2026-04-05T13:10:12,981 Created temporary directory: /tmp/pip-ephem-wheel-cache-k39v98w8
2026-04-05T13:10:12,983 Created temporary directory: /tmp/pip-build-tracker-3py8yzcp
2026-04-05T13:10:12,984 Initialized build tracking at /tmp/pip-build-tracker-3py8yzcp
2026-04-05T13:10:12,984 Created build tracker: /tmp/pip-build-tracker-3py8yzcp
2026-04-05T13:10:12,985 Entered build tracker: /tmp/pip-build-tracker-3py8yzcp
2026-04-05T13:10:12,985 Created temporary directory: /tmp/pip-wheel-lmlza1md
2026-04-05T13:10:12,988 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
2026-04-05T13:10:12,991 Created temporary directory: /tmp/pip-ephem-wheel-cache-vrbal8al
2026-04-05T13:10:13,012 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-04-05T13:10:13,016 2 location(s) to search for versions of pirlygenes:
2026-04-05T13:10:13,016 * https://pypi.org/simple/pirlygenes/
2026-04-05T13:10:13,016 * https://www.piwheels.org/simple/pirlygenes/
2026-04-05T13:10:13,017 Fetching project page and analyzing links: https://pypi.org/simple/pirlygenes/
2026-04-05T13:10:13,018 Getting page https://pypi.org/simple/pirlygenes/
2026-04-05T13:10:13,019 Found index url https://pypi.org/simple
2026-04-05T13:10:13,246 Fetched page https://pypi.org/simple/pirlygenes/ as application/vnd.pypi.simple.v1+json
2026-04-05T13:10:13,250   Skipping link: No binaries permitted for pirlygenes: https://files.pythonhosted.org/packages/2e/66/a994711ece0c32dc4037b2c20acb069375f8eb2c80bdcca3a9efa47fdaee/pirlygenes-1.7.0-py3-none-any.whl (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9)
2026-04-05T13:10:13,251   Found link https://files.pythonhosted.org/packages/17/fe/bcdacc3535105e4aed789ffd67937b0a725f5eaf16e19e2d70d7d9994985/pirlygenes-1.7.0.tar.gz (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9), version: 1.7.0
2026-04-05T13:10:13,252   Skipping link: No binaries permitted for pirlygenes: https://files.pythonhosted.org/packages/59/b0/3e2df98a4c7e570e430d5a43b78c4325669dc94f670df919535730ad97e4/pirlygenes-1.8.0-py3-none-any.whl (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9)
2026-04-05T13:10:13,253   Found link https://files.pythonhosted.org/packages/4b/7c/57808dd823cb43e0775fef54e28607a61d6e34549ef6c21f02e85567e13a/pirlygenes-1.8.0.tar.gz (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9), version: 1.8.0
2026-04-05T13:10:13,254   Skipping link: No binaries permitted for pirlygenes: https://files.pythonhosted.org/packages/9a/8d/f18f1d145c3cc415d28137493c5cb8e758516d9ac9633fc74cb4f86a318a/pirlygenes-1.8.1-py3-none-any.whl (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9)
2026-04-05T13:10:13,255   Found link https://files.pythonhosted.org/packages/61/0c/c3f0aff27c3758ba3f3ee1f4a63a05238e02043251af230032d9ba555624/pirlygenes-1.8.1.tar.gz (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9), version: 1.8.1
2026-04-05T13:10:13,255   Skipping link: No binaries permitted for pirlygenes: https://files.pythonhosted.org/packages/24/35/2c1111a823202625bf5719038d745faaa60ed3613bc790db7a365d0d9e91/pirlygenes-1.9.0-py3-none-any.whl (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9)
2026-04-05T13:10:13,256   Found link https://files.pythonhosted.org/packages/00/21/33762d0e1497cb8f52920f8804591991b077145275a9bb472d54cb34bd3b/pirlygenes-1.9.0.tar.gz (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9), version: 1.9.0
2026-04-05T13:10:13,257   Skipping link: No binaries permitted for pirlygenes: https://files.pythonhosted.org/packages/da/14/c0e64534396352276e63b247458c9b5db4f43c4d36ecba3f447203f1bed8/pirlygenes-2.0.0-py3-none-any.whl (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9)
2026-04-05T13:10:13,258   Found link https://files.pythonhosted.org/packages/1a/15/da113c10028ce6cef9359672f0d6309ef13174410f74bd641ab56fe968e1/pirlygenes-2.0.0.tar.gz (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9), version: 2.0.0
2026-04-05T13:10:13,259   Skipping link: No binaries permitted for pirlygenes: https://files.pythonhosted.org/packages/ef/67/1ca24d76bbfbb8547103f0c887d0215b8689b9d68ca03b8e63245446d85f/pirlygenes-2.0.1-py3-none-any.whl (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9)
2026-04-05T13:10:13,260   Found link https://files.pythonhosted.org/packages/f0/57/519f98c3e3ce7414973c34a35b56e0123e63c2397c1c28a40f52096110e8/pirlygenes-2.0.1.tar.gz (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9), version: 2.0.1
2026-04-05T13:10:13,260   Skipping link: No binaries permitted for pirlygenes: https://files.pythonhosted.org/packages/b2/a5/eb85bc710dc92ed90930681df0d0727ba7c8adce5f597218b60c8e749abb/pirlygenes-2.1.0-py3-none-any.whl (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9)
2026-04-05T13:10:13,261   Found link https://files.pythonhosted.org/packages/ac/1c/535ab059a16f501c104975a9afdbe26292625c5f6b4565dfaff29827dae5/pirlygenes-2.1.0.tar.gz (from https://pypi.org/simple/pirlygenes/) (requires-python:>=3.9), version: 2.1.0
2026-04-05T13:10:13,262 Fetching project page and analyzing links: https://www.piwheels.org/simple/pirlygenes/
2026-04-05T13:10:13,262 Getting page https://www.piwheels.org/simple/pirlygenes/
2026-04-05T13:10:13,263 Found index url https://www.piwheels.org/simple
2026-04-05T13:10:13,524 Fetched page https://www.piwheels.org/simple/pirlygenes/ as text/html
2026-04-05T13:10:13,527   Skipping link: No binaries permitted for pirlygenes: https://www.piwheels.org/simple/pirlygenes/pirlygenes-2.0.1-py3-none-any.whl#sha256=0956b5fd3f21d43dea90b38bbc06628b327c49504aa0fc53d3d81d55208c6f5f (from https://www.piwheels.org/simple/pirlygenes/) (requires-python:>=3.9)
2026-04-05T13:10:13,528   Skipping link: No binaries permitted for pirlygenes: https://www.piwheels.org/simple/pirlygenes/pirlygenes-2.0.0-py3-none-any.whl#sha256=de738501d014cdb6760b96e01afa7d18cb8dac3d863d433e9ce8fce0172641f5 (from https://www.piwheels.org/simple/pirlygenes/) (requires-python:>=3.9)
2026-04-05T13:10:13,528   Skipping link: No binaries permitted for pirlygenes: https://www.piwheels.org/simple/pirlygenes/pirlygenes-1.9.0-py3-none-any.whl#sha256=3be90370a11cc9b33de80e02b84f99700133addc5994e35bcb8b80b76f09f8ae (from https://www.piwheels.org/simple/pirlygenes/) (requires-python:>=3.9)
2026-04-05T13:10:13,529   Skipping link: No binaries permitted for pirlygenes: https://www.piwheels.org/simple/pirlygenes/pirlygenes-1.8.1-py3-none-any.whl#sha256=35f8427ceac3714bb6339609b7f3602ea81ea8b5642c4e760931e9a28263a28b (from https://www.piwheels.org/simple/pirlygenes/) (requires-python:>=3.9)
2026-04-05T13:10:13,529   Skipping link: No binaries permitted for pirlygenes: https://www.piwheels.org/simple/pirlygenes/pirlygenes-1.8.0-py3-none-any.whl#sha256=202a232caf63d7ad6c6d202e8d8c6c3f52bb57aa7bd124b14be89597a4637f02 (from https://www.piwheels.org/simple/pirlygenes/) (requires-python:>=3.9)
2026-04-05T13:10:13,530   Skipping link: No binaries permitted for pirlygenes: https://www.piwheels.org/simple/pirlygenes/pirlygenes-1.7.0-py3-none-any.whl#sha256=01a45cdf8948ae1d8a8034363ecd9357088d1df4c99ffb9370f8d68432ff4fa7 (from https://www.piwheels.org/simple/pirlygenes/) (requires-python:>=3.9)
2026-04-05T13:10:13,531 Skipping link: not a file: https://www.piwheels.org/simple/pirlygenes/
2026-04-05T13:10:13,531 Skipping link: not a file: https://pypi.org/simple/pirlygenes/
2026-04-05T13:10:13,551 Given no hashes to check 1 links for project 'pirlygenes': discarding no candidates
2026-04-05T13:10:13,568 Collecting pirlygenes==2.1.0
2026-04-05T13:10:13,570   Created temporary directory: /tmp/pip-unpack-a9gmq16z
2026-04-05T13:10:13,720   Downloading pirlygenes-2.1.0.tar.gz (668 kB)
2026-04-05T13:10:14,028   Added pirlygenes==2.1.0 from https://files.pythonhosted.org/packages/ac/1c/535ab059a16f501c104975a9afdbe26292625c5f6b4565dfaff29827dae5/pirlygenes-2.1.0.tar.gz to build tracker '/tmp/pip-build-tracker-3py8yzcp'
2026-04-05T13:10:14,034   Created temporary directory: /tmp/pip-build-env-2qorvkys
2026-04-05T13:10:14,040   Installing build dependencies: started
2026-04-05T13:10:14,041   Running command pip subprocess to install build dependencies
2026-04-05T13:10:15,418   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-04-05T13:10:15,858   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
2026-04-05T13:10:15,882   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-04-05T13:10:17,663   Collecting setuptools>=60
2026-04-05T13:10:17,749     Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB)
2026-04-05T13:10:18,136   Collecting setuptools-scm>=8.0
2026-04-05T13:10:18,150     Using cached https://www.piwheels.org/simple/setuptools-scm/setuptools_scm-10.0.5-py3-none-any.whl (21 kB)
2026-04-05T13:10:18,230   Collecting vcs-versioning>=1.0.0.dev0
2026-04-05T13:10:18,246     Using cached https://www.piwheels.org/simple/vcs-versioning/vcs_versioning-1.1.1-py3-none-any.whl (79 kB)
2026-04-05T13:10:18,426   Collecting packaging>=20
2026-04-05T13:10:18,442     Using cached https://www.piwheels.org/simple/packaging/packaging-26.0-py3-none-any.whl (74 kB)
2026-04-05T13:10:21,513   Installing collected packages: setuptools, packaging, vcs-versioning, setuptools-scm
2026-04-05T13:10:25,137     Creating /tmp/pip-build-env-2qorvkys/overlay/local/bin
2026-04-05T13:10:25,140     changing mode of /tmp/pip-build-env-2qorvkys/overlay/local/bin/vcs-versioning to 755
2026-04-05T13:10:25,255     changing mode of /tmp/pip-build-env-2qorvkys/overlay/local/bin/setuptools-scm to 755
2026-04-05T13:10:25,284   Successfully installed packaging-26.0 setuptools-82.0.1 setuptools-scm-10.0.5 vcs-versioning-1.1.1
2026-04-05T13:10:25,580   Installing build dependencies: finished with status 'done'
2026-04-05T13:10:25,595   Getting requirements to build wheel: started
2026-04-05T13:10:25,597   Running command Getting requirements to build wheel
2026-04-05T13:10:26,259   toml section missing PosixPath('pyproject.toml') does not contain any of the tool sections: ['setuptools_scm', 'vcs-versioning']
2026-04-05T13:10:26,371   /tmp/pip-build-env-2qorvkys/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-04-05T13:10:26,372   !!

2026-04-05T13:10:26,373           ********************************************************************************
2026-04-05T13:10:26,373           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-04-05T13:10:26,374           License :: OSI Approved :: Apache Software License

2026-04-05T13:10:26,376           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-04-05T13:10:26,376           ********************************************************************************

2026-04-05T13:10:26,377   !!
2026-04-05T13:10:26,378     dist._finalize_license_expression()
2026-04-05T13:10:26,379   /tmp/pip-build-env-2qorvkys/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-04-05T13:10:26,379   !!

2026-04-05T13:10:26,381           ********************************************************************************
2026-04-05T13:10:26,381           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-04-05T13:10:26,383           License :: OSI Approved :: Apache Software License

2026-04-05T13:10:26,384           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-04-05T13:10:26,385           ********************************************************************************

2026-04-05T13:10:26,385   !!
2026-04-05T13:10:26,386     self._finalize_license_expression()
2026-04-05T13:10:26,386   running egg_info
2026-04-05T13:10:26,395   writing pirlygenes.egg-info/PKG-INFO
2026-04-05T13:10:26,399   writing dependency_links to pirlygenes.egg-info/dependency_links.txt
2026-04-05T13:10:26,401   writing entry points to pirlygenes.egg-info/entry_points.txt
2026-04-05T13:10:26,402   writing requirements to pirlygenes.egg-info/requires.txt
2026-04-05T13:10:26,403   writing top-level names to pirlygenes.egg-info/top_level.txt
2026-04-05T13:10:26,445   /tmp/pip-build-env-2qorvkys/overlay/local/lib/python3.11/dist-packages/vcs_versioning/overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly.
2026-04-05T13:10:26,445     return get_active_overrides().subprocess_timeout
2026-04-05T13:10:26,452   listing git files failed - pretending there aren't any
2026-04-05T13:10:26,462   reading manifest file 'pirlygenes.egg-info/SOURCES.txt'
2026-04-05T13:10:26,469   adding license file 'LICENSE'
2026-04-05T13:10:26,474   writing manifest file 'pirlygenes.egg-info/SOURCES.txt'
2026-04-05T13:10:26,580   Getting requirements to build wheel: finished with status 'done'
2026-04-05T13:10:26,583   Created temporary directory: /tmp/pip-modern-metadata-9pnha_k3
2026-04-05T13:10:26,586   Preparing metadata (pyproject.toml): started
2026-04-05T13:10:26,587   Running command Preparing metadata (pyproject.toml)
2026-04-05T13:10:27,198   toml section missing PosixPath('pyproject.toml') does not contain any of the tool sections: ['setuptools_scm', 'vcs-versioning']
2026-04-05T13:10:27,306   /tmp/pip-build-env-2qorvkys/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-04-05T13:10:27,306   !!

2026-04-05T13:10:27,308           ********************************************************************************
2026-04-05T13:10:27,308           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-04-05T13:10:27,309           License :: OSI Approved :: Apache Software License

2026-04-05T13:10:27,310           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-04-05T13:10:27,311           ********************************************************************************

2026-04-05T13:10:27,312   !!
2026-04-05T13:10:27,313     dist._finalize_license_expression()
2026-04-05T13:10:27,313   /tmp/pip-build-env-2qorvkys/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-04-05T13:10:27,314   !!

2026-04-05T13:10:27,315           ********************************************************************************
2026-04-05T13:10:27,316           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-04-05T13:10:27,317           License :: OSI Approved :: Apache Software License

2026-04-05T13:10:27,318           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-04-05T13:10:27,318           ********************************************************************************

2026-04-05T13:10:27,320   !!
2026-04-05T13:10:27,320     self._finalize_license_expression()
2026-04-05T13:10:27,321   running dist_info
2026-04-05T13:10:27,335   creating /tmp/pip-modern-metadata-9pnha_k3/pirlygenes.egg-info
2026-04-05T13:10:27,336   writing /tmp/pip-modern-metadata-9pnha_k3/pirlygenes.egg-info/PKG-INFO
2026-04-05T13:10:27,340   writing dependency_links to /tmp/pip-modern-metadata-9pnha_k3/pirlygenes.egg-info/dependency_links.txt
2026-04-05T13:10:27,342   writing entry points to /tmp/pip-modern-metadata-9pnha_k3/pirlygenes.egg-info/entry_points.txt
2026-04-05T13:10:27,343   writing requirements to /tmp/pip-modern-metadata-9pnha_k3/pirlygenes.egg-info/requires.txt
2026-04-05T13:10:27,344   writing top-level names to /tmp/pip-modern-metadata-9pnha_k3/pirlygenes.egg-info/top_level.txt
2026-04-05T13:10:27,346   writing manifest file '/tmp/pip-modern-metadata-9pnha_k3/pirlygenes.egg-info/SOURCES.txt'
2026-04-05T13:10:27,382   /tmp/pip-build-env-2qorvkys/overlay/local/lib/python3.11/dist-packages/vcs_versioning/overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly.
2026-04-05T13:10:27,382     return get_active_overrides().subprocess_timeout
2026-04-05T13:10:27,388   listing git files failed - pretending there aren't any
2026-04-05T13:10:27,396   reading manifest file '/tmp/pip-modern-metadata-9pnha_k3/pirlygenes.egg-info/SOURCES.txt'
2026-04-05T13:10:27,398   adding license file 'LICENSE'
2026-04-05T13:10:27,401   writing manifest file '/tmp/pip-modern-metadata-9pnha_k3/pirlygenes.egg-info/SOURCES.txt'
2026-04-05T13:10:27,402   creating '/tmp/pip-modern-metadata-9pnha_k3/pirlygenes-2.1.0.dist-info'
2026-04-05T13:10:27,537   Preparing metadata (pyproject.toml): finished with status 'done'
2026-04-05T13:10:27,542   Source in /tmp/pip-wheel-lmlza1md/pirlygenes_f506eac8379b419896d18bb4a2cbaf38 has version 2.1.0, which satisfies requirement pirlygenes==2.1.0 from https://files.pythonhosted.org/packages/ac/1c/535ab059a16f501c104975a9afdbe26292625c5f6b4565dfaff29827dae5/pirlygenes-2.1.0.tar.gz
2026-04-05T13:10:27,543   Removed pirlygenes==2.1.0 from https://files.pythonhosted.org/packages/ac/1c/535ab059a16f501c104975a9afdbe26292625c5f6b4565dfaff29827dae5/pirlygenes-2.1.0.tar.gz from build tracker '/tmp/pip-build-tracker-3py8yzcp'
2026-04-05T13:10:27,549 Created temporary directory: /tmp/pip-unpack-br5u53qy
2026-04-05T13:10:27,550 Building wheels for collected packages: pirlygenes
2026-04-05T13:10:27,554   Created temporary directory: /tmp/pip-wheel-zh12sba7
2026-04-05T13:10:27,555   Destination directory: /tmp/pip-wheel-zh12sba7
2026-04-05T13:10:27,557   Building wheel for pirlygenes (pyproject.toml): started
2026-04-05T13:10:27,559   Running command Building wheel for pirlygenes (pyproject.toml)
2026-04-05T13:10:28,146   toml section missing PosixPath('pyproject.toml') does not contain any of the tool sections: ['setuptools_scm', 'vcs-versioning']
2026-04-05T13:10:28,244   /tmp/pip-build-env-2qorvkys/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-04-05T13:10:28,245   !!

2026-04-05T13:10:28,246           ********************************************************************************
2026-04-05T13:10:28,247           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-04-05T13:10:28,248           License :: OSI Approved :: Apache Software License

2026-04-05T13:10:28,249           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-04-05T13:10:28,250           ********************************************************************************

2026-04-05T13:10:28,251   !!
2026-04-05T13:10:28,251     dist._finalize_license_expression()
2026-04-05T13:10:28,252   /tmp/pip-build-env-2qorvkys/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-04-05T13:10:28,253   !!

2026-04-05T13:10:28,254           ********************************************************************************
2026-04-05T13:10:28,254           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-04-05T13:10:28,256           License :: OSI Approved :: Apache Software License

2026-04-05T13:10:28,257           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-04-05T13:10:28,258           ********************************************************************************

2026-04-05T13:10:28,259   !!
2026-04-05T13:10:28,259     self._finalize_license_expression()
2026-04-05T13:10:28,259   running bdist_wheel
2026-04-05T13:10:28,279   running build
2026-04-05T13:10:28,279   running build_py
2026-04-05T13:10:28,281   creating build/lib/pirlygenes
2026-04-05T13:10:28,283   copying pirlygenes/transcript_to_gene.py -> build/lib/pirlygenes
2026-04-05T13:10:28,285   copying pirlygenes/gene_names.py -> build/lib/pirlygenes
2026-04-05T13:10:28,287   copying pirlygenes/cli.py -> build/lib/pirlygenes
2026-04-05T13:10:28,289   copying pirlygenes/gene_ids.py -> build/lib/pirlygenes
2026-04-05T13:10:28,291   copying pirlygenes/plot.py -> build/lib/pirlygenes
2026-04-05T13:10:28,293   copying pirlygenes/common.py -> build/lib/pirlygenes
2026-04-05T13:10:28,295   copying pirlygenes/version.py -> build/lib/pirlygenes
2026-04-05T13:10:28,297   copying pirlygenes/gene_sets_cancer.py -> build/lib/pirlygenes
2026-04-05T13:10:28,299   copying pirlygenes/aggregate_gene_expression.py -> build/lib/pirlygenes
2026-04-05T13:10:28,301   copying pirlygenes/__init__.py -> build/lib/pirlygenes
2026-04-05T13:10:28,303   copying pirlygenes/gene_sets_old.py -> build/lib/pirlygenes
2026-04-05T13:10:28,305   copying pirlygenes/load_dataset.py -> build/lib/pirlygenes
2026-04-05T13:10:28,306   copying pirlygenes/plot_data_helpers.py -> build/lib/pirlygenes
2026-04-05T13:10:28,309   copying pirlygenes/load_expression.py -> build/lib/pirlygenes
2026-04-05T13:10:28,311   running egg_info
2026-04-05T13:10:28,325   writing pirlygenes.egg-info/PKG-INFO
2026-04-05T13:10:28,329   writing dependency_links to pirlygenes.egg-info/dependency_links.txt
2026-04-05T13:10:28,330   writing entry points to pirlygenes.egg-info/entry_points.txt
2026-04-05T13:10:28,331   writing requirements to pirlygenes.egg-info/requires.txt
2026-04-05T13:10:28,332   writing top-level names to pirlygenes.egg-info/top_level.txt
2026-04-05T13:10:28,362   /tmp/pip-build-env-2qorvkys/overlay/local/lib/python3.11/dist-packages/vcs_versioning/overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly.
2026-04-05T13:10:28,362     return get_active_overrides().subprocess_timeout
2026-04-05T13:10:28,369   listing git files failed - pretending there aren't any
2026-04-05T13:10:28,376   reading manifest file 'pirlygenes.egg-info/SOURCES.txt'
2026-04-05T13:10:28,381   adding license file 'LICENSE'
2026-04-05T13:10:28,386   writing manifest file 'pirlygenes.egg-info/SOURCES.txt'
2026-04-05T13:10:28,388   /tmp/pip-build-env-2qorvkys/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pirlygenes.data' is absent from the `packages` configuration.
2026-04-05T13:10:28,389   !!

2026-04-05T13:10:28,390           ********************************************************************************
2026-04-05T13:10:28,391           ############################
2026-04-05T13:10:28,391           # Package would be ignored #
2026-04-05T13:10:28,392           ############################
2026-04-05T13:10:28,392           Python recognizes 'pirlygenes.data' as an importable package[^1],
2026-04-05T13:10:28,393           but it is absent from setuptools' `packages` configuration.

2026-04-05T13:10:28,394           This leads to an ambiguous overall configuration. If you want to distribute this
2026-04-05T13:10:28,394           package, please make sure that 'pirlygenes.data' is explicitly added
2026-04-05T13:10:28,395           to the `packages` configuration field.

2026-04-05T13:10:28,396           Alternatively, you can also rely on setuptools' discovery methods
2026-04-05T13:10:28,396           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-04-05T13:10:28,397           instead of `find_packages(...)`/`find:`).

2026-04-05T13:10:28,398           You can read more about "package discovery" on setuptools documentation page:

2026-04-05T13:10:28,399           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-04-05T13:10:28,400           If you don't want 'pirlygenes.data' to be distributed and are
2026-04-05T13:10:28,400           already explicitly excluding 'pirlygenes.data' via
2026-04-05T13:10:28,401           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-04-05T13:10:28,402           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-04-05T13:10:28,402           combination with a more fine grained `package-data` configuration.

2026-04-05T13:10:28,403           You can read more about "package data files" on setuptools documentation page:

2026-04-05T13:10:28,404           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-04-05T13:10:28,405           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-04-05T13:10:28,405                 even if it does not contain any `.py` files.
2026-04-05T13:10:28,406                 On the other hand, currently there is no concept of package data
2026-04-05T13:10:28,406                 directory, all directories are treated like packages.
2026-04-05T13:10:28,406           ********************************************************************************

2026-04-05T13:10:28,407   !!
2026-04-05T13:10:28,408     check.warn(importable)
2026-04-05T13:10:28,408   copying pirlygenes/PLAN-1.4.0-radioligand.md -> build/lib/pirlygenes
2026-04-05T13:10:28,409   creating build/lib/pirlygenes/data
2026-04-05T13:10:28,409   copying pirlygenes/data/ADC-approved.csv -> build/lib/pirlygenes/data
2026-04-05T13:10:28,410   copying pirlygenes/data/ADC-trials.csv -> build/lib/pirlygenes/data
2026-04-05T13:10:28,410   copying pirlygenes/data/ADC-withdrawn.csv -> build/lib/pirlygenes/data
2026-04-05T13:10:28,411   copying pirlygenes/data/CAR-T-approved.csv -> build/lib/pirlygenes/data
2026-04-05T13:10:28,411   copying pirlygenes/data/TCR-T-approved.csv -> build/lib/pirlygenes/data
2026-04-05T13:10:28,412   copying pirlygenes/data/TCR-T-trials.csv -> build/lib/pirlygenes/data
2026-04-05T13:10:28,412   copying pirlygenes/data/bispecific-antibodies-approved.csv -> build/lib/pirlygenes/data
2026-04-05T13:10:28,415   copying pirlygenes/data/cancer-driver-genes.csv -> build/lib/pirlygenes/data
2026-04-05T13:10:28,418   copying pirlygenes/data/cancer-driver-variants.csv -> build/lib/pirlygenes/data
2026-04-05T13:10:28,421   copying pirlygenes/data/cancer-testis-antigens.csv -> build/lib/pirlygenes/data
2026-04-05T13:10:28,424   copying pirlygenes/data/class1-mhc-presentation-pathway.csv -> build/lib/pirlygenes/data
2026-04-05T13:10:28,427   copying pirlygenes/data/interferon-response.csv -> build/lib/pirlygenes/data
2026-04-05T13:10:28,430   copying pirlygenes/data/multispecific-tcell-engager-trials.csv -> build/lib/pirlygenes/data
2026-04-05T13:10:28,432   copying pirlygenes/data/radioligand-targets.csv -> build/lib/pirlygenes/data
2026-04-05T13:10:28,450   installing to build/bdist.linux-armv7l/wheel
2026-04-05T13:10:28,451   running install
2026-04-05T13:10:28,473   running install_lib
2026-04-05T13:10:28,482   creating build/bdist.linux-armv7l/wheel
2026-04-05T13:10:28,484   creating build/bdist.linux-armv7l/wheel/pirlygenes
2026-04-05T13:10:28,485   copying build/lib/pirlygenes/transcript_to_gene.py -> build/bdist.linux-armv7l/wheel/./pirlygenes
2026-04-05T13:10:28,488   copying build/lib/pirlygenes/PLAN-1.4.0-radioligand.md -> build/bdist.linux-armv7l/wheel/./pirlygenes
2026-04-05T13:10:28,490   copying build/lib/pirlygenes/gene_names.py -> build/bdist.linux-armv7l/wheel/./pirlygenes
2026-04-05T13:10:28,492   copying build/lib/pirlygenes/cli.py -> build/bdist.linux-armv7l/wheel/./pirlygenes
2026-04-05T13:10:28,494   copying build/lib/pirlygenes/gene_ids.py -> build/bdist.linux-armv7l/wheel/./pirlygenes
2026-04-05T13:10:28,496   copying build/lib/pirlygenes/plot.py -> build/bdist.linux-armv7l/wheel/./pirlygenes
2026-04-05T13:10:28,499   copying build/lib/pirlygenes/common.py -> build/bdist.linux-armv7l/wheel/./pirlygenes
2026-04-05T13:10:28,500   copying build/lib/pirlygenes/version.py -> build/bdist.linux-armv7l/wheel/./pirlygenes
2026-04-05T13:10:28,502   copying build/lib/pirlygenes/gene_sets_cancer.py -> build/bdist.linux-armv7l/wheel/./pirlygenes
2026-04-05T13:10:28,504   copying build/lib/pirlygenes/aggregate_gene_expression.py -> build/bdist.linux-armv7l/wheel/./pirlygenes
2026-04-05T13:10:28,507   copying build/lib/pirlygenes/__init__.py -> build/bdist.linux-armv7l/wheel/./pirlygenes
2026-04-05T13:10:28,508   copying build/lib/pirlygenes/gene_sets_old.py -> build/bdist.linux-armv7l/wheel/./pirlygenes
2026-04-05T13:10:28,510   copying build/lib/pirlygenes/load_dataset.py -> build/bdist.linux-armv7l/wheel/./pirlygenes
2026-04-05T13:10:28,512   copying build/lib/pirlygenes/plot_data_helpers.py -> build/bdist.linux-armv7l/wheel/./pirlygenes
2026-04-05T13:10:28,515   creating build/bdist.linux-armv7l/wheel/pirlygenes/data
2026-04-05T13:10:28,516   copying build/lib/pirlygenes/data/bispecific-antibodies-approved.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data
2026-04-05T13:10:28,518   copying build/lib/pirlygenes/data/class1-mhc-presentation-pathway.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data
2026-04-05T13:10:28,520   copying build/lib/pirlygenes/data/interferon-response.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data
2026-04-05T13:10:28,522   copying build/lib/pirlygenes/data/ADC-trials.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data
2026-04-05T13:10:28,525   copying build/lib/pirlygenes/data/multispecific-tcell-engager-trials.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data
2026-04-05T13:10:28,527   copying build/lib/pirlygenes/data/CAR-T-approved.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data
2026-04-05T13:10:28,529   copying build/lib/pirlygenes/data/ADC-approved.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data
2026-04-05T13:10:28,531   copying build/lib/pirlygenes/data/cancer-driver-variants.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data
2026-04-05T13:10:28,535   copying build/lib/pirlygenes/data/TCR-T-trials.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data
2026-04-05T13:10:28,538   copying build/lib/pirlygenes/data/TCR-T-approved.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data
2026-04-05T13:10:28,539   copying build/lib/pirlygenes/data/radioligand-targets.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data
2026-04-05T13:10:28,541   copying build/lib/pirlygenes/data/cancer-driver-genes.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data
2026-04-05T13:10:28,544   copying build/lib/pirlygenes/data/cancer-testis-antigens.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data
2026-04-05T13:10:28,548   copying build/lib/pirlygenes/data/ADC-withdrawn.csv -> build/bdist.linux-armv7l/wheel/./pirlygenes/data
2026-04-05T13:10:28,549   copying build/lib/pirlygenes/load_expression.py -> build/bdist.linux-armv7l/wheel/./pirlygenes
2026-04-05T13:10:28,551   running install_egg_info
2026-04-05T13:10:28,559   Copying pirlygenes.egg-info to build/bdist.linux-armv7l/wheel/./pirlygenes-2.1.0-py3.11.egg-info
2026-04-05T13:10:28,570   running install_scripts
2026-04-05T13:10:28,582   creating build/bdist.linux-armv7l/wheel/pirlygenes-2.1.0.dist-info/WHEEL
2026-04-05T13:10:28,585   creating '/tmp/pip-wheel-zh12sba7/.tmp-x2ly2b9z/pirlygenes-2.1.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-04-05T13:10:28,588   adding 'pirlygenes/PLAN-1.4.0-radioligand.md'
2026-04-05T13:10:28,589   adding 'pirlygenes/__init__.py'
2026-04-05T13:10:28,591   adding 'pirlygenes/aggregate_gene_expression.py'
2026-04-05T13:10:28,593   adding 'pirlygenes/cli.py'
2026-04-05T13:10:28,594   adding 'pirlygenes/common.py'
2026-04-05T13:10:28,596   adding 'pirlygenes/gene_ids.py'
2026-04-05T13:10:28,598   adding 'pirlygenes/gene_names.py'
2026-04-05T13:10:28,601   adding 'pirlygenes/gene_sets_cancer.py'
2026-04-05T13:10:28,602   adding 'pirlygenes/gene_sets_old.py'
2026-04-05T13:10:28,604   adding 'pirlygenes/load_dataset.py'
2026-04-05T13:10:28,605   adding 'pirlygenes/load_expression.py'
2026-04-05T13:10:28,607   adding 'pirlygenes/plot.py'
2026-04-05T13:10:28,609   adding 'pirlygenes/plot_data_helpers.py'
2026-04-05T13:10:28,611   adding 'pirlygenes/transcript_to_gene.py'
2026-04-05T13:10:28,612   adding 'pirlygenes/version.py'
2026-04-05T13:10:28,614   adding 'pirlygenes/data/ADC-approved.csv'
2026-04-05T13:10:28,618   adding 'pirlygenes/data/ADC-trials.csv'
2026-04-05T13:10:28,620   adding 'pirlygenes/data/ADC-withdrawn.csv'
2026-04-05T13:10:28,621   adding 'pirlygenes/data/CAR-T-approved.csv'
2026-04-05T13:10:28,622   adding 'pirlygenes/data/TCR-T-approved.csv'
2026-04-05T13:10:28,626   adding 'pirlygenes/data/TCR-T-trials.csv'
2026-04-05T13:10:28,627   adding 'pirlygenes/data/bispecific-antibodies-approved.csv'
2026-04-05T13:10:28,632   adding 'pirlygenes/data/cancer-driver-genes.csv'
2026-04-05T13:10:28,635   adding 'pirlygenes/data/cancer-driver-variants.csv'
2026-04-05T13:10:28,641   adding 'pirlygenes/data/cancer-testis-antigens.csv'
2026-04-05T13:10:28,643   adding 'pirlygenes/data/class1-mhc-presentation-pathway.csv'
2026-04-05T13:10:28,644   adding 'pirlygenes/data/interferon-response.csv'
2026-04-05T13:10:28,646   adding 'pirlygenes/data/multispecific-tcell-engager-trials.csv'
2026-04-05T13:10:28,648   adding 'pirlygenes/data/radioligand-targets.csv'
2026-04-05T13:10:28,651   adding 'pirlygenes-2.1.0.dist-info/licenses/LICENSE'
2026-04-05T13:10:28,653   adding 'pirlygenes-2.1.0.dist-info/METADATA'
2026-04-05T13:10:28,654   adding 'pirlygenes-2.1.0.dist-info/WHEEL'
2026-04-05T13:10:28,655   adding 'pirlygenes-2.1.0.dist-info/entry_points.txt'
2026-04-05T13:10:28,656   adding 'pirlygenes-2.1.0.dist-info/top_level.txt'
2026-04-05T13:10:28,657   adding 'pirlygenes-2.1.0.dist-info/RECORD'
2026-04-05T13:10:28,660   removing build/bdist.linux-armv7l/wheel
2026-04-05T13:10:28,775   Building wheel for pirlygenes (pyproject.toml): finished with status 'done'
2026-04-05T13:10:28,782   Created wheel for pirlygenes: filename=pirlygenes-2.1.0-py3-none-any.whl size=91274 sha256=6e0978a40a4b6a16e6e44012574ac0838b0abf01a40770a2b4c8e7db2aa583a6
2026-04-05T13:10:28,783   Stored in directory: /tmp/pip-ephem-wheel-cache-vrbal8al/wheels/5a/68/32/f5d5fc27e78705918958f5faa48c64ba16a04ec9a0f4cab054
2026-04-05T13:10:28,797 Successfully built pirlygenes
2026-04-05T13:10:28,803 Removed build tracker: '/tmp/pip-build-tracker-3py8yzcp'