AmberTools 24 breaks Mac ChimeraX verification

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.9.dev202408060516 (2024-08-06 05:16:11 UTC)
Description
Yesterday's Mac ChimeraX daily build said "developer unknown" when I downloaded and tried to start it.  The build log claimed the notarization succeeded.  We saw this several months ago when AmberTools was updated, and Eric just updated AmberTools last week, so we reverted to the old AmberTools 20 version last night and the builds last night now open correctly.

So it appears that AmberTools 24 introduces some problem that the Mac notarization/verification does not like.  The one thing I have seen cause this in the past is binaries or libraries referencing dynamically loaded non-system libraries outside the ChimeraX app.  A first step to fix this would be to look for such library dependencies (with otool) in all AmberTools 24 binaries.  If that turns up nothing you could remove all the AmberTools binaries and notarize and see if it opens (might need to download from web too).  Assuming that works, start adding back binaries until you find the one Apple does not like.

Unfortunately when I tried debugging this in the past Apple's notarytool including verification did not indicate any problem.  But it would be worth check the build output to see if notarization output gives any clues.


Log:
UCSF ChimeraX version: 1.9.dev202408060516 (2024-08-06)  
© 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 M1 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Model Number: MK1H3LL/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 10151.121.1

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 14 days, 2 hours, 37 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.14
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.5
    ChimeraX-AtomicLibrary: 14.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    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: 2.2.5
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9.dev202408060516
    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-DeepMutationalScan: 1.0
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    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-Foldseek: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.3
    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: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.7
    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: 2.1.5
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NIHPresets: 1.1.18
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.1.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.13
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18
    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
    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: 1.40.1
    ChimeraX-Ummbas-Anaglyph: 0.1
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.2.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.5
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.15.4
    fonttools: 4.53.1
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    Jinja2: 3.1.4
    joblib: 1.4.2
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.11
    kiwisolver: 1.4.5
    line_profiler: 4.1.3
    llvmlite: 0.43.0
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.9.1
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numba: 0.60.0
    numexpr: 2.10.1
    numpy: 1.26.4
    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: 4.2.2
    prompt_toolkit: 3.0.47
    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
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynndescent: 0.5.13
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject_hooks: 1.1.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.2
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.2
    PyQt6-WebEngineSubwheel-Qt6: 6.7.2
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.1.0
    qtconsole: 5.5.2
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.32.3
    scikit-learn: 1.5.1
    scipy: 1.14.0
    setuptools: 72.1.0
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    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: 3.8.0
    tcia_utils: 1.5.1
    threadpoolctl: 3.5.0
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.1
    tqdm: 4.66.4
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.1
    umap-learn: 0.5.6
    urllib3: 2.2.2
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11