Changes between Initial Version and Version 1 of Ticket #6680


Ignore:
Timestamp:
Apr 25, 2022, 10:32:33 AM (3 years ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #6680

    • Property Cc Tom Goddard added
    • Property Component Unassigned → Core
    • Property Owner set to Eric Pettersen
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → accepted
    • Property Summary ChimeraX bug report submission → Crash in strlen

  • Ticket #6680 – Description

    initial v1  
    66Last time you used ChimeraX it crashed.
    77Please describe steps that led to the crash here.
     8
     9
     10{"app_name":"ChimeraX","timestamp":"2022-04-21 18:34:23.00 +0200","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":"6A4DEB0D-D3BF-43D3-8135-08FBD57AB766","name":"ChimeraX"}
     11{
     12  "uptime" : 490000,
     13  "procLaunch" : "2022-04-21 18:27:09.3035 +0200",
     14  "procRole" : "Background",
     15  "version" : 2,
     16  "userID" : 503,
     17  "deployVersion" : 210,
     18  "modelCode" : "MacBookPro17,1",
     19  "procStartAbsTime" : 11822602304853,
     20  "coalitionID" : 61743,
     21  "osVersion" : {
     22    "train" : "macOS 12.2.1",
     23    "build" : "21D62",
     24    "releaseType" : "User"
     25  },
     26  "captureTime" : "2022-04-21 18:34:22.7143 +0200",
     27  "incident" : "6A4DEB0D-D3BF-43D3-8135-08FBD57AB766",
     28  "bug_type" : "309",
     29  "pid" : 18590,
     30  "procExitAbsTime" : 11833003072885,
     31  "translated" : true,
     32  "cpuType" : "X86-64",
     33  "procName" : "ChimeraX",
     34  "procPath" : "\/private\/var\/folders\/*\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
     35  "parentProc" : "launchd",
     36  "parentPid" : 1,
     37  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
     38  "crashReporterKey" : "54176689-DFA0-CE96-87A1-CEC6B246D0CD",
     39  "wakeTime" : 2204,
     40  "sleepWakeUUID" : "ABFCB01C-B504-44EE-98CC-CFD8303D42B9",
     41  "sip" : "enabled",
     42  "vmRegionInfo" : "0x108bec1d0 is in 0x1089ed000-0x108c56000;  bytes after start: 2093520  bytes before end: 433711\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      Rosetta Generic             1089eb000-1089ec000    [    4K] rw-\/rwx SM=PRV  \n      GAP OF 0x1000 BYTES\n--->  mapped file                 1089ed000-108c56000    [ 2468K] r-x\/rwx SM=COW  ...t_id=c3469681\n      mapped file                 108c56000-108c90000    [  232K] rw-\/rwx SM=COW  ...t_id=c2546281",
     43  "isCorpse" : 1,
     44  "exception" : {"codes":"0x000000000000000a, 0x0000000108bec1d0","rawCodes":[10,4441686480],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_MEMORY_ERROR at 0x0000000108bec1d0"},
     45  "termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"exc handler","byPid":18590},
     46  "ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Object is not alive\nVM - Object is not alive\nVM - Object is not alive\n",
     47  "vmregioninfo" : "0x108bec1d0 is in 0x1089ed000-0x108c56000;  bytes after start: 2093520  bytes before end: 433711\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      Rosetta Generic             1089eb000-1089ec000    [    4K] rw-\/rwx SM=PRV  \n      GAP OF 0x1000 BYTES\n--->  mapped file                 1089ed000-108c56000    [ 2468K] r-x\/rwx SM=COW  ...t_id=c3469681\n      mapped file                 108c56000-108c90000    [  232K] rw-\/rwx SM=COW  ...t_id=c2546281",
     48  "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},
     49  "faultingThread" : 0,
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     97    "base" : 140703388618752,
     98    "CFBundleShortVersionString" : "6.9",
     99    "CFBundleIdentifier" : "com.apple.CoreFoundation",
     100    "size" : 5246976,
     101    "uuid" : "1d1db08b-810c-316e-b9d9-eecdff8ee6e3",
     102    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
     103    "name" : "CoreFoundation",
     104    "CFBundleVersion" : "1856.107"
     105  }
     106],
     107  "sharedCache" : {
     108  "base" : 140703385059328,
     109  "size" : 15218196480,
     110  "uuid" : "5c9ff5db-8827-329a-8a37-2483935a9ea1"
     111},
     112  "vmSummary" : "ReadOnly portion of Libraries: Total=206.0M resident=0K(0%) swapped_out_or_unallocated=206.0M(100%)\nWritable regions: Total=2.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.2G(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                           220K       21 \nColorSync                          236K       27 \nCoreAnimation                      152K       12 \nCoreGraphics                        12K        2 \nCoreUI image data                 2816K       20 \nFoundation                          16K        1 \nKernel Alloc Once                    8K        1 \nMALLOC                           372.2M       74 \nMALLOC guard page                  192K        8 \nMALLOC_MEDIUM (reserved)         880.0M        8         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)\nMach message                        16K        4 \nOpenGL GLSL                        384K        5 \nRosetta Arena                     4096K        2 \nRosetta Generic                   1448K      359 \nRosetta IndirectBranch            2048K        1 \nRosetta JIT                      128.0M        1 \nRosetta Return Stack               760K       76 \nRosetta Thread Context             760K       76 \nSTACK GUARD                         44K       11 \nStack                            162.1M       39 \nStack Guard                       56.1M       28 \nVM_ALLOCATE                      105.8M      187 \nVM_ALLOCATE (reserved)           160.1M       13         reserved VM address space (unallocated)\n__DATA                             355K       45 \n__DATA_CONST                      3031K       40 \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               1184K        3 \nmapped file                        6.5G      932 \nshared memory                     3340K       38 \nunshared pmap                     10.3M        8 \n===========                     =======  ======= \nTOTAL                              9.0G     2137 \nTOTAL, minus reserved VM space     7.7G     2137 \n",
     113  "legacyInfo" : {
     114  "threadTriggered" : {
     115    "name" : "CrBrowserMain",
     116    "queue" : "com.apple.main-thread"
     117  }
     118},
     119  "trialInfo" : {
     120  "rollouts" : [
     121    {
     122      "rolloutId" : "602ad4dac86151000cf27e46",
     123      "factorPackIds" : {
     124        "SIRI_DICTATION_ASSETS" : "61fb0e87c773c43cde3bb80e"
     125      },
     126      "deploymentId" : 240000305
     127    },
     128    {
     129      "rolloutId" : "60da5e84ab0ca017dace9abf",
     130      "factorPackIds" : {
     131
     132      },
     133      "deploymentId" : 240000008
     134    },
     135    {
     136      "rolloutId" : "607844aa04477260f58a8077",
     137      "factorPackIds" : {
     138        "SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
     139      },
     140      "deploymentId" : 240000066
     141    },
     142    {
     143      "rolloutId" : "601d9415f79519000ccd4b69",
     144      "factorPackIds" : {
     145        "SIRI_TEXT_TO_SPEECH" : "622657ce37186c771d5404ad"
     146      },
     147      "deploymentId" : 240000412
     148    },
     149    {
     150      "rolloutId" : "60356660bbe37970735c5624",
     151      "factorPackIds" : {
     152
     153      },
     154      "deploymentId" : 240000027
     155    },
     156    {
     157      "rolloutId" : "5fb4245a1bbfe8005e33a1e1",
     158      "factorPackIds" : {
     159
     160      },
     161      "deploymentId" : 240000015
     162    },
     163    {
     164      "rolloutId" : "5ffde50ce2aacd000d47a95f",
     165      "factorPackIds" : {
     166
     167      },
     168      "deploymentId" : 240000136
     169    },
     170    {
     171      "rolloutId" : "5fc94383418129005b4e9ae0",
     172      "factorPackIds" : {
     173
     174      },
     175      "deploymentId" : 240000334
     176    }
     177  ],
     178  "experiments" : [
     179
     180  ]
     181}
     182}
     183===== Log before crash start =====
     184Startup Messages 
     185--- 
     186note | available bundle cache has not been initialized yet 
     187 
     188UCSF ChimeraX version: 1.4.dev202204210713 (2022-04-21) 
     189© 2016-2022 Regents of the University of California. All rights reserved. 
     190How to cite UCSF ChimeraX 
     191
     192
     193===== Log before crash end =====
     194
     195Log:
     196UCSF ChimeraX version: 1.4.dev202204210713 (2022-04-21) 
     197© 2016-2022 Regents of the University of California. All rights reserved. 
     198How to cite UCSF ChimeraX 
     199
     200
     201
     202
     203OpenGL version: 4.1 Metal - 76.3
     204OpenGL renderer: Apple M1
     205OpenGL vendor: Apple
     206
     207Python: 3.9.11
     208Locale: UTF-8
     209Qt version: PyQt6 6.2.3, Qt 6.2.3
     210Qt runtime version: 6.2.4
     211Qt platform: cocoa
     212Hardware:
     213
     214    Hardware Overview:
     215
     216      Model Name: MacBook Pro
     217      Model Identifier: MacBookPro17,1
     218      Processor Name: Unknown
     219      Processor Speed: 2,4 GHz
     220      Number of Processors: 1
     221      Total Number of Cores: 8
     222      L2 Cache: 8 MB
     223      Memory: 8 GB
     224
     225Software:
     226
     227    System Software Overview:
     228
     229      System Version: macOS 12.2.1 (21D62)
     230      Kernel Version: Darwin 21.3.0
     231      Time since boot: 40 days 8:17
     232
     233Graphics/Displays:
     234
     235    Apple M1:
     236
     237      Chipset Model: Apple M1
     238      Type: GPU
     239      Bus: Built-In
     240      Total Number of Cores: 8
     241      Vendor: Apple (0x106b)
     242      Metal Family: Supported, Metal GPUFamily Apple 7
     243      Displays:
     244        Color LCD:
     245          Display Type: Built-In Retina LCD
     246          Resolution: 2560 x 1600 Retina
     247          Main Display: Yes
     248          Mirror: Off
     249          Online: Yes
     250          Automatically Adjust Brightness: No
     251          Display Asleep: Yes
     252          Connection Type: Internal
     253
     254
     255Installed Packages:
     256    alabaster: 0.7.12
     257    appdirs: 1.4.4
     258    appnope: 0.1.3
     259    Babel: 2.10.1
     260    backcall: 0.2.0
     261    blockdiag: 3.0.0
     262    certifi: 2021.10.8
     263    cftime: 1.6.0
     264    charset-normalizer: 2.0.12
     265    ChimeraX-AddCharge: 1.2.3
     266    ChimeraX-AddH: 2.1.11
     267    ChimeraX-AlignmentAlgorithms: 2.0
     268    ChimeraX-AlignmentHdrs: 3.2.1
     269    ChimeraX-AlignmentMatrices: 2.0
     270    ChimeraX-Alignments: 2.4.2
     271    ChimeraX-AlphaFold: 1.0
     272    ChimeraX-AltlocExplorer: 1.0.2
     273    ChimeraX-AmberInfo: 1.0
     274    ChimeraX-Arrays: 1.0
     275    ChimeraX-Atomic: 1.38.1
     276    ChimeraX-AtomicLibrary: 7.0
     277    ChimeraX-AtomSearch: 2.0.1
     278    ChimeraX-AxesPlanes: 2.1
     279    ChimeraX-BasicActions: 1.1
     280    ChimeraX-BILD: 1.0
     281    ChimeraX-BlastProtein: 2.1.1
     282    ChimeraX-BondRot: 2.0
     283    ChimeraX-BugReporter: 1.0
     284    ChimeraX-BuildStructure: 2.7
     285    ChimeraX-Bumps: 1.0
     286    ChimeraX-BundleBuilder: 1.1
     287    ChimeraX-ButtonPanel: 1.0
     288    ChimeraX-CageBuilder: 1.0
     289    ChimeraX-CellPack: 1.0
     290    ChimeraX-Centroids: 1.2
     291    ChimeraX-ChemGroup: 2.0
     292    ChimeraX-Clashes: 2.2.3
     293    ChimeraX-ColorActions: 1.0
     294    ChimeraX-ColorGlobe: 1.0
     295    ChimeraX-ColorKey: 1.5.1
     296    ChimeraX-CommandLine: 1.2.3
     297    ChimeraX-ConnectStructure: 2.0.1
     298    ChimeraX-Contacts: 1.0
     299    ChimeraX-Core: 1.4.dev202204210713
     300    ChimeraX-CoreFormats: 1.1
     301    ChimeraX-coulombic: 1.3.2
     302    ChimeraX-Crosslinks: 1.0
     303    ChimeraX-Crystal: 1.0
     304    ChimeraX-CrystalContacts: 1.0
     305    ChimeraX-DataFormats: 1.2.2
     306    ChimeraX-Dicom: 1.1
     307    ChimeraX-DistMonitor: 1.1.5
     308    ChimeraX-Dssp: 2.0
     309    ChimeraX-EMDB-SFF: 1.0
     310    ChimeraX-ExperimentalCommands: 1.0
     311    ChimeraX-FileHistory: 1.0
     312    ChimeraX-FunctionKey: 1.0
     313    ChimeraX-Geometry: 1.2
     314    ChimeraX-gltf: 1.0
     315    ChimeraX-Graphics: 1.1
     316    ChimeraX-Hbonds: 2.1.2
     317    ChimeraX-Help: 1.2
     318    ChimeraX-HKCage: 1.3
     319    ChimeraX-IHM: 1.1
     320    ChimeraX-ImageFormats: 1.2
     321    ChimeraX-IMOD: 1.0
     322    ChimeraX-IO: 1.0.1
     323    ChimeraX-ItemsInspection: 1.0
     324    ChimeraX-Label: 1.1
     325    ChimeraX-ListInfo: 1.1.1
     326    ChimeraX-Log: 1.1.5
     327    ChimeraX-LookingGlass: 1.1
     328    ChimeraX-Maestro: 1.8.1
     329    ChimeraX-Map: 1.1
     330    ChimeraX-MapData: 2.0
     331    ChimeraX-MapEraser: 1.0
     332    ChimeraX-MapFilter: 2.0
     333    ChimeraX-MapFit: 2.0
     334    ChimeraX-MapSeries: 2.1
     335    ChimeraX-Markers: 1.0
     336    ChimeraX-Mask: 1.0
     337    ChimeraX-MatchMaker: 2.0.6
     338    ChimeraX-MDcrds: 2.6
     339    ChimeraX-MedicalToolbar: 1.0.1
     340    ChimeraX-Meeting: 1.0
     341    ChimeraX-MLP: 1.1
     342    ChimeraX-mmCIF: 2.7
     343    ChimeraX-MMTF: 2.1
     344    ChimeraX-Modeller: 1.5.5
     345    ChimeraX-ModelPanel: 1.3.2
     346    ChimeraX-ModelSeries: 1.0
     347    ChimeraX-Mol2: 2.0
     348    ChimeraX-Morph: 1.0
     349    ChimeraX-MouseModes: 1.1
     350    ChimeraX-Movie: 1.0
     351    ChimeraX-Neuron: 1.0
     352    ChimeraX-Nucleotides: 2.0.2
     353    ChimeraX-OpenCommand: 1.9
     354    ChimeraX-PDB: 2.6.6
     355    ChimeraX-PDBBio: 1.0
     356    ChimeraX-PDBLibrary: 1.0.2
     357    ChimeraX-PDBMatrices: 1.0
     358    ChimeraX-PickBlobs: 1.0
     359    ChimeraX-Positions: 1.0
     360    ChimeraX-PresetMgr: 1.1
     361    ChimeraX-PubChem: 2.1
     362    ChimeraX-ReadPbonds: 1.0.1
     363    ChimeraX-Registration: 1.1
     364    ChimeraX-RemoteControl: 1.0
     365    ChimeraX-ResidueFit: 1.0
     366    ChimeraX-RestServer: 1.1
     367    ChimeraX-RNALayout: 1.0
     368    ChimeraX-RotamerLibMgr: 2.0.1
     369    ChimeraX-RotamerLibsDunbrack: 2.0
     370    ChimeraX-RotamerLibsDynameomics: 2.0
     371    ChimeraX-RotamerLibsRichardson: 2.0
     372    ChimeraX-SaveCommand: 1.5
     373    ChimeraX-SchemeMgr: 1.0
     374    ChimeraX-SDF: 2.0
     375    ChimeraX-Segger: 1.0
     376    ChimeraX-Segment: 1.0
     377    ChimeraX-SelInspector: 1.0
     378    ChimeraX-SeqView: 2.6
     379    ChimeraX-Shape: 1.0.1
     380    ChimeraX-Shell: 1.0
     381    ChimeraX-Shortcuts: 1.1
     382    ChimeraX-ShowAttr: 1.0
     383    ChimeraX-ShowSequences: 1.0
     384    ChimeraX-SideView: 1.0
     385    ChimeraX-Smiles: 2.1
     386    ChimeraX-SmoothLines: 1.0
     387    ChimeraX-SpaceNavigator: 1.0
     388    ChimeraX-StdCommands: 1.8
     389    ChimeraX-STL: 1.0
     390    ChimeraX-Storm: 1.0
     391    ChimeraX-StructMeasure: 1.0.1
     392    ChimeraX-Struts: 1.0.1
     393    ChimeraX-Surface: 1.0
     394    ChimeraX-SwapAA: 2.0
     395    ChimeraX-SwapRes: 2.1.1
     396    ChimeraX-TapeMeasure: 1.0
     397    ChimeraX-Test: 1.0
     398    ChimeraX-Toolbar: 1.1
     399    ChimeraX-ToolshedUtils: 1.2.1
     400    ChimeraX-Tug: 1.0
     401    ChimeraX-UI: 1.16.5
     402    ChimeraX-uniprot: 2.2
     403    ChimeraX-UnitCell: 1.0
     404    ChimeraX-ViewDockX: 1.1.2
     405    ChimeraX-VIPERdb: 1.0
     406    ChimeraX-Vive: 1.1
     407    ChimeraX-VolumeMenu: 1.0
     408    ChimeraX-VTK: 1.0
     409    ChimeraX-WavefrontOBJ: 1.0
     410    ChimeraX-WebCam: 1.0
     411    ChimeraX-WebServices: 1.1.0
     412    ChimeraX-Zone: 1.0
     413    colorama: 0.4.4
     414    cxservices: 1.2
     415    cycler: 0.11.0
     416    Cython: 0.29.26
     417    debugpy: 1.6.0
     418    decorator: 5.1.1
     419    docutils: 0.17.1
     420    entrypoints: 0.4
     421    filelock: 3.4.2
     422    fonttools: 4.32.0
     423    funcparserlib: 1.0.0a1
     424    grako: 3.16.5
     425    h5py: 3.6.0
     426    html2text: 2020.1.16
     427    idna: 3.3
     428    ihm: 0.27
     429    imagecodecs: 2021.11.20
     430    imagesize: 1.3.0
     431    ipykernel: 6.6.1
     432    ipython: 7.31.1
     433    ipython-genutils: 0.2.0
     434    jedi: 0.18.1
     435    Jinja2: 3.0.3
     436    jupyter-client: 7.1.0
     437    jupyter-core: 4.10.0
     438    kiwisolver: 1.4.2
     439    line-profiler: 3.4.0
     440    lxml: 4.7.1
     441    lz4: 3.1.10
     442    MarkupSafe: 2.1.1
     443    matplotlib: 3.5.1
     444    matplotlib-inline: 0.1.3
     445    msgpack: 1.0.3
     446    nest-asyncio: 1.5.5
     447    netCDF4: 1.5.8
     448    networkx: 2.6.3
     449    numexpr: 2.8.1
     450    numpy: 1.22.1
     451    openvr: 1.16.802
     452    packaging: 21.0
     453    ParmEd: 3.4.3
     454    parso: 0.8.3
     455    pexpect: 4.8.0
     456    pickleshare: 0.7.5
     457    Pillow: 9.0.1
     458    pip: 21.3.1
     459    pkginfo: 1.8.2
     460    prompt-toolkit: 3.0.29
     461    psutil: 5.9.0
     462    ptyprocess: 0.7.0
     463    pycollada: 0.7.2
     464    pydicom: 2.2.2
     465    Pygments: 2.11.2
     466    PyOpenGL: 3.1.5
     467    PyOpenGL-accelerate: 3.1.5
     468    pyparsing: 3.0.8
     469    PyQt6-commercial: 6.2.3
     470    PyQt6-Qt6: 6.2.4
     471    PyQt6-sip: 13.2.1
     472    PyQt6-WebEngine-commercial: 6.2.1
     473    PyQt6-WebEngine-Qt6: 6.2.4
     474    python-dateutil: 2.8.2
     475    pytz: 2022.1
     476    pyzmq: 22.3.0
     477    qtconsole: 5.3.0
     478    QtPy: 2.0.1
     479    RandomWords: 0.3.0
     480    requests: 2.27.1
     481    scipy: 1.7.3
     482    setuptools: 59.8.0
     483    sfftk-rw: 0.7.1
     484    six: 1.16.0
     485    snowballstemmer: 2.2.0
     486    sortedcontainers: 2.4.0
     487    Sphinx: 4.3.2
     488    sphinx-autodoc-typehints: 1.15.2
     489    sphinxcontrib-applehelp: 1.0.2
     490    sphinxcontrib-blockdiag: 3.0.0
     491    sphinxcontrib-devhelp: 1.0.2
     492    sphinxcontrib-htmlhelp: 2.0.0
     493    sphinxcontrib-jsmath: 1.0.1
     494    sphinxcontrib-qthelp: 1.0.3
     495    sphinxcontrib-serializinghtml: 1.1.5
     496    suds-community: 1.0.0
     497    tables: 3.7.0
     498    tifffile: 2021.11.2
     499    tinyarray: 1.2.4
     500    tornado: 6.1
     501    traitlets: 5.1.1
     502    urllib3: 1.26.9
     503    wcwidth: 0.2.5
     504    webcolors: 1.11.1
     505    wheel: 0.37.1
     506    wheel-filename: 1.3.0
     507
     508}}}