Opened 4 years ago

Closed 4 years ago

#6369 closed defect (duplicate)

Qt6 shell tab-completion crash

Reported by: Tony Schaefer Owned by: Zach Pearson
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.4.dev202203120056 (2022-03-12 00:56:56 UTC)
Description
Last time you used ChimeraX it crashed.
I pressed tab to autocomplete something on the shell
Windows fatal exception: access violation

Thread 0x0000c4c0 (most recent call first):
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\selectors.py", line 315 in _select
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\selectors.py", line 324 in select
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\asyncio\base_events.py", line 1854 in _run_once
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\asyncio\base_events.py", line 596 in run_forever
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\site-packages\tornado\platform\asyncio.py", line 199 in start
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\site-packages\ipykernel\iostream.py", line 81 in _thread_main
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\threading.py", line 910 in run
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000ceac (most recent call first):
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\threading.py", line 312 in wait
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\threading.py", line 574 in wait
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\site-packages\IPython\core\history.py", line 829 in run
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\site-packages\IPython\core\history.py", line 58 in needs_sqlite
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\site-packages\decorator.py", line 232 in fun
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\threading.py", line 930 in _bootstrap

Current thread 0x0000ce40 (most recent call first):
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\site-packages\qtconsole\console_widget.py", line 1696 in _get_block_plain_text
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\site-packages\qtconsole\frontend_widget.py", line 70 in highlightBlock
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\site-packages\qtconsole\console_widget.py", line 1089 in _fill_temporary_buffer
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\site-packages\qtconsole\completion_html.py", line 350 in _update_list
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\site-packages\qtconsole\completion_html.py", line 323 in show_items
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\site-packages\qtconsole\console_widget.py", line 1078 in _complete_with_items
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\site-packages\qtconsole\jupyter_widget.py", line 179 in _handle_complete_reply
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\site-packages\qtconsole\base_frontend_mixin.py", line 138 in _dispatch
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\site-packages\qtconsole\inprocess.py", line 46 in call_handlers
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\site-packages\qtconsole\inprocess.py", line 42 in 
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\runpy.py", line 87 in _run_code
  File "E:\ChimeraX 1.4.dev202203120056\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UI Theme  

> cd C:\Users\normn/Desktop

Current working directory is: C:\Users\normn\Desktop  

> graphics selection width 2

UCSF ChimeraX version: 1.4.dev202203120056 (2022-03-12)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Shell


===== Log before crash end =====

Log:
UI Theme  

> cd C:\Users\normn/Desktop

Current working directory is: C:\Users\normn\Desktop  

> graphics selection width 2

UCSF ChimeraX version: 1.4.dev202203120056 (2022-03-12)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 497.29
OpenGL renderer: NVIDIA GeForce RTX 2070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Locale: en_US.cp1252
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt platform: windows

Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Microsoft Windows 10 Home (Build 19044)
Memory: 17,107,529,728
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 2700X Eight-Core Processor         
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.36.2
    ChimeraX-AtomicLibrary: 6.1.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202203120056
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.4
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.8
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.8
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-themes: 0.3.1
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16.2
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.5.1
    decorator: 5.1.1
    dill: 0.3.4
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.30.0
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.26
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    joblib: 1.1.0
    jupyter-client: 7.1.0
    jupyter-core: 4.9.2
    kiwisolver: 1.3.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.0
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    multiprocess: 0.70.12.2
    nest-asyncio: 1.5.4
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pathos: 0.2.8
    pdb-objects: 0.1.3
    pickleshare: 0.7.5
    Pillow: 9.0.0
    pip: 21.3.1
    pkginfo: 1.8.2
    pox: 0.3.0
    ppft: 1.6.6.4
    prompt-toolkit: 3.0.28
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.7
    PyQt6-commercial: 6.2.3
    PyQt6-sip: 13.2.0
    PyQt6-WebEngine-commercial: 6.2.1
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 303
    pyzmq: 22.3.0
    qtconsole: 5.2.2
    QtPy: 2.0.1
    RandomWords: 0.3.0
    requests: 2.27.1
    scikit-learn: 1.0.2
    scipy: 1.7.3
    Send2Trash: 1.8.0
    SEQCROW: 1.4a2
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    threadpoolctl: 3.1.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.8
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Window Toolkit
Owner: set to Zach Pearson
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Qt6 shell tab-completion crash

comment:2 by Eric Pettersen, 4 years ago

Resolution: → duplicate
Status: assigned → closed

Duplicate of #6363; adding Tony to recipient list for that ticket

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