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

[Jean Thioulouse]

I did not run any of the Catalina betas and have no problem with Catalina/XQuartz.

Jean

—-
Jean THIOULOUSE - orcid.org/0000-0001-7664-0598
http://lbbe.univ-lyon1.fr/-Thioulouse-Jean-.html
https://www.springer.com/fr/book/9781493988488




> Le 9 oct. 2019 à 15:20, Kasper Daniel Hansen <kasperdanielhansen using gmail.com> a écrit :
> 
> 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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> 
> 
> -- 
> Best,
> Kasper
> 
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