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#16250 feedback defect

KVFinder: error in "pip install" error handling

Reported by:	yongquan0043@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Surface/Binding Analysis	Version:
Keywords:		Cc:	chimera-programmers
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.9rc202411012347 (2024-11-01 23:47:45 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9rc202411012347 (2024-11-01)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "S:/alphafold predict/mTORC2 电镜扫描结构/6zwo.pdb"

6zwo.pdb title:  
Cryo-em structure of human mtor complex 2, focused on one half [more info...]  
  
Chain information for 6zwo.pdb #1  
---  
Chain | Description | UniProt  
B | serine/threonine-protein kinase mtor | MTOR_HUMAN 1-2549  
D | target of rapamycin complex subunit LST8 | LST8_HUMAN 1-326  
F | rapamycin-insensitive companion of mtor | RICTR_HUMAN 1-1708  
H | target of rapamycin complex 2 subunit MAPKAP1 | SIN1_HUMAN 2-522  
  
Non-standard residues in 6zwo.pdb #1  
---  
ACE — acetyl group  
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5&#x27;-(3-thiotriphosphate);adenosine 5&#x27;-(γ-thiotriphosphate);
adenosine-5&#x27;-diphosphate monothiophosphate)  
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)  
ZN — zinc ion  
  

> select /B:791-2549

12841 atoms, 13126 bonds, 4 pseudobonds, 1592 residues, 2 models selected  

> select /B:791-2549

12841 atoms, 13126 bonds, 4 pseudobonds, 1592 residues, 2 models selected  

> select /B:791-2549

12841 atoms, 13126 bonds, 4 pseudobonds, 1592 residues, 2 models selected  

> select /B:791-2549

12841 atoms, 13126 bonds, 4 pseudobonds, 1592 residues, 2 models selected  

> select /B:791-2549

12841 atoms, 13126 bonds, 4 pseudobonds, 1592 residues, 2 models selected  

> color (#!1 & sel) yellow

> color (#!1 & sel) light sea green

>

Incomplete command: sequence  

> help help:user

> select sequence "chain B"

Nothing selected  

> help help:user

> lighting simple

[Repeated 3 time(s)]

> select /B:791-2549

12841 atoms, 13126 bonds, 4 pseudobonds, 1592 residues, 2 models selected  

> 1026

Unknown command: sequence 1026  

> 1026, chainB

Unknown command: sequence 1026, chainB  

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> select clear

[Repeated 3 time(s)]

> select
> /B:792-809,816-829,836-847,855-861,863-871,877-892,895-902,929-936,946-960,967-983,989-1023,1027-1039,1048-1064,1066-1084,1090-1101,1115-1123,1128-1142,1149-1165,1169-1182,1185-1189,1191-1202,1206-1218,1228-1238,1265-1270,1276-1294,1297-1308,1310-1327,1330-1348,1350-1366,1376-1389,1392-1407,1409-1423,1425-1440,1446-1453,1455-1468,1476-1499,1505-1534,1540-1554,1558-1579,1582-1608,1611-1624,1629-1641,1650-1663,1665-1678,1693-1708,1711-1729,1739-1763,1768-1784,1786-1809,1875-1896,1899-1914,1916-1930,1932-1944,1950-1968,1972-1981,1984-1999,2003-2059,2064-2091,2093-2113,2123-2127,2192-2217,2246-2257,2262-2272,2274-2293,2297-2306,2309-2335,2380-2385,2394-2423,2429-2433,2493-2508,2520-2546

9638 atoms, 9784 bonds, 1176 residues, 1 model selected  

> select clear

> select
> /B:792-809,816-829,836-847,855-861,863-871,877-892,895-902,929-936,946-960,967-983,989-1023,1027-1039,1048-1064,1066-1084,1090-1101,1115-1123,1128-1142,1149-1165,1169-1182,1185-1189,1191-1202,1206-1218,1228-1238,1265-1270,1276-1294,1297-1308,1310-1327,1330-1348,1350-1366,1376-1389,1392-1407,1409-1423,1425-1440,1446-1453,1455-1468,1476-1499,1505-1534,1540-1554,1558-1579,1582-1608,1611-1624,1629-1641,1650-1663,1665-1678,1693-1708,1711-1729,1739-1763,1768-1784,1786-1809,1875-1896,1899-1914,1916-1930,1932-1944,1950-1968,1972-1981,1984-1999,2003-2059,2064-2091,2093-2113,2123-2127,2192-2217,2246-2257,2262-2272,2274-2293,2297-2306,2309-2335,2380-2385,2394-2423,2429-2433,2493-2508,2520-2546

9638 atoms, 9784 bonds, 1176 residues, 1 model selected  

> select /B:1028

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /B:1028

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel target ab

> view sel

> select /F:463

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /F:463

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add /F:464

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select subtract /F:463

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add /F:463

18 atoms, 16 bonds, 2 residues, 1 model selected  

> show sel target ab

> undo

> select subtract /F:463

9 atoms, 8 bonds, 1 residue, 1 model selected  

> view sel

> show sel target ab

> select add /B:1028@CZ

10 atoms, 8 bonds, 2 residues, 1 model selected  

> show sel target ab

> ui tool show H-Bonds

> hbonds sel reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /F PRO 27 N; /H PRO 134 N; /H PRO 133 N; /F PRO 642 N; /F PRO
34 N  

2 hydrogen bonds found  

> select clear

> hide #!1 models

> show #!1 models

> ui tool show "Find Cavities"

pyKVFinder module not installed; fetching from PyPi repository...  
Traceback (most recent call last):  
File "S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 37, in register_command  
import pyKVFinder  
ModuleNotFoundError: No module named 'pyKVFinder'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 42, in register_command  
run(logger.session, "pip install pyKVFinder", log=False)  
File "S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\core\commands\pip.py", line 88, in pip  
run_logged_pip(pip_cmd, session.logger)  
File "S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\core\python_utils.py", line 143, in run_logged_pip  
raise RuntimeError(s)  
RuntimeError  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 330, in _register_cmd  
api._api_caller.register_command(api, self, ci, logger)  
File "S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1403, in register_command  
return cls._get_func(api, "register_command")(ci.name, logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 44, in register_command  
from chimerax.core.logger import report_exception  
ImportError: cannot import name 'report_exception' from 'chimerax.core.logger'
(S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\core\logger.py)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2475, in lazy_register  
deferred.call()  
File "S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2403, in call  
return self.proxy()  
^^^^^^^^^^^^  
File "S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 320, in cb  
s._register_cmd(ci, logger)  
File "S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 332, in _register_cmd  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: register_command() failed for command
kvfinder in bundle ChimeraX-KVFinder:  
cannot import name 'report_exception' from 'chimerax.core.logger'
(S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\core\logger.py)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 67, in find_cavities  
run(self.session, "kvfinder %s" % concise_model_spec(self.session, structures,  
File "S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3139, in run  
self._find_command_name(final, used_aliases=_used_aliases)  
File "S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2863, in _find_command_name  
what.lazy_register(cmd_name)  
File "S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2477, in lazy_register  
raise RuntimeError(  
RuntimeError: delayed command registration for 'kvfinder' failed
(register_command() failed for command kvfinder in bundle ChimeraX-KVFinder:  
cannot import name 'report_exception' from 'chimerax.core.logger'
(S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\core\logger.py))  
  
RuntimeError: delayed command registration for 'kvfinder' failed
(register_command() failed for command kvfinder in bundle ChimeraX-KVFinder:  
cannot import name 'report_exception' from 'chimerax.core.logger'
(S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\core\logger.py))  
  
File "S:\ChimeraX\ChimeraX 1.9rc202411012347\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2477, in lazy_register  
raise RuntimeError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 551.86
OpenGL renderer: NVIDIA GeForce GTX 1650/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: LENOVO
Model: 82B6
OS: Microsoft Windows 10 家庭版 (Build 19045)
Memory: 16,505,966,592
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 4600H with Radeon Graphics         
OSLanguage: zh-CN

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 2.4.1
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9rc202411012347
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.5
    ChimeraX-DistMonitor: 1.4.2
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2
    ChimeraX-Label: 1.1.11
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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-Segmentations: 3.2.4
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.7
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.54.1
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.1
    numpy: 2.1.3
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    plotly: 5.24.1
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.1
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tenacity: 9.0.0
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    toml: 0.10.2
    tornado: 6.4.1
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 12 months ago

Component:	Unassigned → Surface/Binding Analysis
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → KVFinder: error in "pip install" error handling

comment:2 by Eric Pettersen, 12 months ago

Cc:	chimera-programmers added
Status:	accepted → feedback

Hi,

Thanks for reporting this problem. Your machine had a problem installing the pyKVFinder module from the PyPi repository, and the error-processing code had a bug in it, so you got the confusing error message you saw. Tomorrow's builds have a corrected version of the error-processing code.
Nonetheless, this doesn't address the underlying problem of your machine not being able to install pyKVFinder from the PyPi repository. Can you run the command "pip install pyKVFinder" (in the ChimeraX command line) and let me know what happens?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

Last edited 12 months ago by Eric Pettersen (previous) (diff)

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