Opened 20 months ago

Closed 20 months ago

Last modified 20 months ago

#14765 closed defect (wontfix)

Missing dynamic libraries

Reported by: markus.meier@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Platform Version:
Keywords: Cc: chimera@…
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.1.57-gentoo-x86_64-AMD_Ryzen_9_6900HX_with_Radeon_Graphics-with-glibc2.38
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Hi, so far ChimeraX is working well for me on my Gentoo Linux system. I just wanted to bring to your attention that the following dynamic libraries are missing in the ChimeraX distribution (I installed generic ChimeraX-1.7.1.tar.gz):

libQt63DCore.so.6
libQt63DRender.so.6
libQt63DQuick.so.6
libQt63DQuickScene2D.so.6
libQt63DAnimation.so.6 
libQt63DExtras.so.6
libQt63DInput.so.6
libQt63DLogic.so.6
libQt6WebView.so.6
libQt6WebViewQuick.so.6
libQt6QmlXmlListModel.so.6
libQt6QmlLocalStorage.so.6
libQt6Quick3DParticleEffects.so.6

Gentoo performs an automated dependency analysis during installation. Details below:

 * QA Notice: Unresolved soname dependencies:
 * /usr/lib64/ucsf-chimerax/lib/python3.11/site-packages/PyQt6/Qt6/plugins/geometryloaders/libdefaultgeometryloader.so: libQt63DCore.so.6 libQt63DRender.so.6
 * /usr/lib64/ucsf-chimerax/lib/python3.11/site-packages/PyQt6/Qt6/plugins/geometryloaders/libgltfgeometryloader.so: libQt63DCore.so.6 libQt63DRender.so.6
 * /usr/lib64/ucsf-chimerax/lib/python3.11/site-packages/PyQt6/Qt6/plugins/renderers/libopenglrenderer.so: libQt63DCore.so.6 libQt63DRender.so.6
 * /usr/lib64/ucsf-chimerax/lib/python3.11/site-packages/PyQt6/Qt6/plugins/renderers/librhirenderer.so: libQt63DCore.so.6 libQt63DRender.so.6
 * /usr/lib64/ucsf-chimerax/lib/python3.11/site-packages/PyQt6/Qt6/plugins/renderplugins/libscene2d.so: libQt63DCore.so.6 libQt63DQuick.so.6 libQt63DQuickScene2D.so.6 libQt63DRender.so.6
 * /usr/lib64/ucsf-chimerax/lib/python3.11/site-packages/PyQt6/Qt6/plugins/sceneparsers/libassimpsceneimport.so: libQt63DAnimation.so.6 libQt63DCore.so.6 libQt63DExtras.so.6 libQt63DInput.so.6 libQt63DLogic.so.6 libQt63DRender.so.6
 * /usr/lib64/ucsf-chimerax/lib/python3.11/site-packages/PyQt6/Qt6/plugins/sceneparsers/libgltfsceneexport.so: libQt63DCore.so.6 libQt63DExtras.so.6 libQt63DInput.so.6 libQt63DLogic.so.6 libQt63DRender.so.6
 * /usr/lib64/ucsf-chimerax/lib/python3.11/site-packages/PyQt6/Qt6/plugins/sceneparsers/libgltfsceneimport.so: libQt63DCore.so.6 libQt63DExtras.so.6 libQt63DInput.so.6 libQt63DLogic.so.6 libQt63DRender.so.6
 * /usr/lib64/ucsf-chimerax/lib/python3.11/site-packages/PyQt6/Qt6/plugins/webview/libqtwebview_webengine.so: libQt6WebView.so.6 libQt6WebViewQuick.so.6
 * /usr/lib64/ucsf-chimerax/lib/python3.11/site-packages/PyQt6/Qt6/qml/QtQml/XmlListModel/libqmlxmllistmodelplugin.so: libQt6QmlXmlListModel.so.6
 * /usr/lib64/ucsf-chimerax/lib/python3.11/site-packages/PyQt6/Qt6/qml/QtQuick/LocalStorage/libqmllocalstorageplugin.so: libQt6QmlLocalStorage.so.6
 * /usr/lib64/ucsf-chimerax/lib/python3.11/site-packages/PyQt6/Qt6/qml/QtQuick/Scene2D/libqtquickscene2dplugin.so: libQt63DCore.so.6 libQt63DQuick.so.6 libQt63DQuickScene2D.so.6 libQt63DRender.so.6
 * /usr/lib64/ucsf-chimerax/lib/python3.11/site-packages/PyQt6/Qt6/qml/QtQuick/Scene3D/libqtquickscene3dplugin.so: libQt63DAnimation.so.6 libQt63DCore.so.6 libQt63DInput.so.6 libQt63DLogic.so.6 libQt63DRender.so.6
 * /usr/lib64/ucsf-chimerax/lib/python3.11/site-packages/PyQt6/Qt6/qml/QtQuick3D/ParticleEffects/libqtquick3dparticleeffectsplugin.so: libQt6Quick3DParticleEffects.so.6


Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 470.223.02
OpenGL renderer: NVIDIA GeForce RTX 3070 Ti Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_CA.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=xfce
XDG_SESSION_DESKTOP=XFCE
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:0.0
Manufacturer: ASUSTeK COMPUTER INC.
Model: ROG Strix G513RW_G513RW
OS: Gentoo 2.14 n/a
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 AMD Ryzen 9 6900HX with Radeon Graphics
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            14Gi       3.6Gi       161Mi        39Mi        11Gi        10Gi
	Swap:           31Gi       0.0Ki        31Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104 [Geforce RTX 3070 Ti Laptop GPU] [10de:24a0] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. GA104 [Geforce RTX 3070 Ti Laptop GPU] [1043:1cb2]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    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: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    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-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: 1.7.1
    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: 2.6.1
    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: 1.5.14
    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: 1.0.4
    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: 1.12.4
    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: 1.33.3
    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: 0.2.1
    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: 4.47.2
    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: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    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
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    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: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    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: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (4)

comment:1 by pett, 20 months ago

Component: Unassigned → Platform
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Missing dynamic libraries

comment:2 by Greg Couch, 20 months ago

Resolution: → wontfix
Status: assigned → closed

Those libraries are in chimerax-1.7/lib/python3.11/site-packages/PyQt6/Qt6/lib/. If there were any unresolved dependencies for libQt6core.so, and some others, then ChimeraX wouldn't start up. So that is a kind of a false positive, i.e., a bug in Gentoo. Many pypi.org Python packages include libraries that could trigger that warning.

Anyway, I recommend switching to the experimental flatpak version of ChimeraX -- there's a link at the bottom of the download page. We will be replacing the tar.gz version with the flatpak version before the next release. And then you will have a supported version of ChimeraX. The dependencies needed for the tar.gz version can be difficult to resolve for some versions of Linux.

comment:3 by markus.meier@…, 20 months ago 

Hi Greg,

Thank you for your prompt response! However, I did *not* report libQt6core.so missing.

libQt63DCore.so.6 is a totally different library from libQt6core.so

None of the libraries I listed are in chimerax-1.7/lib/python3.11/site-packages/PyQt6/Qt6/lib/

Neither in the tar.gz file nor in the .deb distribution. I made sure to check before I submitted the report.

The Qt63D libraries are used by certain Qt plugins (the full list is appended in my bug report). You did include these plugins in the ChimeraX distribution, but not the required libraries to load these plugins. Maybe these Qt plugins a not required to run ChimeraX.

It is not a bug in Gentoo.

I am maintaining the package management script (ebuild) for ChimeraX on Gentoo, so it is my job to resolve all dependencies and report inconsistencies upstream. It is up to you to fix or ignore them.

With best regards,
Markus


On 2024-03-14 21:20, ChimeraX wrote:

comment:4 by Greg Couch, 20 months ago

Cc: chimera@… added

You're right, my mistake. We have a commercial license for PyQt, not Qt. So our distribution can't bundle PyQt6-3D because it GPL, not LGPL. There is no issue with third party bundles depending on it.

And note that a fresh compile of ChimeraX is not binary compatible with bundles in the ChimeraX toolshed unless the bundles are compiled on RHEL 8. This is another reason to use the flatpak version when it is no longer experimental (should be ready by the end of this month).

And recognize that the license agreement for ChimeraX does not allow for third party distribution yet. The ebuild script could be considered an improvement. See the "Permitted Use and Restrictions" section of the license agreement. Send email to chimera@… and ask for permission. It will help your case if you could provide us with download statistics that we could report to our funding agencies. And ideally notify us of any commercial downloads. We have not considered this use case yet, so I don't know what the answer will be.

Note: See TracTickets for help on using tickets.