[phenixbb] Phenix installation on macOS 14 Sonoma

[Billy Poon]

Hi everyone,

I have a working fix (see attached screenshot). I'm doing some more
testing and then coming up with instructions (or an installer) for updating
the 1.20 release. The 1.21 release candidates will be updated to work with
Sonoma. Essentially, i backported this commit (
https://github.com/wxWidgets/wxWidgets/commit/c7f6feadfdb866d672f317452eb97e125c308231)
to the wxWidgets in wxPython 3.0. The fix is encapsulated in an updated
wxPython conda package.

--
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 Sat, Sep 30, 2023 at 6:01 AM Billy Poon <BKPoon at lbl.gov> wrote:

> 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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>>
>>
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