<div dir="ltr">Hi everyone,<div><br></div><div>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 (<a href="https://github.com/wxWidgets/wxWidgets/commit/c7f6feadfdb866d672f317452eb97e125c308231">https://github.com/wxWidgets/wxWidgets/commit/c7f6feadfdb866d672f317452eb97e125c308231</a>) to the wxWidgets in wxPython 3.0. The fix is encapsulated in an updated wxPython conda package.</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Sep 30, 2023 at 6:01 AM Billy Poon <<a href="mailto:BKPoon@lbl.gov">BKPoon@lbl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr">I have narrowed down the segmentation fault to some code in wxWidgets (from wxPython). It's a similar problem to this (<a href="https://github.com/wxWidgets/wxWidgets/issues/19005" target="_blank">https://github.com/wxWidgets/wxWidgets/issues/19005</a>) 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.<br clear="all"><div><div dir="ltr" class="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div><br></div><div>--</div><div><span style="font-size:12.8px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Sep 28, 2023 at 9:29 AM Kizziah, James <<a href="mailto:kizziah4@uab.edu" target="_blank">kizziah4@uab.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div>
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<p class="MsoNormal"><span style="font-size:11pt">Hi Billy,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">Thanks for your help. I’m using the v1.20.1-4487 graphical installer currently listed for macOS on the main download page:
<a href="https://phenix-online.org/download/phenix/release/" target="_blank">https://phenix-online.org/download/phenix/release/</a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">Best,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">James<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="MsoNormal" style="margin-bottom:12pt"><b><span style="font-size:12pt;color:black">From:
</span></b><span style="font-size:12pt;color:black">Billy Poon <<a href="mailto:BKPoon@lbl.gov" target="_blank">BKPoon@lbl.gov</a>><br>
<b>Date: </b>Thursday, September 28, 2023 at 11:24 AM<br>
<b>To: </b>Kizziah, James <<a href="mailto:kizziah4@uab.edu" target="_blank">kizziah4@uab.edu</a>><br>
<b>Cc: </b><a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a> <<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a>><br>
<b>Subject: </b>Re: [phenixbb] Phenix installation on macOS 14 Sonoma<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Hi James,<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">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.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">--<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:9.5pt">Billy K. Poon</span><span style="font-size:11pt"><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Research Scientist, Molecular Biophysics and Integrated Bioimaging<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Lawrence Berkeley National Laboratory<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">1 Cyclotron Road, M/S 33R0345<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Berkeley, CA 94720<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Fax: (510) 486-5909<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Web: <a href="https://phenix-online.org/" target="_blank">https://phenix-online.org</a><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">On Thu, Sep 28, 2023 at 8:54 AM Kizziah, James <<a href="mailto:kizziah4@uab.edu" target="_blank">kizziah4@uab.edu</a>> wrote:<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt">Hi all,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"> <u></u><u></u></span></p>
<p>I am having trouble getting Phenix to open on a new mac.
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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:
<u></u><u></u></p>
<p style="margin-left:0.5in">“<span>python[9678:116756] It's not legal to call -layoutSubtreeIfNeeded on a view which is already being laid out.</span><span>
</span><span>If you are implementing the view's -layout method, you can call -[super layout] instead. Break on void _NSDetectedLayoutRecursion(void) to debug.</span><span>
</span><span>This will be logged only once.</span><span>
</span><span>This may break in the future.</span><u></u><u></u></p>
<p> <u></u><u></u></p>
<p style="text-indent:0.5in"><span>[3]</span><span>
</span><span>segmentation fault</span><span>
</span><span>phenix”</span><u></u><u></u></p>
<p><span> </span><u></u><u></u></p>
<p>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. <u></u><u></u></p>
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<p>Any ideas how to solve this problem?<u></u><u></u></p>
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<p>Thanks,<u></u><u></u></p>
<p>James<u></u><u></u></p>
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