id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20308 KVFinder on old MacOS taylor@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.8.5-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description tried to install kvfinder Log: Startup Messages --- warning | No presets found in custom preset folder /Users/becca/Desktop/Postdoc/Computational_references/ChimeraX_presets note | CubeNTube: sphere eraser undo support enabled > volume defaultvalues limitVoxelCount false voxelLimitForPlane > 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true Saved volume settings > graphics silhouettes true > set silhouetteWidth 1.5 > ui mousemode right ""translate selected models"" > isolde shorthand Initialising ISOLDE-specific command aliases: Alias Equivalent full command ------------------------------------------------- st isolde step {arguments} aw isolde add water {arguments} awsf isolde add water {arguments} sim false al isolde add ligand {arguments} aa isolde add aa $1 sel {arguments} ht isolde mod his sel {arguments} so setattr sel atoms occupancy {arguments} ab isolde adjust bfactors {arguments} ss isolde sim start sel rt isolde release torsions sel {arguments} rd isolde release distances sel {arguments} ra rd; rt pf isolde pepflip sel cf isolde cisflip sel cbb color bfactor {arguments} cbo color byattr occupancy {arguments} cbc color {arguments} bychain; color {arguments} byhet cs clipper set contourSensitivity {arguments} > alias t0 transparency 0 > alias t50 transparency 50 > alias t60 transparency 60 > alias t70 transparency 70 > alias t80 transparency 80 > alias t90 transparency 90 > alias fmap ui tool show ""Fit in Map"" > alias delh select H; delete sel > alias ls lighting soft > alias 0 transp 0; lighting soft > alias fit transp 50; lighting simple > alias licorice car style protein modeh default arrows f xsect oval width 1 > thick 1 > functionkey F1 mousemode right 'rotate selected models' > functionkey F2 mousemode right 'translate selected models' > functionkey F3 view sel > functionkey F5 turn x 1 90 > functionkey F6 turn x -1 90 > functionkey F7 turn y 1 90 > functionkey F8 turn y -1 90 > functionkey F9 turn z 1 90 > functionkey F10 turn z -1 90 > cartoon smooth 1 > style stick Changed 0 atom styles > size stickRadius 0.3 Changed 0 bond radii > set bgColor white > alias bbh hide @C,N,O > alias bb show @C,N,O > cartoon all > style stick Changed 0 atom styles > color all byhetero > hide atoms > transparency 0 > lighting soft > color name alphav1 #5786F5 Color 'alphav1' is opaque: rgb(34.1%, 52.5%, 96.1%) hex: #5786f5 > color name alphav2 #2A4B9B Color 'alphav2' is opaque: rgb(16.5%, 29.4%, 60.8%) hex: #2a4b9b > color name betapv1 #53EAF3 Color 'betapv1' is opaque: rgb(32.5%, 91.8%, 95.3%) hex: #53eaf3 > color name betapv2 #759ED9 Color 'betapv2' is opaque: rgb(45.9%, 62%, 85.1%) hex: #759ed9 > color name betav1 #37863D Color 'betav1' is opaque: rgb(21.6%, 52.5%, 23.9%) hex: #37863d > color name betav2 #207B35 Color 'betav2' is opaque: rgb(12.5%, 48.2%, 20.8%) hex: #207b35 > color name deltav1 #CE8041 Color 'deltav1' is opaque: rgb(80.8%, 50.2%, 25.5%) hex: #ce8041 > color name deltav2 #E97408 Color 'deltav2' is opaque: rgb(91.4%, 45.5%, 3.14%) hex: #e97408 > color name epsilonv1 #F06969 Color 'epsilonv1' is opaque: rgb(94.1%, 41.2%, 41.2%) hex: #f06969 > color name gammav1 #2AFF3C Color 'gammav1' is opaque: rgb(16.5%, 100%, 23.5%) hex: #2aff3c > color name gammav2 #61B230 Color 'gammav2' is opaque: rgb(38%, 69.8%, 18.8%) hex: #61b230 > color name zetav1 #E0C819 Color 'zetav1' is opaque: rgb(87.8%, 78.4%, 9.8%) hex: #e0c819 > color name zetav2 #EFE30C Color 'zetav2' is opaque: rgb(93.7%, 89%, 4.71%) hex: #efe30c > color name arf1v1 #FF76AF Color 'arf1v1' is opaque: rgb(100%, 46.3%, 68.6%) hex: #ff76af > color name arf1v2 #EB70A8 Color 'arf1v2' is opaque: rgb(92.2%, 43.9%, 65.9%) hex: #eb70a8 > color name label_red #E32723 Color 'label_red' is opaque: rgb(89%, 15.3%, 13.7%) hex: #e32723 > color name label_purple #6C4896 Color 'label_purple' is opaque: rgb(42.4%, 28.2%, 58.8%) hex: #6c4896 > color name alphav3 #57679E Color 'alphav3' is opaque: rgb(34.1%, 40.4%, 62%) hex: #57679e > color name betapv3 #7ACADA Color 'betapv3' is opaque: rgb(47.8%, 79.2%, 85.5%) hex: #7acada > color name betav3 #447A57 Color 'betav3' is opaque: rgb(26.7%, 47.8%, 34.1%) hex: #447a57 > color name gammav3 #ADE57C Color 'gammav3' is opaque: rgb(67.8%, 89.8%, 48.6%) hex: #ade57c > color name deltav3 #E5AF76 Color 'deltav3' is opaque: rgb(89.8%, 68.6%, 46.3%) hex: #e5af76 > color name epsilonv3 #EB8675 Color 'epsilonv3' is opaque: rgb(92.2%, 52.5%, 45.9%) hex: #eb8675 > color name zetav3 #F0E07B Color 'zetav3' is opaque: rgb(94.1%, 87.8%, 48.2%) hex: #f0e07b > color name arf1v3 #EB8BCA Color 'arf1v3' is opaque: rgb(92.2%, 54.5%, 79.2%) hex: #eb8bca > color name label_red_v3 #E51A16 Color 'label_red_v3' is opaque: rgb(89.8%, 10.2%, 8.63%) hex: #e51a16 > color name label_purple_v3 #691099 Color 'label_purple_v3' is opaque: rgb(41.2%, 6.27%, 60%) hex: #691099 > color name lable_purple_v4 #9057AD Color 'lable_purple_v4' is opaque: rgb(56.5%, 34.1%, 67.8%) hex: #9057ad > color name lpta #B03B3B Color 'lpta' is opaque: rgb(69%, 23.1%, 23.1%) hex: #b03b3b > color name lptb #EEB3AA Color 'lptb' is opaque: rgb(93.3%, 70.2%, 66.7%) hex: #eeb3aa > color name lptc #EB8BD7 Color 'lptc' is opaque: rgb(92.2%, 54.5%, 84.3%) hex: #eb8bd7 > color name lptd #617FBF Color 'lptd' is opaque: rgb(38%, 49.8%, 74.9%) hex: #617fbf > color name lpte #FF8533 Color 'lpte' is opaque: rgb(100%, 52.2%, 20%) hex: #ff8533 > color name lptf #A6D5A5 Color 'lptf' is opaque: rgb(65.1%, 83.5%, 64.7%) hex: #a6d5a5 > color name lptg #75CDDE Color 'lptg' is opaque: rgb(45.9%, 80.4%, 87.1%) hex: #75cdde > color name lps #FDCB80 Color 'lps' is opaque: rgb(99.2%, 79.6%, 50.2%) hex: #fdcb80 UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/becca/Documents/Kahne lab materials/Lpt bridge paper/Structural > data/P24 - Krios - ordered > LPS/P24_2026_final_models/P24_Combined_Final_RenamedChains-coot-2.pdb"" Chain information for P24_Combined_Final_RenamedChains-coot-2.pdb #1 --- Chain | Description B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available > open ""/Users/becca/Documents/Kahne lab materials/Lpt bridge paper/Structural > data/P24 - Krios - ordered > LPS/P24_2026_final_models/P24_ForDisplay_notFit_useThis.pdb"" Chain information for P24_ForDisplay_notFit_useThis.pdb #2 --- Chain | Description B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available X | No description available > open ""/Users/becca/Documents/Kahne lab materials/Lpt bridge paper/Structural > data/P31 - Krios - ordered C > helix/P31_2026_final_models/P31_ModelWithPeriplasm_ForDisplay.pdb"" Chain information for P31_ModelWithPeriplasm_ForDisplay.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available > open ""/Users/becca/Documents/Kahne lab materials/Lpt bridge paper/Structural > data/P31 - Krios - ordered C > helix/P31_2026_final_models/P31_Revised_Combined_RenamedChain-coot-3.pdb"" Chain information for P31_Revised_Combined_RenamedChain-coot-3.pdb #4 --- Chain | Description B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!1 models > show #!3 models > hide #!1,3 atoms > show #!1,3 cartoons Computing secondary structure [Repeated 1 time(s)] > ui tool show Matchmaker > matchmaker #!2-4 to #1/D pairing bs Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker P24_Combined_Final_RenamedChains-coot-2.pdb, chain D (#1) with P24_ForDisplay_notFit_useThis.pdb, chain D (#2), sequence alignment score = 3983.7 RMSD between 752 pruned atom pairs is 0.004 angstroms; (across all 752 pairs: 0.004) Matchmaker P24_Combined_Final_RenamedChains-coot-2.pdb, chain D (#1) with P31_ModelWithPeriplasm_ForDisplay.pdb, chain D (#3), sequence alignment score = 3805.7 RMSD between 743 pruned atom pairs is 0.524 angstroms; (across all 752 pairs: 0.751) Matchmaker P24_Combined_Final_RenamedChains-coot-2.pdb, chain D (#1) with P31_Revised_Combined_RenamedChain-coot-3.pdb, chain D (#4), sequence alignment score = 3805.7 RMSD between 743 pruned atom pairs is 0.524 angstroms; (across all 752 pairs: 0.751) > hide #!3 models > show #!3 models > hide #!1 models > ui mousemode right select > select #3/A:116 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 19 atom styles > select clear > hide #!3 models pyKVFinder module not installed; fetching from PyPi repository... 'pip install pyKVFinder' failed. Error from pip: error: subprocess-exited- with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/55/xpl116m117d7c2r7578q0b1h0000gp/T/pip-build- env-30odsb9k/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py"", line 48, in check_pyKVFinder import pyKVFinder ModuleNotFoundError: No module named 'pyKVFinder' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 330, in _register_cmd api._api_caller.register_command(api, self, ci, logger) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py"", line 1404, in register_command return cls._get_func(api, ""register_command"")(ci.name, logger) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py"", line 36, in register_command check_pyKVFinder(logger) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py"", line 54, in check_pyKVFinder run(logger.session, pip_cmd, log=False) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3237, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/pip.py"", line 84, in pip run_logged_pip(pip_cmd, session.logger) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/python_utils.py"", line 148, in run_logged_pip raise RuntimeError(s) RuntimeError: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/55/xpl116m117d7c2r7578q0b1h0000gp/T/pip-build- env-30odsb9k/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2492, in lazy_register deferred.call() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2420, in call return self.proxy() ^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 320, in cb s._register_cmd(ci, logger) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/55/xpl116m117d7c2r7578q0b1h0000gp/T/pip-build- env-30odsb9k/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 322, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3163, in run self._find_command_name(final, used_aliases=_used_aliases) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2883, in _find_command_name what.lazy_register(cmd_name) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2494, in lazy_register raise RuntimeError( RuntimeError: delayed command registration for 'kvfinder' failed (register_command() failed for command kvfinder in bundle ChimeraX-KVFinder: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/55/xpl116m117d7c2r7578q0b1h0000gp/T/pip-build- env-30odsb9k/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder ) RuntimeError: delayed command registration for 'kvfinder' failed (register_command() failed for command kvfinder in bundle ChimeraX-KVFinder: error: subprocess-exited-with-error × Building wheel for pyKVFinder (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [58 lines of output] running bdist_wheel running build running build_py creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/hydropathy.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/export.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/spatial.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/depth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/constitutional.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/geometry.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/cavity.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/openings.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid copying pyKVFinder/grid/detect.py -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid running egg_info writing pyKVFinder.egg-info/PKG-INFO writing dependency_links to pyKVFinder.egg-info/dependency_links.txt writing entry points to pyKVFinder.egg-info/entry_points.txt writing requirements to pyKVFinder.egg-info/requires.txt writing top-level names to pyKVFinder.egg-info/top_level.txt reading manifest file 'pyKVFinder.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'requirements.txt' adding license file 'LICENSE' writing manifest file 'pyKVFinder.egg-info/SOURCES.txt' creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests running build_ext building 'pyKVFinder._pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.macosx-10.9-universal2-cpython-311/C clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/private/var/folders/55/xpl116m117d7c2r7578q0b1h0000gp/T/pip-build- env-30odsb9k/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.11.1.app/Contents/include/python3.11 -c C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o -Xpreprocessor -fopenmp=libomp -O3 -ffast-math error: unknown argument: '-fopenmp=libomp' error: command '/usr/bin/clang' failed with exit code 1 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for pyKVFinder error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> pyKVFinder ) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2494, in lazy_register raise RuntimeError( See log for complete Python traceback. OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.9 Locale: UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,7 Model Number: Z16S000N6D/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: mBoot-18000.101.7 OS Loader Version: 10151.140.19.701.1 Software: System Software Overview: System Version: macOS 14.8.5 (23J423) Kernel Version: Darwin 23.6.0 Time since boot: 5 days, 15 hours, 17 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL P2422H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-CircosContacts: 0.4.21 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.26.1 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-CubeNTube: 1.1.0 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ISOLDE: 1.11.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.0.1 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: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 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: 1.19.1 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: 2.5.2 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: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 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: 1.1.5 ChimeraX-XMAS: 1.1.3 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 et_xmlfile: 2.0.0 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openpyxl: 3.1.5 openvr: 1.26.701 packaging: 25.0 pandas: 3.0.2 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 QtRangeSlider: 0.1.5 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 seaborn: 0.13.2 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 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 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect closed normal Surface/Binding Analysis limitation all ChimeraX