2025-06-07T05:20:32,498 Created temporary directory: /tmp/pip-build-tracker-zrzx6sri
2025-06-07T05:20:32,500 Initialized build tracking at /tmp/pip-build-tracker-zrzx6sri
2025-06-07T05:20:32,500 Created build tracker: /tmp/pip-build-tracker-zrzx6sri
2025-06-07T05:20:32,501 Entered build tracker: /tmp/pip-build-tracker-zrzx6sri
2025-06-07T05:20:32,502 Created temporary directory: /tmp/pip-wheel-cr734v_o
2025-06-07T05:20:32,507 Created temporary directory: /tmp/pip-ephem-wheel-cache-8_mkpyfv
2025-06-07T05:20:32,558 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-06-07T05:20:32,560 2 location(s) to search for versions of clasv:
2025-06-07T05:20:32,560 * https://pypi.org/simple/clasv/
2025-06-07T05:20:32,560 * https://www.piwheels.org/simple/clasv/
2025-06-07T05:20:32,561 Fetching project page and analyzing links: https://pypi.org/simple/clasv/
2025-06-07T05:20:32,562 Getting page https://pypi.org/simple/clasv/
2025-06-07T05:20:32,563 Found index url https://pypi.org/simple/
2025-06-07T05:20:32,789 Fetched page https://pypi.org/simple/clasv/ as application/vnd.pypi.simple.v1+json
2025-06-07T05:20:32,796   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)
2025-06-07T05:20:32,798   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
2025-06-07T05:20:32,799   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)
2025-06-07T05:20:32,800   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
2025-06-07T05:20:32,801   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)
2025-06-07T05:20:32,802   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
2025-06-07T05:20:32,802   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)
2025-06-07T05:20:32,803   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
2025-06-07T05:20:32,804   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)
2025-06-07T05:20:32,805   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
2025-06-07T05:20:32,805   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)
2025-06-07T05:20:32,806   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
2025-06-07T05:20:32,807   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)
2025-06-07T05:20:32,809   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
2025-06-07T05:20:32,809   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)
2025-06-07T05:20:32,810   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
2025-06-07T05:20:32,811   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)
2025-06-07T05:20:32,811   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
2025-06-07T05:20:32,812 Fetching project page and analyzing links: https://www.piwheels.org/simple/clasv/
2025-06-07T05:20:32,813 Getting page https://www.piwheels.org/simple/clasv/
2025-06-07T05:20:32,814 Found index url https://www.piwheels.org/simple/
2025-06-07T05:20:32,974 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/
2025-06-07T05:20:33,641 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/
2025-06-07T05:20:34,833 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/
2025-06-07T05:20:37,013 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/
2025-06-07T05:20:41,195 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/
2025-06-07T05:20:41,371 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
2025-06-07T05:20:41,372 Skipping link: not a file: https://www.piwheels.org/simple/clasv/
2025-06-07T05:20:41,373 Skipping link: not a file: https://pypi.org/simple/clasv/
2025-06-07T05:20:41,394 Given no hashes to check 1 links for project 'clasv': discarding no candidates
2025-06-07T05:20:41,396 Collecting clasv==1.0.0
2025-06-07T05:20:41,399   Created temporary directory: /tmp/pip-unpack-h1vens6t
2025-06-07T05:20:41,632   Downloading clasv-1.0.0.tar.gz (2.5 MB)
2025-06-07T05:20:42,574   Added clasv==1.0.0 from https://files.pythonhosted.org/packages/25/01/75fa1aecd6564f60afab17af9d5847f73575d1c15c7ada4f4619a1b6c14c/clasv-1.0.0.tar.gz to build tracker '/tmp/pip-build-tracker-zrzx6sri'
2025-06-07T05:20:42,577   Running setup.py (path:/tmp/pip-wheel-cr734v_o/clasv_6b0e0f1b8dd343bdb188b2dfe4d84e0e/setup.py) egg_info for package clasv
2025-06-07T05:20:42,578   Created temporary directory: /tmp/pip-pip-egg-info-zhv3ajv9
2025-06-07T05:20:42,579   Preparing metadata (setup.py): started
2025-06-07T05:20:42,580   Running command python setup.py egg_info
2025-06-07T05:20:43,496   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-07T05:20:43,496   !!

2025-06-07T05:20:43,497           ********************************************************************************
2025-06-07T05:20:43,498           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-07T05:20:43,499           License :: OSI Approved :: MIT License

2025-06-07T05:20:43,500           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-07T05:20:43,500           ********************************************************************************

2025-06-07T05:20:43,501   !!
2025-06-07T05:20:43,501     self._finalize_license_expression()
2025-06-07T05:20:43,526   Running setup...
2025-06-07T05:20:43,527   running egg_info
2025-06-07T05:20:43,556   creating /tmp/pip-pip-egg-info-zhv3ajv9/CLASV.egg-info
2025-06-07T05:20:43,557   writing /tmp/pip-pip-egg-info-zhv3ajv9/CLASV.egg-info/PKG-INFO
2025-06-07T05:20:43,562   writing dependency_links to /tmp/pip-pip-egg-info-zhv3ajv9/CLASV.egg-info/dependency_links.txt
2025-06-07T05:20:43,564   writing entry points to /tmp/pip-pip-egg-info-zhv3ajv9/CLASV.egg-info/entry_points.txt
2025-06-07T05:20:43,567   writing requirements to /tmp/pip-pip-egg-info-zhv3ajv9/CLASV.egg-info/requires.txt
2025-06-07T05:20:43,568   writing top-level names to /tmp/pip-pip-egg-info-zhv3ajv9/CLASV.egg-info/top_level.txt
2025-06-07T05:20:43,569   writing manifest file '/tmp/pip-pip-egg-info-zhv3ajv9/CLASV.egg-info/SOURCES.txt'
2025-06-07T05:20:43,668   reading manifest file '/tmp/pip-pip-egg-info-zhv3ajv9/CLASV.egg-info/SOURCES.txt'
2025-06-07T05:20:43,670   reading manifest template 'MANIFEST.in'
2025-06-07T05:20:43,741   warning: no files found matching '*.png' under directory 'CLASV'
2025-06-07T05:20:43,756   warning: no files found matching 'config' under directory 'CLASV'
2025-06-07T05:20:43,802   warning: no files found matching 'predictions' under directory 'CLASV'
2025-06-07T05:20:43,838   warning: no files found matching 'raw_data' under directory 'CLASV'
2025-06-07T05:20:43,884   warning: no files found matching 'results' under directory 'CLASV'
2025-06-07T05:20:43,932   warning: no files found matching 'visuals' under directory 'CLASV'
2025-06-07T05:20:43,962   adding license file 'LICENSE'
2025-06-07T05:20:43,971   writing manifest file '/tmp/pip-pip-egg-info-zhv3ajv9/CLASV.egg-info/SOURCES.txt'
2025-06-07T05:20:44,082   Preparing metadata (setup.py): finished with status 'done'
2025-06-07T05:20:44,088   Source in /tmp/pip-wheel-cr734v_o/clasv_6b0e0f1b8dd343bdb188b2dfe4d84e0e has version 1.0.0, which satisfies requirement clasv==1.0.0 from https://files.pythonhosted.org/packages/25/01/75fa1aecd6564f60afab17af9d5847f73575d1c15c7ada4f4619a1b6c14c/clasv-1.0.0.tar.gz
2025-06-07T05:20:44,089   Removed clasv==1.0.0 from https://files.pythonhosted.org/packages/25/01/75fa1aecd6564f60afab17af9d5847f73575d1c15c7ada4f4619a1b6c14c/clasv-1.0.0.tar.gz from build tracker '/tmp/pip-build-tracker-zrzx6sri'
2025-06-07T05:20:44,114 Created temporary directory: /tmp/pip-unpack-pvjdzrof
2025-06-07T05:20:44,116 Created temporary directory: /tmp/pip-unpack-r11k27rt
2025-06-07T05:20:44,116 Building wheels for collected packages: clasv
2025-06-07T05:20:44,121   Created temporary directory: /tmp/pip-wheel-wgtjehx4
2025-06-07T05:20:44,122   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
2025-06-07T05:20:44,123   Building wheel for clasv (setup.py): started
2025-06-07T05:20:44,124   Destination directory: /tmp/pip-wheel-wgtjehx4
2025-06-07T05:20:44,124   Running command python setup.py bdist_wheel
2025-06-07T05:20:44,599   Running setup...
2025-06-07T05:20:44,979   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-07T05:20:44,980   !!

2025-06-07T05:20:44,981           ********************************************************************************
2025-06-07T05:20:44,981           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-07T05:20:44,982           License :: OSI Approved :: MIT License

2025-06-07T05:20:44,983           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-07T05:20:44,983           ********************************************************************************

2025-06-07T05:20:44,984   !!
2025-06-07T05:20:44,985     self._finalize_license_expression()
2025-06-07T05:20:44,986   running bdist_wheel
2025-06-07T05:20:45,118   running build
2025-06-07T05:20:45,118   running build_py
2025-06-07T05:20:45,150   creating build/lib/CLASV
2025-06-07T05:20:45,152   copying CLASV/__init__.py -> build/lib/CLASV
2025-06-07T05:20:45,154   copying CLASV/install_seqkit.py -> build/lib/CLASV
2025-06-07T05:20:45,157   copying CLASV/cli.py -> build/lib/CLASV
2025-06-07T05:20:45,159   copying CLASV/pipeline.py -> build/lib/CLASV
2025-06-07T05:20:45,161   copying CLASV/install_nextclade.py -> build/lib/CLASV
2025-06-07T05:20:45,164   copying CLASV/core.py -> build/lib/CLASV
2025-06-07T05:20:45,166   copying CLASV/benchmark_clasv.py -> build/lib/CLASV
2025-06-07T05:20:45,168   copying CLASV/setup.py -> build/lib/CLASV
2025-06-07T05:20:45,171   creating build/lib/CLASV/tools
2025-06-07T05:20:45,172   copying CLASV/tools/__init__.py -> build/lib/CLASV/tools
2025-06-07T05:20:45,175   copying CLASV/tools/benchmark_clasv.py -> build/lib/CLASV/tools
2025-06-07T05:20:45,177   running egg_info
2025-06-07T05:20:45,208   writing CLASV.egg-info/PKG-INFO
2025-06-07T05:20:45,213   writing dependency_links to CLASV.egg-info/dependency_links.txt
2025-06-07T05:20:45,214   writing entry points to CLASV.egg-info/entry_points.txt
2025-06-07T05:20:45,217   writing requirements to CLASV.egg-info/requires.txt
2025-06-07T05:20:45,218   writing top-level names to CLASV.egg-info/top_level.txt
2025-06-07T05:20:45,254   reading manifest file 'CLASV.egg-info/SOURCES.txt'
2025-06-07T05:20:45,259   reading manifest template 'MANIFEST.in'
2025-06-07T05:20:45,303   warning: no files found matching '*.png' under directory 'CLASV'
2025-06-07T05:20:45,313   warning: no files found matching 'config' under directory 'CLASV'
2025-06-07T05:20:45,339   warning: no files found matching 'predictions' under directory 'CLASV'
2025-06-07T05:20:45,367   warning: no files found matching 'raw_data' under directory 'CLASV'
2025-06-07T05:20:45,392   warning: no files found matching 'results' under directory 'CLASV'
2025-06-07T05:20:45,418   warning: no files found matching 'visuals' under directory 'CLASV'
2025-06-07T05:20:45,436   adding license file 'LICENSE'
2025-06-07T05:20:45,444   writing manifest file 'CLASV.egg-info/SOURCES.txt'
2025-06-07T05:20:45,446   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'CLASV.__pycache__' is absent from the `packages` configuration.
2025-06-07T05:20:45,447   !!

2025-06-07T05:20:45,449           ********************************************************************************
2025-06-07T05:20:45,449           ############################
2025-06-07T05:20:45,450           # Package would be ignored #
2025-06-07T05:20:45,450           ############################
2025-06-07T05:20:45,451           Python recognizes 'CLASV.__pycache__' as an importable package[^1],
2025-06-07T05:20:45,451           but it is absent from setuptools' `packages` configuration.

2025-06-07T05:20:45,452           This leads to an ambiguous overall configuration. If you want to distribute this
2025-06-07T05:20:45,453           package, please make sure that 'CLASV.__pycache__' is explicitly added
2025-06-07T05:20:45,453           to the `packages` configuration field.

2025-06-07T05:20:45,454           Alternatively, you can also rely on setuptools' discovery methods
2025-06-07T05:20:45,455           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-06-07T05:20:45,455           instead of `find_packages(...)`/`find:`).

2025-06-07T05:20:45,456           You can read more about "package discovery" on setuptools documentation page:

2025-06-07T05:20:45,457           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-06-07T05:20:45,458           If you don't want 'CLASV.__pycache__' to be distributed and are
2025-06-07T05:20:45,458           already explicitly excluding 'CLASV.__pycache__' via
2025-06-07T05:20:45,459           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-06-07T05:20:45,459           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-06-07T05:20:45,460           combination with a more fine grained `package-data` configuration.

2025-06-07T05:20:45,461           You can read more about "package data files" on setuptools documentation page:

2025-06-07T05:20:45,462           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-06-07T05:20:45,463           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-06-07T05:20:45,464                 even if it does not contain any `.py` files.
2025-06-07T05:20:45,464                 On the other hand, currently there is no concept of package data
2025-06-07T05:20:45,465                 directory, all directories are treated like packages.
2025-06-07T05:20:45,465           ********************************************************************************

2025-06-07T05:20:45,466   !!
2025-06-07T05:20:45,466     check.warn(importable)
2025-06-07T05:20:45,467   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'CLASV.config' is absent from the `packages` configuration.
2025-06-07T05:20:45,468   !!

2025-06-07T05:20:45,469           ********************************************************************************
2025-06-07T05:20:45,469           ############################
2025-06-07T05:20:45,470           # Package would be ignored #
2025-06-07T05:20:45,470           ############################
2025-06-07T05:20:45,471           Python recognizes 'CLASV.config' as an importable package[^1],
2025-06-07T05:20:45,471           but it is absent from setuptools' `packages` configuration.

2025-06-07T05:20:45,473           This leads to an ambiguous overall configuration. If you want to distribute this
2025-06-07T05:20:45,473           package, please make sure that 'CLASV.config' is explicitly added
2025-06-07T05:20:45,474           to the `packages` configuration field.

2025-06-07T05:20:45,475           Alternatively, you can also rely on setuptools' discovery methods
2025-06-07T05:20:45,476           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-06-07T05:20:45,476           instead of `find_packages(...)`/`find:`).

2025-06-07T05:20:45,477           You can read more about "package discovery" on setuptools documentation page:

2025-06-07T05:20:45,479           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-06-07T05:20:45,479           If you don't want 'CLASV.config' to be distributed and are
2025-06-07T05:20:45,480           already explicitly excluding 'CLASV.config' via
2025-06-07T05:20:45,480           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-06-07T05:20:45,481           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-06-07T05:20:45,481           combination with a more fine grained `package-data` configuration.

2025-06-07T05:20:45,482           You can read more about "package data files" on setuptools documentation page:

2025-06-07T05:20:45,483           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-06-07T05:20:45,485           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-06-07T05:20:45,486                 even if it does not contain any `.py` files.
2025-06-07T05:20:45,486                 On the other hand, currently there is no concept of package data
2025-06-07T05:20:45,487                 directory, all directories are treated like packages.
2025-06-07T05:20:45,487           ********************************************************************************

2025-06-07T05:20:45,488   !!
2025-06-07T05:20:45,489     check.warn(importable)
2025-06-07T05:20:45,489   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'CLASV.raw_data' is absent from the `packages` configuration.
2025-06-07T05:20:45,490   !!

2025-06-07T05:20:45,491           ********************************************************************************
2025-06-07T05:20:45,491           ############################
2025-06-07T05:20:45,492           # Package would be ignored #
2025-06-07T05:20:45,493           ############################
2025-06-07T05:20:45,493           Python recognizes 'CLASV.raw_data' as an importable package[^1],
2025-06-07T05:20:45,494           but it is absent from setuptools' `packages` configuration.

2025-06-07T05:20:45,495           This leads to an ambiguous overall configuration. If you want to distribute this
2025-06-07T05:20:45,495           package, please make sure that 'CLASV.raw_data' is explicitly added
2025-06-07T05:20:45,496           to the `packages` configuration field.

2025-06-07T05:20:45,497           Alternatively, you can also rely on setuptools' discovery methods
2025-06-07T05:20:45,498           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-06-07T05:20:45,498           instead of `find_packages(...)`/`find:`).

2025-06-07T05:20:45,500           You can read more about "package discovery" on setuptools documentation page:

2025-06-07T05:20:45,501           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-06-07T05:20:45,502           If you don't want 'CLASV.raw_data' to be distributed and are
2025-06-07T05:20:45,502           already explicitly excluding 'CLASV.raw_data' via
2025-06-07T05:20:45,503           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-06-07T05:20:45,504           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-06-07T05:20:45,504           combination with a more fine grained `package-data` configuration.

2025-06-07T05:20:45,505           You can read more about "package data files" on setuptools documentation page:

2025-06-07T05:20:45,506           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-06-07T05:20:45,508           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-06-07T05:20:45,509                 even if it does not contain any `.py` files.
2025-06-07T05:20:45,510                 On the other hand, currently there is no concept of package data
2025-06-07T05:20:45,510                 directory, all directories are treated like packages.
2025-06-07T05:20:45,511           ********************************************************************************

2025-06-07T05:20:45,513   !!
2025-06-07T05:20:45,513     check.warn(importable)
2025-06-07T05:20:45,514   copying CLASV/MANIFEST.in -> build/lib/CLASV
2025-06-07T05:20:45,514   copying CLASV/README.md -> build/lib/CLASV
2025-06-07T05:20:45,515   copying CLASV/VERSION -> build/lib/CLASV
2025-06-07T05:20:45,515   copying CLASV/predict_lineage.smk -> build/lib/CLASV
2025-06-07T05:20:45,516   copying CLASV/requirements.txt -> build/lib/CLASV
2025-06-07T05:20:45,516   creating build/lib/CLASV/__pycache__
2025-06-07T05:20:45,517   copying CLASV/__pycache__/__init__.cpython-310.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:20:45,517   copying CLASV/__pycache__/__init__.cpython-311.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:20:45,518   copying CLASV/__pycache__/cli.cpython-310.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:20:45,518   copying CLASV/__pycache__/cli.cpython-311.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:20:45,519   copying CLASV/__pycache__/core.cpython-311.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:20:45,519   copying CLASV/__pycache__/install_nextclade.cpython-310.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:20:45,520   copying CLASV/__pycache__/install_nextclade.cpython-311.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:20:45,520   copying CLASV/__pycache__/install_seqkit.cpython-310.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:20:45,521   copying CLASV/__pycache__/install_seqkit.cpython-311.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:20:45,521   copying CLASV/__pycache__/pipeline.cpython-310.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:20:45,522   copying CLASV/__pycache__/pipeline.cpython-311.pyc -> build/lib/CLASV/__pycache__
2025-06-07T05:20:45,523   creating build/lib/CLASV/config
2025-06-07T05:20:45,523   copying CLASV/config/NC_004296.fasta -> build/lib/CLASV/config
2025-06-07T05:20:45,524   copying CLASV/config/RF_LASV_lineage_n500_aa.joblib -> build/lib/CLASV/config
2025-06-07T05:20:45,588   copying CLASV/config/config.yaml -> build/lib/CLASV/config
2025-06-07T05:20:45,590   copying CLASV/config/configs.yaml -> build/lib/CLASV/config
2025-06-07T05:20:45,592   creating build/lib/CLASV/raw_data
2025-06-07T05:20:45,593   copying CLASV/raw_data/Adesina_et_al_2023_EMI.csv -> build/lib/CLASV/raw_data
2025-06-07T05:20:45,597   copying CLASV/raw_data/Adesina_et_al_2023_EMI.fasta -> build/lib/CLASV/raw_data
2025-06-07T05:20:45,603   copying CLASV/raw_data/All_LASV_06_07_24.csv -> build/lib/CLASV/raw_data
2025-06-07T05:20:45,629   copying CLASV/raw_data/All_LASV_06_07_24.fasta -> build/lib/CLASV/raw_data
2025-06-07T05:20:45,784   copying CLASV/raw_data/Bangura_et_al_2024_EMI.csv -> build/lib/CLASV/raw_data
2025-06-07T05:20:45,788   copying CLASV/raw_data/Bangura_et_al_2024_EMI.fasta -> build/lib/CLASV/raw_data
2025-06-07T05:20:45,795   copying CLASV/tools/README-benchmark.md -> build/lib/CLASV/tools
2025-06-07T05:20:45,799   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-06-07T05:20:45,800   !!

2025-06-07T05:20:45,801           ********************************************************************************
2025-06-07T05:20:45,802           Please avoid running ``setup.py`` directly.
2025-06-07T05:20:45,803           Instead, use pypa/build, pypa/installer or other
2025-06-07T05:20:45,803           standards-based tools.

2025-06-07T05:20:45,805           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-06-07T05:20:45,805           or your builds will no longer be supported.

2025-06-07T05:20:45,807           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-06-07T05:20:45,808           ********************************************************************************

2025-06-07T05:20:45,809   !!
2025-06-07T05:20:45,810     self.initialize_options()
2025-06-07T05:20:45,835   installing to build/bdist.linux-armv7l/wheel
2025-06-07T05:20:45,836   running install
2025-06-07T05:20:45,862   running install_lib
2025-06-07T05:20:45,890   creating build/bdist.linux-armv7l/wheel
2025-06-07T05:20:45,892   creating build/bdist.linux-armv7l/wheel/CLASV
2025-06-07T05:20:45,894   copying build/lib/CLASV/__init__.py -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:20:45,896   copying build/lib/CLASV/install_seqkit.py -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:20:45,898   copying build/lib/CLASV/predict_lineage.smk -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:20:45,901   creating build/bdist.linux-armv7l/wheel/CLASV/raw_data
2025-06-07T05:20:45,902   copying build/lib/CLASV/raw_data/Adesina_et_al_2023_EMI.csv -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data
2025-06-07T05:20:45,907   copying build/lib/CLASV/raw_data/All_LASV_06_07_24.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data
2025-06-07T05:20:46,070   copying build/lib/CLASV/raw_data/Bangura_et_al_2024_EMI.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data
2025-06-07T05:20:46,076   copying build/lib/CLASV/raw_data/Bangura_et_al_2024_EMI.csv -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data
2025-06-07T05:20:46,079   copying build/lib/CLASV/raw_data/Adesina_et_al_2023_EMI.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data
2025-06-07T05:20:46,084   copying build/lib/CLASV/raw_data/All_LASV_06_07_24.csv -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data
2025-06-07T05:20:46,112   copying build/lib/CLASV/requirements.txt -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:20:46,114   copying build/lib/CLASV/VERSION -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:20:46,116   creating build/bdist.linux-armv7l/wheel/CLASV/config
2025-06-07T05:20:46,117   copying build/lib/CLASV/config/RF_LASV_lineage_n500_aa.joblib -> build/bdist.linux-armv7l/wheel/./CLASV/config
2025-06-07T05:20:46,186   copying build/lib/CLASV/config/configs.yaml -> build/bdist.linux-armv7l/wheel/./CLASV/config
2025-06-07T05:20:46,188   copying build/lib/CLASV/config/NC_004296.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/config
2025-06-07T05:20:46,190   copying build/lib/CLASV/config/config.yaml -> build/bdist.linux-armv7l/wheel/./CLASV/config
2025-06-07T05:20:46,192   copying build/lib/CLASV/README.md -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:20:46,194   copying build/lib/CLASV/cli.py -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:20:46,196   creating build/bdist.linux-armv7l/wheel/CLASV/__pycache__
2025-06-07T05:20:46,197   copying build/lib/CLASV/__pycache__/install_seqkit.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:20:46,200   copying build/lib/CLASV/__pycache__/core.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:20:46,202   copying build/lib/CLASV/__pycache__/install_nextclade.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:20:46,205   copying build/lib/CLASV/__pycache__/pipeline.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:20:46,207   copying build/lib/CLASV/__pycache__/__init__.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:20:46,210   copying build/lib/CLASV/__pycache__/cli.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:20:46,212   copying build/lib/CLASV/__pycache__/cli.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:20:46,214   copying build/lib/CLASV/__pycache__/pipeline.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:20:46,217   copying build/lib/CLASV/__pycache__/install_seqkit.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:20:46,220   copying build/lib/CLASV/__pycache__/__init__.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:20:46,222   copying build/lib/CLASV/__pycache__/install_nextclade.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__
2025-06-07T05:20:46,225   copying build/lib/CLASV/pipeline.py -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:20:46,227   copying build/lib/CLASV/install_nextclade.py -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:20:46,230   creating build/bdist.linux-armv7l/wheel/CLASV/tools
2025-06-07T05:20:46,232   copying build/lib/CLASV/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./CLASV/tools
2025-06-07T05:20:46,234   copying build/lib/CLASV/tools/README-benchmark.md -> build/bdist.linux-armv7l/wheel/./CLASV/tools
2025-06-07T05:20:46,236   copying build/lib/CLASV/tools/benchmark_clasv.py -> build/bdist.linux-armv7l/wheel/./CLASV/tools
2025-06-07T05:20:46,238   copying build/lib/CLASV/core.py -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:20:46,241   copying build/lib/CLASV/benchmark_clasv.py -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:20:46,243   copying build/lib/CLASV/MANIFEST.in -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:20:46,245   copying build/lib/CLASV/setup.py -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-07T05:20:46,247   running install_egg_info
2025-06-07T05:20:46,288   Copying CLASV.egg-info to build/bdist.linux-armv7l/wheel/./CLASV-1.0.0-py3.11.egg-info
2025-06-07T05:20:46,300   running install_scripts
2025-06-07T05:20:46,301   Installing Nextclade...
2025-06-07T05:20:46,304   Failed to install Nextclade: [Errno 2] No such file or directory: 'python'
2025-06-07T05:20:46,304   Installing Seqkit...
2025-06-07T05:20:46,305   Failed to install Seqkit: [Errno 2] No such file or directory: 'python'
2025-06-07T05:20:46,319   creating build/bdist.linux-armv7l/wheel/clasv-1.0.0.dist-info/WHEEL
2025-06-07T05:20:46,322   creating '/tmp/pip-wheel-wgtjehx4/clasv-1.0.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-06-07T05:20:46,326   adding 'CLASV/MANIFEST.in'
2025-06-07T05:20:46,328   adding 'CLASV/README.md'
2025-06-07T05:20:46,329   adding 'CLASV/VERSION'
2025-06-07T05:20:46,331   adding 'CLASV/__init__.py'
2025-06-07T05:20:46,332   adding 'CLASV/benchmark_clasv.py'
2025-06-07T05:20:46,334   adding 'CLASV/cli.py'
2025-06-07T05:20:46,337   adding 'CLASV/core.py'
2025-06-07T05:20:46,339   adding 'CLASV/install_nextclade.py'
2025-06-07T05:20:46,341   adding 'CLASV/install_seqkit.py'
2025-06-07T05:20:46,343   adding 'CLASV/pipeline.py'
2025-06-07T05:20:46,344   adding 'CLASV/predict_lineage.smk'
2025-06-07T05:20:46,346   adding 'CLASV/requirements.txt'
2025-06-07T05:20:46,347   adding 'CLASV/setup.py'
2025-06-07T05:20:46,349   adding 'CLASV/__pycache__/__init__.cpython-310.pyc'
2025-06-07T05:20:46,350   adding 'CLASV/__pycache__/__init__.cpython-311.pyc'
2025-06-07T05:20:46,352   adding 'CLASV/__pycache__/cli.cpython-310.pyc'
2025-06-07T05:20:46,353   adding 'CLASV/__pycache__/cli.cpython-311.pyc'
2025-06-07T05:20:46,356   adding 'CLASV/__pycache__/core.cpython-311.pyc'
2025-06-07T05:20:46,358   adding 'CLASV/__pycache__/install_nextclade.cpython-310.pyc'
2025-06-07T05:20:46,360   adding 'CLASV/__pycache__/install_nextclade.cpython-311.pyc'
2025-06-07T05:20:46,362   adding 'CLASV/__pycache__/install_seqkit.cpython-310.pyc'
2025-06-07T05:20:46,364   adding 'CLASV/__pycache__/install_seqkit.cpython-311.pyc'
2025-06-07T05:20:46,365   adding 'CLASV/__pycache__/pipeline.cpython-310.pyc'
2025-06-07T05:20:46,367   adding 'CLASV/__pycache__/pipeline.cpython-311.pyc'
2025-06-07T05:20:46,369   adding 'CLASV/config/NC_004296.fasta'
2025-06-07T05:20:46,660   adding 'CLASV/config/RF_LASV_lineage_n500_aa.joblib'
2025-06-07T05:20:46,688   adding 'CLASV/config/config.yaml'
2025-06-07T05:20:46,689   adding 'CLASV/config/configs.yaml'
2025-06-07T05:20:46,693   adding 'CLASV/raw_data/Adesina_et_al_2023_EMI.csv'
2025-06-07T05:20:46,703   adding 'CLASV/raw_data/Adesina_et_al_2023_EMI.fasta'
2025-06-07T05:20:46,748   adding 'CLASV/raw_data/All_LASV_06_07_24.csv'
2025-06-07T05:20:50,016   adding 'CLASV/raw_data/All_LASV_06_07_24.fasta'
2025-06-07T05:20:50,076   adding 'CLASV/raw_data/Bangura_et_al_2024_EMI.csv'
2025-06-07T05:20:50,132   adding 'CLASV/raw_data/Bangura_et_al_2024_EMI.fasta'
2025-06-07T05:20:50,136   adding 'CLASV/tools/README-benchmark.md'
2025-06-07T05:20:50,137   adding 'CLASV/tools/__init__.py'
2025-06-07T05:20:50,140   adding 'CLASV/tools/benchmark_clasv.py'
2025-06-07T05:20:50,143   adding 'clasv-1.0.0.dist-info/licenses/LICENSE'
2025-06-07T05:20:50,144   adding 'clasv-1.0.0.dist-info/METADATA'
2025-06-07T05:20:50,146   adding 'clasv-1.0.0.dist-info/WHEEL'
2025-06-07T05:20:50,146   adding 'clasv-1.0.0.dist-info/entry_points.txt'
2025-06-07T05:20:50,148   adding 'clasv-1.0.0.dist-info/top_level.txt'
2025-06-07T05:20:50,149   adding 'clasv-1.0.0.dist-info/RECORD'
2025-06-07T05:20:50,193   removing build/bdist.linux-armv7l/wheel
2025-06-07T05:20:50,329   Building wheel for clasv (setup.py): finished with status 'done'
2025-06-07T05:20:50,363   Created wheel for clasv: filename=clasv-1.0.0-py3-none-any.whl size=3063324 sha256=57259d69e3ed26589c32ec59cad8baf578af19cc69c1743475c5814f0cc3164e
2025-06-07T05:20:50,364   Stored in directory: /tmp/pip-ephem-wheel-cache-8_mkpyfv/wheels/7f/c6/40/103e7da6c4bc4cca713a43ed0391a091dbffdc9be4e35ab3f0
2025-06-07T05:20:50,381 Successfully built clasv
2025-06-07T05:20:50,471 Removed build tracker: '/tmp/pip-build-tracker-zrzx6sri'