networkx: no libbz2

[murpholinox@…]

The following bug report has been submitted:
Platform:        Linux-5.17.11-300.fc36.x86_64-x86_64-with-glibc2.35
ChimeraX Version: 1.4rc202205290614 (2022-05-29 06:14:06 UTC)
Description
click on color PAE domains... 

Log:
UCSF ChimeraX version: 1.4rc202205290614 (2022-05-29)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold predict
> MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRDPNSSSVDKLMGKEVVFESSGAAVHNHRRHHQQQTNGYHRAAIHQSLNKKKKHCQPRVVKKPRSVSNGTSRTMRHDAILFSNLKPKEFAQEVVGKTNKNDLENPFYIVDIDDVLYKIDLWRKSVPRAKPFYAVKCNDNPIVLEVLAGLGLGFDCASLAEIEAVMSLGVDPSRIIYAHPQKHVSYLHRAHELGVDLMTFDCAEELYKIKAHHPCARLVLRLKVDNKKALFAMGDKFGCSEVEAINLLQLAKDLELSVVGICFHVGSTNQDPGAFTGALAAARRTFDAGRDLGFDLRLLDIGGGYPGEKGLEHVFLKTADIINAGLDKHFPESYGVSIISEPGTFFVASAFTIYTKIIGKRLKESYDDSKPKERMYYINESVYKSFIVSLFDDESVEPEPLQDNEEPLHPSIVWGITCDGVDKIKAVCKLPELAVGEWLYFENMGAYTITINSPFNGFPMADVHYRASKIVEDHLRRKKLILSILDTAAAALEHHHHHH

Running AlphaFold prediction  
[Repeated 2 time(s)]AlphaFold prediction finished  
Results in /home/murphy/Downloads/ChimeraX/AlphaFold/prediction_1  
Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  

atomName: bad atom 50463471  

atomName: bad atom 32530  

> alphafold pae #1 file
> /home/murphy/Downloads/ChimeraX/AlphaFold/prediction_1/best_model_pae.json

> color bfactor #1 palette alphafold

8274 atoms, 529 residues, atom bfactor range 21.1 to 98.9  
Traceback (most recent call last):  
File "/home/murphy/Downloads/chimerax-1.4-rc2022.05.29/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 441, in _color_domains  
self._pae.color_domains(log_command = True)  
File "/home/murphy/Downloads/chimerax-1.4-rc2022.05.29/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 674, in color_domains  
self._clusters = pae_domains(self._pae_matrix,  
File "/home/murphy/Downloads/chimerax-1.4-rc2022.05.29/lib/python3.9/site-
packages/chimerax/alphafold/pae.py", line 837, in pae_domains  
import networkx as nx  
File "/home/murphy/Downloads/chimerax-1.4-rc2022.05.29/lib/python3.9/site-
packages/networkx/__init__.py", line 57, in <module>  
from networkx import utils  
File "/home/murphy/Downloads/chimerax-1.4-rc2022.05.29/lib/python3.9/site-
packages/networkx/utils/__init__.py", line 2, in <module>  
from networkx.utils.decorators import *  
File "/home/murphy/Downloads/chimerax-1.4-rc2022.05.29/lib/python3.9/site-
packages/networkx/utils/decorators.py", line 12, in <module>  
import re, gzip, bz2  
File "/home/murphy/Downloads/chimerax-1.4-rc2022.05.29/lib/python3.9/bz2.py",
line 18, in <module>  
from _bz2 import BZ2Compressor, BZ2Decompressor  
ImportError: libbz2.so.1.0: cannot open shared object file: No such file or
directory  
  
ImportError: libbz2.so.1.0: cannot open shared object file: No such file or
directory  
  
File "/home/murphy/Downloads/chimerax-1.4-rc2022.05.29/lib/python3.9/bz2.py",
line 18, in  
from _bz2 import BZ2Compressor, BZ2Decompressor  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 22.0.3
OpenGL renderer: Mesa Intel(R) Xe Graphics (TGL GT2)
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: LENOVO
Model: 82FE
OS: Fedora Linux 36 
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
Cache Size: 12288 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           7.6Gi       4.3Gi       653Mi       1.2Gi       2.6Gi       1.7Gi
	Swap:          7.6Gi       998Mi       6.6Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation TigerLake-LP GT2 [Iris Xe Graphics] [8086:9a49] (rev 01)	
	Subsystem: Lenovo Device [17aa:3f18]	
	Kernel driver in use: i915

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    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: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4rc202205290614
    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: 1.1
    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: 1.2
    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: 1.1.1
    ChimeraX-LinuxSupport: 1.0
    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: 1.5.5
    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: 1.9
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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: 1.8
    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-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    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
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    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
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.0.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    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
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

[Greg Couch]

Ouch. While I'm tracking this down, you could workaround the problem by adding the symbolic link by hand:

sudo ln -s /usr/lib64/libbz2.so.1.0.8 /usr/lib64/libbz2.so.1.0

But I hope to figure this out quickly and get a fix in today.

[Greg Couch]

So which version of ChimeraX did you download for Fedora 36? You should be using the CentOS 9 rpm. In that version, there is no reference to libbz2.so.1.0. Please install the current release candidate and confirm that it works.

[Greg Couch]

This should be solved by using the existing CentOS 9 release candidate. So it should not hold up making the final 1.4 release.

[goddard@…]

Agree.  I milestoned it 1.4 because the reporter did not yet say which ChimeraX distribution they used.  If they used the wrong one we should probably update the download page so it is clearer which ChimeraX is needed on Fedora XX.

[Greg Couch]

Already done. "Works on Fedora 36" should appear with tonight's builds.

[Tom Goddard]

Ticket retargeted after milestone closed