Opened 5 months ago

Closed 5 months ago

#17779 closed defect (duplicate)

Crash in garbage collection

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-5.15.0-136-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00007f7d08568740 (most recent call first):
  Garbage-collecting
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 157 in asArray
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 146 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 146 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2828 in set_matrix
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 817 in set_projection_matrix
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 725 in _use_shader
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 801 in _opengl_shader
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 698 in shader
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 818 in _draw_geometry
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 787 in draw_self
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 780 in draw
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1567 in _draw_multiple
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1554 in draw_opaque
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/view.py", line 258 in _draw_scene
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.segment._segment, chimerax.mmcif.mmcif_write (total: 53)
===== Log before crash start =====
Startup Messages  
---  
warnings | No presets found in custom preset folder /home/mpimp-
golm.mpg.de/zillmer4400/Downloads/ChimeraX/presets  
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle  
  

> ui tool hide "command line interface"

> ui tool show CliX

UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/mpimp-
> golm.mpg.de/zillmer4400/Desktop/linuxdata/programs/flowr/data/8zvn/8zvn.pdb
> format pdb

Chain information for 8zvn.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select ::name="LIG"

22 atoms, 24 bonds, 1 residue, 1 model selected  

> delete sel

> save /home/mpimp-
> golm.mpg.de/zillmer4400/Desktop/linuxdata/programs/flowr/data/8zvn/8zvn.cif
> relModel #1

> close

> open /home/mpimp-
> golm.mpg.de/zillmer4400/Desktop/linuxdata/programs/flowr/data/8zvn/8zvn.cif
> format mmcif

Chain information for 8zvn.cif #1  
---  
Chain | Description  
A | No description available  
  

> close

> open /home/mpimp-
> golm.mpg.de/zillmer4400/Desktop/linuxdata/programs/flowr/data/8zvn/8zvn.pdb
> format pdb

Chain information for 8zvn.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select ::name="LIG"

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select zone ligand 6

Selected 115 atoms  

> select zone ligand 5

Selected 71 atoms  

> save /home/mpimp-
> golm.mpg.de/zillmer4400/Desktop/linuxdata/programs/flowr/data/8zvn/LIG.pdb
> selectedOnly

Missing "selectedOnly" keyword's argument  

> save /home/mpimp-
> golm.mpg.de/zillmer4400/Desktop/linuxdata/programs/flowr/data/8zvn/LIG.pdb
> #1 selectedOnly

Missing "selectedOnly" keyword's argument  

> log thumbnail

![](data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGQAAABkCAIAAAD/gAIDAAAOp0lEQVR4nO2cd1QU1x7Hv0tVwGeP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%0A)  

> save /home/mpimp-
> golm.mpg.de/zillmer4400/Desktop/linuxdata/programs/flowr/data/8zvn/LIG.pdb
> #1 selectedOnly true

> save /home/mpimp-
> golm.mpg.de/zillmer4400/Desktop/linuxdata/programs/flowr/data/8zvn/8zvn_pocket.pdb
> #1 selectedOnly true

> select #1 ::name="LIG"

22 atoms, 24 bonds, 1 residue, 1 model selected  

> save /home/mpimp-
> golm.mpg.de/zillmer4400/Desktop/linuxdata/programs/flowr/data/8zvn/LIG.pdb
> #1 selectedOnly true

> select zone ligand 5

Selected 71 atoms  

> save /home/mpimp-
> golm.mpg.de/zillmer4400/Desktop/linuxdata/programs/flowr/data/8zvn/8zvn_pocket.cif
> #1 selectedOnly true

Fetching CCD LIG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/LIG/LIG.cif  

> open /home/mpimp-
> golm.mpg.de/zillmer4400/Desktop/linuxdata/programs/flowr/data/8zvn/8zvn_pocket.cif

Summary of feedback from opening /home/mpimp-
golm.mpg.de/zillmer4400/Desktop/linuxdata/programs/flowr/data/8zvn/8zvn_pocket.cif  
---  
warnings | Atom N has no neighbors to form bonds with according to residue
template for VAL /A:96  
Atom CB has no neighbors to form bonds with according to residue template for
VAL /A:96  
Atom CE1 has no neighbors to form bonds with according to residue template for
TYR /A:150  
Atom OH has no neighbors to form bonds with according to residue template for
TYR /A:150  
  
Chain information for 8zvn_pocket.cif #2  
---  
Chain | Description  
A | No description available  
  

> hide #1 models

> hide #2.1 models

> show #2

> close #2

> select zone ligand 5 residues true

Selected 175 atoms  

> show #1 models

> show sel

> select ~sel & ##selected

1929 atoms, 1985 bonds, 249 residues, 1 model selected  

> delete sel

> undo

Undo failed, probably because structures have been modified.  

> save /home/mpimp-
> golm.mpg.de/zillmer4400/Desktop/linuxdata/programs/flowr/data/8zvn/8zvn_pocket.cif
> #1

> open /home/mpimp-
> golm.mpg.de/zillmer4400/Desktop/linuxdata/programs/flowr/data/8zvn/8zvn_pocket.cif

Chain information for 8zvn_pocket.cif #2  
---  
Chain | Description  
A | No description available  
  

> close #1

> show sel

> close #2

> open /home/mpimp-
> golm.mpg.de/zillmer4400/Desktop/linuxdata/programs/flowr/data/8zvn/8zvn.pdb
> format pdb

Chain information for 8zvn.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select zone ligand 5 residues true

Selected 175 atoms  

> show sel

> save /home/mpimp-
> golm.mpg.de/zillmer4400/Desktop/linuxdata/programs/flowr/data/8zvn/8zvn_pocket.cif
> #1 selectedOnly true

> open /home/mpimp-
> golm.mpg.de/zillmer4400/Desktop/linuxdata/programs/flowr/data/8zvn/8zvn_pocket.cif

Chain information for 8zvn_pocket.cif #2  
---  
Chain | Description  
A | No description available  
  

> show sel


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

Log:
Startup Messages  
---  
warnings | No presets found in custom preset folder /home/mpimp-
golm.mpg.de/zillmer4400/Downloads/ChimeraX/presets  
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle  
  

> ui tool hide "command line interface"

> ui tool show CliX

UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 535.183.01
OpenGL renderer: NVIDIA GeForce RTX 3060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 3660
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 12th Gen Intel(R) Core(TM) i9-12900K
Cache Size: 30720 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           62Gi       6.1Gi        39Gi       165Mi        16Gi        55Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2504] (rev a1)	
	Subsystem: Dell Device [1028:c974]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    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: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    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: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-clix: 0.1.10
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    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: 1.1.3
    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: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    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: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    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: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    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: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    pandas: 2.2.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.3.6
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by pett, 5 months ago

Component: UnassignedCore
Owner: set to pett
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionCrash in garbage collection

comment:2 by pett, 5 months ago

Resolution: duplicate
Status: acceptedclosed
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