2026-02-12T12:49:20,655 Created temporary directory: /tmp/pip-ephem-wheel-cache-o6tejygq 2026-02-12T12:49:20,657 Created temporary directory: /tmp/pip-build-tracker-8mza9ljx 2026-02-12T12:49:20,657 Initialized build tracking at /tmp/pip-build-tracker-8mza9ljx 2026-02-12T12:49:20,658 Created build tracker: /tmp/pip-build-tracker-8mza9ljx 2026-02-12T12:49:20,658 Entered build tracker: /tmp/pip-build-tracker-8mza9ljx 2026-02-12T12:49:20,659 Created temporary directory: /tmp/pip-wheel-uk3xb3hl 2026-02-12T12:49:20,662 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-02-12T12:49:20,664 Created temporary directory: /tmp/pip-ephem-wheel-cache-i11wemux 2026-02-12T12:49:20,688 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-02-12T12:49:20,691 2 location(s) to search for versions of pdbfixer: 2026-02-12T12:49:20,691 * https://pypi.org/simple/pdbfixer/ 2026-02-12T12:49:20,691 * https://www.piwheels.org/simple/pdbfixer/ 2026-02-12T12:49:20,692 Fetching project page and analyzing links: https://pypi.org/simple/pdbfixer/ 2026-02-12T12:49:20,693 Getting page https://pypi.org/simple/pdbfixer/ 2026-02-12T12:49:20,694 Found index url https://pypi.org/simple 2026-02-12T12:49:20,906 Fetched page https://pypi.org/simple/pdbfixer/ as application/vnd.pypi.simple.v1+json 2026-02-12T12:49:20,907 Found link https://files.pythonhosted.org/packages/da/bd/394c3185e4b9fbacf803651a374e99e597d3411d316784f8ea6d8fc17af5/pdbfixer-1.12.0.tar.gz (from https://pypi.org/simple/pdbfixer/), version: 1.12.0 2026-02-12T12:49:20,908 Fetching project page and analyzing links: https://www.piwheels.org/simple/pdbfixer/ 2026-02-12T12:49:20,908 Getting page https://www.piwheels.org/simple/pdbfixer/ 2026-02-12T12:49:20,910 Found index url https://www.piwheels.org/simple 2026-02-12T12:49:21,062 Fetched page https://www.piwheels.org/simple/pdbfixer/ as text/html 2026-02-12T12:49:21,063 Skipping link: not a file: https://www.piwheels.org/simple/pdbfixer/ 2026-02-12T12:49:21,064 Skipping link: not a file: https://pypi.org/simple/pdbfixer/ 2026-02-12T12:49:21,082 Given no hashes to check 1 links for project 'pdbfixer': discarding no candidates 2026-02-12T12:49:21,100 Collecting pdbfixer==1.12.0 2026-02-12T12:49:21,102 Created temporary directory: /tmp/pip-unpack-gnaxn4iu 2026-02-12T12:49:21,233 Downloading pdbfixer-1.12.0.tar.gz (665 kB) 2026-02-12T12:49:21,553 Added pdbfixer==1.12.0 from https://files.pythonhosted.org/packages/da/bd/394c3185e4b9fbacf803651a374e99e597d3411d316784f8ea6d8fc17af5/pdbfixer-1.12.0.tar.gz to build tracker '/tmp/pip-build-tracker-8mza9ljx' 2026-02-12T12:49:21,554 Running setup.py (path:/tmp/pip-wheel-uk3xb3hl/pdbfixer_f144f9b55c7449f4bb1fb3762ac9a521/setup.py) egg_info for package pdbfixer 2026-02-12T12:49:21,555 Created temporary directory: /tmp/pip-pip-egg-info-d3k8wtdj 2026-02-12T12:49:21,556 Preparing metadata (setup.py): started 2026-02-12T12:49:21,557 Running command python setup.py egg_info 2026-02-12T12:49:22,459 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-12T12:49:22,460 !! 2026-02-12T12:49:22,461 ******************************************************************************** 2026-02-12T12:49:22,461 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-12T12:49:22,462 License :: OSI Approved :: MIT License 2026-02-12T12:49:22,463 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-12T12:49:22,464 ******************************************************************************** 2026-02-12T12:49:22,465 !! 2026-02-12T12:49:22,466 self._finalize_license_expression() 2026-02-12T12:49:22,490 running egg_info 2026-02-12T12:49:22,517 creating /tmp/pip-pip-egg-info-d3k8wtdj/pdbfixer.egg-info 2026-02-12T12:49:22,518 writing /tmp/pip-pip-egg-info-d3k8wtdj/pdbfixer.egg-info/PKG-INFO 2026-02-12T12:49:22,522 writing dependency_links to /tmp/pip-pip-egg-info-d3k8wtdj/pdbfixer.egg-info/dependency_links.txt 2026-02-12T12:49:22,523 writing entry points to /tmp/pip-pip-egg-info-d3k8wtdj/pdbfixer.egg-info/entry_points.txt 2026-02-12T12:49:22,525 writing requirements to /tmp/pip-pip-egg-info-d3k8wtdj/pdbfixer.egg-info/requires.txt 2026-02-12T12:49:22,526 writing top-level names to /tmp/pip-pip-egg-info-d3k8wtdj/pdbfixer.egg-info/top_level.txt 2026-02-12T12:49:22,528 writing manifest file '/tmp/pip-pip-egg-info-d3k8wtdj/pdbfixer.egg-info/SOURCES.txt' 2026-02-12T12:49:22,629 reading manifest file '/tmp/pip-pip-egg-info-d3k8wtdj/pdbfixer.egg-info/SOURCES.txt' 2026-02-12T12:49:22,630 adding license file 'LICENSE' 2026-02-12T12:49:22,635 writing manifest file '/tmp/pip-pip-egg-info-d3k8wtdj/pdbfixer.egg-info/SOURCES.txt' 2026-02-12T12:49:22,744 Preparing metadata (setup.py): finished with status 'done' 2026-02-12T12:49:22,748 Source in /tmp/pip-wheel-uk3xb3hl/pdbfixer_f144f9b55c7449f4bb1fb3762ac9a521 has version 1.12.0, which satisfies requirement pdbfixer==1.12.0 from https://files.pythonhosted.org/packages/da/bd/394c3185e4b9fbacf803651a374e99e597d3411d316784f8ea6d8fc17af5/pdbfixer-1.12.0.tar.gz 2026-02-12T12:49:22,749 Removed pdbfixer==1.12.0 from https://files.pythonhosted.org/packages/da/bd/394c3185e4b9fbacf803651a374e99e597d3411d316784f8ea6d8fc17af5/pdbfixer-1.12.0.tar.gz from build tracker '/tmp/pip-build-tracker-8mza9ljx' 2026-02-12T12:49:22,754 Created temporary directory: /tmp/pip-unpack-nm7_a903 2026-02-12T12:49:22,754 Building wheels for collected packages: pdbfixer 2026-02-12T12:49:22,758 Created temporary directory: /tmp/pip-wheel-r7btwm78 2026-02-12T12:49:22,759 Building wheel for pdbfixer (setup.py): started 2026-02-12T12:49:22,760 Destination directory: /tmp/pip-wheel-r7btwm78 2026-02-12T12:49:22,761 Running command python setup.py bdist_wheel 2026-02-12T12:49:23,592 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-12T12:49:23,592 !! 2026-02-12T12:49:23,593 ******************************************************************************** 2026-02-12T12:49:23,594 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-12T12:49:23,596 License :: OSI Approved :: MIT License 2026-02-12T12:49:23,597 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-12T12:49:23,598 ******************************************************************************** 2026-02-12T12:49:23,599 !! 2026-02-12T12:49:23,599 self._finalize_license_expression() 2026-02-12T12:49:23,600 running bdist_wheel 2026-02-12T12:49:23,727 running build 2026-02-12T12:49:23,728 running build_py 2026-02-12T12:49:23,760 creating build/lib/pdbfixer 2026-02-12T12:49:23,762 copying pdbfixer/pdbfixer.py -> build/lib/pdbfixer 2026-02-12T12:49:23,766 copying pdbfixer/ui.py -> build/lib/pdbfixer 2026-02-12T12:49:23,769 copying pdbfixer/__init__.py -> build/lib/pdbfixer 2026-02-12T12:49:23,771 copying pdbfixer/uiserver.py -> build/lib/pdbfixer 2026-02-12T12:49:23,773 creating build/lib/pdbfixer/tests 2026-02-12T12:49:23,774 copying pdbfixer/tests/test_removechains.py -> build/lib/pdbfixer/tests 2026-02-12T12:49:23,776 copying pdbfixer/tests/test_add_hydrogens.py -> build/lib/pdbfixer/tests 2026-02-12T12:49:23,778 copying pdbfixer/tests/test_charge_and_solvate.py -> build/lib/pdbfixer/tests 2026-02-12T12:49:23,780 copying pdbfixer/tests/__init__.py -> build/lib/pdbfixer/tests 2026-02-12T12:49:23,782 copying pdbfixer/tests/test_mutate.py -> build/lib/pdbfixer/tests 2026-02-12T12:49:23,784 copying pdbfixer/tests/test_cli.py -> build/lib/pdbfixer/tests 2026-02-12T12:49:23,786 copying pdbfixer/tests/test_build_and_simulate.py -> build/lib/pdbfixer/tests 2026-02-12T12:49:23,798 copying pdbfixer/soft.xml -> build/lib/pdbfixer 2026-02-12T12:49:23,805 creating build/lib/pdbfixer/templates 2026-02-12T12:49:23,806 copying pdbfixer/templates/CYS.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,808 copying pdbfixer/templates/G.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,810 copying pdbfixer/templates/GLY.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,813 copying pdbfixer/templates/C.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,815 copying pdbfixer/templates/DT.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,817 copying pdbfixer/templates/GLN.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,820 copying pdbfixer/templates/U.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,822 copying pdbfixer/templates/DA.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,825 copying pdbfixer/templates/HIS.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,827 copying pdbfixer/templates/TRP.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,829 copying pdbfixer/templates/TYR.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,832 copying pdbfixer/templates/PHE.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,834 copying pdbfixer/templates/DC.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,837 copying pdbfixer/templates/GLU.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,839 copying pdbfixer/templates/ACE.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,842 copying pdbfixer/templates/ASP.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,844 copying pdbfixer/templates/ASN.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,847 copying pdbfixer/templates/ILE.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,849 copying pdbfixer/templates/LYS.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,852 copying pdbfixer/templates/ARG.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,854 copying pdbfixer/templates/THR.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,857 copying pdbfixer/templates/LEU.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,859 copying pdbfixer/templates/PRO.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,862 copying pdbfixer/templates/NME.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,864 copying pdbfixer/templates/ALA.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,867 copying pdbfixer/templates/A.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,870 copying pdbfixer/templates/MET.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,872 copying pdbfixer/templates/DG.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,875 copying pdbfixer/templates/SER.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,878 copying pdbfixer/templates/VAL.pdb -> build/lib/pdbfixer/templates 2026-02-12T12:49:23,883 creating build/lib/pdbfixer/tests/data 2026-02-12T12:49:23,884 copying pdbfixer/tests/data/4JSV.pdb -> build/lib/pdbfixer/tests/data 2026-02-12T12:49:23,967 copying pdbfixer/tests/data/test.pdb -> build/lib/pdbfixer/tests/data 2026-02-12T12:49:23,972 copying pdbfixer/tests/data/alanine-dipeptide.pdb -> build/lib/pdbfixer/tests/data 2026-02-12T12:49:23,974 copying pdbfixer/tests/data/1BHL.pdb -> build/lib/pdbfixer/tests/data 2026-02-12T12:49:23,978 copying pdbfixer/tests/data/CAS.pdb -> build/lib/pdbfixer/tests/data 2026-02-12T12:49:23,980 creating build/lib/pdbfixer/images 2026-02-12T12:49:23,982 copying pdbfixer/images/logo.png -> build/lib/pdbfixer/images 2026-02-12T12:49:23,985 copying pdbfixer/images/logo_small.png -> build/lib/pdbfixer/images 2026-02-12T12:49:23,988 copying pdbfixer/images/logo.svg -> build/lib/pdbfixer/images 2026-02-12T12:49:23,991 copying pdbfixer/images/background.jpg -> build/lib/pdbfixer/images 2026-02-12T12:49:23,995 creating build/lib/pdbfixer/html 2026-02-12T12:49:23,996 copying pdbfixer/html/convertResidues.html -> build/lib/pdbfixer/html 2026-02-12T12:49:23,998 copying pdbfixer/html/removeChains.html -> build/lib/pdbfixer/html 2026-02-12T12:49:24,000 copying pdbfixer/html/addHeavyAtoms.html -> build/lib/pdbfixer/html 2026-02-12T12:49:24,002 copying pdbfixer/html/addHydrogens.html -> build/lib/pdbfixer/html 2026-02-12T12:49:24,005 copying pdbfixer/html/quit.html -> build/lib/pdbfixer/html 2026-02-12T12:49:24,007 copying pdbfixer/html/error.html -> build/lib/pdbfixer/html 2026-02-12T12:49:24,009 copying pdbfixer/html/addResidues.html -> build/lib/pdbfixer/html 2026-02-12T12:49:24,012 copying pdbfixer/html/saveFile.html -> build/lib/pdbfixer/html 2026-02-12T12:49:24,014 copying pdbfixer/html/start.html -> build/lib/pdbfixer/html 2026-02-12T12:49:24,016 copying pdbfixer/html/header.html -> build/lib/pdbfixer/html 2026-02-12T12:49:24,046 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2026-02-12T12:49:24,047 !! 2026-02-12T12:49:24,048 ******************************************************************************** 2026-02-12T12:49:24,048 Please avoid running ``setup.py`` directly. 2026-02-12T12:49:24,049 Instead, use pypa/build, pypa/installer or other 2026-02-12T12:49:24,049 standards-based tools. 2026-02-12T12:49:24,050 This deprecation is overdue, please update your project and remove deprecated 2026-02-12T12:49:24,051 calls to avoid build errors in the future. 2026-02-12T12:49:24,052 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2026-02-12T12:49:24,053 ******************************************************************************** 2026-02-12T12:49:24,054 !! 2026-02-12T12:49:24,054 self.initialize_options() 2026-02-12T12:49:24,075 installing to build/bdist.linux-armv7l/wheel 2026-02-12T12:49:24,075 running install 2026-02-12T12:49:24,098 running install_lib 2026-02-12T12:49:24,125 creating build/bdist.linux-armv7l/wheel 2026-02-12T12:49:24,127 creating build/bdist.linux-armv7l/wheel/pdbfixer 2026-02-12T12:49:24,129 copying build/lib/pdbfixer/pdbfixer.py -> build/bdist.linux-armv7l/wheel/./pdbfixer 2026-02-12T12:49:24,133 copying build/lib/pdbfixer/ui.py -> build/bdist.linux-armv7l/wheel/./pdbfixer 2026-02-12T12:49:24,136 creating build/bdist.linux-armv7l/wheel/pdbfixer/templates 2026-02-12T12:49:24,138 copying build/lib/pdbfixer/templates/CYS.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,140 copying build/lib/pdbfixer/templates/G.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,142 copying build/lib/pdbfixer/templates/GLY.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,144 copying build/lib/pdbfixer/templates/C.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,146 copying build/lib/pdbfixer/templates/DT.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,148 copying build/lib/pdbfixer/templates/GLN.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,150 copying build/lib/pdbfixer/templates/U.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,151 copying build/lib/pdbfixer/templates/DA.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,153 copying build/lib/pdbfixer/templates/HIS.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,156 copying build/lib/pdbfixer/templates/TRP.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,157 copying build/lib/pdbfixer/templates/TYR.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,159 copying build/lib/pdbfixer/templates/PHE.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,161 copying build/lib/pdbfixer/templates/DC.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,163 copying build/lib/pdbfixer/templates/GLU.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,165 copying build/lib/pdbfixer/templates/ACE.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,167 copying build/lib/pdbfixer/templates/ASP.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,169 copying build/lib/pdbfixer/templates/ASN.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,170 copying build/lib/pdbfixer/templates/ILE.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,172 copying build/lib/pdbfixer/templates/LYS.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,174 copying build/lib/pdbfixer/templates/ARG.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,176 copying build/lib/pdbfixer/templates/THR.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,178 copying build/lib/pdbfixer/templates/LEU.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,180 copying build/lib/pdbfixer/templates/PRO.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,182 copying build/lib/pdbfixer/templates/NME.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,183 copying build/lib/pdbfixer/templates/ALA.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,185 copying build/lib/pdbfixer/templates/A.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,187 copying build/lib/pdbfixer/templates/MET.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,189 copying build/lib/pdbfixer/templates/DG.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,191 copying build/lib/pdbfixer/templates/SER.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,193 copying build/lib/pdbfixer/templates/VAL.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/templates 2026-02-12T12:49:24,195 copying build/lib/pdbfixer/__init__.py -> build/bdist.linux-armv7l/wheel/./pdbfixer 2026-02-12T12:49:24,197 creating build/bdist.linux-armv7l/wheel/pdbfixer/tests 2026-02-12T12:49:24,198 copying build/lib/pdbfixer/tests/test_removechains.py -> build/bdist.linux-armv7l/wheel/./pdbfixer/tests 2026-02-12T12:49:24,200 copying build/lib/pdbfixer/tests/test_add_hydrogens.py -> build/bdist.linux-armv7l/wheel/./pdbfixer/tests 2026-02-12T12:49:24,202 copying build/lib/pdbfixer/tests/test_charge_and_solvate.py -> build/bdist.linux-armv7l/wheel/./pdbfixer/tests 2026-02-12T12:49:24,204 copying build/lib/pdbfixer/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./pdbfixer/tests 2026-02-12T12:49:24,206 copying build/lib/pdbfixer/tests/test_mutate.py -> build/bdist.linux-armv7l/wheel/./pdbfixer/tests 2026-02-12T12:49:24,208 copying build/lib/pdbfixer/tests/test_cli.py -> build/bdist.linux-armv7l/wheel/./pdbfixer/tests 2026-02-12T12:49:24,211 creating build/bdist.linux-armv7l/wheel/pdbfixer/tests/data 2026-02-12T12:49:24,221 copying build/lib/pdbfixer/tests/data/4JSV.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/tests/data 2026-02-12T12:49:24,268 copying build/lib/pdbfixer/tests/data/test.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/tests/data 2026-02-12T12:49:24,271 copying build/lib/pdbfixer/tests/data/alanine-dipeptide.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/tests/data 2026-02-12T12:49:24,273 copying build/lib/pdbfixer/tests/data/1BHL.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/tests/data 2026-02-12T12:49:24,277 copying build/lib/pdbfixer/tests/data/CAS.pdb -> build/bdist.linux-armv7l/wheel/./pdbfixer/tests/data 2026-02-12T12:49:24,279 copying build/lib/pdbfixer/tests/test_build_and_simulate.py -> build/bdist.linux-armv7l/wheel/./pdbfixer/tests 2026-02-12T12:49:24,281 copying build/lib/pdbfixer/soft.xml -> build/bdist.linux-armv7l/wheel/./pdbfixer 2026-02-12T12:49:24,287 creating build/bdist.linux-armv7l/wheel/pdbfixer/images 2026-02-12T12:49:24,288 copying build/lib/pdbfixer/images/logo.png -> build/bdist.linux-armv7l/wheel/./pdbfixer/images 2026-02-12T12:49:24,291 copying build/lib/pdbfixer/images/logo_small.png -> build/bdist.linux-armv7l/wheel/./pdbfixer/images 2026-02-12T12:49:24,293 copying build/lib/pdbfixer/images/logo.svg -> build/bdist.linux-armv7l/wheel/./pdbfixer/images 2026-02-12T12:49:24,296 copying build/lib/pdbfixer/images/background.jpg -> build/bdist.linux-armv7l/wheel/./pdbfixer/images 2026-02-12T12:49:24,299 copying build/lib/pdbfixer/uiserver.py -> build/bdist.linux-armv7l/wheel/./pdbfixer 2026-02-12T12:49:24,302 creating build/bdist.linux-armv7l/wheel/pdbfixer/html 2026-02-12T12:49:24,303 copying build/lib/pdbfixer/html/convertResidues.html -> build/bdist.linux-armv7l/wheel/./pdbfixer/html 2026-02-12T12:49:24,305 copying build/lib/pdbfixer/html/removeChains.html -> build/bdist.linux-armv7l/wheel/./pdbfixer/html 2026-02-12T12:49:24,307 copying build/lib/pdbfixer/html/addHeavyAtoms.html -> build/bdist.linux-armv7l/wheel/./pdbfixer/html 2026-02-12T12:49:24,309 copying build/lib/pdbfixer/html/addHydrogens.html -> build/bdist.linux-armv7l/wheel/./pdbfixer/html 2026-02-12T12:49:24,311 copying build/lib/pdbfixer/html/quit.html -> build/bdist.linux-armv7l/wheel/./pdbfixer/html 2026-02-12T12:49:24,313 copying build/lib/pdbfixer/html/error.html -> build/bdist.linux-armv7l/wheel/./pdbfixer/html 2026-02-12T12:49:24,315 copying build/lib/pdbfixer/html/addResidues.html -> build/bdist.linux-armv7l/wheel/./pdbfixer/html 2026-02-12T12:49:24,316 copying build/lib/pdbfixer/html/saveFile.html -> build/bdist.linux-armv7l/wheel/./pdbfixer/html 2026-02-12T12:49:24,318 copying build/lib/pdbfixer/html/start.html -> build/bdist.linux-armv7l/wheel/./pdbfixer/html 2026-02-12T12:49:24,320 copying build/lib/pdbfixer/html/header.html -> build/bdist.linux-armv7l/wheel/./pdbfixer/html 2026-02-12T12:49:24,322 running install_egg_info 2026-02-12T12:49:24,356 running egg_info 2026-02-12T12:49:24,382 writing pdbfixer.egg-info/PKG-INFO 2026-02-12T12:49:24,385 writing dependency_links to pdbfixer.egg-info/dependency_links.txt 2026-02-12T12:49:24,387 writing entry points to pdbfixer.egg-info/entry_points.txt 2026-02-12T12:49:24,389 writing requirements to pdbfixer.egg-info/requires.txt 2026-02-12T12:49:24,390 writing top-level names to pdbfixer.egg-info/top_level.txt 2026-02-12T12:49:24,428 reading manifest file 'pdbfixer.egg-info/SOURCES.txt' 2026-02-12T12:49:24,434 adding license file 'LICENSE' 2026-02-12T12:49:24,439 writing manifest file 'pdbfixer.egg-info/SOURCES.txt' 2026-02-12T12:49:24,440 Copying pdbfixer.egg-info to build/bdist.linux-armv7l/wheel/./pdbfixer-1.12.0-py3.11.egg-info 2026-02-12T12:49:24,453 running install_scripts 2026-02-12T12:49:24,467 creating build/bdist.linux-armv7l/wheel/pdbfixer-1.12.0.dist-info/WHEEL 2026-02-12T12:49:24,470 creating '/tmp/pip-wheel-r7btwm78/pdbfixer-1.12.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-02-12T12:49:24,472 adding 'pdbfixer/__init__.py' 2026-02-12T12:49:24,482 adding 'pdbfixer/pdbfixer.py' 2026-02-12T12:49:24,493 adding 'pdbfixer/soft.xml' 2026-02-12T12:49:24,496 adding 'pdbfixer/ui.py' 2026-02-12T12:49:24,498 adding 'pdbfixer/uiserver.py' 2026-02-12T12:49:24,500 adding 'pdbfixer/html/addHeavyAtoms.html' 2026-02-12T12:49:24,501 adding 'pdbfixer/html/addHydrogens.html' 2026-02-12T12:49:24,503 adding 'pdbfixer/html/addResidues.html' 2026-02-12T12:49:24,504 adding 'pdbfixer/html/convertResidues.html' 2026-02-12T12:49:24,505 adding 'pdbfixer/html/error.html' 2026-02-12T12:49:24,507 adding 'pdbfixer/html/header.html' 2026-02-12T12:49:24,508 adding 'pdbfixer/html/quit.html' 2026-02-12T12:49:24,509 adding 'pdbfixer/html/removeChains.html' 2026-02-12T12:49:24,510 adding 'pdbfixer/html/saveFile.html' 2026-02-12T12:49:24,511 adding 'pdbfixer/html/start.html' 2026-02-12T12:49:24,518 adding 'pdbfixer/images/background.jpg' 2026-02-12T12:49:24,521 adding 'pdbfixer/images/logo.png' 2026-02-12T12:49:24,523 adding 'pdbfixer/images/logo.svg' 2026-02-12T12:49:24,526 adding 'pdbfixer/images/logo_small.png' 2026-02-12T12:49:24,528 adding 'pdbfixer/templates/A.pdb' 2026-02-12T12:49:24,529 adding 'pdbfixer/templates/ACE.pdb' 2026-02-12T12:49:24,530 adding 'pdbfixer/templates/ALA.pdb' 2026-02-12T12:49:24,532 adding 'pdbfixer/templates/ARG.pdb' 2026-02-12T12:49:24,533 adding 'pdbfixer/templates/ASN.pdb' 2026-02-12T12:49:24,534 adding 'pdbfixer/templates/ASP.pdb' 2026-02-12T12:49:24,535 adding 'pdbfixer/templates/C.pdb' 2026-02-12T12:49:24,536 adding 'pdbfixer/templates/CYS.pdb' 2026-02-12T12:49:24,537 adding 'pdbfixer/templates/DA.pdb' 2026-02-12T12:49:24,538 adding 'pdbfixer/templates/DC.pdb' 2026-02-12T12:49:24,539 adding 'pdbfixer/templates/DG.pdb' 2026-02-12T12:49:24,541 adding 'pdbfixer/templates/DT.pdb' 2026-02-12T12:49:24,542 adding 'pdbfixer/templates/G.pdb' 2026-02-12T12:49:24,543 adding 'pdbfixer/templates/GLN.pdb' 2026-02-12T12:49:24,544 adding 'pdbfixer/templates/GLU.pdb' 2026-02-12T12:49:24,545 adding 'pdbfixer/templates/GLY.pdb' 2026-02-12T12:49:24,546 adding 'pdbfixer/templates/HIS.pdb' 2026-02-12T12:49:24,547 adding 'pdbfixer/templates/ILE.pdb' 2026-02-12T12:49:24,548 adding 'pdbfixer/templates/LEU.pdb' 2026-02-12T12:49:24,549 adding 'pdbfixer/templates/LYS.pdb' 2026-02-12T12:49:24,551 adding 'pdbfixer/templates/MET.pdb' 2026-02-12T12:49:24,552 adding 'pdbfixer/templates/NME.pdb' 2026-02-12T12:49:24,553 adding 'pdbfixer/templates/PHE.pdb' 2026-02-12T12:49:24,554 adding 'pdbfixer/templates/PRO.pdb' 2026-02-12T12:49:24,555 adding 'pdbfixer/templates/SER.pdb' 2026-02-12T12:49:24,556 adding 'pdbfixer/templates/THR.pdb' 2026-02-12T12:49:24,557 adding 'pdbfixer/templates/TRP.pdb' 2026-02-12T12:49:24,559 adding 'pdbfixer/templates/TYR.pdb' 2026-02-12T12:49:24,560 adding 'pdbfixer/templates/U.pdb' 2026-02-12T12:49:24,561 adding 'pdbfixer/templates/VAL.pdb' 2026-02-12T12:49:24,563 adding 'pdbfixer/tests/__init__.py' 2026-02-12T12:49:24,564 adding 'pdbfixer/tests/test_add_hydrogens.py' 2026-02-12T12:49:24,566 adding 'pdbfixer/tests/test_build_and_simulate.py' 2026-02-12T12:49:24,567 adding 'pdbfixer/tests/test_charge_and_solvate.py' 2026-02-12T12:49:24,569 adding 'pdbfixer/tests/test_cli.py' 2026-02-12T12:49:24,570 adding 'pdbfixer/tests/test_mutate.py' 2026-02-12T12:49:24,571 adding 'pdbfixer/tests/test_removechains.py' 2026-02-12T12:49:24,591 adding 'pdbfixer/tests/data/1BHL.pdb' 2026-02-12T12:49:24,965 adding 'pdbfixer/tests/data/4JSV.pdb' 2026-02-12T12:49:24,979 adding 'pdbfixer/tests/data/CAS.pdb' 2026-02-12T12:49:24,980 adding 'pdbfixer/tests/data/alanine-dipeptide.pdb' 2026-02-12T12:49:24,989 adding 'pdbfixer/tests/data/test.pdb' 2026-02-12T12:49:24,992 adding 'pdbfixer-1.12.0.dist-info/licenses/LICENSE' 2026-02-12T12:49:24,994 adding 'pdbfixer-1.12.0.dist-info/METADATA' 2026-02-12T12:49:24,995 adding 'pdbfixer-1.12.0.dist-info/WHEEL' 2026-02-12T12:49:24,996 adding 'pdbfixer-1.12.0.dist-info/entry_points.txt' 2026-02-12T12:49:24,996 adding 'pdbfixer-1.12.0.dist-info/top_level.txt' 2026-02-12T12:49:24,998 adding 'pdbfixer-1.12.0.dist-info/RECORD' 2026-02-12T12:49:25,007 removing build/bdist.linux-armv7l/wheel 2026-02-12T12:49:25,139 Building wheel for pdbfixer (setup.py): finished with status 'done' 2026-02-12T12:49:25,149 Created wheel for pdbfixer: filename=pdbfixer-1.12.0-py3-none-any.whl size=681766 sha256=9f89aad749dd3c4efed6594f9268d3ae19d4a9eed38d5f0a0745e7a40b2b5b9e 2026-02-12T12:49:25,150 Stored in directory: /tmp/pip-ephem-wheel-cache-i11wemux/wheels/54/ed/65/df3fc2beff652f88d50b6294da5acbf4a757ab12c4858cb83d 2026-02-12T12:49:25,163 Successfully built pdbfixer 2026-02-12T12:49:25,183 Removed build tracker: '/tmp/pip-build-tracker-8mza9ljx'