Opened 11 months ago

Closed 11 months ago

#16512 closed defect (duplicate)

Various startup errors

Reported by: Eric Pettersen Owned by: Zach Pearson
Priority: normal Milestone:
Component: Build System Version:
Keywords: Cc: chimera-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.6.1-arm64-arm-64bit-Mach-O
ChimeraX Version: 1.10.dev202412210159 (2024-12-21 01:59:55 UTC)
Description
Startup error(s) after building from scratch

Log:
Startup Errors  
---  
errors | Bundle 'ChimeraX-Dicom' custom initialization failed  
Bundle 'ChimeraX-Segmentations' custom initialization failed  
warnings | Traceback (most recent call last):  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/core/toolshed/info.py", line 501, in get_module  
m = importlib.import_module(self.package_name)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/importlib/__init__.py",
line 88, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen importlib._bootstrap>", line 1387, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1360, in _find_and_load  
File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 935, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 1026, in exec_module  
File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/dicom/__init__.py", line 21, in <module>  
from chimerax.dicom.dicom_fetcher import fetchers  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/dicom/dicom_fetcher.py", line 2, in <module>  
from .databases import TCIADatabase  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/dicom/databases/__init__.py", line 1, in <module>  
from .tcia import TCIADatabase  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/dicom/databases/tcia.py", line 24, in <module>  
from tcia_utils import nbia  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/tcia_utils/__init__.py", line 1, in <module>  
from . import nbia  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/tcia_utils/nbia.py", line 12, in <module>  
import matplotlib.pyplot as plt  
File "/Users/pett/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/matplotlib/__init__.py", line 159, in <module>  
from . import _api, _version, cbook, _docstring, rcsetup  
File "/Users/pett/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/matplotlib/cbook.py", line 32, in <module>  
from matplotlib import _api, _c_internal_utils  
ImportError: cannot import name '_c_internal_utils' from partially initialized
module 'matplotlib' (most likely due to a circular import)
(/Users/pett/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/matplotlib/__init__.py)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/core/toolshed/info.py", line 375, in initialize  
api = self._get_api(session.logger)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/core/toolshed/info.py", line 520, in _get_api  
m = self.get_module()  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/core/toolshed/info.py", line 503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-Dicom's
module: cannot import name '_c_internal_utils' from partially initialized
module 'matplotlib' (most likely due to a circular import)
(/Users/pett/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/matplotlib/__init__.py)  
  
Traceback (most recent call last):  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/core/toolshed/info.py", line 376, in initialize  
api._api_caller.initialize(api, session, self)  
~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/core/toolshed/__init__.py", line 1411, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/segmentations/bundle.py", line 11, in initialize  
from .segmentation_tracker import register_model_trigger_handlers  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/segmentations/segmentation_tracker.py", line 28, in <module>  
from chimerax.dicom import Study  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/dicom/__init__.py", line 21, in <module>  
from chimerax.dicom.dicom_fetcher import fetchers  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/dicom/dicom_fetcher.py", line 2, in <module>  
from .databases import TCIADatabase  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/dicom/databases/__init__.py", line 1, in <module>  
from .tcia import TCIADatabase  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/dicom/databases/tcia.py", line 24, in <module>  
from tcia_utils import nbia  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/tcia_utils/__init__.py", line 1, in <module>  
from . import nbia  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/tcia_utils/nbia.py", line 12, in <module>  
import matplotlib.pyplot as plt  
File "/Users/pett/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/matplotlib/__init__.py", line 159, in <module>  
from . import _api, _version, cbook, _docstring, rcsetup  
File "/Users/pett/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/matplotlib/cbook.py", line 32, in <module>  
from matplotlib import _api, _c_internal_utils  
ImportError: cannot import name '_c_internal_utils' from partially initialized
module 'matplotlib' (most likely due to a circular import)
(/Users/pett/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/matplotlib/__init__.py)  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202412210159 (2024-12-21)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Traceback (most recent call last):  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 87, in _expose_event  
self._create_opengl_context()  
~~~~~~~~~~~~~~~~~~~~~~~~~~~^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 120, in _create_opengl_context  
r.initialize_opengl(lw, lh)  
~~~~~~~~~~~~~~~~~~~^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/opengl.py", line 1165, in initialize_opengl  
vao = GL.glGenVertexArrays(1)  
File "src/latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src/wrapper.pyx", line 303, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/wrapper.pyx", line 88, in
OpenGL_accelerate.wrapper.CArgCalculator.c_call  
File "src/wrapper.pyx", line 69, in
OpenGL_accelerate.wrapper.CArgCalculatorElement.c_call  
File "src/wrapper.pyx", line 64, in
OpenGL_accelerate.wrapper.CArgCalculatorElement.c_call  
File "src/arraydatatype.pyx", line 355, in
OpenGL_accelerate.arraydatatype.SizedOutputOrInput.c_call  
File "src/arraydatatype.pyx", line 224, in
OpenGL_accelerate.arraydatatype.ArrayDatatype.c_zeros  
File "src/arraydatatype.pyx", line 69, in
OpenGL_accelerate.arraydatatype.HandlerRegistry.c_get_output_handler  
File "src/arraydatatype.pyx", line 80, in
OpenGL_accelerate.arraydatatype.HandlerRegistry.c_handler_by_plugin_name  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/OpenGL/plugins.py", line 18, in load  
return importByName( self.import_path )  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/OpenGL/plugins.py", line 45, in importByName  
module = __import__( ".".join(moduleName), {}, {}, moduleName)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/OpenGL/arrays/numpymodule.py", line 28, in <module>  
from OpenGL_accelerate.numpy_formathandler import NumpyHandler  
File "src/numpy_formathandler.pyx", line 1, in init
OpenGL_accelerate.numpy_formathandler  
ValueError: ('numpy.dtype size changed, may indicate binary incompatibility.
Expected 96 from C header, got 88 from PyObject', 1,
<OpenGL.platform.baseplatform.glGenVertexArrays object at 0x11e768350>)  
  
ValueError: ('numpy.dtype size changed, may indicate binary incompatibility.
Expected 96 from C header, got 88 from PyObject', 1, )  
  
File "src/numpy_formathandler.pyx", line 1, in init
OpenGL_accelerate.numpy_formathandler  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event  
self.status(self._last_message, self._last_color)  
~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 155, in status  
self._draw_text(msg, color, secondary)  
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 161, in _draw_text  
self._update_texture(msg, color, secondary)  
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 176, in _update_texture  
lw, lh = self._renderer.render_size()  
~~~~~~~~~~~~~~~~~~~~~~~~~~^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/opengl.py", line 639, in render_size  
x, y, w, h = fb.viewport  
^^^^^^^^^^  
TypeError: cannot unpack non-iterable NoneType object  
  
TypeError: cannot unpack non-iterable NoneType object  
  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/opengl.py", line 639, in render_size  
x, y, w, h = fb.viewport  
^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event  
self.status(self._last_message, self._last_color)  
~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 155, in status  
self._draw_text(msg, color, secondary)  
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 165, in _draw_text  
draw_overlays(dlist, self._renderer)  
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 1608, in draw_overlays  
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)  
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 1567, in _draw_multiple  
d.draw(renderer, draw_pass)  
~~~~~~^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 780, in draw  
self.draw_self(renderer, draw_pass)  
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 791, in draw_self  
self._draw_geometry(renderer, transparent_only = any_opaque)  
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 814, in _draw_geometry  
ds.activate_bindings(renderer)  
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 1923, in activate_bindings  
bi.activate()  
~~~~~~~~~~~^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/opengl.py", line 2605, in activate  
self._vao_id = GL.glGenVertexArrays(1)  
~~~~~~~~~~~~~~~~~~~~^^^  
File "src/latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src/wrapper.pyx", line 303, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/wrapper.pyx", line 88, in
OpenGL_accelerate.wrapper.CArgCalculator.c_call  
File "src/wrapper.pyx", line 69, in
OpenGL_accelerate.wrapper.CArgCalculatorElement.c_call  
File "src/wrapper.pyx", line 64, in
OpenGL_accelerate.wrapper.CArgCalculatorElement.c_call  
File "src/arraydatatype.pyx", line 355, in
OpenGL_accelerate.arraydatatype.SizedOutputOrInput.c_call  
File "src/arraydatatype.pyx", line 224, in
OpenGL_accelerate.arraydatatype.ArrayDatatype.c_zeros  
File "src/arraydatatype.pyx", line 69, in
OpenGL_accelerate.arraydatatype.HandlerRegistry.c_get_output_handler  
File "src/arraydatatype.pyx", line 80, in
OpenGL_accelerate.arraydatatype.HandlerRegistry.c_handler_by_plugin_name  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/OpenGL/plugins.py", line 18, in load  
return importByName( self.import_path )  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/OpenGL/plugins.py", line 45, in importByName  
module = __import__( ".".join(moduleName), {}, {}, moduleName)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/OpenGL/arrays/numpymodule.py", line 28, in <module>  
from OpenGL_accelerate.numpy_formathandler import NumpyHandler  
File "src/numpy_formathandler.pyx", line 1, in init
OpenGL_accelerate.numpy_formathandler  
KeyError: ('__reduce_cython__', 1,
<OpenGL.platform.baseplatform.glGenVertexArrays object at 0x11e768350>)  
  
KeyError: ('__reduce_cython__', 1, )  
  
File "src/numpy_formathandler.pyx", line 1, in init
OpenGL_accelerate.numpy_formathandler  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event  
self.status(self._last_message, self._last_color)  
~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 155, in status  
self._draw_text(msg, color, secondary)  
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 165, in _draw_text  
draw_overlays(dlist, self._renderer)  
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 1608, in draw_overlays  
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)  
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 1567, in _draw_multiple  
d.draw(renderer, draw_pass)  
~~~~~~^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 780, in draw  
self.draw_self(renderer, draw_pass)  
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 791, in draw_self  
self._draw_geometry(renderer, transparent_only = any_opaque)  
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 814, in _draw_geometry  
ds.activate_bindings(renderer)  
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 1923, in activate_bindings  
bi.activate()  
~~~~~~~~~~~^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/opengl.py", line 2605, in activate  
self._vao_id = GL.glGenVertexArrays(1)  
~~~~~~~~~~~~~~~~~~~~^^^  
File "src/latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src/wrapper.pyx", line 303, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/wrapper.pyx", line 88, in
OpenGL_accelerate.wrapper.CArgCalculator.c_call  
File "src/wrapper.pyx", line 69, in
OpenGL_accelerate.wrapper.CArgCalculatorElement.c_call  
File "src/wrapper.pyx", line 64, in
OpenGL_accelerate.wrapper.CArgCalculatorElement.c_call  
File "src/arraydatatype.pyx", line 355, in
OpenGL_accelerate.arraydatatype.SizedOutputOrInput.c_call  
File "src/arraydatatype.pyx", line 224, in
OpenGL_accelerate.arraydatatype.ArrayDatatype.c_zeros  
File "src/arraydatatype.pyx", line 69, in
OpenGL_accelerate.arraydatatype.HandlerRegistry.c_get_output_handler  
File "src/arraydatatype.pyx", line 80, in
OpenGL_accelerate.arraydatatype.HandlerRegistry.c_handler_by_plugin_name  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/OpenGL/plugins.py", line 18, in load  
return importByName( self.import_path )  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/OpenGL/plugins.py", line 45, in importByName  
module = __import__( ".".join(moduleName), {}, {}, moduleName)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/OpenGL/arrays/numpymodule.py", line 28, in <module>  
from OpenGL_accelerate.numpy_formathandler import NumpyHandler  
File "src/numpy_formathandler.pyx", line 1, in init
OpenGL_accelerate.numpy_formathandler  
ValueError: ('numpy.dtype size changed, may indicate binary incompatibility.
Expected 96 from C header, got 88 from PyObject', 1,
<OpenGL.platform.baseplatform.glGenVertexArrays object at 0x11e768350>)  
  
ValueError: ('numpy.dtype size changed, may indicate binary incompatibility.
Expected 96 from C header, got 88 from PyObject', 1, )  
  
File "src/numpy_formathandler.pyx", line 1, in init
OpenGL_accelerate.numpy_formathandler  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event  
self.status(self._last_message, self._last_color)  
~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 155, in status  
self._draw_text(msg, color, secondary)  
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 165, in _draw_text  
draw_overlays(dlist, self._renderer)  
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 1608, in draw_overlays  
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)  
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 1567, in _draw_multiple  
d.draw(renderer, draw_pass)  
~~~~~~^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 780, in draw  
self.draw_self(renderer, draw_pass)  
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 791, in draw_self  
self._draw_geometry(renderer, transparent_only = any_opaque)  
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 814, in _draw_geometry  
ds.activate_bindings(renderer)  
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 1923, in activate_bindings  
bi.activate()  
~~~~~~~~~~~^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/opengl.py", line 2605, in activate  
self._vao_id = GL.glGenVertexArrays(1)  
~~~~~~~~~~~~~~~~~~~~^^^  
File "src/latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src/wrapper.pyx", line 303, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/wrapper.pyx", line 88, in
OpenGL_accelerate.wrapper.CArgCalculator.c_call  
File "src/wrapper.pyx", line 69, in
OpenGL_accelerate.wrapper.CArgCalculatorElement.c_call  
File "src/wrapper.pyx", line 64, in
OpenGL_accelerate.wrapper.CArgCalculatorElement.c_call  
File "src/arraydatatype.pyx", line 355, in
OpenGL_accelerate.arraydatatype.SizedOutputOrInput.c_call  
File "src/arraydatatype.pyx", line 224, in
OpenGL_accelerate.arraydatatype.ArrayDatatype.c_zeros  
File "src/arraydatatype.pyx", line 69, in
OpenGL_accelerate.arraydatatype.HandlerRegistry.c_get_output_handler  
File "src/arraydatatype.pyx", line 80, in
OpenGL_accelerate.arraydatatype.HandlerRegistry.c_handler_by_plugin_name  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/OpenGL/plugins.py", line 18, in load  
return importByName( self.import_path )  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/OpenGL/plugins.py", line 45, in importByName  
module = __import__( ".".join(moduleName), {}, {}, moduleName)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/OpenGL/arrays/numpymodule.py", line 28, in <module>  
from OpenGL_accelerate.numpy_formathandler import NumpyHandler  
File "src/numpy_formathandler.pyx", line 1, in init
OpenGL_accelerate.numpy_formathandler  
ValueError: ('numpy.dtype size changed, may indicate binary incompatibility.
Expected 96 from C header, got 88 from PyObject', 1,
<OpenGL.platform.baseplatform.glGenVertexArrays object at 0x11e768350>)  
  
ValueError: ('numpy.dtype size changed, may indicate binary incompatibility.
Expected 96 from C header, got 88 from PyObject', 1, )  
  
File "src/numpy_formathandler.pyx", line 1, in init
OpenGL_accelerate.numpy_formathandler  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event  
self.status(self._last_message, self._last_color)  
~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 155, in status  
self._draw_text(msg, color, secondary)  
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 165, in _draw_text  
draw_overlays(dlist, self._renderer)  
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 1608, in draw_overlays  
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)  
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 1567, in _draw_multiple  
d.draw(renderer, draw_pass)  
~~~~~~^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 780, in draw  
self.draw_self(renderer, draw_pass)  
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 791, in draw_self  
self._draw_geometry(renderer, transparent_only = any_opaque)  
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 814, in _draw_geometry  
ds.activate_bindings(renderer)  
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 1923, in activate_bindings  
bi.activate()  
~~~~~~~~~~~^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/opengl.py", line 2605, in activate  
self._vao_id = GL.glGenVertexArrays(1)  
~~~~~~~~~~~~~~~~~~~~^^^  
File "src/latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src/wrapper.pyx", line 303, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/wrapper.pyx", line 88, in
OpenGL_accelerate.wrapper.CArgCalculator.c_call  
File "src/wrapper.pyx", line 69, in
OpenGL_accelerate.wrapper.CArgCalculatorElement.c_call  
File "src/wrapper.pyx", line 64, in
OpenGL_accelerate.wrapper.CArgCalculatorElement.c_call  
File "src/arraydatatype.pyx", line 355, in
OpenGL_accelerate.arraydatatype.SizedOutputOrInput.c_call  
File "src/arraydatatype.pyx", line 224, in
OpenGL_accelerate.arraydatatype.ArrayDatatype.c_zeros  
File "src/arraydatatype.pyx", line 69, in
OpenGL_accelerate.arraydatatype.HandlerRegistry.c_get_output_handler  
File "src/arraydatatype.pyx", line 80, in
OpenGL_accelerate.arraydatatype.HandlerRegistry.c_handler_by_plugin_name  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/OpenGL/plugins.py", line 18, in load  
return importByName( self.import_path )  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/OpenGL/plugins.py", line 45, in importByName  
module = __import__( ".".join(moduleName), {}, {}, moduleName)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/OpenGL/arrays/numpymodule.py", line 28, in <module>  
from OpenGL_accelerate.numpy_formathandler import NumpyHandler  
File "src/numpy_formathandler.pyx", line 1, in init
OpenGL_accelerate.numpy_formathandler  
ValueError: ('numpy.dtype size changed, may indicate binary incompatibility.
Expected 96 from C header, got 88 from PyObject', 1,
<OpenGL.platform.baseplatform.glGenVertexArrays object at 0x11e768350>)  
  
ValueError: ('numpy.dtype size changed, may indicate binary incompatibility.
Expected 96 from C header, got 88 from PyObject', 1, )  
  
File "src/numpy_formathandler.pyx", line 1, in init
OpenGL_accelerate.numpy_formathandler  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event  
self.status(self._last_message, self._last_color)  
~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 155, in status  
self._draw_text(msg, color, secondary)  
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/ui/statusbar.py", line 165, in _draw_text  
draw_overlays(dlist, self._renderer)  
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 1608, in draw_overlays  
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)  
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 1567, in _draw_multiple  
d.draw(renderer, draw_pass)  
~~~~~~^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 780, in draw  
self.draw_self(renderer, draw_pass)  
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 791, in draw_self  
self._draw_geometry(renderer, transparent_only = any_opaque)  
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 814, in _draw_geometry  
ds.activate_bindings(renderer)  
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/drawing.py", line 1923, in activate_bindings  
bi.activate()  
~~~~~~~~~~~^^  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/graphics/opengl.py", line 2605, in activate  
self._vao_id = GL.glGenVertexArrays(1)  
~~~~~~~~~~~~~~~~~~~~^^^  
File "src/latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src/wrapper.pyx", line 303, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/wrapper.pyx", line 88, in
OpenGL_accelerate.wrapper.CArgCalculator.c_call  
File "src/wrapper.pyx", line 69, in
OpenGL_accelerate.wrapper.CArgCalculatorElement.c_call  
File "src/wrapper.pyx", line 64, in
OpenGL_accelerate.wrapper.CArgCalculatorElement.c_call  
File "src/arraydatatype.pyx", line 355, in
OpenGL_accelerate.arraydatatype.SizedOutputOrInput.c_call  
File "src/arraydatatype.pyx", line 224, in
OpenGL_accelerate.arraydatatype.ArrayDatatype.c_zeros  
File "src/arraydatatype.pyx", line 69, in
OpenGL_accelerate.arraydatatype.HandlerRegistry.c_get_output_handler  
File "src/arraydatatype.pyx", line 80, in
OpenGL_accelerate.arraydatatype.HandlerRegistry.c_handler_by_plugin_name  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/OpenGL/plugins.py", line 18, in load  
return importByName( self.import_path )  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/OpenGL/plugins.py", line 45, in importByName  
module = __import__( ".".join(moduleName), {}, {}, moduleName)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/OpenGL/arrays/numpymodule.py", line 28, in <module>  
from OpenGL_accelerate.numpy_formathandler import NumpyHandler  
File "src/numpy_formathandler.pyx", line 1, in init
OpenGL_accelerate.numpy_formathandler  
ValueError: ('numpy.dtype size changed, may indicate binary incompatibility.
Expected 96 from C header, got 88 from PyObject', 1,
<OpenGL.platform.baseplatform.glGenVertexArrays object at 0x11e768350>)  
  
ValueError: ('numpy.dtype size changed, may indicate binary incompatibility.
Expected 96 from C header, got 88 from PyObject', 1, )  
  
File "src/numpy_formathandler.pyx", line 1, in init
OpenGL_accelerate.numpy_formathandler  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3
OpenGL vendor: Apple

Python: 3.13.1
Locale: en_US.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: iMac
      Model Identifier: Mac15,5
      Model Number: Z19K0011DLL/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 10 hours, 16 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 4.5K (4480 x 2520)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          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: 2024.12.14
    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: 2.16.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.59
    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: 1.0.2
    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: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202412210159
    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: 1.2.7
    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: 1.5.1
    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: 2.7.7
    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-ProfileGrids: 1.0
    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: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.15
    ChimeraX-Shape: 1.1
    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: 1.19.1
    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: 2.5.1
    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: 1.42.2
    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: 1.8.11
    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: 2024.9.22
    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: 5.3.0
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.7.2
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.0.1
    numexpr: 2.10.2
    numpy: 2.1.3
    numpy: 2.2.0
    OpenMM: 8.2.0
    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
    plotly: 5.24.1
    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
    pyKVFinder: 0.7.1
    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: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine: 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: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.1
    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

Change History (6)

comment:1 by Eric Pettersen, 11 months ago

Cc: chimera-programmers added
Component: Unassigned → Build System
Owner: set to Zach Pearson
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Various startup errors

comment:2 by Zach Pearson, 11 months ago

What happens if you go to prereqs/pips, delete the PyOpenGL_accelerate wheel, redownload it and install it?

comment:3 by Eric Pettersen, 11 months ago

Basically the same. Maybe we can see how the daily build works tomorrow to determine if somehow it has to do with my machine or build environment.

comment:4 by Zach Pearson, 11 months ago

I was able to get ahold of a mac ARM daily build and tried it out on Chloe's computer; that worked

comment:5 by Zach Pearson, 11 months ago

I don't see my previous comment, but the gist of it was that I tried the Windows and Ubuntu builds and that I'd get back to you when I had a working mac build to try.

comment:6 by Eric Pettersen, 11 months ago

Resolution: → duplicate
Status: assigned → closed

Closing this one since #16515 is from the actual daily build rather than my personal build.

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