2025-06-07T05:22:59,657 Created temporary directory: /tmp/pip-build-tracker-v14bjnmo
2025-06-07T05:22:59,658 Initialized build tracking at /tmp/pip-build-tracker-v14bjnmo
2025-06-07T05:22:59,658 Created build tracker: /tmp/pip-build-tracker-v14bjnmo
2025-06-07T05:22:59,659 Entered build tracker: /tmp/pip-build-tracker-v14bjnmo
2025-06-07T05:22:59,660 Created temporary directory: /tmp/pip-wheel-yq5tzrwj
2025-06-07T05:22:59,664 Created temporary directory: /tmp/pip-ephem-wheel-cache-nabwx4mb
2025-06-07T05:22:59,713 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-06-07T05:22:59,716 2 location(s) to search for versions of clasv:
2025-06-07T05:22:59,716 * https://pypi.org/simple/clasv/
2025-06-07T05:22:59,716 * https://www.piwheels.org/simple/clasv/
2025-06-07T05:22:59,716 Fetching project page and analyzing links: https://pypi.org/simple/clasv/
2025-06-07T05:22:59,717 Getting page https://pypi.org/simple/clasv/
2025-06-07T05:22:59,719 Found index url https://pypi.org/simple/
2025-06-07T05:22:59,867 Fetched page https://pypi.org/simple/clasv/ as application/vnd.pypi.simple.v1+json
2025-06-07T05:22:59,870   Skipping link: No binaries permitted for clasv: https://files.pythonhosted.org/packages/1a/16/db344cddef30afa227564b37850859df2be84ad92983a4e623cc6d22e358/CLASV-0.1.14-py3-none-any.whl (from https://pypi.org/simple/clasv/) (requires-python:>=3.6)
2025-06-07T05:22:59,872   Found link https://files.pythonhosted.org/packages/1f/ea/a546746ef065df29e7d448b541720187f00fb3d6313c131edfce2458dcfb/clasv-0.1.14.tar.gz (from https://pypi.org/simple/clasv/) (requires-python:>=3.6), version: 0.1.14
2025-06-07T05:22:59,872   Skipping link: No binaries permitted for clasv: https://files.pythonhosted.org/packages/01/a7/fb8fe230851b0d19d0c9df27bb7b096c9c7b0d25d999999213f7fb663bea/CLASV-0.1.15-py3-none-any.whl (from https://pypi.org/simple/clasv/) (requires-python:>=3.6)
2025-06-07T05:22:59,873   Found link https://files.pythonhosted.org/packages/04/88/bb8ba072c5ce1e54697cb4049212cf1520972dadbdb0af3e65bd0caf6307/clasv-0.1.15.tar.gz (from https://pypi.org/simple/clasv/) (requires-python:>=3.6), version: 0.1.15
2025-06-07T05:22:59,873   Skipping link: No binaries permitted for clasv: https://files.pythonhosted.org/packages/2f/01/e66257efeac8ad400c86e8f5041ff0b77719174c6cbbb2910eb7e3f04a7e/CLASV-0.1.16-py3-none-any.whl (from https://pypi.org/simple/clasv/) (requires-python:>=3.6)
2025-06-07T05:22:59,874   Found link https://files.pythonhosted.org/packages/f3/ee/d74f763c762dc4eb56f3f4ac5e6fbde566c9d391e6156bfaabce4cc769ed/clasv-0.1.16.tar.gz (from https://pypi.org/simple/clasv/) (requires-python:>=3.6), version: 0.1.16
2025-06-07T05:22:59,874   Skipping link: No binaries permitted for clasv: https://files.pythonhosted.org/packages/d5/e2/e4c26b7e5bdb7b5cf384a243b22a93158d9636b0f9c13e7bf47121d889cf/clasv-1.0.0-py3-none-any.whl (from https://pypi.org/simple/clasv/) (requires-python:>=3.6)
2025-06-07T05:22:59,875   Found link https://files.pythonhosted.org/packages/25/01/75fa1aecd6564f60afab17af9d5847f73575d1c15c7ada4f4619a1b6c14c/clasv-1.0.0.tar.gz (from https://pypi.org/simple/clasv/) (requires-python:>=3.6), version: 1.0.0
2025-06-07T05:22:59,876   Skipping link: No binaries permitted for clasv: https://files.pythonhosted.org/packages/6f/01/71b5679f21f1605748c639f9e46ed4a65deac4073500ac0600e8371e44c3/clasv-1.0.1-py3-none-any.whl (from https://pypi.org/simple/clasv/) (requires-python:>=3.6)
2025-06-07T05:22:59,876   Found link https://files.pythonhosted.org/packages/8b/8a/0c047f0e3d0ddd5747387676aaa40d63c12b3bb76faddaf031d70ed7060d/clasv-1.0.1.tar.gz (from https://pypi.org/simple/clasv/) (requires-python:>=3.6), version: 1.0.1
2025-06-07T05:22:59,877   Skipping link: No binaries permitted for clasv: https://files.pythonhosted.org/packages/ae/db/d58479423cbcd8bfc12fd34b84f8e98911e6e5585b5be6e7ad9139295b29/clasv-1.0.2-py3-none-any.whl (from https://pypi.org/simple/clasv/) (requires-python:>=3.6)
2025-06-07T05:22:59,877   Found link https://files.pythonhosted.org/packages/d8/8b/fa027f178c8e86e464814497c55bb250f9e751d5281ae8d0f8b628c53c21/clasv-1.0.2.tar.gz (from https://pypi.org/simple/clasv/) (requires-python:>=3.6), version: 1.0.2
2025-06-07T05:22:59,878   Skipping link: No binaries permitted for clasv: https://files.pythonhosted.org/packages/eb/a5/b50674274289535cc79168e5ad0afb33d639d23381a8bc5d6e5e6d17a977/clasv-1.0.4-py3-none-any.whl (from https://pypi.org/simple/clasv/) (requires-python:<3.14,>=3.7)
2025-06-07T05:22:59,879   Found link https://files.pythonhosted.org/packages/d4/f4/4a24334f0238c96ad88300acf9f8f037ae20e612ee75d4c6efd241c10a2c/clasv-1.0.4.tar.gz (from https://pypi.org/simple/clasv/) (requires-python:<3.14,>=3.7), version: 1.0.4
2025-06-07T05:22:59,880   Skipping link: No binaries permitted for clasv: https://files.pythonhosted.org/packages/b4/ac/a546b70abb941263c6a1429ab67608fb4de2e84df444ef2c1c1ff430b98a/clasv-1.0.5-py3-none-any.whl (from https://pypi.org/simple/clasv/) (requires-python:<3.14,>=3.7)
2025-06-07T05:22:59,880   Found link https://files.pythonhosted.org/packages/de/b0/ce608a6857fc6753be849706d938c7252569ac46235997cb33b83cdcff18/clasv-1.0.5.tar.gz (from https://pypi.org/simple/clasv/) (requires-python:<3.14,>=3.7), version: 1.0.5
2025-06-07T05:22:59,881   Skipping link: No binaries permitted for clasv: https://files.pythonhosted.org/packages/a2/4b/20f591f8c5794b8aa5e7cb969237227e4d5f8a0fd3317eb24ec8d9846a25/clasv-1.0.6-py3-none-any.whl (from https://pypi.org/simple/clasv/) (requires-python:<3.14,>=3.7)
2025-06-07T05:22:59,881   Found link https://files.pythonhosted.org/packages/26/da/92a0b688197a1d762ced46693a7ec80d8de0d4406f04a083bac4176b452b/clasv-1.0.6.tar.gz (from https://pypi.org/simple/clasv/) (requires-python:<3.14,>=3.7), version: 1.0.6
2025-06-07T05:22:59,882 Fetching project page and analyzing links: https://www.piwheels.org/simple/clasv/
2025-06-07T05:22:59,883 Getting page https://www.piwheels.org/simple/clasv/
2025-06-07T05:22:59,884 Found index url https://www.piwheels.org/simple/
2025-06-07T05:23:00,040 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/clasv/
2025-06-07T05:23:00,691 WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/clasv/
2025-06-07T05:23:01,840 WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/clasv/
2025-06-07T05:23:04,058 WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/clasv/
2025-06-07T05:23:08,285 WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/clasv/
2025-06-07T05:23:08,500 Could not fetch URL https://www.piwheels.org/simple/clasv/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='www.piwheels.org', port=443): Max retries exceeded with url: /simple/clasv/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))) - skipping
2025-06-07T05:23:08,502 Skipping link: not a file: https://www.piwheels.org/simple/clasv/
2025-06-07T05:23:08,502 Skipping link: not a file: https://pypi.org/simple/clasv/
2025-06-07T05:23:08,521 Given no hashes to check 1 links for project 'clasv': discarding no candidates
2025-06-07T05:23:08,523 Collecting clasv==1.0.1
2025-06-07T05:23:08,526   Created temporary directory: /tmp/pip-unpack-tmw91oeg
2025-06-07T05:23:08,750   Downloading clasv-1.0.1.tar.gz (2.5 MB)
2025-06-07T05:23:09,689   Added clasv==1.0.1 from https://files.pythonhosted.org/packages/8b/8a/0c047f0e3d0ddd5747387676aaa40d63c12b3bb76faddaf031d70ed7060d/clasv-1.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-v14bjnmo'
2025-06-07T05:23:09,691   Running setup.py (path:/tmp/pip-wheel-yq5tzrwj/clasv_3e81894ad09946e9b3bae4b2384c2b1f/setup.py) egg_info for package clasv
2025-06-07T05:23:09,692   Created temporary directory: /tmp/pip-pip-egg-info-ex2f1rcd
2025-06-07T05:23:09,693   Preparing metadata (setup.py): started
2025-06-07T05:23:09,694   Running command python setup.py egg_info
2025-06-07T05:23:10,557   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-07T05:23:10,558   !!

2025-06-07T05:23:10,559           ********************************************************************************
2025-06-07T05:23:10,559           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-07T05:23:10,560           License :: OSI Approved :: MIT License

2025-06-07T05:23:10,561           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-07T05:23:10,562           ********************************************************************************

2025-06-07T05:23:10,563   !!
2025-06-07T05:23:10,563     self._finalize_license_expression()
2025-06-07T05:23:10,587   Running setup...
2025-06-07T05:23:10,587   running egg_info
2025-06-07T05:23:10,614   creating /tmp/pip-pip-egg-info-ex2f1rcd/CLASV.egg-info
2025-06-07T05:23:10,615   writing /tmp/pip-pip-egg-info-ex2f1rcd/CLASV.egg-info/PKG-INFO
2025-06-07T05:23:10,620   writing dependency_links to /tmp/pip-pip-egg-info-ex2f1rcd/CLASV.egg-info/dependency_links.txt
2025-06-07T05:23:10,621   writing entry points to /tmp/pip-pip-egg-info-ex2f1rcd/CLASV.egg-info/entry_points.txt
2025-06-07T05:23:10,624   writing requirements to /tmp/pip-pip-egg-info-ex2f1rcd/CLASV.egg-info/requires.txt
2025-06-07T05:23:10,625   writing top-level names to /tmp/pip-pip-egg-info-ex2f1rcd/CLASV.egg-info/top_level.txt
2025-06-07T05:23:10,626   writing manifest file '/tmp/pip-pip-egg-info-ex2f1rcd/CLASV.egg-info/SOURCES.txt'
2025-06-07T05:23:10,715   reading manifest file '/tmp/pip-pip-egg-info-ex2f1rcd/CLASV.egg-info/SOURCES.txt'
2025-06-07T05:23:10,717   reading manifest template 'MANIFEST.in'
2025-06-07T05:23:10,761   warning: no files found matching '*.png' under directory 'CLASV'
2025-06-07T05:23:10,770   warning: no files found matching 'config' under directory 'CLASV'
2025-06-07T05:23:10,793   warning: no files found matching 'predictions' under directory 'CLASV'
2025-06-07T05:23:10,816   warning: no files found matching 'raw_data' under directory 'CLASV'
2025-06-07T05:23:10,839   warning: no files found matching 'results' under directory 'CLASV'
2025-06-07T05:23:10,861   warning: no files found matching 'visuals' under directory 'CLASV'
2025-06-07T05:23:10,875   adding license file 'LICENSE'
2025-06-07T05:23:10,881   writing manifest file '/tmp/pip-pip-egg-info-ex2f1rcd/CLASV.egg-info/SOURCES.txt'
2025-06-07T05:23:10,987   Preparing metadata (setup.py): finished with status 'done'
2025-06-07T05:23:10,993   Source in /tmp/pip-wheel-yq5tzrwj/clasv_3e81894ad09946e9b3bae4b2384c2b1f has version 1.0.1, which satisfies requirement clasv==1.0.1 from https://files.pythonhosted.org/packages/8b/8a/0c047f0e3d0ddd5747387676aaa40d63c12b3bb76faddaf031d70ed7060d/clasv-1.0.1.tar.gz
2025-06-07T05:23:10,994   Removed clasv==1.0.1 from https://files.pythonhosted.org/packages/8b/8a/0c047f0e3d0ddd5747387676aaa40d63c12b3bb76faddaf031d70ed7060d/clasv-1.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-v14bjnmo'
2025-06-07T05:23:11,019 Created temporary directory: /tmp/pip-unpack-5__m9mgo
2025-06-07T05:23:11,020 Created temporary directory: /tmp/pip-unpack-04ifd7sm
2025-06-07T05:23:11,021 Building wheels for collected packages: clasv
2025-06-07T05:23:11,026   Created temporary directory: /tmp/pip-wheel-6i3snoe1
2025-06-07T05:23:11,027   DEPRECATION: Building 'clasv' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'clasv'. Discussion can be found at https://github.com/pypa/pip/issues/6334
2025-06-07T05:23:11,028   Building wheel for clasv (setup.py): started
2025-06-07T05:23:11,029   Destination directory: /tmp/pip-wheel-6i3snoe1
2025-06-07T05:23:11,030   Running command python setup.py bdist_wheel
2025-06-07T05:23:11,520   Running setup...
2025-06-07T05:23:11,888   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-07T05:23:11,889   !!

2025-06-07T05:23:11,890           ********************************************************************************
2025-06-07T05:23:11,890           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-07T05:23:11,891           License :: OSI Approved :: MIT License

2025-06-07T05:23:11,892           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-07T05:23:11,892           ********************************************************************************

2025-06-07T05:23:11,893   !!
2025-06-07T05:23:11,894     self._finalize_license_expression()
2025-06-07T05:23:11,894   running bdist_wheel
2025-06-07T05:23:12,035   running build
2025-06-07T05:23:12,035   running build_py
2025-06-07T05:23:12,066   creating build/lib/CLASV
2025-06-07T05:23:12,069   copying CLASV/core.py -> build/lib/CLASV
2025-06-07T05:23:12,071   copying CLASV/setup.py -> build/lib/CLASV
2025-06-07T05:23:12,073   copying CLASV/benchmark_clasv.py -> build/lib/CLASV
2025-06-07T05:23:12,075   copying CLASV/cli.py -> build/lib/CLASV
2025-06-07T05:23:12,077   copying CLASV/install_seqkit.py -> build/lib/CLASV
2025-06-07T05:23:12,080   copying CLASV/__init__.py -> build/lib/CLASV
2025-06-07T05:23:12,082   copying CLASV/install_nextclade.py -> build/lib/CLASV
2025-06-07T05:23:12,084   copying CLASV/pipeline.py -> build/lib/CLASV
2025-06-07T05:23:12,086   creating build/lib/CLASV/tools
2025-06-07T05:23:12,087   copying CLASV/tools/benchmark_clasv.py -> build/lib/CLASV/tools
2025-06-07T05:23:12,090   copying CLASV/tools/__init__.py -> build/lib/CLASV/tools
2025-06-07T05:23:12,092   running egg_info
2025-06-07T05:23:12,119   writing CLASV.egg-info/PKG-INFO
2025-06-07T05:23:12,124   writing dependency_links to CLASV.egg-info/dependency_links.txt
2025-06-07T05:23:12,125   writing entry points to CLASV.egg-info/entry_points.txt
2025-06-07T05:23:12,128   writing requirements to CLASV.egg-info/requires.txt
2025-06-07T05:23:12,129   writing top-level names to CLASV.egg-info/top_level.txt
2025-06-07T05:23:12,163   reading manifest file 'CLASV.egg-info/SOURCES.txt'
2025-06-07T05:23:12,167   reading manifest template 'MANIFEST.in'
2025-06-07T05:23:12,209   warning: no files found matching '*.png' under directory 'CLASV'
2025-06-07T05:23:12,217   warning: no files found matching 'config' under directory 'CLASV'
2025-06-07T05:23:12,240   warning: no files found matching 'predictions' under directory 'CLASV'
2025-06-07T05:23:12,262   warning: no files found matching 'raw_data' under directory 'CLASV'
2025-06-07T05:23:12,285   warning: no files found matching 'results' under directory 'CLASV'
2025-06-07T05:23:12,308   warning: no files found matching 'visuals' under directory 'CLASV'
2025-06-07T05:23:12,324   adding license file 'LICENSE'
2025-06-07T05:23:12,330   writing manifest file 'CLASV.egg-info/SOURCES.txt'
2025-06-07T05:23:12,332   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'CLASV.__pycache__' is absent from the `packages` configuration.
2025-06-07T05:23:12,333   !!

2025-06-07T05:23:12,334           ********************************************************************************
2025-06-07T05:23:12,335           ############################
2025-06-07T05:23:12,335           # Package would be ignored #
2025-06-07T05:23:12,336           ############################
2025-06-07T05:23:12,336           Python recognizes 'CLASV.__pycache__' as an importable package[^1],
2025-06-07T05:23:12,337           but it is absent from setuptools' `packages` configuration.

2025-06-07T05:23:12,337           This leads to an ambiguous overall configuration. If you want to distribute this
2025-06-07T05:23:12,338           package, please make sure that 'CLASV.__pycache__' is explicitly added
2025-06-07T05:23:12,338           to the `packages` configuration field.

2025-06-07T05:23:12,339           Alternatively, you can also rely on setuptools' discovery methods
2025-06-07T05:23:12,340           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-06-07T05:23:12,340           instead of `find_packages(...)`/`find:`).

2025-06-07T05:23:12,341           You can read more about "package discovery" on setuptools documentation page:

2025-06-07T05:23:12,342           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-06-07T05:23:12,343           If you don't want 'CLASV.__pycache__' to be distributed and are
2025-06-07T05:23:12,343           already explicitly excluding 'CLASV.__pycache__' via
2025-06-07T05:23:12,344           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-06-07T05:23:12,344           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-06-07T05:23:12,345           combination with a more fine grained `package-data` configuration.

2025-06-07T05:23:12,346           You can read more about "package data files" on setuptools documentation page:

2025-06-07T05:23:12,347           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-06-07T05:23:12,349           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-06-07T05:23:12,349                 even if it does not contain any `.py` files.
2025-06-07T05:23:12,350                 On the other hand, currently there is no concept of package data
2025-06-07T05:23:12,350                 directory, all directories are treated like packages.
2025-06-07T05:23:12,351           ********************************************************************************

2025-06-07T05:23:12,352   !!
2025-06-07T05:23:12,352     check.warn(importable)
2025-06-07T05:23:12,353   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'CLASV.config' is absent from the `packages` configuration.
2025-06-07T05:23:12,353   !!

2025-06-07T05:23:12,354           ********************************************************************************
2025-06-07T05:23:12,355           ############################
2025-06-07T05:23:12,355           # Package would be ignored #
2025-06-07T05:23:12,356           ############################
2025-06-07T05:23:12,356           Python recognizes 'CLASV.config' as an importable package[^1],
2025-06-07T05:23:12,357           but it is absent from setuptools' `packages` configuration.

2025-06-07T05:23:12,358           This leads to an ambiguous overall configuration. If you want to distribute this
2025-06-07T05:23:12,358           package, please make sure that 'CLASV.config' is explicitly added
2025-06-07T05:23:12,359           to the `packages` configuration field.

2025-06-07T05:23:12,360           Alternatively, you can also rely on setuptools' discovery methods
2025-06-07T05:23:12,360           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-06-07T05:23:12,361           instead of `find_packages(...)`/`find:`).

2025-06-07T05:23:12,362           You can read more about "package discovery" on setuptools documentation page:

2025-06-07T05:23:12,363           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-06-07T05:23:12,364           If you don't want 'CLASV.config' to be distributed and are
2025-06-07T05:23:12,365           already explicitly excluding 'CLASV.config' via
2025-06-07T05:23:12,365           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-06-07T05:23:12,365           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-06-07T05:23:12,366           combination with a more fine grained `package-data` configuration.

2025-06-07T05:23:12,367           You can read more about "package data files" on setuptools documentation page:

2025-06-07T05:23:12,368           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-06-07T05:23:12,369           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-06-07T05:23:12,370                 even if it does not contain any `.py` files.
2025-06-07T05:23:12,370                 On the other hand, currently there is no concept of package data
2025-06-07T05:23:12,371                 directory, all directories are treated like packages.
2025-06-07T05:23:12,371           ********************************************************************************

2025-06-07T05:23:12,372   !!
2025-06-07T05:23:12,373     check.warn(importable)
2025-06-07T05:23:12,373   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'CLASV.raw_data' is absent from the `packages` configuration.
2025-06-07T05:23:12,374   !!

2025-06-07T05:23:12,375           ********************************************************************************
2025-06-07T05:23:12,375           ############################
2025-06-07T05:23:12,376           # Package would be ignored #
2025-06-07T05:23:12,376           ############################
2025-06-07T05:23:12,377           Python recognizes 'CLASV.raw_data' as an importable package[^1],
2025-06-07T05:23:12,377           but it is absent from setuptools' `packages` configuration.

2025-06-07T05:23:12,378           This leads to an ambiguous overall configuration. If you want to distribute this
2025-06-07T05:23:12,379           package, please make sure that 'CLASV.raw_data' is explicitly added
2025-06-07T05:23:12,379           to the `packages` configuration field.

2025-06-07T05:23:12,380           Alternatively, you can also rely on setuptools' discovery methods
2025-06-07T05:23:12,380           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-06-07T05:23:12,381           instead of `find_packages(...)`/`find:`).

2025-06-07T05:23:12,382           You can read more about "package discovery" on setuptools documentation page:

2025-06-07T05:23:12,383           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-06-07T05:23:12,384           If you don't want 'CLASV.raw_data' to be distributed and are
2025-06-07T05:23:12,384           already explicitly excluding 'CLASV.raw_data' via
2025-06-07T05:23:12,385           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-06-07T05:23:12,385           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-06-07T05:23:12,386           combination with a more fine grained `package-data` configuration.

2025-06-07T05:23:12,387           You can read more about "package data files" on setuptools documentation page:

2025-06-07T05:23:12,388           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-06-07T05:23:12,390           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-06-07T05:23:12,390                 even if it does not contain any `.py` files.
2025-06-07T05:23:12,391                 On the other hand, currently there is no concept of package data
2025-06-07T05:23:12,391                 directory, all directories are treated like packages.
2025-06-07T05:23:12,392           ********************************************************************************

2025-06-07T05:23:12,393   !!
2025-06-07T05:23:12,393     check.warn(importable)
2025-06-07T05:23:12,394   copying CLASV/MANIFEST.in -> build/lib/CLASV
2025-06-07T05:23:12,394   copying CLASV/README.md -> build/lib/CLASV
2025-06-07T05:23:12,394   copying CLASV/VERSION -> build/lib/CLASV
2025-06-07T05:23:12,395   copying CLASV/predict_lineage.smk -> build/lib/CLASV
2025-06-07T05:23:12,395   copying CLASV/requirements.txt -> build/lib/CLASV
2025-06-07T05:23:12,396   creating build/lib/CLASV/__pycache__
2025-06-07T05:23:12,396   copying CLASV/__pycache__/__init__.cpython-310.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:23:12,397   copying CLASV/__pycache__/__init__.cpython-311.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:23:12,397   copying CLASV/__pycache__/cli.cpython-310.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:23:12,398   copying CLASV/__pycache__/cli.cpython-311.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:23:12,398   copying CLASV/__pycache__/core.cpython-311.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:23:12,398   copying CLASV/__pycache__/install_nextclade.cpython-310.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:23:12,399   copying CLASV/__pycache__/install_nextclade.cpython-311.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:23:12,399   copying CLASV/__pycache__/install_seqkit.cpython-310.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:23:12,400   copying CLASV/__pycache__/install_seqkit.cpython-311.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:23:12,400   copying CLASV/__pycache__/pipeline.cpython-310.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:23:12,401   copying CLASV/__pycache__/pipeline.cpython-311.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:23:12,401   creating build/lib/CLASV/config
2025-06-07T05:23:12,402   copying CLASV/config/NC_004296.fasta -> build/lib/CLASV/config
2025-06-07T05:23:12,402   copying CLASV/config/RF_LASV_lineage_n500_aa.joblib -> build/lib/CLASV/config
2025-06-07T05:23:12,462   copying CLASV/config/config.yaml -> build/lib/CLASV/config
2025-06-07T05:23:12,465   copying CLASV/config/configs.yaml -> build/lib/CLASV/config
2025-06-07T05:23:12,467   creating build/lib/CLASV/raw_data
2025-06-07T05:23:12,468   copying CLASV/raw_data/Adesina_et_al_2023_EMI.csv -> build/lib/CLASV/raw_data
2025-06-07T05:23:12,473   copying CLASV/raw_data/Adesina_et_al_2023_EMI.fasta -> build/lib/CLASV/raw_data
2025-06-07T05:23:12,479   copying CLASV/raw_data/All_LASV_06_07_24.csv -> build/lib/CLASV/raw_data
2025-06-07T05:23:12,503   copying CLASV/raw_data/All_LASV_06_07_24.fasta -> build/lib/CLASV/raw_data
2025-06-07T05:23:12,643   copying CLASV/raw_data/Bangura_et_al_2024_EMI.csv -> build/lib/CLASV/raw_data
2025-06-07T05:23:12,646   copying CLASV/raw_data/Bangura_et_al_2024_EMI.fasta -> build/lib/CLASV/raw_data
2025-06-07T05:23:12,652   copying CLASV/tools/README-benchmark.md -> build/lib/CLASV/tools
2025-06-07T05:23:12,656   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-06-07T05:23:12,657   !!

2025-06-07T05:23:12,658           ********************************************************************************
2025-06-07T05:23:12,658           Please avoid running ``setup.py`` directly.
2025-06-07T05:23:12,659           Instead, use pypa/build, pypa/installer or other
2025-06-07T05:23:12,659           standards-based tools.

2025-06-07T05:23:12,660           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-06-07T05:23:12,661           or your builds will no longer be supported.

2025-06-07T05:23:12,662           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-06-07T05:23:12,662           ********************************************************************************

2025-06-07T05:23:12,663   !!
2025-06-07T05:23:12,664     self.initialize_options()
2025-06-07T05:23:12,687   installing to build/bdist.linux-armv7l/wheel
2025-06-07T05:23:12,688   running install
2025-06-07T05:23:12,712   running install_lib
2025-06-07T05:23:12,738   creating build/bdist.linux-armv7l/wheel
2025-06-07T05:23:12,741   creating build/bdist.linux-armv7l/wheel/CLASV
2025-06-07T05:23:12,742   copying build/lib/CLASV/core.py -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:23:12,745   creating build/bdist.linux-armv7l/wheel/CLASV/config
2025-06-07T05:23:12,746   copying build/lib/CLASV/config/NC_004296.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/config
2025-06-07T05:23:12,748   copying build/lib/CLASV/config/config.yaml -> build/bdist.linux-armv7l/wheel/./CLASV/config
2025-06-07T05:23:12,750   copying build/lib/CLASV/config/RF_LASV_lineage_n500_aa.joblib -> build/bdist.linux-armv7l/wheel/./CLASV/config
2025-06-07T05:23:12,815   copying build/lib/CLASV/config/configs.yaml -> build/bdist.linux-armv7l/wheel/./CLASV/config
2025-06-07T05:23:12,817   copying build/lib/CLASV/VERSION -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:23:12,819   creating build/bdist.linux-armv7l/wheel/CLASV/tools
2025-06-07T05:23:12,820   copying build/lib/CLASV/tools/README-benchmark.md -> build/bdist.linux-armv7l/wheel/./CLASV/tools
2025-06-07T05:23:12,822   copying build/lib/CLASV/tools/benchmark_clasv.py -> build/bdist.linux-armv7l/wheel/./CLASV/tools
2025-06-07T05:23:12,824   copying build/lib/CLASV/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./CLASV/tools
2025-06-07T05:23:12,826   copying build/lib/CLASV/requirements.txt -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:23:12,828   copying build/lib/CLASV/setup.py -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:23:12,830   copying build/lib/CLASV/benchmark_clasv.py -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:23:12,832   copying build/lib/CLASV/cli.py -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:23:12,834   copying build/lib/CLASV/README.md -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:23:12,836   copying build/lib/CLASV/install_seqkit.py -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:23:12,838   copying build/lib/CLASV/__init__.py -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:23:12,840   creating build/bdist.linux-armv7l/wheel/CLASV/__pycache__
2025-06-07T05:23:12,841   copying build/lib/CLASV/__pycache__/__init__.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:23:12,843   copying build/lib/CLASV/__pycache__/pipeline.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:23:12,846   copying build/lib/CLASV/__pycache__/install_nextclade.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:23:12,848   copying build/lib/CLASV/__pycache__/__init__.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:23:12,850   copying build/lib/CLASV/__pycache__/core.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:23:12,852   copying build/lib/CLASV/__pycache__/install_nextclade.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:23:12,854   copying build/lib/CLASV/__pycache__/install_seqkit.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:23:12,856   copying build/lib/CLASV/__pycache__/cli.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:23:12,858   copying build/lib/CLASV/__pycache__/pipeline.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:23:12,860   copying build/lib/CLASV/__pycache__/cli.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:23:12,862   copying build/lib/CLASV/__pycache__/install_seqkit.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:23:12,864   copying build/lib/CLASV/MANIFEST.in -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:23:12,866   copying build/lib/CLASV/install_nextclade.py -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:23:12,868   copying build/lib/CLASV/predict_lineage.smk -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:23:12,871   creating build/bdist.linux-armv7l/wheel/CLASV/raw_data
2025-06-07T05:23:12,872   copying build/lib/CLASV/raw_data/Adesina_et_al_2023_EMI.csv -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data
2025-06-07T05:23:12,875   copying build/lib/CLASV/raw_data/Bangura_et_al_2024_EMI.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data
2025-06-07T05:23:12,880   copying build/lib/CLASV/raw_data/Adesina_et_al_2023_EMI.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data
2025-06-07T05:23:12,885   copying build/lib/CLASV/raw_data/Bangura_et_al_2024_EMI.csv -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data
2025-06-07T05:23:12,888   copying build/lib/CLASV/raw_data/All_LASV_06_07_24.csv -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data
2025-06-07T05:23:12,910   copying build/lib/CLASV/raw_data/All_LASV_06_07_24.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data
2025-06-07T05:23:13,053   copying build/lib/CLASV/pipeline.py -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:23:13,055   running install_egg_info
2025-06-07T05:23:13,090   Copying CLASV.egg-info to build/bdist.linux-armv7l/wheel/./CLASV-1.0.1-py3.11.egg-info
2025-06-07T05:23:13,102   running install_scripts
2025-06-07T05:23:13,103   Installing Nextclade...
2025-06-07T05:23:13,105   Failed to install Nextclade: [Errno 2] No such file or directory: 'python'
2025-06-07T05:23:13,105   Installing Seqkit...
2025-06-07T05:23:13,106   Failed to install Seqkit: [Errno 2] No such file or directory: 'python'
2025-06-07T05:23:13,119   creating build/bdist.linux-armv7l/wheel/clasv-1.0.1.dist-info/WHEEL
2025-06-07T05:23:13,122   creating '/tmp/pip-wheel-6i3snoe1/clasv-1.0.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-06-07T05:23:13,125   adding 'CLASV/MANIFEST.in'
2025-06-07T05:23:13,127   adding 'CLASV/README.md'
2025-06-07T05:23:13,129   adding 'CLASV/VERSION'
2025-06-07T05:23:13,130   adding 'CLASV/__init__.py'
2025-06-07T05:23:13,131   adding 'CLASV/benchmark_clasv.py'
2025-06-07T05:23:13,133   adding 'CLASV/cli.py'
2025-06-07T05:23:13,135   adding 'CLASV/core.py'
2025-06-07T05:23:13,136   adding 'CLASV/install_nextclade.py'
2025-06-07T05:23:13,138   adding 'CLASV/install_seqkit.py'
2025-06-07T05:23:13,139   adding 'CLASV/pipeline.py'
2025-06-07T05:23:13,141   adding 'CLASV/predict_lineage.smk'
2025-06-07T05:23:13,142   adding 'CLASV/requirements.txt'
2025-06-07T05:23:13,144   adding 'CLASV/setup.py'
2025-06-07T05:23:13,146   adding 'CLASV/__pycache__/__init__.cpython-310.pyc'
2025-06-07T05:23:13,147   adding 'CLASV/__pycache__/__init__.cpython-311.pyc'
2025-06-07T05:23:13,148   adding 'CLASV/__pycache__/cli.cpython-310.pyc'
2025-06-07T05:23:13,150   adding 'CLASV/__pycache__/cli.cpython-311.pyc'
2025-06-07T05:23:13,152   adding 'CLASV/__pycache__/core.cpython-311.pyc'
2025-06-07T05:23:13,154   adding 'CLASV/__pycache__/install_nextclade.cpython-310.pyc'
2025-06-07T05:23:13,156   adding 'CLASV/__pycache__/install_nextclade.cpython-311.pyc'
2025-06-07T05:23:13,157   adding 'CLASV/__pycache__/install_seqkit.cpython-310.pyc'
2025-06-07T05:23:13,159   adding 'CLASV/__pycache__/install_seqkit.cpython-311.pyc'
2025-06-07T05:23:13,161   adding 'CLASV/__pycache__/pipeline.cpython-310.pyc'
2025-06-07T05:23:13,162   adding 'CLASV/__pycache__/pipeline.cpython-311.pyc'
2025-06-07T05:23:13,164   adding 'CLASV/config/NC_004296.fasta'
2025-06-07T05:23:13,452   adding 'CLASV/config/RF_LASV_lineage_n500_aa.joblib'
2025-06-07T05:23:13,481   adding 'CLASV/config/config.yaml'
2025-06-07T05:23:13,482   adding 'CLASV/config/configs.yaml'
2025-06-07T05:23:13,486   adding 'CLASV/raw_data/Adesina_et_al_2023_EMI.csv'
2025-06-07T05:23:13,496   adding 'CLASV/raw_data/Adesina_et_al_2023_EMI.fasta'
2025-06-07T05:23:13,540   adding 'CLASV/raw_data/All_LASV_06_07_24.csv'
2025-06-07T05:23:16,949   adding 'CLASV/raw_data/All_LASV_06_07_24.fasta'
2025-06-07T05:23:17,010   adding 'CLASV/raw_data/Bangura_et_al_2024_EMI.csv'
2025-06-07T05:23:17,071   adding 'CLASV/raw_data/Bangura_et_al_2024_EMI.fasta'
2025-06-07T05:23:17,074   adding 'CLASV/tools/README-benchmark.md'
2025-06-07T05:23:17,075   adding 'CLASV/tools/__init__.py'
2025-06-07T05:23:17,078   adding 'CLASV/tools/benchmark_clasv.py'
2025-06-07T05:23:17,081   adding 'clasv-1.0.1.dist-info/licenses/LICENSE'
2025-06-07T05:23:17,082   adding 'clasv-1.0.1.dist-info/METADATA'
2025-06-07T05:23:17,083   adding 'clasv-1.0.1.dist-info/WHEEL'
2025-06-07T05:23:17,084   adding 'clasv-1.0.1.dist-info/entry_points.txt'
2025-06-07T05:23:17,085   adding 'clasv-1.0.1.dist-info/top_level.txt'
2025-06-07T05:23:17,086   adding 'clasv-1.0.1.dist-info/RECORD'
2025-06-07T05:23:17,123   removing build/bdist.linux-armv7l/wheel
2025-06-07T05:23:17,250   Building wheel for clasv (setup.py): finished with status 'done'
2025-06-07T05:23:17,283   Created wheel for clasv: filename=clasv-1.0.1-py3-none-any.whl size=3063291 sha256=e9390e4b39429a31e3b2ee578bb0e1342144a82b447a3601b3e16b3e7bf89380
2025-06-07T05:23:17,285   Stored in directory: /tmp/pip-ephem-wheel-cache-nabwx4mb/wheels/3a/7a/a4/6fbef3841b082b17f6ee10ec1c335ce1b727445f0f3e7aebdf
2025-06-07T05:23:17,300 Successfully built clasv
2025-06-07T05:23:17,376 Removed build tracker: '/tmp/pip-build-tracker-v14bjnmo'