Thank you. dragging the org.xquartz.startx.* to Trash and reinstalling 2.7.11 restored my system to sanity.
________________________________________ From: Duncan Murdoch <murdoch.dun...@gmail.com> 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 <e...@lisse.na> > 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 <r...@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 <e...@lisse.na> > 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 <r...@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.dun...@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 <e...@lisse.na> > 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 <r...@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-boun...@r-project.org> on behalf of Simon Urbanek > <simon.urba...@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 > > _______________________________________________ > 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 > > > _______________________________________________ > 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