id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
6038	ChimeraX Log panel broken on Fedora	paulaj@…	Greg Couch	"{{{
Dear ChimeraX developers,
Since I switched to Fedora, I've been getting an error that does not allow the log and some other tools (such as the start view with the previous structures) to open. I tried to use the bug reporter tool, but when I click submit, nothing happens. The error happens with both the rpm and the tarball version, but the tarball allows me to see the log in the terminal. I appended it here along with the information the bug reporter detects.
Thank you in advance!
Paula

____________ log ___________

Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway.
NOTE: Traceback (most recent call last):
  File ""/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py"", line 554, in start_tool
    ti = api._api_caller.start_tool(api, session, self, tool_info)
  File ""/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py"", line 1264, in start_tool
    return cls._get_func(api, ""start_tool"")(session, ti.name)
  File ""/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/log/__init__.py"", line 39, in start_tool
    return cmd.get_singleton(session, create=True)
  File ""/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/log/cmd.py"", line 19, in get_singleton
    return tools.get_singleton(session, Log, 'Log', create=create)
  File ""/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/tools.py"", line 193, in get_singleton
    tinst = tool_class(session, tool_name, **kw)
  File ""/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/log/tool.py"", line 161, in __init__
    from chimerax.ui.widgets import ChimeraXHtmlView
  File ""/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/ui/widgets/ChimeraXHtmlView.py"", line 20, in <module>
    from Qt.QtWebEngineWidgets import QWebEngineView, QWebEnginePage,
QWebEngineProfile
  File ""/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/Qt/QtWebEngineWidgets.py"", line 4, in <module>
    from PyQt5.QtWebEngineWidgets import *
ImportError: /lib64/libk5crypto.so.3: undefined symbol: EVP_KDF_ctrl, version
OPENSSL_1_1_1b

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File ""/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/tools.py"", line 379, in start_tools
    bi.start_tool(session, tool_name)
  File ""/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py"", line 559, in start_tool
    raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Log in
bundle ChimeraX-Log:
/lib64/libk5crypto.so.3: undefined symbol: EVP_KDF_ctrl, version
OPENSSL_1_1_1b


BUG: Tool ""Log"" failed to start:
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Log in
bundle ChimeraX-Log:
/lib64/libk5crypto.so.3: undefined symbol: EVP_KDF_ctrl, version
OPENSSL_1_1_1b

File ""/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py"", line 559, in start_tool
raise ToolshedError(

 _See log for complete Python traceback._


NOTE: UCSF ChimeraX version: 1.3 (2021-12-08)
NOTE: © 2016-2021 Regents of the University of California.  All rights reserved.
NOTE: [How to cite UCSF ChimeraX](cxcmd:help help:credits.html)

NOTE: Traceback (most recent call last):
  File ""/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/triggerset.py"", line 134, in invoke
    return self._func(self._name, data)
  File ""/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/bug_reporter/crash_report.py"", line 110, in
_delayed_register_log_recorder
    _register_log_recorder(session)
  File ""/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/bug_reporter/crash_report.py"", line 144, in
_register_log_recorder
    log.record_to_file(log_file)
  File ""/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/log/tool.py"", line 396, in record_to_file
    self._log_to_file(self.page_source)
AttributeError: 'Log' object has no attribute 'page_source'


BUG: Error processing trigger ""new frame"":
AttributeError: 'Log' object has no attribute 'page_source'

File ""/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/log/tool.py"", line 396, in record_to_file
self._log_to_file(self.page_source)

 _See log for complete Python traceback._

____________ system info ___________

Platform: Linux-5.15.14-200.fc35.x86_64-x86_64-with-glibc2.34
ChimeraX version: 1.3 (2021-12-08 23:08:33 UTC)

Gathered information:

OpenGL version: 4.6 (Core Profile) Mesa 21.3.4

OpenGL renderer: Mesa Intel(R) HD Graphics 520 (SKL GT2)

OpenGL vendor: Intel

Manufacturer: LENOVO

Model: 80UK

OS: Fedora Linux 35

Architecture: 64bit ELF

Virutal Machine: none

CPU: 4 Intel(R) Core(TM) i5-6200U CPU @ 2.30GHz

Cache Size: 3072 KB

Memory:

              total        used        free      shared  buff/cache   available

Mem:           7.6Gi       3.8Gi       391Mi       872Mi       3.4Gi       2.7Gi

Swap:          7.6Gi        42Mi       7.6Gi


Graphics:

00:02.0 VGA compatible controller [0300]: Intel Corporation Skylake GT2 [HD Graphics 520] [8086:1916] (rev 07)

Subsystem: Lenovo Device [17aa:381d]

Kernel driver in use: i915

Locale: ('en_GB', 'UTF-8')

PyQt5 5.15.2, Qt 5.15.2

Installed Packages:

    alabaster: 0.7.12

    appdirs: 1.4.4

    Babel: 2.9.1

    backcall: 0.2.0

    blockdiag: 2.0.1

    certifi: 2021.10.8

    cftime: 1.5.1.1

    charset-normalizer: 2.0.9

    ChimeraX-AddCharge: 1.2.2

    ChimeraX-AddH: 2.1.11

    ChimeraX-AlignmentAlgorithms: 2.0

    ChimeraX-AlignmentHdrs: 3.2

    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: 1.31

    ChimeraX-AtomicLibrary: 4.2

    ChimeraX-AtomSearch: 2.0

    ChimeraX-AtomSearchLibrary: 1.0

    ChimeraX-AxesPlanes: 2.0

    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

    ChimeraX-CommandLine: 1.1.5

    ChimeraX-ConnectStructure: 2.0

    ChimeraX-Contacts: 1.0

    ChimeraX-Core: 1.3

    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-DistUI: 1.0

    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-LinuxSupport: 1.0

    ChimeraX-ListInfo: 1.1.1

    ChimeraX-Log: 1.1.4

    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: 2.0.4

    ChimeraX-MDcrds: 2.6

    ChimeraX-MedicalToolbar: 1.0.1

    ChimeraX-Meeting: 1.0

    ChimeraX-MLP: 1.1

    ChimeraX-mmCIF: 2.4

    ChimeraX-MMTF: 2.1

    ChimeraX-Modeller: 1.2.6

    ChimeraX-ModelPanel: 1.2.1

    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: 1.7

    ChimeraX-PDB: 2.6.5

    ChimeraX-PDBBio: 1.0

    ChimeraX-PDBLibrary: 1.0.2

    ChimeraX-PDBMatrices: 1.0

    ChimeraX-PickBlobs: 1.0

    ChimeraX-Positions: 1.0

    ChimeraX-PresetMgr: 1.0.1

    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: 2.4.6

    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: 1.6.1

    ChimeraX-STL: 1.0

    ChimeraX-Storm: 1.0

    ChimeraX-Struts: 1.0

    ChimeraX-Surface: 1.0

    ChimeraX-SwapAA: 2.0

    ChimeraX-SwapRes: 2.1

    ChimeraX-TapeMeasure: 1.0

    ChimeraX-Test: 1.0

    ChimeraX-Toolbar: 1.1

    ChimeraX-ToolshedUtils: 1.2

    ChimeraX-Tug: 1.0

    ChimeraX-UI: 1.13.7

    ChimeraX-uniprot: 2.2

    ChimeraX-UnitCell: 1.0

    ChimeraX-ViewDockX: 1.0.1

    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

    cxservices: 1.1

    cycler: 0.11.0

    Cython: 0.29.24

    decorator: 5.1.0

    distro: 1.6.0

    docutils: 0.17.1

    filelock: 3.0.12

    funcparserlib: 0.3.6

    grako: 3.16.5

    h5py: 3.6.0

    html2text: 2020.1.16

    idna: 3.3

    ihm: 0.21

    imagecodecs: 2021.4.28

    imagesize: 1.3.0

    ipykernel: 5.5.5

    ipython: 7.23.1

    ipython-genutils: 0.2.0

    jedi: 0.18.0

    Jinja2: 3.0.1

    jupyter-client: 6.1.12

    jupyter-core: 4.9.1

    kiwisolver: 1.3.2

    line-profiler: 3.3.0

    lxml: 4.6.3

    lz4: 3.1.3

    MarkupSafe: 2.0.1

    matplotlib: 3.4.3

    matplotlib-inline: 0.1.3

    msgpack: 1.0.2

    netCDF4: 1.5.7

    networkx: 2.6.3

    numexpr: 2.8.0

    numpy: 1.21.2

    openvr: 1.16.801

    packaging: 21.3

    ParmEd: 3.2.0

    parso: 0.8.3

    pexpect: 4.8.0

    pickleshare: 0.7.5

    Pillow: 8.3.2

    pip: 21.2.4

    pkginfo: 1.7.1

    prompt-toolkit: 3.0.23

    psutil: 5.8.0

    ptyprocess: 0.7.0

    pycollada: 0.7.1

    pydicom: 2.1.2

    Pygments: 2.10.0

    PyOpenGL: 3.1.5

    PyOpenGL-accelerate: 3.1.5

    pyparsing: 3.0.6

    PyQt5-commercial: 5.15.2

    PyQt5-sip: 12.8.1

    PyQtWebEngine-commercial: 5.15.2

    python-dateutil: 2.8.2

    pytz: 2021.3

    pyzmq: 22.3.0

    qtconsole: 5.1.1

    QtPy: 1.11.3

    RandomWords: 0.3.0

    requests: 2.26.0

    scipy: 1.7.1

    setuptools: 57.5.0

    sfftk-rw: 0.7.1

    six: 1.16.0

    snowballstemmer: 2.2.0

    sortedcontainers: 2.4.0

    Sphinx: 4.2.0

    sphinx-autodoc-typehints: 1.12.0

    sphinxcontrib-applehelp: 1.0.2

    sphinxcontrib-blockdiag: 2.0.0

    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-jurko: 0.6

    tables: 3.6.1

    tifffile: 2021.4.8

    tinyarray: 1.2.3

    tornado: 6.1

    traitlets: 5.1.1

    urllib3: 1.26.7

    wcwidth: 0.2.5

    webcolors: 1.11.1

    wheel: 0.37.0

    wheel-filename: 1.3.0


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