Opened 11 months ago

Closed 11 months ago

Last modified 11 months ago

#16515 closed defect (not a bug)

Startup errors from the 12/21 daily build

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.dev202412210559 (2024-12-21 05:59:26 UTC)
Description
Startup errors from the 12/21 daily build

Log:
Startup Errors  
---  
errors | Bundle 'ChimeraX-Segmentations' custom initialization failed  
Bundle 'ChimeraX-Dicom' custom initialization failed  
warnings | Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily-12-21.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
"/Applications/ChimeraX_Daily-12-21.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
"/Applications/ChimeraX_Daily-12-21.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
"/Applications/ChimeraX_Daily-12-21.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
"/Applications/ChimeraX_Daily-12-21.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
"/Applications/ChimeraX_Daily-12-21.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
"/Applications/ChimeraX_Daily-12-21.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
"/Applications/ChimeraX_Daily-12-21.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
"/Applications/ChimeraX_Daily-12-21.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
"/Applications/ChimeraX_Daily-12-21.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)  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily-12-21.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
"/Applications/ChimeraX_Daily-12-21.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
"/Applications/ChimeraX_Daily-12-21.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
"/Applications/ChimeraX_Daily-12-21.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
"/Applications/ChimeraX_Daily-12-21.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
"/Applications/ChimeraX_Daily-12-21.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
"/Applications/ChimeraX_Daily-12-21.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
"/Applications/ChimeraX_Daily-12-21.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
"/Applications/ChimeraX_Daily-12-21.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
"/Applications/ChimeraX_Daily-12-21.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
"/Applications/ChimeraX_Daily-12-21.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)  
notes | available bundle cache has not been initialized yet  
/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/map/volume.py:3894: SyntaxWarning: invalid escape sequence
'\\*'  
'''  
  
UCSF ChimeraX version: 1.10.dev202412210559 (2024-12-21)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




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

Python: 3.13.1
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: 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: 2 hours, 17 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.dev202412210559
    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
    coverage: 7.6.9
    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
    iniconfig: 2.0.0
    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
    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
    pluggy: 1.5.0
    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: 1.1.1
    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
    pytest: 8.3.4
    pytest-cov: 6.0.0
    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

Component: Unassigned → Build System
Owner: set to Zach Pearson
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Startup errors from the 12/21 daily build

comment:2 by Eric Pettersen, 11 months ago

Cc: chimera-programmers added

comment:3 by Zach Pearson, 11 months ago

OK, this ticket is a significant improvement actually because while the original circular import is there the rest of the errors, which had to do with OpenGL, are gone.

comment:4 by Zach Pearson, 11 months ago

Resolution: → not a bug
Status: assigned → closed

I notice that ChimeraX says you have two versions of matplotlib. One is in /Users/pett/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/ and is undoubtedly built for Python 3.11. The other is in the ChimeraX distribution. Delete the Python 3.11 packages in ~/Library/Application Support/ChimeraX/1.10

comment:5 by Eric Pettersen, 11 months ago

Yep, that cleared the startup errors, though it's unfortunate that this will plague any users where installing bundles caused these packages to go into their user-specific installation area.

comment:6 by Greg Couch, 11 months ago

All toolshed bundle installation is supposed to go into the user-specific installation area. And the bundles should be for a particular ChimeraX version.

Isn't the real problem that a user has installed a bundle and/or associated Python packages, and we changed the version of Python without changing the version of ChimeraX? This should only be an issue with daily builds early in the release cycle.

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