id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20430 KVFinder on old MacOS chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.4-arm64-arm-64bit ChimeraX Version: 1.12rc202605280043 (2026-05-28 00:43:25 UTC) Description I freshly installed and cannot use the find cavities tool Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.12rc202605280043 (2026-05-28) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/matthewwren/Downloads/Ctla2a_full.pdb format pdb Ctla2a_full.pdb title: Alphafold monomer V2.0 prediction for protein CTLA-2-α (P12399) [more info...] Chain information for Ctla2a_full.pdb #1 --- Chain | Description | UniProt A | protein CTLA-2-α | CTL2A_MOUSE 1-137 Computing secondary structure > ui tool show ""Find Cavities"" 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/nj/_jww__pj1gd2mg3wt8lfs53m0000gn/T/pip-build- env-f59apber/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.12-rc2026.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.12-rc2026.06.01.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-1.12-rc2026.06.01.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-1.12-rc2026.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12-rc2026.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py"", line 1400, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12-rc2026.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/kvfinder/__init__.py"", line 42, in start_tool check_pyKVFinder(session.logger) File ""/Applications/ChimeraX-1.12-rc2026.06.01.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-1.12-rc2026.06.01.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-1.12-rc2026.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12-rc2026.06.01.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-1.12-rc2026.06.01.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/nj/_jww__pj1gd2mg3wt8lfs53m0000gn/T/pip-build- env-f59apber/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.12-rc2026.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.12-rc2026.06.01.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-1.12-rc2026.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py"", line 1955, in run(ses, ""ui tool show %s"" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12-rc2026.06.01.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-1.12-rc2026.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12-rc2026.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/cmd.py"", line 219, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12-rc2026.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 578, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities 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/nj/_jww__pj1gd2mg3wt8lfs53m0000gn/T/pip-build- env-f59apber/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.12-rc2026.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.12-rc2026.06.01.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 chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find Cavities 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/nj/_jww__pj1gd2mg3wt8lfs53m0000gn/T/pip-build- env-f59apber/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/Applications/ChimeraX-1.12-rc2026.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11 -I/Applications/ChimeraX-1.12-rc2026.06.01.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-1.12-rc2026.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/info.py"", line 578, in start_tool raise ToolshedError( See log for complete Python traceback. OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.9 Locale: UTF-8 Qt version: PyQt6 6.10.2, Qt 6.10.0 Qt runtime version: 6.10.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac14,2 Model Number: MLY33LL/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 8422.121.1 OS Loader Version: 8422.121.1 Software: System Software Overview: System Version: macOS 13.4 (22F66) Kernel Version: Darwin 22.5.0 Time since boot: 15 days, 23 hours, 53 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.6.2 aiohttp: 3.13.4 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.13.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 26.1.0 babel: 2.18.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.3.3 bs4: 0.0.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.7 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2 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: 1.67.1 ChimeraX-AtomicLibrary: 14.4 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: 1.4.1 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.4 ChimeraX-Cluster: 1.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.12rc202605280043 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.2.1 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-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.8.2 ChimeraX-Label: 1.5 ChimeraX-LightingGUI: 1.0 ChimeraX-ListInfo: 1.3.1 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.3 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-MatchAlign: 1.2 ChimeraX-MatchMaker: 2.4.1 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.9 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.23 ChimeraX-ModelPanel: 1.6.1 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: 1.15.4 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.13 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: 1.6 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.2 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: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.18 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-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.3 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: 2.5.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.4 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.50.7 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.2 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-Zone: 1.0.1 click: 8.4.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.14.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.2.4 debugpy: 1.8.20 decorator: 5.3.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.63.0 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.16.0 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.17 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 2.0.0 iniconfig: 2.3.0 ipykernel: 7.1.0 ipython: 9.9.0 ipython_pygments_lexers: 1.1.1 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.8.0 jupyter_core: 5.9.1 kiwisolver: 1.5.0 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: 0.2.2 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.1 narwhals: 2.21.2 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: 8.4.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.7 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: 4.10.0 plotly: 6.7.0 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.5.2 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: 2.13.4 pydantic-settings: 2.14.1 pydantic_core: 2.46.4 pydata-sphinx-theme: 0.18.0 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.5.1 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: 6.10.2 PyQt6-Qt6: 6.10.2 PyQt6-WebEngine-commercial: 6.10.0 PyQt6-WebEngine-Qt6: 6.10.2 PyQt6_sip: 13.10.3 pytest: 9.0.3 pytest-cov: 7.1.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.2 python-multipart: 0.0.30 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 rpds-py: 2026.5.1 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.1.0 sortedcontainers: 2.4.0 soupsieve: 2.8.4 Sphinx: 9.0.4 sphinx-autodoc-typehints: 3.6.1 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: 3.4.4 stack-data: 0.6.3 starlette: 1.2.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 3.2.1 threadpoolctl: 3.6.0 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.6 tqdm: 4.67.3 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 Unidecode: 1.4.0 urllib3: 2.7.0 uvicorn: 0.48.0 wcwidth: 0.7.0 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 yarl: 1.24.2 }}} " defect closed normal Surface/Binding Analysis limitation all ChimeraX