id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18677 Find Cavities on ARM Linux greenpearz@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-6.8.0-56-generic-aarch64-with-glibc2.40 ChimeraX Version: 1.11.dev202508140657 (2025-08-14 06:57:21 UTC) Description Tools > binding analysis > find cavities works perfectly on Mac (M1 ARM) doesn't work here on ARM Linux (flatpak originated) -- see error below -- Ubuntu 22.04 VM Log: Startup Messages --- warning | Qt: Session management error: Could not open network socket UCSF ChimeraX version: 1.11.dev202508140657 (2025-08-14) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 4ZUD format mmcif fromDatabase pdbe_bio Summary of feedback from opening 4ZUD fetched from pdbe_bio --- warning | Missing or incorrect sequence information. Inferred polymer connectivity. 4ZUD bioassembly 1 title: Crystal Structure of Human Angiotensin Receptor in Complex with Inverse Agonist Olmesartan at 2.8A resolution. [more info...] Chain information for 4ZUD bioassembly 1 #1 --- Chain | Description A | Chimera protein of Soluble cytochrome b562 and Type-1 angiotensin II receptor Non-standard residues in 4ZUD bioassembly 1 #1 --- OLM — (OLM) Computing secondary structure Opened 1 biological assemblies for 4ZUD > 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 ╰─> [50 lines of output] running bdist_wheel running build running build_py file _pyKVFinder.py (for module _pyKVFinder) not found creating build/lib.linux-aarch64-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.linux- aarch64-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.linux- aarch64-cpython-311/pyKVFinder copying pyKVFinder/grid.py -> build/lib.linux-aarch64-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.linux-aarch64-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.linux-aarch64-cpython-311/pyKVFinder 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 file _pyKVFinder.py (for module _pyKVFinder) not found 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.linux-aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data creating build/lib.linux-aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests file _pyKVFinder.py (for module _pyKVFinder) not found running build_ext building '_pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.linux-aarch64-cpython-311/C gcc -pipe -fPIC -std=gnu99 -fstack-protector-strong -DUSE_DYLD_GLOBAL_NAMESPACE -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -g -O3 -Wall -D_FORTIFY=2 -fstack-protector-strong -O3 -Wall -Wextra -D_FORTIFY=2 -I/run/build/chimerax/build/include -fPIC -I/tmp/pip-build- env-1kausaqy/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/app/include/python3.11 -c C/pyKVFinder.c -o build/temp.linux- aarch64-cpython-311/C/pyKVFinder.o -fopenmp -Ofast error: command 'gcc' failed: No such file or directory [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 ""/app/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 ""/app/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 ""/app/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 ""/app/lib/python3.11/site-packages/chimerax/kvfinder/__init__.py"", line 42, in start_tool check_pyKVFinder(session.logger) File ""/app/lib/python3.11/site-packages/chimerax/kvfinder/__init__.py"", line 54, in check_pyKVFinder run(logger.session, pip_cmd, log=False) File ""/app/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 ""/app/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3230, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/app/lib/python3.11/site-packages/chimerax/core/commands/pip.py"", line 88, in pip run_logged_pip(pip_cmd, session.logger) File ""/app/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 ╰─> [50 lines of output] running bdist_wheel running build running build_py file _pyKVFinder.py (for module _pyKVFinder) not found creating build/lib.linux-aarch64-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.linux- aarch64-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.linux- aarch64-cpython-311/pyKVFinder copying pyKVFinder/grid.py -> build/lib.linux-aarch64-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.linux-aarch64-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.linux-aarch64-cpython-311/pyKVFinder 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 file _pyKVFinder.py (for module _pyKVFinder) not found 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.linux-aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data creating build/lib.linux-aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests file _pyKVFinder.py (for module _pyKVFinder) not found running build_ext building '_pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.linux-aarch64-cpython-311/C gcc -pipe -fPIC -std=gnu99 -fstack-protector-strong -DUSE_DYLD_GLOBAL_NAMESPACE -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -g -O3 -Wall -D_FORTIFY=2 -fstack-protector-strong -O3 -Wall -Wextra -D_FORTIFY=2 -I/run/build/chimerax/build/include -fPIC -I/tmp/pip-build- env-1kausaqy/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/app/include/python3.11 -c C/pyKVFinder.c -o build/temp.linux- aarch64-cpython-311/C/pyKVFinder.o -fopenmp -Ofast error: command 'gcc' failed: No such file or directory [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 ""/app/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 1891, in run(ses, ""ui tool show %s"" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/app/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 ""/app/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3230, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/app/lib/python3.11/site-packages/chimerax/ui/cmd.py"", line 219, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/app/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 ╰─> [50 lines of output] running bdist_wheel running build running build_py file _pyKVFinder.py (for module _pyKVFinder) not found creating build/lib.linux-aarch64-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.linux- aarch64-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.linux- aarch64-cpython-311/pyKVFinder copying pyKVFinder/grid.py -> build/lib.linux-aarch64-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.linux-aarch64-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.linux-aarch64-cpython-311/pyKVFinder 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 file _pyKVFinder.py (for module _pyKVFinder) not found 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.linux-aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data creating build/lib.linux-aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests file _pyKVFinder.py (for module _pyKVFinder) not found running build_ext building '_pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.linux-aarch64-cpython-311/C gcc -pipe -fPIC -std=gnu99 -fstack-protector-strong -DUSE_DYLD_GLOBAL_NAMESPACE -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -g -O3 -Wall -D_FORTIFY=2 -fstack-protector-strong -O3 -Wall -Wextra -D_FORTIFY=2 -I/run/build/chimerax/build/include -fPIC -I/tmp/pip-build- env-1kausaqy/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/app/include/python3.11 -c C/pyKVFinder.c -o build/temp.linux- aarch64-cpython-311/C/pyKVFinder.o -fopenmp -Ofast error: command 'gcc' failed: No such file or directory [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 ╰─> [50 lines of output] running bdist_wheel running build running build_py file _pyKVFinder.py (for module _pyKVFinder) not found creating build/lib.linux-aarch64-cpython-311/pyKVFinder copying pyKVFinder/__init__.py -> build/lib.linux- aarch64-cpython-311/pyKVFinder copying pyKVFinder/argparser.py -> build/lib.linux- aarch64-cpython-311/pyKVFinder copying pyKVFinder/grid.py -> build/lib.linux-aarch64-cpython-311/pyKVFinder copying pyKVFinder/main.py -> build/lib.linux-aarch64-cpython-311/pyKVFinder copying pyKVFinder/utils.py -> build/lib.linux-aarch64-cpython-311/pyKVFinder 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 file _pyKVFinder.py (for module _pyKVFinder) not found 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.linux-aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/EisenbergWeiss.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/HessaHeijne.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/KyteDoolittle.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/MoonFleming.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/RadzickaWolfenden.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/WimleyWhite.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/ZhaoLondon.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data copying pyKVFinder/data/vdw.dat -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data creating build/lib.linux-aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/1FMO.xyz -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ADN.xyz -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/C1.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/ClO4.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/PKI.pdb -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/custom-box.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests copying pyKVFinder/data/tests/residues-box.toml -> build/lib.linux- aarch64-cpython-311/pyKVFinder/data/tests file _pyKVFinder.py (for module _pyKVFinder) not found running build_ext building '_pyKVFinder' extension swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i creating build/temp.linux-aarch64-cpython-311/C gcc -pipe -fPIC -std=gnu99 -fstack-protector-strong -DUSE_DYLD_GLOBAL_NAMESPACE -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -g -O3 -Wall -D_FORTIFY=2 -fstack-protector-strong -O3 -Wall -Wextra -D_FORTIFY=2 -I/run/build/chimerax/build/include -fPIC -I/tmp/pip-build- env-1kausaqy/overlay/lib/python3.11/site-packages/numpy/_core/include -IC -I/app/include/python3.11 -c C/pyKVFinder.c -o build/temp.linux- aarch64-cpython-311/C/pyKVFinder.o -fopenmp -Ofast error: command 'gcc' failed: No such file or directory [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 ""/app/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: 4.5 (Core Profile) Mesa 25.1.7 (git-581a4f7e70) OpenGL renderer: llvmpipe (LLVM 19.1.7, 128 bits) OpenGL vendor: Mesa Python: 3.11.13 Locale: en_AU.UTF-8 Qt version: PySide6 6.9.1, Qt 6.9.1 Qt runtime version: 6.9.1 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:99.0 Manufacturer: QEMU Model: QEMU Virtual Machine OS: Freedesktop SDK 24.08 Architecture: 64bit ELF Virtual Machine: detection failed CPU: 4 unknown Cache Size: unknown Memory: total used free shared buff/cache available Mem: 3.8Gi 1.5Gi 682Mi 47Mi 1.9Gi 2.3Gi Swap: 4.1Gi 0B 4.1Gi Graphics: unknown Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 asttokens: 3.0.0 babel: 2.17.0 beautifulsoup4: 4.13.4 blockdiag: 3.0.0 blosc2: 3.7.0 build: 1.2.2.post1 certifi: 2025.8.3 cftime: 1.6.4.post1 charset-normalizer: 3.4.3 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.0.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.12 ChimeraX-AtomicLibrary: 14.1.22 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-Clashes: 2.3 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.dev202508140657 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: 1.1.4 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-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.1 ChimeraX-Label: 1.1.14 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 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-MDcrds: 2.17 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.5.1 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: 1.15.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 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: 1.1.3 ChimeraX-ProfileGrids: 1.1.4 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.4 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: 1.5.2 ChimeraX-Scenes: 0.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.2 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: 1.48.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.3 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 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.10.3 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.2 debugpy: 1.8.16 decorator: 5.2.1 distro: 1.9.0 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.59.1 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.30.1 ipython: 9.4.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.7 jedi: 0.19.2 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 5.3.1 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PySide6: 6.9.1 PySide6_Addons: 6.9.1 PySide6_Essentials: 6.9.1 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.1 qtconsole: 5.6.1 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 requests: 2.32.4 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 shiboken6: 6.9.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 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 stack-data: 0.6.3 superqt: 0.7.5 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.2 traitlets: 5.14.3 typing_extensions: 4.14.1 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Surface/Binding Analysis limitation joao.guerra@… paulo.oliveira@… jvsguerra@… all ChimeraX