Scipy symbol not found

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-11.6-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Attempted to use the Cylinders/Stubs preset

Log:
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/josecarlos/Downloads/Bedaquilina solo cadenas a y c.cxs"

Log from Thu May 15 21:04:09 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/josecarlos/Downloads/7jg9.pdb

7jg9.pdb title:  
Cryo-em structure of bedaquiline-saturated mycobacterium smegmatis atp
synthase rotational state 2 (backbone model) [more info...]  
  
Chain information for 7jg9.pdb #1  
---  
Chain | Description | UniProt  
1 2 3 4 5 6 7 8 9 | atp synthase subunit C | Q5TIX5_MYCSM 1-86  
A B C | atp synthase subunit α |   
D E F | atp synthase subunit β |   
G | atp synthase γ chain |   
H | atp synthase ε chain |   
a | atp synthase subunit A | A0R206_MYCS2 1-252  
b | atp synthase subunit B |   
d | atp synthase subunit B-δ | ATPFD_MYCS2 1-445  
  
Non-standard residues in 7jg9.pdb #1  
---  
BQ1 — bedaquiline  
  

> select ::name="BQ1"

259 atoms, 287 bonds, 7 residues, 1 model selected  

> style sel sphere

Changed 259 atom styles  

> ui tool show "Color Actions"

> color sel sky blue target a

> color sel byhetero target a

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> select /a

828 atoms, 826 bonds, 1 pseudobond, 207 residues, 2 models selected  

> lighting simple

> select /a

828 atoms, 826 bonds, 1 pseudobond, 207 residues, 2 models selected  

> color sel cornflower blue target c

> color sel white target c

> select /a

828 atoms, 826 bonds, 1 pseudobond, 207 residues, 2 models selected  

> color sel medium slate blue target c

> select /b

558 atoms, 557 bonds, 138 residues, 1 model selected  

> select /d

1712 atoms, 1709 bonds, 2 pseudobonds, 428 residues, 2 models selected  

> color sel medium slate blue target c

[Repeated 2 time(s)]

> select /1/2/3/4/5/6/7/8/9

3175 atoms, 3194 bonds, 736 residues, 1 model selected  

> color sel light sea green target c

> color sel light sea green target ac

> color sel medium turquoise target ac

> color sel medium spring green target ac

> color sel magenta target ac

> ui tool show "Color Actions"

> color sel aquamarine target ac

> color sel gray target ac

> color sel medium aquamarine target ac

> color sel aquamarine target ac

> color sel turquoise target ac

> color sel pale turquoise target ac

> color sel dark khaki target ac

> color sel dark turquoise target ac

> color sel light sea green target ac

> color sel spring green target ac

> color sel cadet blue target ac

> select /A/B/C

6144 atoms, 6138 bonds, 3 pseudobonds, 1536 residues, 2 models selected  

> color sel cadet blue target ac

> color sel olive drab target ac

> color sel dark sea green target ac

> select /D/E/F

5568 atoms, 5565 bonds, 1392 residues, 1 model selected  

> color sel rosy brown target ac

> color sel light salmon target ac

> select /G

1116 atoms, 1113 bonds, 2 pseudobonds, 279 residues, 2 models selected  

> color sel plum target ac

> select /H

468 atoms, 467 bonds, 117 residues, 1 model selected  

> color sel turquoise target ac

> color sel dark goldenrod target ac

> color sel teal target ac

> color sel gray target ac

> color sel khaki target ac

> color sel dark khaki target ac

> select /a

828 atoms, 826 bonds, 1 pseudobond, 207 residues, 2 models selected  

> color sel medium slate blue target ac

> color sel cornflower blue target ac

> select /b

558 atoms, 557 bonds, 138 residues, 1 model selected  

> color sel medium spring green target ac

> undo

> select /b

558 atoms, 557 bonds, 138 residues, 1 model selected  

> color sel light coral target ac

> undo

> select /a

828 atoms, 826 bonds, 1 pseudobond, 207 residues, 2 models selected  

> color sel khaki target ac

> undo

> select /d

1712 atoms, 1709 bonds, 2 pseudobonds, 428 residues, 2 models selected  

> color sel dark goldenrod target ac

> undo

> color sel salmon target ac

> undo

> color sel tomato target ac

> undo

> select clear

> select ::name="BQ1"

259 atoms, 287 bonds, 7 residues, 1 model selected  

> color sel sky blue target ac

> color sel byhetero target ac

> select /1/2/3/4/5/6/7/8/9

3175 atoms, 3194 bonds, 736 residues, 1 model selected  

> color sel tan target ac

> undo

> select ::name="BQ1"

259 atoms, 287 bonds, 7 residues, 1 model selected  

> color sel tan target ac

> color sel byhetero target ac

> select clear

> color sky blue target ac

> undo

> select ::name="BQ1"

259 atoms, 287 bonds, 7 residues, 1 model selected  

> color sel sky blue target ac

> color sel byhetero target ac

> color sel pale goldenrod target ac

> color sel light sea green target ac

> undo

[Repeated 1 time(s)]

> select /1/2/3/4/5/6/7/8/9

3175 atoms, 3194 bonds, 736 residues, 1 model selected  

> color sel medium aquamarine target ac

> select ::name="BQ1"

259 atoms, 287 bonds, 7 residues, 1 model selected  

> color sel sky blue target ac

> color sel byhetero target ac

> color sel dark sea green target ac

> undo

> select /1/2/3/4/5/6/7/8/9

3175 atoms, 3194 bonds, 736 residues, 1 model selected  

> color sel medium aquamarine target ac

> undo

> select /1/2/3/4/5/6/7/8/9

3175 atoms, 3194 bonds, 736 residues, 1 model selected  

> color sel khaki target ac

> select ::name="BQ1"

259 atoms, 287 bonds, 7 residues, 1 model selected  

> select ::name="BQ1"

259 atoms, 287 bonds, 7 residues, 1 model selected  

> color sel sky blue target ac

> color sel byhetero target ac

> select /H

468 atoms, 467 bonds, 117 residues, 1 model selected  

> color sel medium aquamarine target ac

> color sel teal target ac

> color sel medium aquamarine target ac

> color sel medium turquoise target ac

> save "/Users/josecarlos/Downloads/Bedaquilina en diana.cxs"

> select /a

828 atoms, 826 bonds, 1 pseudobond, 207 residues, 2 models selected  

> select /b

558 atoms, 557 bonds, 138 residues, 1 model selected  

> select /a

828 atoms, 826 bonds, 1 pseudobond, 207 residues, 2 models selected  

> select /d

1712 atoms, 1709 bonds, 2 pseudobonds, 428 residues, 2 models selected  

> select /a

828 atoms, 826 bonds, 1 pseudobond, 207 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel red target ac

> undo

> select /d

1712 atoms, 1709 bonds, 2 pseudobonds, 428 residues, 2 models selected  

> color sel red target ac

> undo

> select /A/B/C

6144 atoms, 6138 bonds, 3 pseudobonds, 1536 residues, 2 models selected  

> select /G

1116 atoms, 1113 bonds, 2 pseudobonds, 279 residues, 2 models selected  

> color sel red target ac

> undo

> select /a

828 atoms, 826 bonds, 1 pseudobond, 207 residues, 2 models selected  

> select /b

558 atoms, 557 bonds, 138 residues, 1 model selected  

> hide sel atoms

> select /d

1712 atoms, 1709 bonds, 2 pseudobonds, 428 residues, 2 models selected  

> hide sel atoms

> select /A/B/C

6144 atoms, 6138 bonds, 3 pseudobonds, 1536 residues, 2 models selected  

> hide sel atoms

> select /D/E/F

5568 atoms, 5565 bonds, 1392 residues, 1 model selected  

> hide sel atoms

> select /D/E/F

5568 atoms, 5565 bonds, 1392 residues, 1 model selected  

> hide sel atoms

> select /G

1116 atoms, 1113 bonds, 2 pseudobonds, 279 residues, 2 models selected  

> hide sel atoms

> select /H

468 atoms, 467 bonds, 117 residues, 1 model selected  

> hide sel atoms

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 19310 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1906, in
_update_graphics_if_needed  
s[i].update_graphics_if_needed()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 363, in update_graphics_if_needed  
self._create_ribbon_graphics()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 673, in _create_ribbon_graphics  
ribbons_drawing.compute_ribbons(self)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 630, in compute_ribbons  
_make_ribbon_graphics(structure, self)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 142, in _make_ribbon_graphics  
centers = _arc_helix_geometry(coords, xs_mgr, displays, start, end, geometry)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 1010, in _arc_helix_geometry  
hc = HelixCylinder(coords[start:end])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/sse.py", line 198, in __init__  
self._try_curved()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/sse.py", line 403, in _try_curved  
self._curved_optimize(c_center, c_axis, c_radius)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/sse.py", line 447, in _curved_optimize  
opt = OptArc(self.coords, center, axis, major_radius)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/sse.py", line 96, in __init__  
from scipy.optimize import minimize  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/__init__.py", line 414, in <module>  
from ._optimize import *  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_optimize.py", line 40, in <module>  
from ._numdiff import approx_derivative  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_numdiff.py", line 8, in <module>  
from ._group_columns import group_dense, group_sparse  
ImportError:
dlopen(/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_group_columns.cpython-311-darwin.so, 2): Symbol not
found:
__ZTTNSt3__119basic_ostringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE  
Referenced from:
/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_group_columns.cpython-311-darwin.so (which was built
for Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  
in
/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_group_columns.cpython-311-darwin.so  
  
Error processing trigger "graphics update":  
ImportError:
dlopen(/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_group_columns.cpython-311-darwin.so, 2): Symbol not
found:
__ZTTNSt3__119basic_ostringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE  
Referenced from:
/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_group_columns.cpython-311-darwin.so (which was built
for Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  
in
/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_group_columns.cpython-311-darwin.so  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_numdiff.py", line 8, in  
from ._group_columns import group_dense, group_sparse  
  
See log for complete Python traceback.  
  

> select /a

828 atoms, 826 bonds, 1 pseudobond, 207 residues, 2 models selected  

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> select /1/2/3/4/5/6/7/8/9

3175 atoms, 3194 bonds, 736 residues, 1 model selected  

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> hide sel atoms

> show sel cartoons

> select /1/2/3/4/5/6/7/8/9

3175 atoms, 3194 bonds, 736 residues, 1 model selected  

> hide sel atoms

[Repeated 1 time(s)]

> select clear

> hide atoms

> save "/Users/josecarlos/Downloads/Bedaquilina solo cadenas a y d.cxs"

——— End of log from Thu May 15 21:04:09 2025 ———

opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1906, in
_update_graphics_if_needed  
s[i].update_graphics_if_needed()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 363, in update_graphics_if_needed  
self._create_ribbon_graphics()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 673, in _create_ribbon_graphics  
ribbons_drawing.compute_ribbons(self)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 630, in compute_ribbons  
_make_ribbon_graphics(structure, self)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 142, in _make_ribbon_graphics  
centers = _arc_helix_geometry(coords, xs_mgr, displays, start, end, geometry)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 1010, in _arc_helix_geometry  
hc = HelixCylinder(coords[start:end])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/sse.py", line 198, in __init__  
self._try_curved()  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/sse.py", line 403, in _try_curved  
self._curved_optimize(c_center, c_axis, c_radius)  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/sse.py", line 447, in _curved_optimize  
opt = OptArc(self.coords, center, axis, major_radius)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/sse.py", line 96, in __init__  
from scipy.optimize import minimize  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/__init__.py", line 414, in <module>  
from ._optimize import *  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_optimize.py", line 40, in <module>  
from ._numdiff import approx_derivative  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_numdiff.py", line 8, in <module>  
from ._group_columns import group_dense, group_sparse  
ImportError:
dlopen(/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_group_columns.cpython-311-darwin.so, 2): Symbol not
found:
__ZTTNSt3__119basic_ostringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE  
Referenced from:
/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_group_columns.cpython-311-darwin.so (which was built
for Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  
in
/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_group_columns.cpython-311-darwin.so  
  
Error processing trigger "graphics update":  
ImportError:
dlopen(/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_group_columns.cpython-311-darwin.so, 2): Symbol not
found:
__ZTTNSt3__119basic_ostringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE  
Referenced from:
/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_group_columns.cpython-311-darwin.so (which was built
for Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  
in
/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_group_columns.cpython-311-darwin.so  
  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_numdiff.py", line 8, in  
from ._group_columns import group_dense, group_sparse  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 71.7.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 6723.140.2
      OS Loader Version: 6723.140.2

Software:

    System Software Overview:

      System Version: macOS 11.6 (20G165)
      Kernel Version: Darwin 20.6.0
      Time since boot: 2:38

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Resolution: 2880 x 1800
          UI Looks like: 1440 x 900 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

[Eric Pettersen]

Possibly duplicate of #17079 (this is 1.9 vs 1.10 for the other ticket though)

[Zach Pearson]

I think this is a duplicate. We should note that the 1.9 release is actually more restricted than we think it is on our website (I will make that change shortly).

The basic problem is that scipy has two macOS arm64 wheels up, and one is targeting a higher MACOSX_DEPLOYMENT_TARGET than the other. I think pip ignores this environment variable when selecting packages, so without qualifying that we need the lower deployment target version, pip selects the higher one on build machines.

This user needs to use a daily build or release candidate. I would advocate for cutting a 1.9.1 release, we're pretty close to 1.10 and it's not worth the effort.