Looks like an authorization problem. xclockk did not appear, so I had a look at system.log.
Here’s a sample. --------------------------------------------------------------- Feb 18 20:40:09 Rosie org.macosforge.xquartz.startx[10388]: waiting for X server to begin accepting connections Feb 18 20:40:09 Rosie org.macosforge.xquartz.startx[10388]: /opt/X11/bin/xinit: giving up Feb 18 20:40:09 Rosie org.macosforge.xquartz.startx[10388]: /opt/X11/bin/xinit: unable to connect to X server: Operation timed out Feb 18 20:40:09 Rosie org.macosforge.xquartz.startx[10388]: /opt/X11/bin/xinit: /opt/X11/bin/xinit: server error Feb 18 20:40:09 Rosie org.macosforge.xquartz.startx[10388]: /opt/X11/bin/xinit: Feb 18 21:51:40 Rosie org.macosforge.xquartz.startx[75167]: xauth: file /Users/pbw/.serverauth.75168 does not exist Feb 18 21:51:40 Rosie org.macosforge.xquartz.X11.stub[75265]: Xquartz: Unable to locate waiting server: org.macosforge.xquartz.X11 Feb 18 21:51:40 Rosie Xquartz[75272]: no path for address 0x7ffdffcec000 Feb 18 21:51:40 Rosie org.macosforge.xquartz.X11.stub[75272]: Xquartz: Starting X server: /Applications/Utilities/XQuartz.app/Contents/MacOS/X11 --listenonly Feb 18 21:51:40 Rosie org.macosforge.xquartz.privileged_startx[54309]: /System/Library/Fonts/fonts.scale: fopen(w): Operation not permitted Feb 18 21:51:40 Rosie org.macosforge.xquartz.privileged_startx[54309]: /System/Library/Fonts/fonts.dir: fopen(w): Operation not permitted Feb 18 21:51:40 Rosie org.macosforge.xquartz.privileged_startx[54309]: /System/Library/Fonts/Supplemental/fonts.scale: fopen(w): Operation not permitted Feb 18 21:51:40 Rosie org.macosforge.xquartz.privileged_startx[54309]: /System/Library/Fonts/Supplemental/fonts.dir: fopen(w): Operation not permitted Feb 18 21:51:42 Rosie org.macosforge.xquartz.startx[75167]: Feb 18 21:51:44 Rosie org.macosforge.xquartz.startx[75167]: waiting for X server to begin accepting connections Feb 18 21:52:04 --- last message repeated 9 times --- Feb 18 21:52:04 Rosie org.macosforge.xquartz.X11.stub[75265]: Xquartz: bootstrap_look_up(): Unknown service name Feb 18 21:52:05 Rosie org.macosforge.xquartz.startx[75167]: waiting for X server to begin accepting connections Feb 18 21:52:05 Rosie org.macosforge.xquartz.startx[75167]: waiting for X server to begin accepting connections giving up Feb 18 21:52:05 Rosie org.macosforge.xquartz.startx[75167]: /opt/X11/bin/xinit: unable to connect to X server: Connection refused Feb 18 21:52:05 Rosie org.macosforge.xquartz.startx[75167]: /opt/X11/bin/xinit: unable to connect to X server/opt/X11/bin/xinit: server error Feb 18 21:52:05 Rosie org.macosforge.xquartz.startx[75167]: /opt/X11/bin/xinit: unable to connect to X server Feb 18 21:52:06 Rosie org.macosforge.xquartz.privileged_startx[54309]: /opt/X11/bin/font_cache: line 92: /System/Library/Fonts/fonts.list: Operation not permitted Feb 18 21:52:06 Rosie org.macosforge.xquartz.privileged_startx[54309]: /opt/X11/bin/font_cache: line 92: /System/Library/Fonts/Supplemental/fonts.list: Operation not permitted Feb 18 21:52:06 Rosie org.macosforge.xquartz.startx[75566]: expr: syntax error Feb 18 21:52:06 --- last message repeated 2 times --- @ Feb 18 21:52:30 --- last message repeated 7 times --- Feb 18 21:52:30 Rosie org.macosforge.xquartz.X11.stub[75664]: Xquartz: bootstrap_look_up(): Unknown service name Feb 18 21:52:31 Rosie org.macosforge.xquartz.startx[75566]: waiting for X server to begin accepting connections Feb 18 21:52:31 Rosie org.macosforge.xquartz.startx[75566]: waiting for X server to begin accepting connections giving up Feb 18 21:52:31 Rosie org.macosforge.xquartz.startx[75566]: /opt/X11/bin/xinit: unable to connect to X server: Connection refused Feb 18 21:52:31 Rosie org.macosforge.xquartz.startx[75566]: waiting for X server to begin accepting connections /opt/X11/bin/xinit: server error Feb 18 21:52:31 Rosie org.macosforge.xquartz.startx[75566]: waiting for X server to begin accepting connections Feb 18 21:52:32 Rosie org.macosforge.xquartz.startx[75977]: expr: syntax error Feb 18 21:52:32 --- last message repeated 2 times --- Feb 18 21:52:32 Rosie org.macosforge.xquartz.privileged_startx[54309]: /opt/X11/bin/font_cache: line 92: /System/Library/Fonts/fonts.list: Operation not permitted Feb 18 21:52:32 Rosie org.macosforge.xquartz.privileged_startx[54309]: /opt/X11/bin/font_cache: line 92: /System/Library/Fonts/Supplemental/fonts.list: Operation not permitted Feb 18 21:52:32 Rosie org.macosforge.xquartz.startx[75977]: xauth: file /Users/pbw/.serverauth.75978 does not exist Feb 18 21:52:32 Rosie org.macosforge.xquartz.X11.stub[76064]: Xquartz: Unable to locate waiting server: org.macosforge.xquartz.X11 Feb 18 21:52:32 Rosie Xquartz[76068]: no path for address 0x7ffdffcdd000 Feb 18 21:52:32 Rosie org.macosforge.xquartz.X11.stub[76068]: Xquartz: Starting X server: /Applications/Utilities/XQuartz.app/Contents/MacOS/X11 --listenonly Feb 18 21:52:32 Rosie org.macosforge.xquartz.privileged_startx[54309]: /System/Library/Fonts/fonts.scale: fopen(w): Operation not permitted Feb 18 21:52:32 Rosie org.macosforge.xquartz.privileged_startx[54309]: /System/Library/Fonts/fonts.dir: fopen(w): Operation not permitted Feb 18 21:52:32 Rosie org.macosforge.xquartz.privileged_startx[54309]: /System/Library/Fonts/Supplemental/fonts.scale: fopen(w): Operation not permitted Feb 18 21:52:32 Rosie org.macosforge.xquartz.privileged_startx[54309]: /System/Library/Fonts/Supplemental/fonts.dir: fopen(w): Operation not permitted Feb 18 21:52:34 Rosie org.macosforge.xquartz.startx[75977]: Feb 18 21:52:36 Rosie org.macosforge.xquartz.startx[75977]: waiting for X server to begin accepting connections--------------------------------------------------------------- > On 18 Feb 2021, at 9:30 pm, Duncan Murdoch <murdoch.dun...@gmail.com> wrote: > > On 18/02/2021 6:14 a.m., Peter West wrote: >> Yes, I went through that process. I have no org.xquartz.* files in /Library >> Launch* now. > > If you run x11(), does it cause the same issue? > > What about not starting R at all, and just running some X11 app like xclock > from the terminal? > > Duncan Murdoch > >>> On 18 Feb 2021, at 9:08 pm, Duncan Murdoch <murdoch.dun...@gmail.com >>> <mailto:murdoch.dun...@gmail.com>> wrote: >>> >>> On 17/02/2021 10:13 p.m., Peter West wrote: >>>> And speaking of M1 Silicon: >>>> My XQuartz version is 2.7.11. >>>> Started R 4.0.4. >>>> Stopped R 4.0.4 >>>> Started RStudio >>>>> install.packages("rgl") >>>> trying URL >>>> 'https://cran.rstudio.com/bin/macosx/contrib/4.0/rgl_0.105.13.tgz >>>> <https://cran.rstudio.com/bin/macosx/contrib/4.0/rgl_0.105.13.tgz>' >>>> Content type 'application/x-gzip' length 6446159 bytes (6.1 MB) >>>> ================================================== >>>> downloaded 6.1 MB >>>> The downloaded binary packages are in >>>> /var/folders/jf/mkyz74311796dl4mxx_7tcx80000gn/T//RtmpflD1wL/downloaded_packages >>>>> library(rgl) >>>> RStudio hangs indefinitely. >>>> My RStudio is at 1.4.1103. >>> >>> That looks a lot like the issue Rich had last week (which I think is >>> unrelated to the one posted today). Have you tried the solution I posted >>> for that? Here's a copy: >>> >>>> 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. >>> >>> I suspect it would be sufficient to just delete the >>> /Library/LaunchAgents/org.xquartz.startx.plist and >>> /Library/LaunchDaemons/org.xquartz.startx.plist files and reboot, but I >>> haven't tried that. >>> >>> Duncan Murdoch > [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac