2025-10-24T01:01:38,864 Created temporary directory: /tmp/pip-ephem-wheel-cache-owo1ckt0 2025-10-24T01:01:38,866 Created temporary directory: /tmp/pip-build-tracker-365pwlcm 2025-10-24T01:01:38,867 Initialized build tracking at /tmp/pip-build-tracker-365pwlcm 2025-10-24T01:01:38,867 Created build tracker: /tmp/pip-build-tracker-365pwlcm 2025-10-24T01:01:38,868 Entered build tracker: /tmp/pip-build-tracker-365pwlcm 2025-10-24T01:01:38,869 Created temporary directory: /tmp/pip-wheel-sf74e_cb 2025-10-24T01:01:38,872 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 2025-10-24T01:01:38,874 Created temporary directory: /tmp/pip-ephem-wheel-cache-hj6bfps1 2025-10-24T01:01:38,899 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-10-24T01:01:38,902 2 location(s) to search for versions of rnapolis: 2025-10-24T01:01:38,902 * https://pypi.org/simple/rnapolis/ 2025-10-24T01:01:38,902 * https://www.piwheels.org/simple/rnapolis/ 2025-10-24T01:01:38,903 Fetching project page and analyzing links: https://pypi.org/simple/rnapolis/ 2025-10-24T01:01:38,904 Getting page https://pypi.org/simple/rnapolis/ 2025-10-24T01:01:38,906 Found index url https://pypi.org/simple 2025-10-24T01:01:39,142 Fetched page https://pypi.org/simple/rnapolis/ as application/vnd.pypi.simple.v1+json 2025-10-24T01:01:39,170 Skipping link: No binaries permitted for rnapolis: 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https://archive1.piwheels.org/simple/rnapolis/RNApolis-0.0.5-py3-none-any.whl#sha256=c4bf0586d41d024fc9c8890b8a27a046cb8ee57941b4b9abc4a372e7b6b51c48 (from https://www.piwheels.org/simple/rnapolis/) 2025-10-24T01:01:39,524 Skipping link: No binaries permitted for rnapolis: https://archive1.piwheels.org/simple/rnapolis/RNApolis-0.0.4-py3-none-any.whl#sha256=8640cf34d414ada87c900a3b34de94fb6cdcd2086abde453c136c58f37162ae0 (from https://www.piwheels.org/simple/rnapolis/) 2025-10-24T01:01:39,525 Skipping link: No binaries permitted for rnapolis: https://archive1.piwheels.org/simple/rnapolis/RNApolis-0.0.3-py3-none-any.whl#sha256=1c57dc38a33c0d7fc3e7e0474a5df8c9bcccb634073a7338006da23faf506da2 (from https://www.piwheels.org/simple/rnapolis/) 2025-10-24T01:01:39,525 Skipping link: No binaries permitted for rnapolis: https://archive1.piwheels.org/simple/rnapolis/RNApolis-0.0.1-py3-none-any.whl#sha256=d31b368d8b29ee7bef0f5d81b066aea46724c4d516dbd154e3c305dfcfca560c (from https://www.piwheels.org/simple/rnapolis/) 2025-10-24T01:01:39,526 Skipping link: not a file: https://www.piwheels.org/simple/rnapolis/ 2025-10-24T01:01:39,527 Skipping link: not a file: https://pypi.org/simple/rnapolis/ 2025-10-24T01:01:39,555 Given no hashes to check 1 links for project 'rnapolis': discarding no candidates 2025-10-24T01:01:39,573 Collecting rnapolis==0.10.6 2025-10-24T01:01:39,575 Created temporary directory: /tmp/pip-unpack-9c0dq2lt 2025-10-24T01:01:39,708 Downloading rnapolis-0.10.6.tar.gz (699 kB) 2025-10-24T01:01:40,294 Added rnapolis==0.10.6 from https://files.pythonhosted.org/packages/92/4e/7d69a9b28ce8c4100fc340d2dbde41d49690ac74aa314ef4fb6d325dfdbd/rnapolis-0.10.6.tar.gz to build tracker '/tmp/pip-build-tracker-365pwlcm' 2025-10-24T01:01:40,297 Created temporary directory: /tmp/pip-build-env-l0c3klyv 2025-10-24T01:01:40,302 Installing build dependencies: started 2025-10-24T01:01:40,303 Running command pip subprocess to install build dependencies 2025-10-24T01:01:41,432 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2025-10-24T01:01:42,037 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 2025-10-24T01:01:42,060 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-10-24T01:01:43,775 Collecting setuptools>=61.0 2025-10-24T01:01:43,863 Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB) 2025-10-24T01:01:46,745 Installing collected packages: setuptools 2025-10-24T01:01:50,354 Successfully installed setuptools-80.9.0 2025-10-24T01:01:50,615 Installing build dependencies: finished with status 'done' 2025-10-24T01:01:50,621 Getting requirements to build wheel: started 2025-10-24T01:01:50,623 Running command Getting requirements to build wheel 2025-10-24T01:01:51,201 /tmp/pip-build-env-l0c3klyv/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-10-24T01:01:51,201 !! 2025-10-24T01:01:51,202 ******************************************************************************** 2025-10-24T01:01:51,202 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-10-24T01:01:51,204 License :: OSI Approved :: MIT License 2025-10-24T01:01:51,205 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-10-24T01:01:51,206 ******************************************************************************** 2025-10-24T01:01:51,207 !! 2025-10-24T01:01:51,207 self._finalize_license_expression() 2025-10-24T01:01:51,227 running egg_info 2025-10-24T01:01:51,234 writing src/RNApolis.egg-info/PKG-INFO 2025-10-24T01:01:51,239 writing dependency_links to src/RNApolis.egg-info/dependency_links.txt 2025-10-24T01:01:51,241 writing entry points to src/RNApolis.egg-info/entry_points.txt 2025-10-24T01:01:51,243 writing requirements to src/RNApolis.egg-info/requires.txt 2025-10-24T01:01:51,244 writing top-level names to src/RNApolis.egg-info/top_level.txt 2025-10-24T01:01:51,337 reading manifest file 'src/RNApolis.egg-info/SOURCES.txt' 2025-10-24T01:01:51,341 adding license file 'LICENSE' 2025-10-24T01:01:51,345 writing manifest file 'src/RNApolis.egg-info/SOURCES.txt' 2025-10-24T01:01:51,433 Getting requirements to build wheel: finished with status 'done' 2025-10-24T01:01:51,436 Created temporary directory: /tmp/pip-modern-metadata-s9yo3msk 2025-10-24T01:01:51,438 Preparing metadata (pyproject.toml): started 2025-10-24T01:01:51,440 Running command Preparing metadata (pyproject.toml) 2025-10-24T01:01:51,967 /tmp/pip-build-env-l0c3klyv/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-10-24T01:01:51,968 !! 2025-10-24T01:01:51,969 ******************************************************************************** 2025-10-24T01:01:51,969 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-10-24T01:01:51,970 License :: OSI Approved :: MIT License 2025-10-24T01:01:51,971 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-10-24T01:01:51,971 ******************************************************************************** 2025-10-24T01:01:51,972 !! 2025-10-24T01:01:51,973 self._finalize_license_expression() 2025-10-24T01:01:51,995 running dist_info 2025-10-24T01:01:52,007 creating /tmp/pip-modern-metadata-s9yo3msk/RNApolis.egg-info 2025-10-24T01:01:52,008 writing /tmp/pip-modern-metadata-s9yo3msk/RNApolis.egg-info/PKG-INFO 2025-10-24T01:01:52,013 writing dependency_links to /tmp/pip-modern-metadata-s9yo3msk/RNApolis.egg-info/dependency_links.txt 2025-10-24T01:01:52,015 writing entry points to /tmp/pip-modern-metadata-s9yo3msk/RNApolis.egg-info/entry_points.txt 2025-10-24T01:01:52,016 writing requirements to /tmp/pip-modern-metadata-s9yo3msk/RNApolis.egg-info/requires.txt 2025-10-24T01:01:52,017 writing top-level names to /tmp/pip-modern-metadata-s9yo3msk/RNApolis.egg-info/top_level.txt 2025-10-24T01:01:52,018 writing manifest file '/tmp/pip-modern-metadata-s9yo3msk/RNApolis.egg-info/SOURCES.txt' 2025-10-24T01:01:52,045 reading manifest file '/tmp/pip-modern-metadata-s9yo3msk/RNApolis.egg-info/SOURCES.txt' 2025-10-24T01:01:52,047 adding license file 'LICENSE' 2025-10-24T01:01:52,051 writing manifest file '/tmp/pip-modern-metadata-s9yo3msk/RNApolis.egg-info/SOURCES.txt' 2025-10-24T01:01:52,052 creating '/tmp/pip-modern-metadata-s9yo3msk/rnapolis-0.10.6.dist-info' 2025-10-24T01:01:52,183 Preparing metadata (pyproject.toml): finished with status 'done' 2025-10-24T01:01:52,192 Source in /tmp/pip-wheel-sf74e_cb/rnapolis_7ee632889d8345c0941c155eb6cdd546 has version 0.10.6, which satisfies requirement rnapolis==0.10.6 from https://files.pythonhosted.org/packages/92/4e/7d69a9b28ce8c4100fc340d2dbde41d49690ac74aa314ef4fb6d325dfdbd/rnapolis-0.10.6.tar.gz 2025-10-24T01:01:52,193 Removed rnapolis==0.10.6 from https://files.pythonhosted.org/packages/92/4e/7d69a9b28ce8c4100fc340d2dbde41d49690ac74aa314ef4fb6d325dfdbd/rnapolis-0.10.6.tar.gz from build tracker '/tmp/pip-build-tracker-365pwlcm' 2025-10-24T01:01:52,205 Created temporary directory: /tmp/pip-unpack-hvqprzfq 2025-10-24T01:01:52,205 Building wheels for collected packages: rnapolis 2025-10-24T01:01:52,210 Created temporary directory: /tmp/pip-wheel-xt7bg2wu 2025-10-24T01:01:52,210 Destination directory: /tmp/pip-wheel-xt7bg2wu 2025-10-24T01:01:52,212 Building wheel for rnapolis (pyproject.toml): started 2025-10-24T01:01:52,214 Running command Building wheel for rnapolis (pyproject.toml) 2025-10-24T01:01:52,950 /tmp/pip-build-env-l0c3klyv/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-10-24T01:01:52,950 !! 2025-10-24T01:01:52,951 ******************************************************************************** 2025-10-24T01:01:52,952 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-10-24T01:01:52,953 License :: OSI Approved :: MIT License 2025-10-24T01:01:52,954 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-10-24T01:01:52,955 ******************************************************************************** 2025-10-24T01:01:52,956 !! 2025-10-24T01:01:52,957 self._finalize_license_expression() 2025-10-24T01:01:52,983 running bdist_wheel 2025-10-24T01:01:53,013 running build 2025-10-24T01:01:53,014 running build_py 2025-10-24T01:01:53,024 creating build/lib/rnapolis 2025-10-24T01:01:53,026 copying src/rnapolis/parser.py -> build/lib/rnapolis 2025-10-24T01:01:53,028 copying src/rnapolis/adapter.py -> build/lib/rnapolis 2025-10-24T01:01:53,032 copying src/rnapolis/tertiary_v2.py -> build/lib/rnapolis 2025-10-24T01:01:53,035 copying src/rnapolis/rfam_folder.py -> build/lib/rnapolis 2025-10-24T01:01:53,037 copying src/rnapolis/metareader.py -> build/lib/rnapolis 2025-10-24T01:01:53,039 copying src/rnapolis/aligner.py -> build/lib/rnapolis 2025-10-24T01:01:53,041 copying src/rnapolis/common.py -> build/lib/rnapolis 2025-10-24T01:01:53,044 copying src/rnapolis/util.py -> build/lib/rnapolis 2025-10-24T01:01:53,046 copying src/rnapolis/tertiary.py -> build/lib/rnapolis 2025-10-24T01:01:53,049 copying src/rnapolis/annotator.py -> build/lib/rnapolis 2025-10-24T01:01:53,052 copying src/rnapolis/motif_extractor.py -> build/lib/rnapolis 2025-10-24T01:01:53,053 copying src/rnapolis/transformer.py -> build/lib/rnapolis 2025-10-24T01:01:53,056 copying src/rnapolis/splitter.py -> build/lib/rnapolis 2025-10-24T01:01:53,275 copying src/rnapolis/parser_v2.py -> build/lib/rnapolis 2025-10-24T01:01:53,278 copying src/rnapolis/clashfinder.py -> build/lib/rnapolis 2025-10-24T01:01:53,281 copying src/rnapolis/unifier.py -> build/lib/rnapolis 2025-10-24T01:01:53,283 copying src/rnapolis/molecule_filter.py -> build/lib/rnapolis 2025-10-24T01:01:53,285 copying src/rnapolis/distiller.py -> build/lib/rnapolis 2025-10-24T01:01:53,287 running egg_info 2025-10-24T01:01:53,299 writing src/RNApolis.egg-info/PKG-INFO 2025-10-24T01:01:53,305 writing dependency_links to src/RNApolis.egg-info/dependency_links.txt 2025-10-24T01:01:53,306 writing entry points to src/RNApolis.egg-info/entry_points.txt 2025-10-24T01:01:53,308 writing requirements to src/RNApolis.egg-info/requires.txt 2025-10-24T01:01:53,309 writing top-level names to src/RNApolis.egg-info/top_level.txt 2025-10-24T01:01:53,320 reading manifest file 'src/RNApolis.egg-info/SOURCES.txt' 2025-10-24T01:01:53,324 adding license file 'LICENSE' 2025-10-24T01:01:53,328 writing manifest file 'src/RNApolis.egg-info/SOURCES.txt' 2025-10-24T01:01:53,332 copying src/rnapolis/component_A.csv -> build/lib/rnapolis 2025-10-24T01:01:53,334 copying src/rnapolis/component_C.csv -> build/lib/rnapolis 2025-10-24T01:01:53,336 copying src/rnapolis/component_G.csv -> build/lib/rnapolis 2025-10-24T01:01:53,339 copying src/rnapolis/component_U.csv -> build/lib/rnapolis 2025-10-24T01:01:53,341 copying src/rnapolis/mmcif_pdbx_v50.dic -> build/lib/rnapolis 2025-10-24T01:01:53,438 copying src/rnapolis/py.typed -> build/lib/rnapolis 2025-10-24T01:01:53,456 installing to build/bdist.linux-armv7l/wheel 2025-10-24T01:01:53,457 running install 2025-10-24T01:01:53,481 running install_lib 2025-10-24T01:01:53,490 creating build/bdist.linux-armv7l/wheel 2025-10-24T01:01:53,492 creating build/bdist.linux-armv7l/wheel/rnapolis 2025-10-24T01:01:53,493 copying build/lib/rnapolis/parser.py -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,496 copying build/lib/rnapolis/adapter.py -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,500 copying build/lib/rnapolis/tertiary_v2.py -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,503 copying build/lib/rnapolis/rfam_folder.py -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,505 copying build/lib/rnapolis/metareader.py -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,507 copying build/lib/rnapolis/aligner.py -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,509 copying build/lib/rnapolis/common.py -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,511 copying build/lib/rnapolis/util.py -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,513 copying build/lib/rnapolis/component_A.csv -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,515 copying build/lib/rnapolis/tertiary.py -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,518 copying build/lib/rnapolis/component_U.csv -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,520 copying build/lib/rnapolis/annotator.py -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,523 copying build/lib/rnapolis/motif_extractor.py -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,526 copying build/lib/rnapolis/transformer.py -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,528 copying build/lib/rnapolis/splitter.py -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,530 copying build/lib/rnapolis/parser_v2.py -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,533 copying build/lib/rnapolis/component_G.csv -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,536 copying build/lib/rnapolis/clashfinder.py -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,539 copying build/lib/rnapolis/component_C.csv -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,541 copying build/lib/rnapolis/mmcif_pdbx_v50.dic -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,653 copying build/lib/rnapolis/unifier.py -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,655 copying build/lib/rnapolis/molecule_filter.py -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,657 copying build/lib/rnapolis/distiller.py -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,660 copying build/lib/rnapolis/py.typed -> build/bdist.linux-armv7l/wheel/./rnapolis 2025-10-24T01:01:53,661 running install_egg_info 2025-10-24T01:01:53,674 Copying src/RNApolis.egg-info to build/bdist.linux-armv7l/wheel/./RNApolis-0.10.6-py3.11.egg-info 2025-10-24T01:01:53,686 running install_scripts 2025-10-24T01:01:53,697 creating build/bdist.linux-armv7l/wheel/rnapolis-0.10.6.dist-info/WHEEL 2025-10-24T01:01:53,700 creating '/tmp/pip-wheel-xt7bg2wu/.tmp-24ce1p5z/rnapolis-0.10.6-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-10-24T01:01:53,708 adding 'rnapolis/adapter.py' 2025-10-24T01:01:53,710 adding 'rnapolis/aligner.py' 2025-10-24T01:01:53,713 adding 'rnapolis/annotator.py' 2025-10-24T01:01:53,715 adding 'rnapolis/clashfinder.py' 2025-10-24T01:01:53,719 adding 'rnapolis/common.py' 2025-10-24T01:01:53,720 adding 'rnapolis/component_A.csv' 2025-10-24T01:01:53,722 adding 'rnapolis/component_C.csv' 2025-10-24T01:01:53,723 adding 'rnapolis/component_G.csv' 2025-10-24T01:01:53,725 adding 'rnapolis/component_U.csv' 2025-10-24T01:01:53,729 adding 'rnapolis/distiller.py' 2025-10-24T01:01:53,731 adding 'rnapolis/metareader.py' 2025-10-24T01:01:54,076 adding 'rnapolis/mmcif_pdbx_v50.dic' 2025-10-24T01:01:54,113 adding 'rnapolis/molecule_filter.py' 2025-10-24T01:01:54,114 adding 'rnapolis/motif_extractor.py' 2025-10-24T01:01:54,117 adding 'rnapolis/parser.py' 2025-10-24T01:01:54,121 adding 'rnapolis/parser_v2.py' 2025-10-24T01:01:54,123 adding 'rnapolis/py.typed' 2025-10-24T01:01:54,124 adding 'rnapolis/rfam_folder.py' 2025-10-24T01:01:54,126 adding 'rnapolis/splitter.py' 2025-10-24T01:01:54,130 adding 'rnapolis/tertiary.py' 2025-10-24T01:01:54,134 adding 'rnapolis/tertiary_v2.py' 2025-10-24T01:01:54,136 adding 'rnapolis/transformer.py' 2025-10-24T01:01:54,138 adding 'rnapolis/unifier.py' 2025-10-24T01:01:54,139 adding 'rnapolis/util.py' 2025-10-24T01:01:54,141 adding 'rnapolis-0.10.6.dist-info/licenses/LICENSE' 2025-10-24T01:01:54,144 adding 'rnapolis-0.10.6.dist-info/METADATA' 2025-10-24T01:01:54,146 adding 'rnapolis-0.10.6.dist-info/WHEEL' 2025-10-24T01:01:54,147 adding 'rnapolis-0.10.6.dist-info/entry_points.txt' 2025-10-24T01:01:54,148 adding 'rnapolis-0.10.6.dist-info/top_level.txt' 2025-10-24T01:01:54,148 adding 'rnapolis-0.10.6.dist-info/RECORD' 2025-10-24T01:01:54,157 removing build/bdist.linux-armv7l/wheel 2025-10-24T01:01:54,258 Building wheel for rnapolis (pyproject.toml): finished with status 'done' 2025-10-24T01:01:54,276 Created wheel for rnapolis: filename=rnapolis-0.10.6-py3-none-any.whl size=693646 sha256=df91fa57ee212dc7c89482444335713a9e0067d2085b64d6e67779de0289aa9f 2025-10-24T01:01:54,277 Stored in directory: /tmp/pip-ephem-wheel-cache-hj6bfps1/wheels/7e/55/3d/81de50064e917200f92684b958d7ee56935d54acd536298084 2025-10-24T01:01:54,299 Successfully built rnapolis 2025-10-24T01:01:54,324 Removed build tracker: '/tmp/pip-build-tracker-365pwlcm'