Changes between Initial Version and Version 1 of Ticket #6426


Ignore:
Timestamp:
Mar 22, 2022, 9:48:20 AM (4 years ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
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  • Ticket #6426

    • Property Component UnassignedWindow Toolkit
    • Property Owner set to Tom Goddard
    • Property Platformall
    • Property ProjectChimeraX
    • Property Status newassigned
    • Property Summary ChimeraX bug report submissionCrash in self.graphics_window.mapFromGlobal(QCursor.pos())
  • Ticket #6426 – Description

    initial v1  
    1313  File "/private/var/folders/d5/32cnx92x3j90t8qyqsk66k1r0000gn/T/AppTranslocation/E2C81661-E619-4B7F-B28B-8A4E579BBC8B/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 140 in _redraw_timer_callback
    1414  File "/private/var/folders/d5/32cnx92x3j90t8qyqsk66k1r0000gn/T/AppTranslocation/E2C81661-E619-4B7F-B28B-8A4E579BBC8B/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py301event_loop/private/var/folders/d5/32cnx92x3j90t8qyqsk66k1r0000gn/T/AppTranslocation/E2C81661-E619-4B7F-B28B-8A4E579BBC8B/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py867init/private/var/folders/d5/32cnx92x3j90t8qyqsk66k1r0000gn/T/AppTranslocation/E2C81661-E619-4B7F-B28B-8A4E579BBC8B/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py1018/private/var/folders/d5/32cnx92x3j90t8qyqsk66k1r0000gn/T/AppTranslocation/E2C81661-E619-4B7F-B28B-8A4E579BBC8B/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py87_run_code/private/var/folders/d5/32cnx92x3j90t8qyqsk66k1r0000gn/T/AppTranslocation/E2C81661-E619-4B7F-B28B-8A4E579BBC8B/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py197_run_module_as_main
     15
     16{"app_name":"ChimeraX","timestamp":"2022-03-21 22:03:58.00 +0000","app_version":"","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"","platform":1,"share_with_app_devs":0,"is_first_party":1,"bug_type":"309","os_version":"macOS 12.2.1 (21D62)","incident_id":"34F5F925-E9FE-465C-B336-7119F697F267","name":"ChimeraX"}
     17{
     18  "uptime" : 93000,
     19  "procLaunch" : "2022-03-21 22:01:44.9893 +0000",
     20  "procRole" : "Background",
     21  "version" : 2,
     22  "userID" : 501,
     23  "deployVersion" : 210,
     24  "modelCode" : "MacBookPro17,1",
     25  "procStartAbsTime" : 2229679948605,
     26  "coalitionID" : 15006,
     27  "osVersion" : {
     28    "train" : "macOS 12.2.1",
     29    "build" : "21D62",
     30    "releaseType" : "User"
     31  },
     32  "captureTime" : "2022-03-21 22:03:57.9154 +0000",
     33  "incident" : "34F5F925-E9FE-465C-B336-7119F697F267",
     34  "bug_type" : "309",
     35  "pid" : 19923,
     36  "procExitAbsTime" : 2232869602972,
     37  "translated" : true,
     38  "cpuType" : "X86-64",
     39  "procName" : "ChimeraX",
     40  "procPath" : "\/private\/var\/folders\/*\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
     41  "parentProc" : "launchd",
     42  "parentPid" : 1,
     43  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
     44  "crashReporterKey" : "67917E8B-5E8A-6D38-1B8F-04211C93A8DF",
     45  "wakeTime" : 320,
     46  "sleepWakeUUID" : "A5DFE8CF-D230-4F2A-924E-F13A2F199D9C",
     47  "sip" : "enabled",
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     49  "isCorpse" : 1,
     50  "exception" : {"codes":"0x000000000000000a, 0x000000012a44c020","rawCodes":[10,5004116000],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_MEMORY_ERROR at 0x000000012a44c020"},
     51  "ktriageinfo" : "VM - Object is not alive\n",
     52  "vmregioninfo" : "0x12a44c020 is in 0x12a302000-0x12a471000;  bytes after start: 1351712  bytes before end: 151519\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      Mach message                12a2ff000-12a300000    [    4K] rw-\/rwx SM=PRV  \n      GAP OF 0x2000 BYTES\n--->  mapped file                 12a302000-12a471000    [ 1468K] r-x\/rwx SM=COW  ...t_id=6c5581c9\n      mapped file                 12a471000-12a489000    [   96K] rw-\/rwx SM=COW  ...t_id=64e79ac9",
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     126  "vmSummary" : "ReadOnly portion of Libraries: Total=206.0M resident=0K(0%) swapped_out_or_unallocated=206.0M(100%)\nWritable regions: Total=2.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.1G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               512K        4 \nActivity Tracing                   256K        1 \nCG backing stores                 2176K        4 \nCG image                          1572K       51 \nColorSync                          240K       28 \nCoreAnimation                     2488K       22 \nCoreGraphics                        12K        2 \nCoreUI image data                 4660K       34 \nFoundation                          16K        1 \nKernel Alloc Once                    8K        1 \nMALLOC                           363.2M       70 \nMALLOC guard page                  192K        9 \nMALLOC_MEDIUM (reserved)         888.0M        8         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)\nMach message                        24K        6 \nOpenGL GLSL                        384K        5 \nRosetta Arena                     4096K        2 \nRosetta Generic                   1676K      416 \nRosetta IndirectBranch            2048K        1 \nRosetta JIT                      128.0M        1 \nRosetta Return Stack               520K       52 \nRosetta Thread Context             520K       52 \nSTACK GUARD                         40K       10 \nStack                            133.6M       27 \nStack Guard                       56.1M       17 \nVM_ALLOCATE                      102.3M      187 \nVM_ALLOCATE (reserved)           160.0M        8         reserved VM address space (unallocated)\n__DATA                             355K       45 \n__DATA_CONST                      3031K       39 \n__DATA_DIRTY                        79K       24 \n__LINKEDIT                       193.1M        7 \n__OBJC_RO                         81.8M        1 \n__OBJC_RW                         3136K        2 \n__TEXT                            12.9M       50 \n__UNICODE                          588K        1 \ndyld private memory               1024K        1 \nmapped file                        6.8G      874 \nshared memory                     4056K       35 \nunshared pmap                     10.8M        9 \n===========                     =======  ======= \nTOTAL                              9.3G     2108 \nTOTAL, minus reserved VM space     7.9G     2108 \n",
     127  "legacyInfo" : {
     128  "threadTriggered" : {
     129    "name" : "CrBrowserMain",
     130    "queue" : "com.apple.main-thread"
     131  }
     132},
     133  "trialInfo" : {
     134  "rollouts" : [
     135    {
     136      "rolloutId" : "607844aa04477260f58a8077",
     137      "factorPackIds" : {
     138        "SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
     139      },
     140      "deploymentId" : 240000066
     141    },
     142    {
     143      "rolloutId" : "60da5e84ab0ca017dace9abf",
     144      "factorPackIds" : {
     145
     146      },
     147      "deploymentId" : 240000008
     148    },
     149    {
     150      "rolloutId" : "602ad4dac86151000cf27e46",
     151      "factorPackIds" : {
     152        "SIRI_DICTATION_ASSETS" : "61fb0e87c773c43cde3bb80e"
     153      },
     154      "deploymentId" : 240000303
     155    },
     156    {
     157      "rolloutId" : "60356660bbe37970735c5624",
     158      "factorPackIds" : {
     159
     160      },
     161      "deploymentId" : 240000027
     162    },
     163    {
     164      "rolloutId" : "601d9415f79519000ccd4b69",
     165      "factorPackIds" : {
     166        "SIRI_TEXT_TO_SPEECH" : "622657ce37186c771d5404ad"
     167      },
     168      "deploymentId" : 240000416
     169    },
     170    {
     171      "rolloutId" : "5ffde50ce2aacd000d47a95f",
     172      "factorPackIds" : {
     173
     174      },
     175      "deploymentId" : 240000123
     176    },
     177    {
     178      "rolloutId" : "5fc94383418129005b4e9ae0",
     179      "factorPackIds" : {
     180
     181      },
     182      "deploymentId" : 240000287
     183    }
     184  ],
     185  "experiments" : [
     186
     187  ]
     188}
     189}
     190===== Log before crash start =====
     191UCSF ChimeraX version: 1.3 (2021-12-08) 
     192© 2016-2021 Regents of the University of California. All rights reserved. 
     193How to cite UCSF ChimeraX 
     194Updating list of available bundles failed: Internal Server Error 
     195
     196
     197===== Log before crash end =====
     198
     199Log:
     200UCSF ChimeraX version: 1.3 (2021-12-08) 
     201© 2016-2021 Regents of the University of California. All rights reserved. 
     202How to cite UCSF ChimeraX 
     203
     204
     205
     206
     207OpenGL version: 4.1 Metal - 76.3
     208OpenGL renderer: Apple M1
     209OpenGL vendor: AppleHardware:
     210
     211    Hardware Overview:
     212
     213      Model Name: MacBook Pro
     214      Model Identifier: MacBookPro17,1
     215      Processor Name: Unknown
     216      Processor Speed: 2.4 GHz
     217      Number of Processors: 1
     218      Total Number of Cores: 8
     219      L2 Cache: 8 MB
     220      Memory: 16 GB
     221
     222Software:
     223
     224    System Software Overview:
     225
     226      System Version: macOS 12.2.1 (21D62)
     227      Kernel Version: Darwin 21.3.0
     228      Time since boot: 5 days 7:24
     229
     230Graphics/Displays:
     231
     232    Apple M1:
     233
     234      Chipset Model: Apple M1
     235      Type: GPU
     236      Bus: Built-In
     237      Total Number of Cores: 8
     238      Vendor: Apple (0x106b)
     239      Metal Family: Supported, Metal GPUFamily Apple 7
     240      Displays:
     241        Color LCD:
     242          Display Type: Built-In Retina LCD
     243          Resolution: 2560 x 1600 Retina
     244          Main Display: Yes
     245          Mirror: Off
     246          Online: Yes
     247          Automatically Adjust Brightness: No
     248          Connection Type: Internal
     249
     250Locale: (None, 'UTF-8')
     251PyQt5 5.15.2, Qt 5.15.2
     252Installed Packages:
     253    alabaster: 0.7.12
     254    appdirs: 1.4.4
     255    appnope: 0.1.2
     256    Babel: 2.9.1
     257    backcall: 0.2.0
     258    blockdiag: 2.0.1
     259    certifi: 2021.5.30
     260    cftime: 1.5.1.1
     261    charset-normalizer: 2.0.9
     262    ChimeraX-AddCharge: 1.2.2
     263    ChimeraX-AddH: 2.1.11
     264    ChimeraX-AlignmentAlgorithms: 2.0
     265    ChimeraX-AlignmentHdrs: 3.2
     266    ChimeraX-AlignmentMatrices: 2.0
     267    ChimeraX-Alignments: 2.2.3
     268    ChimeraX-AlphaFold: 1.0
     269    ChimeraX-AltlocExplorer: 1.0.1
     270    ChimeraX-AmberInfo: 1.0
     271    ChimeraX-Arrays: 1.0
     272    ChimeraX-Atomic: 1.31
     273    ChimeraX-AtomicLibrary: 4.2
     274    ChimeraX-AtomSearch: 2.0
     275    ChimeraX-AtomSearchLibrary: 1.0
     276    ChimeraX-AxesPlanes: 2.0
     277    ChimeraX-BasicActions: 1.1
     278    ChimeraX-BILD: 1.0
     279    ChimeraX-BlastProtein: 2.0
     280    ChimeraX-BondRot: 2.0
     281    ChimeraX-BugReporter: 1.0
     282    ChimeraX-BuildStructure: 2.6.1
     283    ChimeraX-Bumps: 1.0
     284    ChimeraX-BundleBuilder: 1.1
     285    ChimeraX-ButtonPanel: 1.0
     286    ChimeraX-CageBuilder: 1.0
     287    ChimeraX-CellPack: 1.0
     288    ChimeraX-Centroids: 1.2
     289    ChimeraX-ChemGroup: 2.0
     290    ChimeraX-Clashes: 2.2.2
     291    ChimeraX-ColorActions: 1.0
     292    ChimeraX-ColorGlobe: 1.0
     293    ChimeraX-ColorKey: 1.5
     294    ChimeraX-CommandLine: 1.1.5
     295    ChimeraX-ConnectStructure: 2.0
     296    ChimeraX-Contacts: 1.0
     297    ChimeraX-Core: 1.3
     298    ChimeraX-CoreFormats: 1.1
     299    ChimeraX-coulombic: 1.3.2
     300    ChimeraX-Crosslinks: 1.0
     301    ChimeraX-Crystal: 1.0
     302    ChimeraX-CrystalContacts: 1.0
     303    ChimeraX-DataFormats: 1.2.2
     304    ChimeraX-Dicom: 1.0
     305    ChimeraX-DistMonitor: 1.1.5
     306    ChimeraX-DistUI: 1.0
     307    ChimeraX-Dssp: 2.0
     308    ChimeraX-EMDB-SFF: 1.0
     309    ChimeraX-ExperimentalCommands: 1.0
     310    ChimeraX-FileHistory: 1.0
     311    ChimeraX-FunctionKey: 1.0
     312    ChimeraX-Geometry: 1.1
     313    ChimeraX-gltf: 1.0
     314    ChimeraX-Graphics: 1.1
     315    ChimeraX-Hbonds: 2.1.2
     316    ChimeraX-Help: 1.2
     317    ChimeraX-HKCage: 1.3
     318    ChimeraX-IHM: 1.1
     319    ChimeraX-ImageFormats: 1.2
     320    ChimeraX-IMOD: 1.0
     321    ChimeraX-IO: 1.0.1
     322    ChimeraX-ItemsInspection: 1.0
     323    ChimeraX-Label: 1.1
     324    ChimeraX-ListInfo: 1.1.1
     325    ChimeraX-Log: 1.1.4
     326    ChimeraX-LookingGlass: 1.1
     327    ChimeraX-Maestro: 1.8.1
     328    ChimeraX-Map: 1.1
     329    ChimeraX-MapData: 2.0
     330    ChimeraX-MapEraser: 1.0
     331    ChimeraX-MapFilter: 2.0
     332    ChimeraX-MapFit: 2.0
     333    ChimeraX-MapSeries: 2.1
     334    ChimeraX-Markers: 1.0
     335    ChimeraX-Mask: 1.0
     336    ChimeraX-MatchMaker: 2.0.4
     337    ChimeraX-MDcrds: 2.6
     338    ChimeraX-MedicalToolbar: 1.0.1
     339    ChimeraX-Meeting: 1.0
     340    ChimeraX-MLP: 1.1
     341    ChimeraX-mmCIF: 2.4
     342    ChimeraX-MMTF: 2.1
     343    ChimeraX-Modeller: 1.2.6
     344    ChimeraX-ModelPanel: 1.2.1
     345    ChimeraX-ModelSeries: 1.0
     346    ChimeraX-Mol2: 2.0
     347    ChimeraX-Morph: 1.0
     348    ChimeraX-MouseModes: 1.1
     349    ChimeraX-Movie: 1.0
     350    ChimeraX-Neuron: 1.0
     351    ChimeraX-Nucleotides: 2.0.2
     352    ChimeraX-OpenCommand: 1.7
     353    ChimeraX-PDB: 2.6.5
     354    ChimeraX-PDBBio: 1.0
     355    ChimeraX-PDBLibrary: 1.0.2
     356    ChimeraX-PDBMatrices: 1.0
     357    ChimeraX-PickBlobs: 1.0
     358    ChimeraX-Positions: 1.0
     359    ChimeraX-PresetMgr: 1.0.1
     360    ChimeraX-PubChem: 2.1
     361    ChimeraX-ReadPbonds: 1.0.1
     362    ChimeraX-Registration: 1.1
     363    ChimeraX-RemoteControl: 1.0
     364    ChimeraX-ResidueFit: 1.0
     365    ChimeraX-RestServer: 1.1
     366    ChimeraX-RNALayout: 1.0
     367    ChimeraX-RotamerLibMgr: 2.0.1
     368    ChimeraX-RotamerLibsDunbrack: 2.0
     369    ChimeraX-RotamerLibsDynameomics: 2.0
     370    ChimeraX-RotamerLibsRichardson: 2.0
     371    ChimeraX-SaveCommand: 1.5
     372    ChimeraX-SchemeMgr: 1.0
     373    ChimeraX-SDF: 2.0
     374    ChimeraX-Segger: 1.0
     375    ChimeraX-Segment: 1.0
     376    ChimeraX-SelInspector: 1.0
     377    ChimeraX-SeqView: 2.4.6
     378    ChimeraX-Shape: 1.0.1
     379    ChimeraX-Shell: 1.0
     380    ChimeraX-Shortcuts: 1.1
     381    ChimeraX-ShowAttr: 1.0
     382    ChimeraX-ShowSequences: 1.0
     383    ChimeraX-SideView: 1.0
     384    ChimeraX-Smiles: 2.1
     385    ChimeraX-SmoothLines: 1.0
     386    ChimeraX-SpaceNavigator: 1.0
     387    ChimeraX-StdCommands: 1.6.1
     388    ChimeraX-STL: 1.0
     389    ChimeraX-Storm: 1.0
     390    ChimeraX-Struts: 1.0
     391    ChimeraX-Surface: 1.0
     392    ChimeraX-SwapAA: 2.0
     393    ChimeraX-SwapRes: 2.1
     394    ChimeraX-TapeMeasure: 1.0
     395    ChimeraX-Test: 1.0
     396    ChimeraX-Toolbar: 1.1
     397    ChimeraX-ToolshedUtils: 1.2
     398    ChimeraX-Tug: 1.0
     399    ChimeraX-UI: 1.13.7
     400    ChimeraX-uniprot: 2.2
     401    ChimeraX-UnitCell: 1.0
     402    ChimeraX-ViewDockX: 1.0.1
     403    ChimeraX-VIPERdb: 1.0
     404    ChimeraX-Vive: 1.1
     405    ChimeraX-VolumeMenu: 1.0
     406    ChimeraX-VTK: 1.0
     407    ChimeraX-WavefrontOBJ: 1.0
     408    ChimeraX-WebCam: 1.0
     409    ChimeraX-WebServices: 1.0
     410    ChimeraX-Zone: 1.0
     411    colorama: 0.4.4
     412    cxservices: 1.1
     413    cycler: 0.11.0
     414    Cython: 0.29.24
     415    decorator: 5.1.0
     416    docutils: 0.17.1
     417    filelock: 3.0.12
     418    funcparserlib: 0.3.6
     419    grako: 3.16.5
     420    h5py: 3.6.0
     421    html2text: 2020.1.16
     422    idna: 3.3
     423    ihm: 0.21
     424    imagecodecs: 2021.4.28
     425    imagesize: 1.3.0
     426    ipykernel: 5.5.5
     427    ipython: 7.23.1
     428    ipython-genutils: 0.2.0
     429    jedi: 0.18.0
     430    Jinja2: 3.0.1
     431    jupyter-client: 6.1.12
     432    jupyter-core: 4.9.1
     433    kiwisolver: 1.3.2
     434    lxml: 4.6.3
     435    lz4: 3.1.3
     436    MarkupSafe: 2.0.1
     437    matplotlib: 3.4.3
     438    matplotlib-inline: 0.1.3
     439    msgpack: 1.0.2
     440    netCDF4: 1.5.7
     441    networkx: 2.6.3
     442    numexpr: 2.8.0
     443    numpy: 1.21.2
     444    openvr: 1.16.801
     445    packaging: 21.0
     446    ParmEd: 3.2.0
     447    parso: 0.8.3
     448    pexpect: 4.8.0
     449    pickleshare: 0.7.5
     450    Pillow: 8.3.2
     451    pip: 21.2.4
     452    pkginfo: 1.7.1
     453    prompt-toolkit: 3.0.23
     454    psutil: 5.8.0
     455    ptyprocess: 0.7.0
     456    pycollada: 0.7.1
     457    pydicom: 2.1.2
     458    Pygments: 2.10.0
     459    PyOpenGL: 3.1.5
     460    PyOpenGL-accelerate: 3.1.5
     461    pyparsing: 3.0.6
     462    PyQt5-commercial: 5.15.2
     463    PyQt5-sip: 12.8.1
     464    PyQtWebEngine-commercial: 5.15.2
     465    python-dateutil: 2.8.2
     466    pytz: 2021.3
     467    pyzmq: 22.3.0
     468    qtconsole: 5.1.1
     469    QtPy: 1.11.3
     470    RandomWords: 0.3.0
     471    requests: 2.26.0
     472    scipy: 1.7.1
     473    setuptools: 57.5.0
     474    sfftk-rw: 0.7.1
     475    six: 1.16.0
     476    snowballstemmer: 2.2.0
     477    sortedcontainers: 2.4.0
     478    Sphinx: 4.2.0
     479    sphinx-autodoc-typehints: 1.12.0
     480    sphinxcontrib-applehelp: 1.0.2
     481    sphinxcontrib-blockdiag: 2.0.0
     482    sphinxcontrib-devhelp: 1.0.2
     483    sphinxcontrib-htmlhelp: 2.0.0
     484    sphinxcontrib-jsmath: 1.0.1
     485    sphinxcontrib-qthelp: 1.0.3
     486    sphinxcontrib-serializinghtml: 1.1.5
     487    suds-jurko: 0.6
     488    tifffile: 2021.4.8
     489    tinyarray: 1.2.3
     490    tornado: 6.1
     491    traitlets: 5.1.1
     492    urllib3: 1.26.7
     493    wcwidth: 0.2.5
     494    webcolors: 1.11.1
     495    wheel: 0.37.0
     496    wheel-filename: 1.3.0
     497
     498}}}