id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16505	error in running kvfinder	vincent.chaptal@…	Eric Pettersen	"{{{
Hi,

by typing the command ""kvfinder #2"" I got the following error message.

I tried to report the bug using the bug reporter but it couldn't reach 
internet so couldn't be sent (but internet connection is working)

perhaps a firewall issue? (but my firewall is configured correctly for 
chimeraX, but is it different for python?)

Thanks

Vincent

Chimera X version: 1.9 (2024-12-11 19:11:19 UTC)

Platform: macOS-14.6.1-arm64-arm-64bit

Could not install pyKVFinder module from PyPi repository: RuntimeError: 
WARNING: Retrying (Retry(total=4, connect=None, read=None, 
redirect=None, status=None)) after connection broken by 
'ProxyError('Your proxy appears to only use HTTP and not HTTPS, try 
changing your proxy URL to be HTTP. See: 
https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#https-proxy-error-http-proxy', 
SSLError(SSLError(1, '[SSL: WRONG_VERSION_NUMBER] wrong version number 
(_ssl.c:1002)')))': /simple/pykvfinder/ WARNING: Retrying 
(Retry(total=3, connect=None, read=None, redirect=None, status=None)) 
after connection broken by 'ProxyError('Your proxy appears to only use 
HTTP and not HTTPS, try changing your proxy URL to be HTTP. See: 
https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#https-proxy-error-http-proxy', 
SSLError(SSLError(1, '[SSL: WRONG_VERSION_NUMBER] wrong version number 
(_ssl.c:1002)')))': /simple/pykvfinder/ WARNING: Retrying 
(Retry(total=2, connect=None, read=None, redirect=None, status=None)) 
after connection broken by 'ProxyError('Your proxy appears to only use 
HTTP and not HTTPS, try changing your proxy URL to be HTTP. See: 
https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#https-proxy-error-http-proxy', 
SSLError(SSLError(1, '[SSL: WRONG_VERSION_NUMBER] wrong version number 
(_ssl.c:1002)')))': /simple/pykvfinder/ WARNING: Retrying 
(Retry(total=1, connect=None, read=None, redirect=None, status=None)) 
after connection broken by 'ProxyError('Your proxy appears to only use 
HTTP and not HTTPS, try changing your proxy URL to be HTTP. See: 
https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#https-proxy-error-http-proxy', 
SSLError(SSLError(1, '[SSL: WRONG_VERSION_NUMBER] wrong version number 
(_ssl.c:1002)')))': /simple/pykvfinder/ WARNING: Retrying 
(Retry(total=0, connect=None, read=None, redirect=None, status=None)) 
after connection broken by 'ProxyError('Your proxy appears to only use 
HTTP and not HTTPS, try changing your proxy URL to be HTTP. See: 
https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#https-proxy-error-http-proxy', 
SSLError(SSLError(1, '[SSL: WRONG_VERSION_NUMBER] wrong version number 
(_ssl.c:1002)')))': /simple/pykvfinder/ ERROR: Could not find a version 
that satisfies the requirement pyKVFinder (from versions: none) ERROR: 
No matching distribution found for pyKVFinder File 
""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/python_utils.py"", 
line 143, in run_logged_pip raise RuntimeError(s) See log for complete 
Python traceback.

Gathered information:

OpenGL version: 4.1 Metal - 88.1

OpenGL renderer: Apple M3 Pro

OpenGL vendor: Apple

Python: 3.11.4

Locale: UTF-8

Qt version: PyQt6 6.7.1, Qt 6.7.1

Qt runtime version: 6.7.3

Qt platform: cocoa

Hardware:

Hardware Overview:

Model Name: MacBook Pro

Model Identifier: Mac15,7

Model Number: Z1AJ00112FN/A

Chip: Apple M3 Pro

Total Number of Cores: 12 (6 performance and 6 efficiency)

Memory: 36 GB

System Firmware Version: 10151.140.19

OS Loader Version: 10151.140.19

Software:

System Software Overview:

System Version: macOS 14.6.1 (23G93)

Kernel Version: Darwin 23.6.0

Time since boot: 29 jours, 21 heures et 41 minutes

Graphics/Displays:

Apple M3 Pro:

Chipset Model: Apple M3 Pro

Type: GPU

Bus: Built-In

Total Number of Cores: 18

Vendor: Apple (0x106b)

Metal Support: Metal 3

Displays:

Color LCD:

Display Type: Built-in Liquid Retina XDR Display

Resolution: 3456 x 2234 Retina

Main Display: Yes

Mirror: Off

Online: Yes

Automatically Adjust Brightness: Yes

Connection Type: Internal

PL3480WQ:

Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)

UI Looks like: 3440 x 1440 @ 100.00Hz

Mirror: Off

Online: Yes

Rotation: Supported

Installed Packages:

alabaster: 1.0.0

anyio: 4.7.0

appdirs: 1.4.4

appnope: 0.1.4

asttokens: 3.0.0

auditwheel: 6.1.0

babel: 2.16.0

beautifulsoup4: 4.12.3

blockdiag: 3.0.0

blosc2: 3.0.0

build: 1.2.1

certifi: 2023.11.17

cftime: 1.6.4.post1

charset-normalizer: 3.4.0

ChimeraX-AddCharge: 1.5.18

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: 1.58.8

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: 3.0.0

ChimeraX-BondRot: 2.0.4

ChimeraX-BugReporter: 1.0.1

ChimeraX-BuildStructure: 2.13.1

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: 1.9

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: 1.2.6

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: 1.2.1

ChimeraX-Label: 1.1.14

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: 2.7.2

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: 1.5.18

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: 1.6.2

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: 3.5.6

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

contourpy: 1.3.1

cxservices: 1.2.3

cycler: 0.12.1

Cython: 3.0.10

debugpy: 1.8.9

decorator: 5.1.1

docutils: 0.21.2

executing: 2.1.0

filelock: 3.15.4

fonttools: 4.55.3

funcparserlib: 2.0.0a0

glfw: 2.8.0

grako: 3.16.5

h11: 0.14.0

h5py: 3.12.1

html2text: 2024.2.26

httpcore: 1.0.7

httpx: 0.28.1

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: 2.10.2

numpy: 1.26.4

openvr: 1.26.701

packaging: 23.2

ParmEd: 4.2.2

parso: 0.8.4

pep517: 0.13.1

pexpect: 4.9.0

pillow: 10.4.0

pip: 24.2

pkginfo: 1.11.1

platformdirs: 4.3.6

prompt_toolkit: 3.0.48

psutil: 6.0.0

ptyprocess: 0.7.0

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

pyzmq: 26.2.0

qtconsole: 5.5.2

QtPy: 2.4.2

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

sniffio: 1.3.1

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

tifffile: 2024.7.24

tinyarray: 1.2.4

tornado: 6.4.2

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

-- 

Vincent Chaptal, PhD

Director of GdR APPICOM

Drug Resistance and Membrane Proteins Lab

MMSB -UMR5086

7 passage du Vercors

69007 LYON

FRANCE

+33 4 37 65 29 01

http://www.appicom.cnrs.fr

http://mmsb.cnrs.fr/en/
}}}
"	defect	closed	normal		Input/Output		fixed						all	ChimeraX