Context Navigation

← Previous Ticket
Next Ticket →

#15267 closed defect (limitation)

Scipy: Symbol not found, macOS 11

Reported by:	chimerax-bug-report@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Core	Version:
Keywords:		Cc:	Greg Couch
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        macOS-11.7.9-arm64-arm-64bit
ChimeraX Version: 1.9.dev202405202355 (2024-05-20 23:55:30 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.9.dev202405202355 (2024-05-20)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/avabostjancic/Downloads/SP-15-Bostjancic-celotna-struktura-
> cartoon.cxs

Log from Mon May 20 19:42:07 2024UCSF ChimeraX version: 1.8rc202405102050
(2024-05-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open C:/Users/janhv/Documents/Šola/FKKT/Struktura/Ava/SP-15-Bostjancic-
> celotna-struktura.cxs

Log from Mon May 20 19:32:43 2024 Startup Messages  
---  
notes | available bundle cache has not been initialized yet  
Database-fetch provider 'redo' in bundle Map specified unknown data format
'MTZ'  
  
UCSF ChimeraX version: 1.8rc202405102050 (2024-05-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/janhv/Downloads/8qv2.cif

8qv2.cif title:  
Structure of the native y-Tubulin Ring Complex (yTuRC) capping microtubule
minus ends at the spindle pole body [more info...]  
  
Chain information for 8qv2.cif #1  
---  
Chain | Description | UniProt  
Ab Ac Ad Ae Af Ag Ah Ai Aj Ak Al Am An Ao Ap Aq Ar | Tubulin alpha-1 chain | TBA1_YEAST 1-447  
Bb Bc Bd Be Bf Bg Bh Bi Bj Bk Bl Bm Bn Bo Bp Bq Br | Tubulin beta chain | A0A6A5PXT5_YEASX 1-457  
C E G I K M O | Spindle pole body component | A0A8H4C290_YEASX 1-823  
D F H J L N P | Spindle pole body component | A0A8H4BVY6_YEASX 1-846  
Sa Sb Sc Sd Se Sf Sg Sh Si Sj Sk Sl Sm Sn | Spindle pole body component 110 | A0A8H8UNQ3_YEASX 1-944  
Ua Ub Uc Ud Ue Uf Ug Uh Ui Uj Uk Ul Um Un | Unkown protein |   
a b c d e f g h i j k l m n | Tubulin gamma chain | A0A8H4BZN3_YEASX 1-473  
  
Non-standard residues in 8qv2.cif #1  
---  
GDP — guanosine-5'-diphosphate  
GTP — guanosine-5'-triphosphate  
  

> sequence chain
> #1/Ab#1/Ac#1/Ad#1/Ae#1/Af#1/Ag#1/Ah#1/Ai#1/Aj#1/Ak#1/Al#1/Am#1/An#1/Ao#1/Ap#1/Aq#1/Ar

Alignment identifier is 1  

> select clear

> select
> #1/Ab#1/Ac#1/Ad#1/Ae#1/Af#1/Ag#1/Ah#1/Ai#1/Aj#1/Ak#1/Al#1/Am#1/An#1/Ao#1/Ap#1/Aq#1/Ar

58320 atoms, 59608 bonds, 1 pseudobond, 7463 residues, 2 models selected  

> select clear

> select
> #1/Ab#1/Ac#1/Ad#1/Ae#1/Af#1/Ag#1/Ah#1/Ai#1/Aj#1/Ak#1/Al#1/Am#1/An#1/Ao#1/Ap#1/Aq#1/Ar

58320 atoms, 59608 bonds, 1 pseudobond, 7463 residues, 2 models selected  

> color (#!1 & sel) #689ed9ff

> color (#!1 & sel) #3bd995ff

> color (#!1 & sel) #a78ef5ff

> color (#!1 & sel) #3bd995ff

> color (#!1 & sel) #a78ef5ff

> select clear

> select /Bb/Bc/Bd/Be/Bf/Bg/Bh/Bi/Bj/Bk/Bl/Bm/Bn/Bo/Bp/Bq/Br

56735 atoms, 57974 bonds, 1 pseudobond, 7246 residues, 2 models selected  

> color (#!1 & sel) #3bd9cbff

> color (#!1 & sel) #eb8ef5ff

> select clear

> select /Ua/Ub/Uc/Ud/Ue/Uf/Ug/Uh/Ui/Uj/Uk/Ul/Um/Un

4277 atoms, 4256 bonds, 861 residues, 1 model selected  

> select clear

> select /C/D/E/F/G/H/I/J/K/L/M/N/O/P

79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected  

> select /Sa/Sb/Sc/Sd/Se/Sf/Sg/Sh/Si/Sj/Sk/Sl/Sm/Sn

6933 atoms, 6978 bonds, 825 residues, 1 model selected  

> select /a/b/c/d/e/f/g/h/i/j/k/l/m/n

49343 atoms, 50397 bonds, 7 pseudobonds, 6265 residues, 2 models selected  

> color (#!1 & sel) #3bb4d9ff

> color (#!1 & sel) #f58ecaff

> select clear

> select /C/D/E/F/G/H/I/J/K/L/M/N/O/P

79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected  

> color (#!1 & sel) #3b83d9ff

> color (#!1 & sel) #f58e8eff

> select clear

> select /a/b/c/d/e/f/g/h/i/j/k/l/m/n

49343 atoms, 50397 bonds, 7 pseudobonds, 6265 residues, 2 models selected  

> color (#!1 & sel) #a78ef5ff

> color (#!1 & sel) #aa7df0ff

> select clear

> select /Bb/Bc/Bd/Be/Bf/Bg/Bh/Bi/Bj/Bk/Bl/Bm/Bn/Bo/Bp/Bq/Br

56735 atoms, 57974 bonds, 1 pseudobond, 7246 residues, 2 models selected  

> select /Ab/Ac/Ad/Ae/Af/Ag/Ah/Ai/Aj/Ak/Al/Am/An/Ao/Ap/Aq/Ar

58320 atoms, 59608 bonds, 1 pseudobond, 7463 residues, 2 models selected  

> color (#!1 & sel) #eb8ef5ff

> color (#!1 & sel) #f07da1ff

> select clear

> select /Bb/Bc/Bd/Be/Bf/Bg/Bh/Bi/Bj/Bk/Bl/Bm/Bn/Bo/Bp/Bq/Br

56735 atoms, 57974 bonds, 1 pseudobond, 7246 residues, 2 models selected  

> color (#!1 & sel) #f58ecaff

> color (#!1 & sel) #cf7df0ff

> select clear

> select /C/D/E/F/G/H/I/J/K/L/M/N/O/P

79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected  

> color (#!1 & sel) #3b83d9ff

> color (#!1 & sel) #98554fff

> select clear

> select /C/D/E/F/G/H/I/J/K/L/M/N/O/P

79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected  

> color (#!1 & sel) #3b83d9ff

> color (#!1 & sel) #d2766dff

> select clear

[Repeated 1 time(s)]

> select /Ua/Ub/Uc/Ud/Ue/Uf/Ug/Uh/Ui/Uj/Uk/Ul/Um/Un

4277 atoms, 4256 bonds, 861 residues, 1 model selected  

> color sel #ffffffff

> color sel #9ef07dff

> select clear

[Repeated 1 time(s)]

> select /C/D/E/F/G/H/I/J/K/L/M/N/O/P

79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected  

> color (#!1 & sel) #d2766dff

> color (#!1 & sel) #847df0ff

> select clear

> select /Ab/Ac/Ad/Ae/Af/Ag/Ah/Ai/Aj/Ak/Al/Am/An/Ao/Ap/Aq/Ar

58320 atoms, 59608 bonds, 1 pseudobond, 7463 residues, 2 models selected  

> color (#!1 & sel) #a78ef5ff

> color (#!1 & sel) #ecc3f0ff

> select clear

> select /Bb/Bc/Bd/Be/Bf/Bg/Bh/Bi/Bj/Bk/Bl/Bm/Bn/Bo/Bp/Bq/Br

56735 atoms, 57974 bonds, 1 pseudobond, 7246 residues, 2 models selected  

> color (#!1 & sel) #f07da1ff

> color (#!1 & sel) #e673f0ff

> select clear

> select /a/b/c/d/e/f/g/h/i/j/k/l/m/n

49343 atoms, 50397 bonds, 7 pseudobonds, 6265 residues, 2 models selected  

> color (#!1 & sel) #f58ecaff

> color (#!1 & sel) #9473f0ff

> select clear

[Repeated 1 time(s)]

> select /Ua/Ub/Uc/Ud/Ue/Uf/Ug/Uh/Ui/Uj/Uk/Ul/Um/Un

4277 atoms, 4256 bonds, 861 residues, 1 model selected  

> style sel ball

Changed 4277 atom styles  

> cartoon sel

> style sel sphere

Changed 4277 atom styles  

> select clear

> select /Ua/Ub/Uc/Ud/Ue/Uf/Ug/Uh/Ui/Uj/Uk/Ul/Um/Un

4277 atoms, 4256 bonds, 861 residues, 1 model selected  

> hide sel target a

> cartoon hide sel

> surface sel

> surface hidePatches (#!1 & sel)

> style (#!1 & sel) ringFill thick

Changed 861 residue ring styles  

> show (#!1 & sel) target ab

> select clear

> undo

[Repeated 9 time(s)]

> select clear

> select /Ua/Ub/Uc/Ud/Ue/Uf/Ug/Uh/Ui/Uj/Uk/Ul/Um/Un

4277 atoms, 4256 bonds, 861 residues, 1 model selected  

> cartoon hide (#!1 & sel)

> style (#!1 & sel) ringFill thick

Changed 861 residue ring styles  

> show (#!1 & sel) target ab

> style (#!1 & sel) stick

Changed 4277 atom styles  

> style (#!1 & sel) ringFill thick

Changed 861 residue ring styles  

> style (#!1 & sel) ball

Changed 4277 atom styles  

> style (#!1 & sel) ringFill thin

Changed 861 residue ring styles  

> style (#!1 & sel) ringFill thick

Changed 861 residue ring styles  

> show (#!1 & sel) target ab

> hide (#!1 & sel) target a

> style (#!1 & sel) sphere

Changed 4277 atom styles  

> show (#!1 & sel) target ab

> select clear

> select /C/D/E/F/G/H/I/J/K/L/M/N/O/P

79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected  

> color (#!1 & sel) #d2766dff

> color (#!1 & sel) #f0ae73ff

> select clear

> select /Sa/Sb/Sc/Sd/Se/Sf/Sg/Sh/Si/Sj/Sk/Sl/Sm/Sn

6933 atoms, 6978 bonds, 825 residues, 1 model selected  

> color sel #3b51d9ff

> color sel #f0d173ff

> color sel #d2766dff

> color sel #f0ae73ff

> color sel #f0d173ff

> select clear

> select /Ua/Ub/Uc/Ud/Ue/Uf/Ug/Uh/Ui/Uj/Uk/Ul/Um/Un

4277 atoms, 4256 bonds, 861 residues, 1 model selected  

> color (#!1 & sel) #74c4dbff

> color (#!1 & sel) #73f0d2ff

> select clear

> save test.png format png width 3840 height 2160 supersample 9
> transparentBackground true

> select /Ua/Ub/Uc/Ud/Ue/Uf/Ug/Uh/Ui/Uj/Uk/Ul/Um/Un

4277 atoms, 4256 bonds, 861 residues, 1 model selected  

> color (#!1 & sel) #b29a05ff

> color (#!1 & sel) #73bcf0ff

> select clear

> save test1.png format png width 3840 height 2160 supersample 9
> transparentBackground true

> save C:/Users/janhv/Documents/Šola/FKKT/Struktura/Ava/barvetest1.cxs

> select /C/D/E/F/G/H/I/J/K/L/M/N/O/P

79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected  

> color (#!1 & sel) #acb935ff

> color (#!1 & sel) #f073b8ff

> select clear

> select /C/D/E/F/G/H/I/J/K/L/M/N/O/P

79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected  

> color (#!1 & sel) #68d97fff

> color (#!1 & sel) #bd73f0ff

> color (#!1 & sel) #f073b8ff

> select clear

> select /Sa/Sb/Sc/Sd/Se/Sf/Sg/Sh/Si/Sj/Sk/Sl/Sm/Sn

6933 atoms, 6978 bonds, 825 residues, 1 model selected  

> color sel #bd73f0ff

> select clear

> select /C/D/E/F/G/H/I/J/K/L/M/N/O/P

79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected  

> color (#!1 & sel) #689ed9ff

> color (#!1 & sel) #ffbae0ff

> select clear

> color #fab6ddff

> color #936b82ff

> color #90697fff

> color #664a5aff

> undo

[Repeated 3 time(s)]

> select /C/D/E/F/G/H/I/J/K/L/M/N/O/P

79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected  

> color (#!1 & sel) #ffbae0ff

> color (#!1 & sel) #fdb9dfff

> color (#!1 & sel) #cf97b7ff

> color (#!1 & sel) #ce96b6ff

> color (#!1 & sel) #c28eabff

> color (#!1 & sel) #be8ba8ff

> color (#!1 & sel) #846075ff

> color (#!1 & sel) #866276ff

> color (#!1 & sel) #ac7d98ff

> color (#!1 & sel) #ad7e99ff

> color (#!1 & sel) #c18daaff

> select clear

> lighting full

> lighting soft

> lighting full

> lighting simple

> lighting soft

> lighting full

> save test2.png format png width 3840 height 2160 supersample 9
> transparentBackground true

> select /Ua/Ub/Uc/Ud/Ue/Uf/Ug/Uh/Ui/Uj/Uk/Ul/Um/Un

4277 atoms, 4256 bonds, 861 residues, 1 model selected  

> color (#!1 & sel) #ffffffff

> color (#!1 & sel) #73bcf0ff

> color (#!1 & sel) #74c4dbff

> color (#!1 & sel) #73bcf0ff

> color (#!1 & sel) #ffffffff

> color (#!1 & sel) #c3f0e5ff

> color (#!1 & sel) #73f07eff

> color (#!1 & sel) #acf073ff

> color (#!1 & sel) #ffffffff

> color (#!1 & sel) #acf073ff

> select clear

> save test3.png format png width 3840 height 2160 supersample 9
> transparentBackground true

> select clear

> select /C/D/E/F/G/H/I/J/K/L/M/N/O/P

79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected  

> color (#!1 & sel) #ffffffff

> undo

> color (#!1 & sel) #dee9adff

> color (#!1 & sel) #bd8aa6ff

> color (#!1 & sel) #e8a9ccff

> color (#!1 & sel) #e2a5c6ff

> color (#!1 & sel) #efafd2ff

> color (#!1 & sel) #ffddffff

> color (#!1 & sel) #ffffffff

> color (#!1 & sel) #ddeeeeff

> color (#!1 & sel) #dee9adff

> color (#!1 & sel) #dee9afff

> color (#!1 & sel) #ddeeeeff

> color (#!1 & sel) #ffbae0ff

> color (#!1 & sel) #fab6ddff

> color (#!1 & sel) #cf97b7ff

> select clear

> select /Ua/Ub/Uc/Ud/Ue/Uf/Ug/Uh/Ui/Uj/Uk/Ul/Um/Un

4277 atoms, 4256 bonds, 861 residues, 1 model selected  

> cartoon style (#!1 & sel) modeHelix tube sides 20

> cartoon (#!1 & sel)

> hide (#!1 & sel) target a

> cartoon style (#!1 & sel & coil) xsection oval

> cartoon style (#!1 & sel) xsection barbell modeHelix default

> cartoon style (#!1 & sel) xsection rectangle modeHelix default

> cartoon style (#!1 & sel) xsection oval modeHelix default

> cartoon hide (#!1 & sel)

> show (#!1 & sel) target ab

> select clear

> select /C

5778 atoms, 5890 bonds, 5 pseudobonds, 693 residues, 2 models selected  

> select /C/E

11625 atoms, 11851 bonds, 10 pseudobonds, 1394 residues, 2 models selected  

> select /C/E/G/I/K/M/O

40860 atoms, 41656 bonds, 35 pseudobonds, 4899 residues, 2 models selected  

> color (#!1 & sel) #d198b8ff

> color (#!1 & sel) #c690afff

> color (#!1 & sel) #d39abaff

> color (#!1 & sel) #c892b1ff

> color (#!1 & sel) #c690afff

> color (#!1 & sel) #a37790ff

> color (#!1 & sel) #a57892ff

> color (#!1 & sel) #79586bff

> color (#!1 & sel) #ffbae0ff

> color (#!1 & sel) #fdb9dfff

> color (#!1 & sel) #836074ff

> color (#!1 & sel) #846075ff

> color (#!1 & sel) #6b4e5eff

> select clear

> save SP-S15-Bostjancic-celotna-struktura.png format png width 3840 height
> 2160 supersample 9 transparentBackground true

[Repeated 1 time(s)]

> select

255200 atoms, 260432 bonds, 52 pseudobonds, 32242 residues, 2 models selected  

> style (#!1 & sel) ringFill thick

Changed 32242 residue ring styles  

> select clear

> select

255200 atoms, 260432 bonds, 52 pseudobonds, 32242 residues, 2 models selected  

> hide (#!1 & sel) target a

> show (#!1 & sel) target ab

> select clear

> save C:/Users/janhv/Documents/Šola/FKKT/Struktura/Ava/SP-15-Bostjancic-
> celotna-struktura.cxs

——— End of log from Mon May 20 19:32:43 2024 ———

opened ChimeraX session  

> select

255200 atoms, 260432 bonds, 52 pseudobonds, 32242 residues, 2 models selected  

> hide (#!1 & sel) target a

> cartoon (#!1 & sel)

> cartoon style (#!1 & sel) modeHelix tube sides 20

> select clear

> save C:/Users/janhv/Documents/Šola/FKKT/Struktura/Ava/SP-15-Bostjancic-
> celotna-struktura-cartoon.cxs

——— End of log from Mon May 20 19:42:07 2024 ———

opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 357, in update_graphics_if_needed  
self._create_ribbon_graphics()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 667, in _create_ribbon_graphics  
ribbons_drawing.compute_ribbons(self)  
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/__init__.py", line 413, in <module>  
from ._optimize import *  
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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_Daily.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 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
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: 8 GB
      System Firmware Version: 8422.141.2
      OS Loader Version: 6723.140.2

Software:

    System Software Overview:

      System Version: macOS 11.7.9 (20G1426)
      Kernel Version: Darwin 20.6.0
      Time since boot: 9:36

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      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: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58
    ChimeraX-AtomicLibrary: 14.0.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.4
    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: 2.2.4
    ChimeraX-ColorActions: 1.0.4
    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.dev202405202355
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.3
    ChimeraX-DiffPlot: 1.0
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.16
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.4
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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: 3.0.4
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    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: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.1
    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: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.51.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    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: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.32.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.2
    typing-extensions: 4.11.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10

Change History (2)

comment:1 by pett, 17 months ago

Cc:	Greg Couch added
Component:	Unassigned → Core
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Scipy: Symbol not found

comment:2 by Tom Goddard, 17 months ago

Resolution:	→ limitation
Status:	assigned → closed
Summary:	Scipy: Symbol not found → Scipy: Symbol not found, macOS 11

Unfortunately the PyPi SciPy wheels for Mac ARM are for macOS 12. This user has macOS 11 and that is why they get the missing symbol. I don't think it is worth trying to build our own SciPy to support the old macOS 11 (current macOS version is 14.5). ChimeraX does not use SciPy too heavily. Tube helices and ISOLDE are the features that hit this error.

Note: See TracTickets for help on using tickets.

Download in other formats: