Opened 19 months ago

Closed 19 months ago

#14778 closed defect (limitation)

scipy built for MacOS 12

Reported by: m.patzschke@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Build System Version:
Keywords: Cc: Tony Schaefer, Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-11.7.10-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Errors  
---  
errors | Bundle 'SEQCROW' custom initialization failed  
Bundle 'SEQCROW' custom initialization failed  
warnings | Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1298, in init_manager  
return cls._get_func(api, "init_manager")(session, bi, name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/michaelp/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/SEQCROW/__init__.py", line 335,
in init_manager  
from .managers import FileReaderManager  
File "/Users/michaelp/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/SEQCROW/managers/__init__.py",
line 1, in <module>  
from .filereader_manager import FileReaderManager, FILEREADER_CHANGE,
FILEREADER_REMOVED, FILEREADER_ADDED, ADD_FILEREADER  
File "/Users/michaelp/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/SEQCROW/managers/filereader_manager.py", line 10, in <module>  
from AaronTools.fileIO import FileReader  
File "/Users/michaelp/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/AaronTools/fileIO.py", line 15,
in <module>  
from AaronTools.orbitals import Orbitals  
File "/Users/michaelp/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/AaronTools/orbitals.py", line 5,
in <module>  
from scipy.spatial import distance_matrix  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/spatial/__init__.py", line 116, in <module>  
from ._geometric_slerp import geometric_slerp  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/spatial/_geometric_slerp.py", line 9, in <module>  
from scipy.spatial.distance import euclidean  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/spatial/distance.py", line 121, in <module>  
from ..special import rel_entr  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/__init__.py", line 772, in <module>  
from . import _ufuncs  
File "scipy/special/_ufuncs.pyx", line 1, in init scipy.special._ufuncs  
ImportError:
dlopen(/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so, 2): Symbol not
found:
__ZNKSt3__115basic_stringbufIcNS_11char_traitsIcEENS_9allocatorIcEEE3strEv  
Referenced from:
/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so (which was built for
Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  
  
  
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 376, in initialize  
api._api_caller.initialize(api, session, self)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1294, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/michaelp/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/SEQCROW/__init__.py", line 73,
in initialize  
from SEQCROW.mouse_modes import (  
File "/Users/michaelp/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/SEQCROW/mouse_modes.py", line
23, in <module>  
from SEQCROW.managers.filereader_manager import apply_seqcrow_preset  
File "/Users/michaelp/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/SEQCROW/managers/__init__.py",
line 1, in <module>  
from .filereader_manager import FileReaderManager, FILEREADER_CHANGE,
FILEREADER_REMOVED, FILEREADER_ADDED, ADD_FILEREADER  
File "/Users/michaelp/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/SEQCROW/managers/filereader_manager.py", line 10, in <module>  
from AaronTools.fileIO import FileReader  
File "/Users/michaelp/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/AaronTools/fileIO.py", line 15,
in <module>  
from AaronTools.orbitals import Orbitals  
File "/Users/michaelp/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/AaronTools/orbitals.py", line 5,
in <module>  
from scipy.spatial import distance_matrix  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/spatial/__init__.py", line 116, in <module>  
from ._geometric_slerp import geometric_slerp  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/spatial/_geometric_slerp.py", line 9, in <module>  
from scipy.spatial.distance import euclidean  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/spatial/distance.py", line 121, in <module>  
from ..special import rel_entr  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/__init__.py", line 772, in <module>  
from . import _ufuncs  
File "scipy/special/_ufuncs.pyx", line 1, in init scipy.special._ufuncs  
ImportError:
dlopen(/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so, 2): Symbol not
found:
__ZNKSt3__115basic_stringbufIcNS_11char_traitsIcEENS_9allocatorIcEEE3strEv  
Referenced from:
/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so (which was built for
Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/michaelp/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/SEQCROW/__init__.py", line 60,
in <lambda>  
lambda *args, ses=session: _SEQCROW_API.register_selector_menus(ses)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/michaelp/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/SEQCROW/__init__.py", line 1062,
in register_selector_menus  
from AaronTools.substituent import Substituent  
File "/Users/michaelp/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/AaronTools/substituent.py", line
14, in <module>  
from AaronTools.fileIO import FileReader, read_types  
File "/Users/michaelp/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/AaronTools/fileIO.py", line 15,
in <module>  
from AaronTools.orbitals import Orbitals  
File "/Users/michaelp/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/AaronTools/orbitals.py", line 5,
in <module>  
from scipy.spatial import distance_matrix  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/spatial/__init__.py", line 116, in <module>  
from ._geometric_slerp import geometric_slerp  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/spatial/_geometric_slerp.py", line 9, in <module>  
from scipy.spatial.distance import euclidean  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/spatial/distance.py", line 121, in <module>  
from ..special import rel_entr  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/__init__.py", line 772, in <module>  
from . import _ufuncs  
File "scipy/special/_ufuncs.pyx", line 1, in init scipy.special._ufuncs  
ImportError:
dlopen(/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so, 2): Symbol not
found:
__ZNKSt3__115basic_stringbufIcNS_11char_traitsIcEENS_9allocatorIcEEE3strEv  
Referenced from:
/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so (which was built for
Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  
  
  
Error processing trigger "ready":  
ImportError:
dlopen(/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so, 2): Symbol not
found:
__ZNKSt3__115basic_stringbufIcNS_11char_traitsIcEENS_9allocatorIcEEE3strEv  
Referenced from:
/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/special/_ufuncs_cxx.cpython-311-darwin.so (which was built for
Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  
  
  
File "scipy/special/_ufuncs.pyx", line 1, in init scipy.special._ufuncs  
  
See log for complete Python traceback.  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 71.7.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.61.4
      OS Loader Version: 6723.140.2

Software:

    System Software Overview:

      System Version: macOS 11.7.10 (20G1427)
      Kernel Version: Darwin 20.6.0
      Time since boot: 69 days 23:38

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Resolution: 3360 x 2100
          UI Looks like: 1680 x 1050 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    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
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    Send2Trash: 1.8.2
    SEQCROW: 1.8.7
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 19 months ago

Cc: Tony Schaefer Greg Couch added
Component: Unassigned → Build System
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → scipy built for MacOS 12

Reported by Michael Patzschke

comment:2 by Tom Goddard, 19 months ago

Resolution: → limitation
Status: assigned → closed

Unfortunately the Mac ARM scipy PyPi distribution requires macOS 12 or newer. ChimeraX uses scipy only for computing curved helix tubes, rarely used. This bug was from seqcrow. We will not build our own scipy on older macOS, too little benefit and too much maintenance burden. Users who stay with obsolete macOS versions can also stick with old ChimeraX versions. I think ChimeraX 1.6 or 1.5 has working scipy on macos 11.

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