This is happening as a result of the Launch* startx and privileged_startx execution. The Operation not permitted stuff just scrolls on by.
> On 18 Feb 2021, at 9:58 pm, Peter West <p...@pbw.id.au> wrote: > > 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 _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
