Opened 3 weeks ago

Closed 8 days ago

#19769 closed defect (invalid)

Wayland causing scipy problem?

Reported by: chimerax-bug-report@… Owned by: Zach Pearson
Priority: normal Milestone:
Component: Platform Version:
Keywords: Cc: Tony Schaefer, chimera-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.14.0-37-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Errors  
---  
errors | Bundle 'SEQCROW' custom initialization failed  
Bundle 'SEQCROW' custom initialization failed  
warnings | Traceback (most recent call last):  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/__init__.py", line 83, in <module>  
from scipy._lib._ccallback import LowLevelCallable  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/_lib/_ccallback.py", line 1, in <module>  
from . import _ccallback_c  
ImportError: cannot import name '_ccallback_c' from 'scipy._lib'
(/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/_lib/__init__.py)  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 387, in init_manager  
return api._api_caller.init_manager(api, session, self, name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1416, in init_manager  
return cls._get_func(api, "init_manager")(session, bi, name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/SEQCROW/__init__.py", line 347, in init_manager  
from .managers import FileReaderManager  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/SEQCROW/managers/__init__.py", line 1, in <module>  
from .filereader_manager import FileReaderManager, FILEREADER_CHANGE,
FILEREADER_REMOVED, FILEREADER_ADDED, ADD_FILEREADER  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/SEQCROW/managers/filereader_manager.py", line 10, in <module>  
from AaronTools.fileIO import FileReader  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/AaronTools/fileIO.py", line 16, in <module>  
from AaronTools.orbitals import Orbitals  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 6, in <module>  
from scipy.spatial.distance import pdist, cdist, squareform  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/__init__.py", line 88, in <module>  
raise ImportError(msg) from e  
ImportError: The `scipy` install you are using seems to be broken, (extension
modules cannot be imported), please try reinstalling.  
  
Traceback (most recent call last):  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/__init__.py", line 83, in <module>  
from scipy._lib._ccallback import LowLevelCallable  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/_lib/_ccallback.py", line 1, in <module>  
from . import _ccallback_c  
ImportError: cannot import name '_ccallback_c' from 'scipy._lib'
(/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/_lib/__init__.py)  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 376, in initialize  
api._api_caller.initialize(api, session, self)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1412, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/SEQCROW/__init__.py", line 73, in initialize  
from SEQCROW.mouse_modes import (  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/SEQCROW/mouse_modes.py", line 23, in <module>  
from SEQCROW.managers.filereader_manager import apply_seqcrow_preset  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/SEQCROW/managers/__init__.py", line 1, in <module>  
from .filereader_manager import FileReaderManager, FILEREADER_CHANGE,
FILEREADER_REMOVED, FILEREADER_ADDED, ADD_FILEREADER  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/SEQCROW/managers/filereader_manager.py", line 10, in <module>  
from AaronTools.fileIO import FileReader  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/AaronTools/fileIO.py", line 16, in <module>  
from AaronTools.orbitals import Orbitals  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/AaronTools/orbitals.py", line 6, in <module>  
from scipy.spatial.distance import pdist, cdist, squareform  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/__init__.py", line 88, in <module>  
raise ImportError(msg) from e  
ImportError: The `scipy` install you are using seems to be broken, (extension
modules cannot be imported), please try reinstalling.  
  
GBM is not supported with the current configuration. Fallback to Vulkan
rendering in Chromium.  
  
Traceback (most recent call last):  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/__init__.py", line 83, in <module>  
from scipy._lib._ccallback import LowLevelCallable  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/_lib/_ccallback.py", line 1, in <module>  
from . import _ccallback_c  
ImportError: cannot import name '_ccallback_c' from 'scipy._lib'
(/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/_lib/__init__.py)  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/SEQCROW/__init__.py", line 60, in <lambda>  
lambda *args, ses=session: _SEQCROW_API.register_selector_menus(ses)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/SEQCROW/__init__.py", line 1145, in register_selector_menus  
from AaronTools.geometry import Geometry  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/AaronTools/geometry.py", line 11, in <module>  
from scipy.spatial import distance_matrix, distance  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/__init__.py", line 88, in <module>  
raise ImportError(msg) from e  
ImportError: The `scipy` install you are using seems to be broken, (extension
modules cannot be imported), please try reinstalling.  
  
Error processing trigger "ready":  
ImportError: The `scipy` install you are using seems to be broken, (extension
modules cannot be imported), please try reinstalling.  
  
File "/home/wangyunjin/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/scipy/__init__.py", line 88, in  
raise ImportError(msg) from e  
  
See log for complete Python traceback.  
  
UCSF ChimeraX version: 1.11 (2025-12-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 580.126.09
OpenGL renderer: NVIDIA GeForce GTX 1070 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.13
Locale: zh_CN.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu-wayland
XDG_SESSION_DESKTOP=ubuntu-wayland
XDG_CURRENT_DESKTOP=ubuntu:GNOME
GNOME_SETUP_DISPLAY=:2
DISPLAY=:1
WAYLAND_DISPLAY=wayland-0
Manufacturer: HUANANZHI
Model: 
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 88 Intel(R) Xeon(R) CPU E5-2696 v4 @ 2.20GHz
Cache Size: 56320 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           125Gi       7.2Gi       108Gi       253Mi        11Gi       118Gi
	Swap:          8.0Gi          0B       8.0Gi

Graphics:
	05:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Lexa XT [Radeon PRO WX 3100] [1002:6985]	
	Subsystem: Dell Lexa XT [Radeon PRO WX 3100] [1028:0b0c]	
	Kernel driver in use: amdgpu

Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.0
    appdirs: 1.4.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2025.11.12
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DAQplugin: 0.13.0
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    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: 1.0.1
    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: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.11
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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: 2.5.2
    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: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.25.1
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.2.5
    pyproject_hooks: 1.2.0
    PyQt6: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pytz: 2025.2
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.0.0
    roman-numerals-py: 4.0.0
    rpds-py: 0.30.0
    scipy: 1.16.1
    scipy: 1.14.0
    SEQCROW: 1.9.7
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    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
    sse-starlette: 3.0.4
    stack-data: 0.6.3
    starlette: 0.50.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2025.3
    urllib3: 2.6.2
    uvicorn: 0.38.0
    wcwidth: 0.2.14
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    yarl: 1.22.0

Change History (4)

comment:1 by Eric Pettersen, 3 weeks ago

Cc: Tony Schaefer chimera-programmers added
Component: Unassigned → Platform
Owner: set to Zach Pearson
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Wayland causing scipy problem?

comment:2 by Zach Pearson, 2 weeks ago

scipy is listed twice in your list of installed packages. One is 1.14.0 and the other is 1.16.1

If SEQCROW is installing its own version of scipy, you could pin it to the version ChimeraX uses (1.14.0)

comment:3 by Tony Schaefer, 2 weeks ago 

Zach,

seqcrow does list scipy as a dependency, but it does not request a specific
version of scipy. I could be mistaken, but I don't think that would trigger
scipy to get installed. It's possible this report is not the first time the
user encountered this error, and tried to run `pip install scipy upgrade
true` prior to reporting to try to fix this. I'm not exactly sure what's
going on here, though.

Best,

Tony

On Wed, Jan 28, 2026 at 2:32 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>

comment:4 by Zach Pearson, 8 days ago

Resolution: → invalid
Status: assigned → closed

Hm. We've had situations before where numpy was installed once in ChimeraX and another time in the user site-packages directory, but things ran fine because the ChimeraX numpy loaded first. I'm not sure if that happens deterministically for all dependencies of all bundles or not, but the user's program is in essentially an "undefined" state. They should delete the second scipy, see if the error still occurs, and open a new ticket if so.

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