Opened 7 weeks ago

Closed 7 weeks ago

Last modified 6 weeks ago

#18677 closed defect (limitation)

Find Cavities on ARM Linux

Reported by: greenpearz@… Owned by: pett
Priority: normal Milestone:
Component: Surface/Binding Analysis Version:
Keywords: Cc: joao.guerra@…, paulo.oliveira@…, jvsguerra@…
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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
<lambda>  
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
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    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

Change History (4)

comment:1 by pett, 7 weeks ago

Cc: joao.guerra@… paulo.oliveira@… jvsguerra@… added
Component: Unassigned → Surface/Binding Analysis
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Find Cavities on ARM Linux

comment:2 by pett, 7 weeks ago

Resolution: → limitation
Status: accepted → closed

Hi Bill,

The Find Cavities tool carries out its search using the pyKVFinder package downloaded from PyPi. That package currently only has versions for x86 Linux. It's possible the maintainers might add an ARM Linux version in the future, but for right now Find Cavities simply will not work on ARM Linux. Sorry!

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

Version 0, edited 7 weeks ago by pett (next)

comment:3 by greenpearz@…, 7 weeks ago 

Hi Eric thank you hugely for your reply and explanation.

Appreciate it. Bill.

On Wed, 3 Sept 2025 at 03:33, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>
>
>
>

comment:4 by joao.guerra@…, 6 weeks ago 

Hi Bill,

I’m pleased to inform you that starting with pyKVFinder v0.8.2<https://github.com/LBC-LNBio/pyKVFinder/releases/tag/v0.8.2>, prebuilt wheels are now available for both ARM64 Linux and x86.

You should now be able to run the Find Cavities tool in ChimeraX on ARM systems without any issues.

Kind regards,
--
João Victor Guerra, MSc. PhD
Especialista em Desenvolvimento Tecnológico Jr

Laboratório Nacional de Biociências - LNBio
Centro Nacional de Pesquisa em Energia e Materiais – CNPEM
Rua Giuseppe Maximo Scolfaro, 10000
Campinas, SP Brasil 13083-100
Fone: +55 19 3512-1113
lnbio.cnpem.br

João Victor Guerra, MSc. PhD
Specialist in Technological Development

Brazilian Biosciences National Laboratory - LNBio
Brazilian Center for Research in Energy and Materials  – CNPEM
10,000 Giuseppe Maximo Scolfaro St
Campinas, SP Brazil 13083-100
Phone: +55 19 3512-1113
lnbio.cnpem.br/en

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, September 4, 2025 12:07 AM
To: greenpearz@gmail.com <greenpearz@gmail.com>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Cc: Joao Victor da Silva Guerra <joao.guerra@lnbio.cnpem.br>; jvsguerra <jvsguerra@gmail.com>; paulo.oliveira@lnbio.cnpem.br <paulo.oliveira@lnbio.cnpem.br>
Subject: Re: [ChimeraX] #18677: Find Cavities on ARM Linux

[You don't often get email from chimerax-bugs-admin@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]

#18677: Find Cavities on ARM Linux
-----------------------------------------------+--------------------
          Reporter:  greenpearz@…              |      Owner:  pett
              Type:  defect                    |     Status:  closed
          Priority:  normal                    |  Milestone:
         Component:  Surface/Binding Analysis  |    Version:
        Resolution:  limitation                |   Keywords:
        Blocked By:                            |   Blocking:
Notify when closed:                            |   Platform:  all
           Project:  ChimeraX                  |
-----------------------------------------------+--------------------
Comment (by greenpearz@…):

 {{{
 Hi Eric thank you hugely for your reply and explanation.

 Appreciate it. Bill.

 On Wed, 3 Sept 2025 at 03:33, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
 wrote:

 >
 >
 >
 >
 >
 >
 }}}
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/18677#comment:3>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker


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