[phenixbb] Phenix installation on macOS 14 Sonoma

[Billy Poon]

I have narrowed down the segmentation fault to some code in wxWidgets (from
wxPython). It's a similar problem to this (
https://github.com/wxWidgets/wxWidgets/issues/19005)  I'm testing some
fixes and I think I can provide a way to update the wxPython package in
1.20. The 1.21 release candidates will be updated to have the fixes.

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Fax: (510) 486-5909
Web: https://phenix-online.org


On Thu, Sep 28, 2023 at 9:29 AM Kizziah, James <kizziah4 at uab.edu> wrote:

> Hi Billy,
>
>
>
> Thanks for your help. I’m using the v1.20.1-4487 graphical installer
> currently listed for macOS on the main download page:
> https://phenix-online.org/download/phenix/release/
>
>
>
> Best,
>
> James
>
>
>
>
>
> *From: *Billy Poon <BKPoon at lbl.gov>
> *Date: *Thursday, September 28, 2023 at 11:24 AM
> *To: *Kizziah, James <kizziah4 at uab.edu>
> *Cc: *phenixbb at phenix-online.org <phenixbb at phenix-online.org>
> *Subject: *Re: [phenixbb] Phenix installation on macOS 14 Sonoma
>
> Hi James,
>
>
>
> Which installer are you using (version and graphical or command-line)? I
> have not updated my laptop to Sonoma yet, so I am not able to test.
>
>
>
> --
>
> Billy K. Poon
>
> Research Scientist, Molecular Biophysics and Integrated Bioimaging
>
> Lawrence Berkeley National Laboratory
>
> 1 Cyclotron Road, M/S 33R0345
>
> Berkeley, CA 94720
>
> Fax: (510) 486-5909
>
> Web: https://phenix-online.org
>
>
>
>
>
> On Thu, Sep 28, 2023 at 8:54 AM Kizziah, James <kizziah4 at uab.edu> wrote:
>
> Hi all,
>
>
>
> I am having trouble getting Phenix to open on a new mac.
>
> I downloaded the latest official release of the point-and-click installer,
> ran xattr -c on it, and installed without issue. Initially, I can create
> the first project directory (or recreate it if I remove the .phenix
> directory), but then I get a notice that another instance of Phenix is
> running with the associated PID. If I continue anyway, python quits
> unexpectedly, and if Phenix is opened in the command line, this reply is
> given:
>
> “python[9678:116756] It's not legal to call -layoutSubtreeIfNeeded on a
> view which is already being laid out.  If you are implementing the view's
> -layout method, you can call -[super layout] instead. Break on void
> _NSDetectedLayoutRecursion(void) to debug.  This will be logged only once.
> This may break in the future.
>
>
>
> [3]    segmentation fault  phenix”
>
>
>
> However, the PID for this supposed other instance doesn’t exist. This
> occurs every time Phenix is run from Applications or in the command line,
> even after restarting the laptop (without resuming programs) or deleting
> and reinstalling Phenix.
>
>
>
> Any ideas how to solve this problem?
>
>
>
> Thanks,
>
> James
>
>
>
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