sse.py → scipy cannot import _uarray

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-8.1-6.3.9600
ChimeraX Version: 0.94 (2020-04-28)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.94.dev202004282203 (2020-04-28)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed 'ChimeraX_UI-1.0-py3-none-any.whl'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing c:\users\yonathan
arfi\appdata\local\ucsf\chimerax\cache\0.94\installers\chimerax_ui-1.0-py3-none-
any.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Core>=0.9 in
c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-UI==1.0)
(0.94.dev202004282203)  
Installing collected packages: ChimeraX-UI  
Attempting uninstall: ChimeraX-UI  
Found existing installation: ChimeraX-UI 1.0  
Uninstalling ChimeraX-UI-1.0:  
Successfully uninstalled ChimeraX-UI-1.0  
Successfully installed ChimeraX-UI-1.0  
Lock 900644913992 acquired on C:\Users\Yonathan
ARFI\AppData\Local\UCSF\ChimeraX\Cache\0.94\toolshed\bundle_info.cache.lock  
Lock 900644913992 released on C:\Users\Yonathan
ARFI\AppData\Local\UCSF\ChimeraX\Cache\0.94\toolshed\bundle_info.cache.lock  
  

WARNING: You are using pip version 20.0.2; however, version 20.1 is available.  
You should consider upgrading via the 'C:\Program
Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip' command.  
  

> open 6n2y format mmCIF fromDatabase pdb

6n2y title:  
Bacillus PS3 ATP synthase class 1 [more info...]  
  
Chain information for 6n2y #1  
---  
Chain | Description  
A B C | ATP synthase subunit α  
D E F | ATP synthase subunit β  
G | ATP synthase γ chain  
H | ATP synthase ε chain  
I | ATP synthase subunit δ  
a | ATP synthase subunit a  
b1 | ATP synthase subunit b  
b2 | ATP synthase subunit b  
c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c  
  
Non-standard residues in 6n2y #1  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
PO4 — phosphate ion  
  
  

> preset cartoons/nucleotides cylinders/stubs

Changed 34914 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1559, in
_update_graphics_if_needed  
s[i]._update_graphics_if_needed()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 297, in
_update_graphics_if_needed  
self._create_ribbon_graphics()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 550, in _create_ribbon_graphics  
ribbons_drawing.compute_ribbons(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\ribbon.py", line 586, in compute_ribbons  
_make_ribbon_graphics(structure, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\ribbon.py", line 128, in _make_ribbon_graphics  
centers = _arc_helix_geometry(coords, xs_mgr, displays, start, end, geometry)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\ribbon.py", line 957, in _arc_helix_geometry  
hc = HelixCylinder(coords[start:end])  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\atomic\sse.py",
line 185, in __init__  
self._straight_optimize()  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\atomic\sse.py",
line 398, in _straight_optimize  
opt = OptLine(self.coords, centroid, axis)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\atomic\sse.py",
line 25, in __init__  
from scipy.optimize import minimize  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\scipy\\__init__.py",
line 156, in <module>  
from . import fft  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\scipy\fft\\__init__.py",
line 76, in <module>  
from ._basic import (  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\scipy\fft\\_basic.py",
line 1, in <module>  
from scipy._lib.uarray import generate_multimethod, Dispatchable  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\scipy\\_lib\uarray.py",
line 27, in <module>  
from ._uarray import *  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\scipy\\_lib\\_uarray\\__init__.py", line 114, in <module>  
from ._backend import *  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\scipy\\_lib\\_uarray\\_backend.py", line 15, in <module>  
from . import _uarray # type: ignore  
ImportError: DLL load failed: Le module spécifié est introuvable.  
  
Error processing trigger "graphics update":  
ImportError: DLL load failed: Le module spécifié est introuvable.  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\scipy\\_lib\\_uarray\\_backend.py", line 15, in  
from . import _uarray # type: ignore  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 344.42
OpenGL renderer: GeForce GTX 965M/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: GS60 2QD
OS: Microsoft Windows 8.1 (Build 9600)
Memory: 8,503,721,984
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-4720HQ CPU @ 2.60GHz"

[Tom Goddard]

scipy could not import one of its private compiled libraries _uarray with DLL not found error message. Probably this was a linking problem, possibly because the error was on a Windows 8 machine. We only support Windows 10. scipy was being used to compute tube helices.

[Greg Couch]

Was this assigned to the Build System component because of the Chimera-UI update? That is probably a bug, but not this one.

[Eric Pettersen]

Well, it was a link failure. Could have been "Build System" (not getting the right link path set) or "Platform" (Windows specific).

I ignored the Chimera-UI update problem for the purposes of this ticket and sent separate email instead.