[R-SIG-Mac] Apparent interaction between XQuartz and the Catalina (10.15) macOS upgrade

[Kasper Daniel Hansen]

Bob,

You ran the betas. On issues like this, that could be a big difference. So
Im not sure it is yet an issue that could be user dependent.

Best,
Kasper

On Tue, Oct 8, 2019 at 10:00 PM Bob Rudis <bob using rud.is> wrote:

> I've been running Catalina since the first beta and upgraded to GM the day
> of release. Apart from having to stick R things into Full Disk Access I've
> had no issues with R nor XQuartz.
>
> I read through the links provided and, while I do have said symlink in the
> relocated items folder Apple creates (this is new behavior for the GM), it
> gets re-created fine for me & XQuartz works fine (and the minor pkg deps I
> have installed that use it also work fine.
>
> This would appear to be a YMMV situation.
>
> -Bob
>
> > On Oct 8, 2019, at 4:19 PM, Luis Puerto <luiss.puerto using gmail.com> wrote:
> >
> > Thanks a lot for the heads up!
> >
> > Cheers!
> > Luis
> >
> >> On 8 Oct 2019, at 22:49, Marc Schwartz via R-SIG-Mac <
> r-sig-mac using r-project.org> wrote:
> >>
> >> Hi All,
> >>
> >> Perhaps I missed something relevant along the way someplace, but I ran
> the upgrade to Catalina (10.15) last night. I wanted to give folks a heads
> up on an issue that you may face, especially if you have XQuartz installed
> alongside R.
> >>
> >> One of the sequelae of the upgrade is that some files may get relocated
> during the upgrade, likely in part due to the macOS SIP.
> >>
> >> In my case, this involved the symlink for XQuartz, 'usr/X11R6', which
> gets placed into a "Relocated Items" folder on the Desktop. That folder,
> which is actually an alias to /Users/Shared, contains a folder tree with:
> Security/usr/X11R6. Naively, after seeing this, I elected to move the
> entire folder to the Trash.
> >>
> >> That led me into a cycle of trying to figure out how to then delete
> that folder tree from the Trash, as I would get various OS errors in the
> course of doing so.
> >>
> >> That led me to some Google searches, with incremental attempts at
> solutions, but eventually landing on the following thread in the Apple
> Community forums:
> >>
> >> https://discussions.apple.com/thread/250712783
> >>
> >> After the first review of the thread there, and before user 'faikbey'
> posted a possible solution using Recovery Mode, I filed an Issue on the
> XQuartz github repo here:
> >>
> >> https://github.com/XQuartz/XQuartz/issues/1
> >>
> >> It would seem that, at some level, one workaround would be to uninstall
> XQuartz fully before the Catalina upgrade, but there is no uninstall
> program provided by them. There is a series of CLI commands in a github
> gist here:
> >>
> >>
> https://gist.github.com/pwnsdx/d127873e24cef159d4d603accaf37ee4#file-gistfile1-txt
> >>
> >> which appears to work, but would likely be best used prior to the
> Catalina upgrade, and then re-install XQuartz after the upgrade is complete.
> >>
> >> The solution to the problem posted by 'faikbey' in the Apple forum
> appears to work in the original scenario, albeit, as I noted in my reply in
> that thread, I needed to first mount the user volume in Recovery Mode using
> Disk Utility, before I could proceed with the additional steps of deleting
> the files from the Trash, then rebooting into normal mode.
> >>
> >> If anyone else has experienced this and knows of an alternative/better
> solution, let us know.
> >>
> >> Otherwise, let's see what the XQuartz folks might come up with on this,
> as this was not an issue with prior macOS upgrades.
> >>
> >> Regards,
> >>
> >> Marc Schwartz
> >>
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> >
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-- 
Best,
Kasper

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