[R-SIG-Mac] more rgl problems

Thu Feb 18 12:58:36 CET 2021

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.duncan using 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.duncan using gmail.com <mailto:murdoch.duncan using 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
> 

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