[R-SIG-Mac] more rgl problems

Thu Feb 18 13:06:24 CET 2021

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 <pbw using 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.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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