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

Duncan Murdoch murdoch@dunc@n @end|ng |rom gm@||@com
Sun Feb 14 02:42:55 CET 2021 

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 <el using lisse.na>
> Sent: Saturday, February 13, 2021 6:50 PM
> To: Duncan Murdoch; R-SIG-Mac; Richard M. Heiberger
> Cc: el using 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 <rmh using temple.edu>, 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 <el using lisse.na>
> Sent: Saturday, February 13, 2021 4:44 PM
> To: Duncan Murdoch; R-SIG-Mac; Richard M. Heiberger
> Cc: el using 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 <rmh using temple.edu>, 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 <murdoch.duncan using gmail.com>
> 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 <el using lisse.na>
> Sent: Saturday, February 13, 2021 3:33 AM
> To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
> Cc: el using 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 <rmh using temple.edu>, 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 <r-sig-mac-bounces using r-project.org> on behalf of Simon Urbanek <simon.urbanek using R-project.org>
> 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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