id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
8874	Invalid code signature	dchakka@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6rc202304140213 (2023-04-14 02:13:32 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
{""app_name"":""ChimeraX"",""timestamp"":""2023-04-19 15:12:09.00 -0500"",""app_version"":""1.6.0"",""slice_uuid"":""5df621ee-554e-36a8-b448-93b2334e5480"",""build_version"":""1.6.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.1 (22C65)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""E9E51D77-375B-482B-9F96-300183D9F93A""}
{
  ""uptime"" : 530000,
  ""procRole"" : ""Default"",
  ""version"" : 2,
  ""userID"" : 118146003,
  ""deployVersion"" : 210,
  ""modelCode"" : ""iMac18,3"",
  ""coalitionID"" : 78287,
  ""osVersion"" : {
    ""train"" : ""macOS 13.1"",
    ""build"" : ""22C65"",
    ""releaseType"" : ""User""
  },
  ""captureTime"" : ""2023-04-19 15:12:09.3161 -0500"",
  ""incident"" : ""E9E51D77-375B-482B-9F96-300183D9F93A"",
  ""pid"" : 98543,
  ""cpuType"" : ""X86-64"",
  ""roots_installed"" : 0,
  ""bug_type"" : ""309"",
  ""procLaunch"" : ""2023-04-19 15:12:09.2164 -0500"",
  ""procStartAbsTime"" : 535826356695606,
  ""procExitAbsTime"" : 535826455969080,
  ""procName"" : ""ChimeraX"",
  ""procPath"" : ""\/private\/var\/folders\/*\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX"",
  ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.0"",""CFBundleVersion"":""1.6.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""},
  ""storeInfo"" : {""deviceIdentifierForVendor"":""471B0B06-EFA9-57FC-A0A8-8A72CC205415"",""thirdParty"":true},
  ""parentProc"" : ""launchd"",
  ""parentPid"" : 1,
  ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"",
  ""crashReporterKey"" : ""C8BC94E2-D988-7F8C-FDD6-05F4001788FA"",
  ""throttleTimeout"" : 2147483647,
  ""sip"" : ""enabled"",
  ""exception"" : {""codes"":""0x0000000000000000, 0x0000000000000000"",""rawCodes"":[0,0],""type"":""EXC_CRASH"",""signal"":""SIGABRT""},
  ""termination"" : {""code"":1,""flags"":518,""namespace"":""DYLD"",""indicator"":""Library missing"",""details"":[""(terminated at launch; ignore backtrace)""],""reasons"":[""Library not loaded: @rpath\/Versions\/3.9\/Python"",""Referenced from:  \/private\/var\/folders\/*\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX"",""Reason: tried: '\/private\/var\/folders\/hw\/5c7mzchj28b6bj5mlph4cz6h3hnhyl\/T\/AppTranslocation\/F5DAEB7E-F83A-4C69-BAEC-E20EAC89FB22\/d\/ChimeraX_Daily.app\/Contents\/lib\/Versions\/3.9\/Python' (no such file), '\/private\/var\/folders\/hw\/5c7mzchj28b6bj5mlph4cz6h3hnhyl\/T\/AppTranslocation\/F5DAEB7E-F83A-4C69-BAEC-E20EAC89FB22\/d\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python' (code signature invalid in  '\/private\/var\/folders\/hw\/5c7mzchj28b6bj5mlph4cz6h3hnhyl\/T\/AppTranslocation\/F5DAEB7E-F83A-4C69-BAEC-E20EAC89FB22\/d\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python' (errno=1) sliceOffset=0x00004000, codeBlobOffset=0x00380270, codeBlobSize=0x000102A0), '\/private\/v""]},
  ""extMods"" : {""caller"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""system"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""targeted"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""warnings"":0},
  ""faultingThread"" : 0,
  ""threads"" : [{""triggered"":true,""id"":7440469,""threadState"":{""r13"":{""value"":140701997090896},""rax"":{""value"":33554953},""rflags"":{""value"":582},""cpu"":{""value"":0},""r14"":{""value"":1},""rsi"":{""value"":1},""r8"":{""value"":140701997089872},""cr2"":{""value"":4352266240},""rdx"":{""value"":140701997090896},""r10"":{""value"":203},""r9"":{""value"":0},""r15"":{""value"":6},""rbx"":{""value"":0},""trap"":{""value"":133},""err"":{""value"":33554953},""r11"":{""value"":582},""rip"":{""value"":140703325346634,""matchesCrashFrame"":1},""rbp"":{""value"":140701997089840},""rsp"":{""value"":140701997089768},""r12"":{""value"":203},""rcx"":{""value"":140701997089768},""flavor"":""x86_THREAD_STATE"",""rdi"":{""value"":6}},""frames"":[{""imageOffset"":432970,""symbol"":""__abort_with_payload"",""symbolLocation"":10,""imageIndex"":0},{""imageOffset"":535815,""symbol"":""abort_with_payload_wrapper_internal"",""symbolLocation"":82,""imageIndex"":0},{""imageOffset"":535865,""symbol"":""abort_with_payload"",""symbolLocation"":9,""imageIndex"":0},{""imageOffset"":41441,""symbol"":""dyld4::halt(char const*)"",""symbolLocation"":375,""imageIndex"":0},{""imageOffset"":30304,""symbol"":""dyld4::prepare(dyld4::APIs&, dyld3::MachOAnalyzer const*)"",""symbolLocation"":4502,""imageIndex"":0},{""imageOffset"":25217,""symbol"":""start"",""symbolLocation"":2289,""imageIndex"":0}]}],
  ""usedImages"" : [
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703324913664,
    ""size"" : 609392,
    ""uuid"" : ""bb7a0970-8c62-3dce-a7a2-5cec9c501f11"",
    ""path"" : ""\/usr\/lib\/dyld"",
    ""name"" : ""dyld""
  }
],
  ""sharedCache"" : {
  ""base"" : 140703324307456,
  ""size"" : 21474836480,
  ""uuid"" : ""ea7f9772-219e-3ece-a4d9-20aeee3bc80f""
},
  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=182.3M resident=0K(0%) swapped_out_or_unallocated=182.3M(100%)\nWritable regions: Total=8708K written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=8708K(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nSTACK GUARD                       56.0M        1 \nStack                             8192K        1 \nVM_ALLOCATE                          8K        2 \n__DATA                              15K        2 \n__DATA_CONST                        20K        1 \n__DATA_DIRTY                         7K        1 \n__LINKEDIT                       181.7M        3 \n__TEXT                             600K        2 \ndyld private memory                512K        2 \nshared memory                        4K        1 \n===========                     =======  ======= \nTOTAL                            246.9M       16 \n"",
  ""legacyInfo"" : {
  ""threadTriggered"" : {

  }
},
  ""trialInfo"" : {
  ""rollouts"" : [
    {
      ""rolloutId"" : ""62699e1ec1ff2978b47f6c3b"",
      ""factorPackIds"" : {
        ""SIRI_FIND_MY_CONFIGURATION_FILES"" : ""631f72d1de559130376df1fb""
      },
      ""deploymentId"" : 240000023
    },
    {
      ""rolloutId"" : ""60356660bbe37970735c5624"",
      ""factorPackIds"" : {

      },
      ""deploymentId"" : 240000027
    }
  ],
  ""experiments"" : [
    {
      ""treatmentId"" : ""c28e4ee6-1b08-4f90-8e05-2809e78310a3"",
      ""experimentId"" : ""6317d2003d24842ff850182a"",
      ""deploymentId"" : 400000013
    }
  ]
}
}


Log:
UCSF ChimeraX version: 1.6rc202304140213 (2023-04-14)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 ATI-4.9.51
OpenGL renderer: AMD Radeon Pro 570 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 3.4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 16 GB
      System Firmware Version: 499.40.2.0.0
      OS Loader Version: 564.40.4~55
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 13.1 (22C65)
      Kernel Version: Darwin 22.2.0
      Time since boot: 6 days, 4 hours, 55 minutes

Graphics/Displays:

    Radeon Pro 570:

      Chipset Model: Radeon Pro 570
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c5
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1L-025
      EFI Driver Version: 01.00.931
      Metal Support: Metal 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2718Q:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 4K8X777U1NFL
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9
    ChimeraX-AddH: 2.2.4
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    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: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    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: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6rc202304140213
    ChimeraX-CoreFormats: 1.1
    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: 1.1.1
    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: 1.2.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.2
    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: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.3.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.2.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    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: 2.4
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

}}}
"	defect	feedback	normal		Platform				Tom Goddard				all	ChimeraX