, I hate that auto-launch "feature" since it tries to start XQuartz 
even if you don't want it].

Cheers,
Simon


> On Feb 14, 2021, at 9:50 AM, Richard M. Heiberger  wrote:
> 
> I tried this.  It made no difference.  Both before and after running
> sudo xcode-select —install
> I ran (in both cases, in a brand new *R* sessio n)
> 
>> X11()
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> 
> 
> My prior was that the xcode call was irrelevant is that X11() using XQuart 
> 8.0.3beta
> worked with intel R_4.0.3 on the Mac M1.
> 
> 
> From: Dr Eberhard W Lisse 
> Sent: Saturday, February 13, 2021 3:33 AM
> To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
> Cc: e...@lisse.na
> Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC
> 
> that has nothing to do with Xquartz but means you need to install the Command 
> line tools
> 
> sudo xcode-select —install
> 
> —
> Sent from Dr Lisse’s iPhone
> On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
> Using the intel R_4.0.4RC on the Mac M1.
> 
> Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
> 8.0.3beta.
> X11() now does not work at all.
> 
> X11()
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> C-c C-c C-c C-c
> 
> Force-Killing XQuartz from the Activity Monitor doesn't help.
> I have to Force-kill the R process.
> 
> 
> From: R-SIG-Mac  on behalf of Simon Urbanek 
> 
> Sent: Friday, February 12, 2021 6:50 PM
> To: R-SIG-Mac
> Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC
> 
> Dear macOS useRs,
> 
> please test the latest R 4.0.4 RC builds from
> 
> https://mac.r-project.org/
> 
> especially if you are running macOS Big Sur. The known issues introduced by 
> Big Sur have been fixed, but I cannot replicate nor test the spurious 
> touchbar warning.
> 
> Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - 
> they are betas for a reason (=unstable) and break things.
> 
> Cheers,
> Simon
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> ___
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Re: [R-SIG-Mac] Problem with read.table in my Mac. "No such file or directory"

2021-02-13 Thread Dr Eberhard W Lisse
space in a directory name?

put the file in ~/Desktop and see what happens then.

If it is a CSV make it moabsitechem.csv and see what that doesn.

el

—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 22:29 +0200, Parkhurst, David F. , wrote:
> I’m still having trouble with read.table, as follows (and there IS a plain 
> text document called moabsitechem in this directory:
> > getwd()
> [1] "/Users/DFP/Documents/Documents - David’s iMac/ae/FriendsMonroe"
> > read.table("moabsitechem")
> Error in file(file, "rt") : cannot open the connection
> In addition: Warning message:
> In file(file, "rt") :
>   cannot open file 'moabsitechem': No such file or directory
>
> How can I fix this problem?
>
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Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Please test R 4.0.4 RC

2021-02-13 Thread Dr Eberhard W Lisse
the Xcode Command line tools are missing. Install them and see what happens.

Did you recently upgrade MacOS?

el

—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 23:21 +0200, Richard M. Heiberger , wrote:
> That is next. Again a fresh session.
>
>
> > setwd('/Users/rmh/Rwd/')
> > Sys.setenv(DISPLAY=":0.0")
> > X11()
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, :
> unable to start device X11
> In addition: Warning messages:
> 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
> running command ''otool' -L 
> '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
> 2: In X11() : unable to open connection to X11 display ''
> >
>
>
> and the R session is still alive.
>
>
> This rasies for me a different question. Why should I want X11()?
>
> When X11 was working it was very slow, and didn't allow paging back through
> previous images.
>
> In favor of X11, I think it uses the display space better. X11() has better 
> size and spacing for xlab, ylab, and main than quartz(). But that isn't a 
> strong enough
> reason to use it while develkoping a graph. When I want it to look good,
> I go directly to pdf() and get the spacing that I think looks better.
>
> 
> From: Duncan Murdoch 
> Sent: Saturday, February 13, 2021 4:05 PM
> To: Richard M. Heiberger; R-SIG-Mac
> Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R 
> 4.0.4 RC
>
> Have you tried the change to DISPLAY, i.e.
>
> Sys.setenv(DISPLAY=":0.0")
>
> before running X11()?
>
> Duncan Murdoch
>
> On 13/02/2021 3:50 p.m., Richard M. Heiberger wrote:
> > I tried this. It made no difference. Both before and after running
> > sudo xcode-select —install
> > I ran (in both cases, in a brand new *R* sessio n)
> >
> > > X11()
> > xcrun: error: invalid active developer path 
> > (/Library/Developer/CommandLineTools), missing xcrun at: 
> > /Library/Developer/CommandLineTools/usr/bin/xcrun
> >
> >
> > My prior was that the xcode call was irrelevant is that X11() using XQuart 
> > 8.0.3beta
> > worked with intel R_4.0.3 on the Mac M1.
> >
> > 
> > From: Dr Eberhard W Lisse 
> > Sent: Saturday, February 13, 2021 3:33 AM
> > To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
> > Cc: e...@lisse.na
> > Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC
> >
> > that has nothing to do with Xquartz but means you need to install the 
> > Command line tools
> >
> > sudo xcode-select —install
> >
> > —
> > Sent from Dr Lisse’s iPhone
> > On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
> > Using the intel R_4.0.4RC on the Mac M1.
> >
> > Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
> > 8.0.3beta.
> > X11() now does not work at all.
> >
> > X11()
> > xcrun: error: invalid active developer path 
> > (/Library/Developer/CommandLineTools), missing xcrun at: 
> > /Library/Developer/CommandLineTools/usr/bin/xcrun
> > C-c C-c C-c C-c
> >
> > Force-Killing XQuartz from the Activity Monitor doesn't help.
> > I have to Force-kill the R process.
> >
> > 
> > From: R-SIG-Mac  on behalf of Simon 
> > Urbanek 
> > Sent: Friday, February 12, 2021 6:50 PM
> > To: R-SIG-Mac
> > Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC
> >
> > Dear macOS useRs,
> >
> > please test the latest R 4.0.4 RC builds from
> >
> > https://mac.r-project.org/
> >
> > especially if you are running macOS Big Sur. The known issues introduced by 
> > Big Sur have been fixed, but I cannot replicate nor test the spurious 
> > touchbar warning.
> >
> > Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - 
> > they are betas for a reason (=unstable) and break things.
> >
> > Cheers,
> > Simon
> >
> > ___
> > 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
> >
> > ___
> > 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] [External] Re: [External] Re: [External] Please test R 4.0.4 RC

2021-02-13 Thread Richard M. Heiberger
That is next.  Again a fresh session.


> setwd('/Users/rmh/Rwd/')
> Sys.setenv(DISPLAY=":0.0")
> X11()
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun
Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  :
  unable to start device X11
In addition: Warning messages:
1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
  running command ''otool' -L 
'/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
2: In X11() : unable to open connection to X11 display ''
>


and the R session is still alive.


This rasies for me a different question.  Why should I want X11()?

When X11 was working it was very slow, and didn't allow paging back through
previous images.

In favor of X11, I think it uses the display space better.  X11() has better 
size and spacing for xlab, ylab, and main than quartz().  But that isn't a 
strong enough
reason to use it while develkoping a graph.  When I want it to look good,
I go directly to pdf() and get the spacing that I  think looks better.


From: Duncan Murdoch 
Sent: Saturday, February 13, 2021 4:05 PM
To: Richard M. Heiberger; R-SIG-Mac
Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R 
4.0.4 RC

Have you tried the change to DISPLAY, i.e.

Sys.setenv(DISPLAY=":0.0")

before running X11()?

Duncan Murdoch

On 13/02/2021 3:50 p.m., Richard M. Heiberger wrote:
> I tried this.  It made no difference.  Both before and after running
> sudo xcode-select —install
> I ran (in both cases, in a brand new *R* sessio n)
>
>> X11()
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
>
>
> My prior was that the xcode call was irrelevant is that X11() using XQuart 
> 8.0.3beta
> worked with intel R_4.0.3 on the Mac M1.
>
> 
> From: Dr Eberhard W Lisse 
> Sent: Saturday, February 13, 2021 3:33 AM
> To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
> Cc: e...@lisse.na
> Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC
>
> that has nothing to do with Xquartz but means you need to install the Command 
> line tools
>
> sudo xcode-select —install
>
> —
> Sent from Dr Lisse’s iPhone
> On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
> Using the intel R_4.0.4RC on the Mac M1.
>
> Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
> 8.0.3beta.
> X11() now does not work at all.
>
> X11()
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> C-c C-c C-c C-c
>
> Force-Killing XQuartz from the Activity Monitor doesn't help.
> I have to Force-kill the R process.
>
> 
> From: R-SIG-Mac  on behalf of Simon Urbanek 
> 
> Sent: Friday, February 12, 2021 6:50 PM
> To: R-SIG-Mac
> Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC
>
> Dear macOS useRs,
>
> please test the latest R 4.0.4 RC builds from
>
> https://mac.r-project.org/
>
> especially if you are running macOS Big Sur. The known issues introduced by 
> Big Sur have been fixed, but I cannot replicate nor test the spurious 
> touchbar warning.
>
> Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - 
> they are betas for a reason (=unstable) and break things.
>
> Cheers,
> Simon
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> ___
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> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> ___
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> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>

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Re: [R-SIG-Mac] [External] Re: [External] Please test R 4.0.4 RC

2021-02-13 Thread Duncan Murdoch

Have you tried the change to DISPLAY, i.e.

Sys.setenv(DISPLAY=":0.0")

before running X11()?

Duncan Murdoch

On 13/02/2021 3:50 p.m., Richard M. Heiberger wrote:

I tried this.  It made no difference.  Both before and after running
sudo xcode-select —install
I ran (in both cases, in a brand new *R* sessio n)


X11()

xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun


My prior was that the xcode call was irrelevant is that X11() using XQuart 
8.0.3beta
worked with intel R_4.0.3 on the Mac M1.


From: Dr Eberhard W Lisse 
Sent: Saturday, February 13, 2021 3:33 AM
To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
Cc: e...@lisse.na
Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC

that has nothing to do with Xquartz but means you need to install the Command 
line tools

sudo xcode-select —install

—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
Using the intel R_4.0.4RC on the Mac M1.

Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
8.0.3beta.
X11() now does not work at all.

X11()
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun
C-c C-c C-c C-c

Force-Killing XQuartz from the Activity Monitor doesn't help.
I have to Force-kill the R process.


From: R-SIG-Mac  on behalf of Simon Urbanek 

Sent: Friday, February 12, 2021 6:50 PM
To: R-SIG-Mac
Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC

Dear macOS useRs,

please test the latest R 4.0.4 RC builds from

https://mac.r-project.org/

especially if you are running macOS Big Sur. The known issues introduced by Big 
Sur have been fixed, but I cannot replicate nor test the spurious touchbar 
warning.

Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - 
they are betas for a reason (=unstable) and break things.

Cheers,
Simon

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Re: [R-SIG-Mac] [External] Re: [External] Please test R 4.0.4 RC

2021-02-13 Thread Richard M. Heiberger
I tried this.  It made no difference.  Both before and after running
sudo xcode-select —install
I ran (in both cases, in a brand new *R* sessio n)

> X11()
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun


My prior was that the xcode call was irrelevant is that X11() using XQuart 
8.0.3beta
worked with intel R_4.0.3 on the Mac M1.


From: Dr Eberhard W Lisse 
Sent: Saturday, February 13, 2021 3:33 AM
To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
Cc: e...@lisse.na
Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC

that has nothing to do with Xquartz but means you need to install the Command 
line tools

sudo xcode-select —install

—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
Using the intel R_4.0.4RC on the Mac M1.

Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
8.0.3beta.
X11() now does not work at all.

X11()
xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun
C-c C-c C-c C-c

Force-Killing XQuartz from the Activity Monitor doesn't help.
I have to Force-kill the R process.


From: R-SIG-Mac  on behalf of Simon Urbanek 

Sent: Friday, February 12, 2021 6:50 PM
To: R-SIG-Mac
Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC

Dear macOS useRs,

please test the latest R 4.0.4 RC builds from

https://mac.r-project.org/

especially if you are running macOS Big Sur. The known issues introduced by Big 
Sur have been fixed, but I cannot replicate nor test the spurious touchbar 
warning.

Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - 
they are betas for a reason (=unstable) and break things.

Cheers,
Simon

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Re: [R-SIG-Mac] Problem with read.table in my Mac. "No such file or directory"

2021-02-13 Thread Parkhurst, David F.
Thanks.  I switched from years using PCs about a year ago when MS would no 
longer support Windows 7.  I have missed seeing extensions on files (probably 
.txt for this one).  It�s good to learn that I can change that.

From: Bryan Hanson 
Date: Saturday, February 13, 2021 at 3:37 PM
To: Parkhurst, David F. 
Cc: r-sig-mac@r-project.org 
Subject: Re: [R-SIG-Mac] Problem with read.table in my Mac. "No such file or 
directory"
Try

list.files()

to see the names of the files in the current directory, and make certain you 
are where you think you are, the file is there, has the name you think it has 
etc.  You may need to add the extension, presumably something like �.csv� to 
your read.table call.

A possible point of confusion is that  you may have your Mac set to not display 
file extensions, and life is generally easier in my opinion if those extensions 
are turned on.   Plenty of advice on the internet as to how to turn this on for 
all files.

Bryan

> On Feb 13, 2021, at 1:29 PM, Parkhurst, David F.  wrote:
>
> I�m still having trouble with read.table, as follows (and there IS a plain 
> text document called moabsitechem in this directory:
>> getwd()
> [1] "/Users/DFP/Documents/Documents - David�s iMac/ae/FriendsMonroe"
>> read.table("moabsitechem")
> Error in file(file, "rt") : cannot open the connection
> In addition: Warning message:
> In file(file, "rt") :
>   cannot open file 'moabsitechem': No such file or directory
>
> How can I fix this problem?
>
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> R-SIG-Mac@r-project.org
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Re: [R-SIG-Mac] Problem with read.table in my Mac. "No such file or directory"

2021-02-13 Thread Bryan Hanson
Try

list.files()

to see the names of the files in the current directory, and make certain you 
are where you think you are, the file is there, has the name you think it has 
etc.  You may need to add the extension, presumably something like “.csv” to 
your read.table call.

A possible point of confusion is that  you may have your Mac set to not display 
file extensions, and life is generally easier in my opinion if those extensions 
are turned on.   Plenty of advice on the internet as to how to turn this on for 
all files.

Bryan

> On Feb 13, 2021, at 1:29 PM, Parkhurst, David F.  wrote:
> 
> I’m still having trouble with read.table, as follows (and there IS a plain 
> text document called moabsitechem in this directory:
>> getwd()
> [1] "/Users/DFP/Documents/Documents - David’s iMac/ae/FriendsMonroe"
>> read.table("moabsitechem")
> Error in file(file, "rt") : cannot open the connection
> In addition: Warning message:
> In file(file, "rt") :
>   cannot open file 'moabsitechem': No such file or directory
> 
> How can I fix this problem?
> 
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[R-SIG-Mac] Problem with read.table in my Mac. "No such file or directory"

2021-02-13 Thread Parkhurst, David F.
I’m still having trouble with read.table, as follows (and there IS a plain text 
document called moabsitechem in this directory:
> getwd()
[1] "/Users/DFP/Documents/Documents - David’s iMac/ae/FriendsMonroe"
> read.table("moabsitechem")
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'moabsitechem': No such file or directory

How can I fix this problem?

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Re: [R-SIG-Mac] How to find the path for a file to be read with read.table() in a Mac

2021-02-13 Thread Jeff Newmiller
Even better is to learn one of the many ways to start R in a working directory 
of your choice, so you don't have to mix code and data from different projects 
together in one directory just because that happens to be where your default R 
icon sets it up.

Some ways:
a) Use Terminal and the cd command before invoking R.
b) Create a .RData file with nothing in it in the desired directory. 
Double-click that to automatically set the working directory there in R.
c) Use RStudio, which lets you create an Rproj file that serves the same 
purpose as the .RData file but doesn't risk injecting broken code or old data 
into your working environment.

On February 13, 2021 8:02:54 AM PST, "Parkhurst, David F." 
 wrote:
>Ah.  That will simplify the process a lot!
>
>From: Duncan Murdoch 
>Date: Saturday, February 13, 2021 at 10:52 AM
>To: Parkhurst, David F. , r-sig-mac@r-project.org
>
>Subject: Re: [R-SIG-Mac] How to find the path for a file to be read
>with read.table() in a Mac
>On 13/02/2021 10:42 a.m., Parkhurst, David F. wrote:
>> I�ve several times to figure this out with no luck.  I�ve moved a tab
>delimited text file (created from excel) to the desktop to simplify the
>path.  If I click on the file and ask Get Info, it lists �Where� as 
>iCloud Drive > Desktop.  If I copy that to the clipboard and paste that
>into a read.table command in the R console, it comes up as
>/Users/DFP/Desktop.  But if I try
>read.table("\\Users\\DFP\\Desktop\\moabsitechem"),
>I get No such file or directory.  How can I get that file into a data
>frame?
>>
>> Is there some place in my Mac that I can put the file so I could
>enter just the file name, and not the whole path?
>
>Sorry, forget to answer your actual question:
>
>You can use getwd() to find the working directory.  If you put the file
>there, you won't need to specify the path.
>
>Duncan Murdoch
>
>   [[alternative HTML version deleted]]

-- 
Sent from my phone. Please excuse my brevity.

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Re: [R-SIG-Mac] How to find the path for a file to be read with read.table() in a Mac

2021-02-13 Thread Bryan Hanson
You can also point R to the directory where the file of interest is, rather 
than moving the file to the directory where R is currently pointing.

setwd(“~/Desktop”)

Bryan

> On Feb 13, 2021, at 9:02 AM, Parkhurst, David F.  wrote:
> 
> Thank you.  I thought I�d seen in some book that in a Mac, one had to specify 
> paths in the way I tried.
> 
> From: Duncan Murdoch 
> Date: Saturday, February 13, 2021 at 10:49 AM
> To: Parkhurst, David F. , r-sig-mac@r-project.org 
> 
> Subject: Re: [R-SIG-Mac] How to find the path for a file to be read with 
> read.table() in a Mac
> On 13/02/2021 10:42 a.m., Parkhurst, David F. wrote:
>> I�ve several times to figure this out with no luck.  I�ve moved a tab 
>> delimited text file (created from excel) to the desktop to simplify the 
>> path.  If I click on the file and ask Get Info, it lists �Where� as  iCloud 
>> Drive > Desktop.  If I copy that to the clipboard and paste that into a 
>> read.table command in the R console, it comes up as /Users/DFP/Desktop.  But 
>> if I try 
>> read.table("\\Users\\DFP\\Desktop\\moabsitechem"),
>>  I get No such file or directory.  How can I get that file into a data frame?
>> 
>> Is there some place in my Mac that I can put the file so I could enter just 
>> the file name, and not the whole path?
> 
> It doesn't make sense to use backslashes in the path:  macOS will see
> those as part of the name, not as path separators.  Just use
> read.table("/Users/DFP/Desktop/moabsitechm") if that's the filename.
> 
> Duncan Murdoch
> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] How to find the path for a file to be read with read.table() in a Mac

2021-02-13 Thread Parkhurst, David F.
Ah.  That will simplify the process a lot!

From: Duncan Murdoch 
Date: Saturday, February 13, 2021 at 10:52 AM
To: Parkhurst, David F. , r-sig-mac@r-project.org 

Subject: Re: [R-SIG-Mac] How to find the path for a file to be read with 
read.table() in a Mac
On 13/02/2021 10:42 a.m., Parkhurst, David F. wrote:
> I�ve several times to figure this out with no luck.  I�ve moved a tab 
> delimited text file (created from excel) to the desktop to simplify the path. 
>  If I click on the file and ask Get Info, it lists �Where� as  iCloud Drive > 
> Desktop.  If I copy that to the clipboard and paste that into a read.table 
> command in the R console, it comes up as /Users/DFP/Desktop.  But if I try 
> read.table("\\Users\\DFP\\Desktop\\moabsitechem"),
>  I get No such file or directory.  How can I get that file into a data frame?
>
> Is there some place in my Mac that I can put the file so I could enter just 
> the file name, and not the whole path?

Sorry, forget to answer your actual question:

You can use getwd() to find the working directory.  If you put the file
there, you won't need to specify the path.

Duncan Murdoch

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Re: [R-SIG-Mac] How to find the path for a file to be read with read.table() in a Mac

2021-02-13 Thread Parkhurst, David F.
Thank you.  I thought I�d seen in some book that in a Mac, one had to specify 
paths in the way I tried.

From: Duncan Murdoch 
Date: Saturday, February 13, 2021 at 10:49 AM
To: Parkhurst, David F. , r-sig-mac@r-project.org 

Subject: Re: [R-SIG-Mac] How to find the path for a file to be read with 
read.table() in a Mac
On 13/02/2021 10:42 a.m., Parkhurst, David F. wrote:
> I�ve several times to figure this out with no luck.  I�ve moved a tab 
> delimited text file (created from excel) to the desktop to simplify the path. 
>  If I click on the file and ask Get Info, it lists �Where� as  iCloud Drive > 
> Desktop.  If I copy that to the clipboard and paste that into a read.table 
> command in the R console, it comes up as /Users/DFP/Desktop.  But if I try 
> read.table("\\Users\\DFP\\Desktop\\moabsitechem"),
>  I get No such file or directory.  How can I get that file into a data frame?
>
> Is there some place in my Mac that I can put the file so I could enter just 
> the file name, and not the whole path?

It doesn't make sense to use backslashes in the path:  macOS will see
those as part of the name, not as path separators.  Just use
read.table("/Users/DFP/Desktop/moabsitechm") if that's the filename.

Duncan Murdoch


[[alternative HTML version deleted]]

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Re: [R-SIG-Mac] How to find the path for a file to be read with read.table() in a Mac

2021-02-13 Thread Duncan Murdoch

On 13/02/2021 10:42 a.m., Parkhurst, David F. wrote:

I’ve several times to figure this out with no luck.  I’ve moved a tab delimited text file 
(created from excel) to the desktop to simplify the path.  If I click on the file and ask 
Get Info, it lists “Where” as  iCloud Drive > Desktop.  If I copy that to the clipboard 
and paste that into a read.table command in the R console, it comes up as 
/Users/DFP/Desktop.  But if I try 
read.table("\\Users\\DFP\\Desktop\\moabsitechem"), I get No such file or 
directory.  How can I get that file into a data frame?

Is there some place in my Mac that I can put the file so I could enter just the 
file name, and not the whole path?


Sorry, forget to answer your actual question:

You can use getwd() to find the working directory.  If you put the file 
there, you won't need to specify the path.


Duncan Murdoch

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Re: [R-SIG-Mac] How to find the path for a file to be read with read.table() in a Mac

2021-02-13 Thread Duncan Murdoch

On 13/02/2021 10:42 a.m., Parkhurst, David F. wrote:

I’ve several times to figure this out with no luck.  I’ve moved a tab delimited text file 
(created from excel) to the desktop to simplify the path.  If I click on the file and ask 
Get Info, it lists “Where” as  iCloud Drive > Desktop.  If I copy that to the clipboard 
and paste that into a read.table command in the R console, it comes up as 
/Users/DFP/Desktop.  But if I try 
read.table("\\Users\\DFP\\Desktop\\moabsitechem"), I get No such file or 
directory.  How can I get that file into a data frame?

Is there some place in my Mac that I can put the file so I could enter just the 
file name, and not the whole path?


It doesn't make sense to use backslashes in the path:  macOS will see 
those as part of the name, not as path separators.  Just use 
read.table("/Users/DFP/Desktop/moabsitechm") if that's the filename.


Duncan Murdoch

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[R-SIG-Mac] How to find the path for a file to be read with read.table() in a Mac

2021-02-13 Thread Parkhurst, David F.
I’ve several times to figure this out with no luck.  I’ve moved a tab delimited 
text file (created from excel) to the desktop to simplify the path.  If I click 
on the file and ask Get Info, it lists “Where” as  iCloud Drive > Desktop.  If 
I copy that to the clipboard and paste that into a read.table command in the R 
console, it comes up as /Users/DFP/Desktop.  But if I try 
read.table("\\Users\\DFP\\Desktop\\moabsitechem"), I get No such file or 
directory.  How can I get that file into a data frame?

Is there some place in my Mac that I can put the file so I could enter just the 
file name, and not the whole path?

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Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC

2021-02-13 Thread Duncan Murdoch

On 12/02/2021 11:12 p.m., Richard M. Heiberger wrote:

Using the intel R_4.0.4RC on the Mac M1.

Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
8.0.3beta.
X11() now does not work at all.


X11()

xcrun: error: invalid active developer path 
(/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun
   C-c C-c  C-c C-c

Force-Killing XQuartz from the Activity Monitor doesn't help.
I have to Force-kill the R process.


I've received reports about this related to rgl.  Some unconfirmed 
reports suggest that setting Sys.setenv(DISPLAY=":0.0") fixes it. 
Others say that didn't work.


I'm still running the beta, and haven't seen any issues.  Maybe I'll try 
going back to 2.7.11 to see if I can trigger things.


Duncan Murdoch

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Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC

2021-02-13 Thread Dr Eberhard W Lisse
that has nothing to do with Xquartz but means you need to install the Command 
line tools

sudo xcode-select —install

—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger , wrote:
> Using the intel R_4.0.4RC on the Mac M1.
>
> Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 
> 8.0.3beta.
> X11() now does not work at all.
>
> > X11()
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> C-c C-c C-c C-c
>
> Force-Killing XQuartz from the Activity Monitor doesn't help.
> I have to Force-kill the R process.
>
> 
> From: R-SIG-Mac  on behalf of Simon Urbanek 
> 
> Sent: Friday, February 12, 2021 6:50 PM
> To: R-SIG-Mac
> Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC
>
> Dear macOS useRs,
>
> please test the latest R 4.0.4 RC builds from
>
> https://mac.r-project.org/
>
> especially if you are running macOS Big Sur. The known issues introduced by 
> Big Sur have been fixed, but I cannot replicate nor test the spurious 
> touchbar warning.
>
> Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - 
> they are betas for a reason (=unstable) and break things.
>
> Cheers,
> Simon
>
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Re: [R-SIG-Mac] Please test R 4.0.4 RC

2021-02-13 Thread Simon Urbanek
Thanks for testing and the reports!

Unfortunately, I cannot reproduce the touch-bar issue, because it doesn''t 
appear when run in Xcode with touch-bar emulation and I don't have a Mac with 
Big Sur and a touch-bar. Moreover, R is not providing custom touch-bar icons so 
I can't even find out which element it is complaining about. If anyone has any 
leads, let me know. If we ever find a work-arournd, it should be possible to do 
in the GUI alone so possibly after the release (unlike the Quartz bug which 
needed changes in core R).

Other projects have seen the same issue so it's likely a macOS bug, but the fix 
that worked for others (re-compile with Xcode 12) did not work for us (the last 
build was using the latests Xcode 12.4). 

Cheers,
Simon



> On Feb 13, 2021, at 3:05 PM, John Fox  wrote:
> 
> Dear Simon,
> 
> I'm still seeing the warning on a MacBook Pro with a touchbar running Big Sur:
> 
> --- snip 
> 
> R version 4.0.4 RC (2021-02-12 r79998) -- "Lost Library Book"
> Copyright (C) 2021 The R Foundation for Statistical Computing
> Platform: x86_64-apple-darwin17.0 (64-bit)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
>  Natural language support but running in an English locale
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
> 
> [R.app GUI 1.74 (7929) x86_64-apple-darwin17.0]
> 
> [History restored from /Users/johnfox/.Rapp.history]
> 
> 2021-02-12 21:00:21.163 R[19677:11057750] Warning: Expected min height of 
> view: () to be less than or 
> equal to 30 but got a height of 32.00. This error will be logged once per 
> view in violation.
> 
> > sessionInfo()
> R version 4.0.4 RC (2021-02-12 r79998)
> Platform: x86_64-apple-darwin17.0 (64-bit)
> Running under: macOS Big Sur 10.16
> 
> Matrix products: default
> BLAS: 
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/4.0/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] stats graphics  grDevices utils datasets  methods   base
> 
> loaded via a namespace (and not attached):
> [1] compiler_4.0.4
> 
> --- snip 
> 
> I hope this helps,
> John
> 
> John Fox, Professor Emeritus
> McMaster University
> Hamilton, Ontario, Canada
> web: https://socialsciences.mcmaster.ca/jfox/
> 
> On 2021-02-12 6:50 p.m., Simon Urbanek wrote:
>> Dear macOS useRs,
>> please test the latest R 4.0.4 RC builds from
>> https://mac.r-project.org/
>> especially if you are running macOS Big Sur. The known issues introduced by 
>> Big Sur have been fixed, but I cannot replicate nor test the spurious 
>> touchbar warning.
>> Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - 
>> they are betas for a reason (=unstable) and break things.
>> Cheers,
>> Simon
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 

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Re: [R-SIG-Mac] Optional Libraries, Frameworks and Applications for macOS

2021-02-13 Thread Simon Urbanek
The libraries are used to build the packages - they are all static, so the 
package binaries will include them. It is not intended for users, but rather if 
you were to compile packages on your own and wanted to replicate the CRAN setup.

Cheers,
Simon



> On Feb 13, 2021, at 7:33 PM, Peter West  wrote:
> 
> Are the various libraries at different versions (e.g. geos-3.7.2 & 
> geos-3.8.1) dependencies for different packages? I don’t suppose there’s a 
> list of reverse package dependencies?
> 
> Peter
> 
> 
> —
> p...@ehealth.id.au
> “What comes out of a person is what defiles him.”
> 
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