2025-06-09T21:12:57,009 Created temporary directory: /tmp/pip-build-tracker-8_2bivv_
2025-06-09T21:12:57,010 Initialized build tracking at /tmp/pip-build-tracker-8_2bivv_
2025-06-09T21:12:57,011 Created build tracker: /tmp/pip-build-tracker-8_2bivv_
2025-06-09T21:12:57,011 Entered build tracker: /tmp/pip-build-tracker-8_2bivv_
2025-06-09T21:12:57,012 Created temporary directory: /tmp/pip-wheel-lepxfftg
2025-06-09T21:12:57,016 Created temporary directory: /tmp/pip-ephem-wheel-cache-w8jzzak2
2025-06-09T21:12:57,065 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-06-09T21:12:57,068 2 location(s) to search for versions of clasv:
2025-06-09T21:12:57,068 * https://pypi.org/simple/clasv/
2025-06-09T21:12:57,068 * https://www.piwheels.org/simple/clasv/
2025-06-09T21:12:57,069 Fetching project page and analyzing links: https://pypi.org/simple/clasv/
2025-06-09T21:12:57,069 Getting page https://pypi.org/simple/clasv/
2025-06-09T21:12:57,071 Found index url https://pypi.org/simple/
2025-06-09T21:12:57,300 Fetched page https://pypi.org/simple/clasv/ as application/vnd.pypi.simple.v1+json
2025-06-09T21:12:57,303   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)
2025-06-09T21:12:57,304   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
2025-06-09T21:12:57,305   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)
2025-06-09T21:12:57,306   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
2025-06-09T21:12:57,306   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)
2025-06-09T21:12:57,307   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
2025-06-09T21:12:57,308   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)
2025-06-09T21:12:57,309   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
2025-06-09T21:12:57,310   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)
2025-06-09T21:12:57,310   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
2025-06-09T21:12:57,311   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)
2025-06-09T21:12:57,312   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
2025-06-09T21:12:57,312   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)
2025-06-09T21:12:57,314   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
2025-06-09T21:12:57,315   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)
2025-06-09T21:12:57,315   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
2025-06-09T21:12:57,316   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)
2025-06-09T21:12:57,316   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
2025-06-09T21:12:57,317 Fetching project page and analyzing links: https://www.piwheels.org/simple/clasv/
2025-06-09T21:12:57,318 Getting page https://www.piwheels.org/simple/clasv/
2025-06-09T21:12:57,319 Found index url https://www.piwheels.org/simple/
2025-06-09T21:12:57,489 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/
2025-06-09T21:12:58,151 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/
2025-06-09T21:12:59,310 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/
2025-06-09T21:13:01,473 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/
2025-06-09T21:13:05,639 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/
2025-06-09T21:13:05,806 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
2025-06-09T21:13:05,807 Skipping link: not a file: https://www.piwheels.org/simple/clasv/
2025-06-09T21:13:05,808 Skipping link: not a file: https://pypi.org/simple/clasv/
2025-06-09T21:13:05,828 Given no hashes to check 1 links for project 'clasv': discarding no candidates
2025-06-09T21:13:05,830 Collecting clasv==1.0.2
2025-06-09T21:13:05,833   Created temporary directory: /tmp/pip-unpack-j3alcu5x
2025-06-09T21:13:06,306   Downloading clasv-1.0.2.tar.gz (1.9 MB)
2025-06-09T21:13:07,072   Added clasv==1.0.2 from https://files.pythonhosted.org/packages/d8/8b/fa027f178c8e86e464814497c55bb250f9e751d5281ae8d0f8b628c53c21/clasv-1.0.2.tar.gz to build tracker '/tmp/pip-build-tracker-8_2bivv_'
2025-06-09T21:13:07,074   Running setup.py (path:/tmp/pip-wheel-lepxfftg/clasv_7975b303a7a745ed9dc6e1bbebf37d31/setup.py) egg_info for package clasv
2025-06-09T21:13:07,075   Created temporary directory: /tmp/pip-pip-egg-info-_r24olny
2025-06-09T21:13:07,076   Preparing metadata (setup.py): started
2025-06-09T21:13:07,077   Running command python setup.py egg_info
2025-06-09T21:13:07,974   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-09T21:13:07,974   !!

2025-06-09T21:13:07,975           ********************************************************************************
2025-06-09T21:13:07,975           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-09T21:13:07,976           License :: OSI Approved :: MIT License

2025-06-09T21:13:07,978           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-09T21:13:07,978           ********************************************************************************

2025-06-09T21:13:07,979   !!
2025-06-09T21:13:07,980     self._finalize_license_expression()
2025-06-09T21:13:08,004   Running setup...
2025-06-09T21:13:08,005   running egg_info
2025-06-09T21:13:08,032   creating /tmp/pip-pip-egg-info-_r24olny/CLASV.egg-info
2025-06-09T21:13:08,033   writing /tmp/pip-pip-egg-info-_r24olny/CLASV.egg-info/PKG-INFO
2025-06-09T21:13:08,038   writing dependency_links to /tmp/pip-pip-egg-info-_r24olny/CLASV.egg-info/dependency_links.txt
2025-06-09T21:13:08,039   writing entry points to /tmp/pip-pip-egg-info-_r24olny/CLASV.egg-info/entry_points.txt
2025-06-09T21:13:08,042   writing requirements to /tmp/pip-pip-egg-info-_r24olny/CLASV.egg-info/requires.txt
2025-06-09T21:13:08,043   writing top-level names to /tmp/pip-pip-egg-info-_r24olny/CLASV.egg-info/top_level.txt
2025-06-09T21:13:08,045   writing manifest file '/tmp/pip-pip-egg-info-_r24olny/CLASV.egg-info/SOURCES.txt'
2025-06-09T21:13:08,139   reading manifest file '/tmp/pip-pip-egg-info-_r24olny/CLASV.egg-info/SOURCES.txt'
2025-06-09T21:13:08,141   reading manifest template 'MANIFEST.in'
2025-06-09T21:13:08,142   warning: no files found matching 'CLASV/config/config.yaml'
2025-06-09T21:13:08,175   warning: no files found matching '*.png' under directory 'CLASV'
2025-06-09T21:13:08,183   warning: no files found matching 'config' under directory 'CLASV'
2025-06-09T21:13:08,201   warning: no files found matching 'predictions' under directory 'CLASV'
2025-06-09T21:13:08,221   warning: no files found matching 'raw_data' under directory 'CLASV'
2025-06-09T21:13:08,239   warning: no files found matching 'results' under directory 'CLASV'
2025-06-09T21:13:08,259   warning: no files found matching 'visuals' under directory 'CLASV'
2025-06-09T21:13:08,273   adding license file 'LICENSE'
2025-06-09T21:13:08,278   writing manifest file '/tmp/pip-pip-egg-info-_r24olny/CLASV.egg-info/SOURCES.txt'
2025-06-09T21:13:08,395   Preparing metadata (setup.py): finished with status 'done'
2025-06-09T21:13:08,401   Source in /tmp/pip-wheel-lepxfftg/clasv_7975b303a7a745ed9dc6e1bbebf37d31 has version 1.0.2, which satisfies requirement clasv==1.0.2 from https://files.pythonhosted.org/packages/d8/8b/fa027f178c8e86e464814497c55bb250f9e751d5281ae8d0f8b628c53c21/clasv-1.0.2.tar.gz
2025-06-09T21:13:08,402   Removed clasv==1.0.2 from https://files.pythonhosted.org/packages/d8/8b/fa027f178c8e86e464814497c55bb250f9e751d5281ae8d0f8b628c53c21/clasv-1.0.2.tar.gz from build tracker '/tmp/pip-build-tracker-8_2bivv_'
2025-06-09T21:13:08,428 Created temporary directory: /tmp/pip-unpack-t0l7n94z
2025-06-09T21:13:08,429 Created temporary directory: /tmp/pip-unpack-x8j71l_p
2025-06-09T21:13:08,430 Building wheels for collected packages: clasv
2025-06-09T21:13:08,434   Created temporary directory: /tmp/pip-wheel-wmhr2j40
2025-06-09T21:13:08,434   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
2025-06-09T21:13:08,436   Building wheel for clasv (setup.py): started
2025-06-09T21:13:08,437   Destination directory: /tmp/pip-wheel-wmhr2j40
2025-06-09T21:13:08,437   Running command python setup.py bdist_wheel
2025-06-09T21:13:08,919   Running setup...
2025-06-09T21:13:09,302   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-09T21:13:09,302   !!

2025-06-09T21:13:09,303           ********************************************************************************
2025-06-09T21:13:09,304           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-09T21:13:09,305           License :: OSI Approved :: MIT License

2025-06-09T21:13:09,306           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-09T21:13:09,307           ********************************************************************************

2025-06-09T21:13:09,308   !!
2025-06-09T21:13:09,309     self._finalize_license_expression()
2025-06-09T21:13:09,309   running bdist_wheel
2025-06-09T21:13:09,449   running build
2025-06-09T21:13:09,450   running build_py
2025-06-09T21:13:09,483   creating build/lib/CLASV
2025-06-09T21:13:09,485   copying CLASV/cli.py -> build/lib/CLASV
2025-06-09T21:13:09,487   copying CLASV/__init__.py -> build/lib/CLASV
2025-06-09T21:13:09,489   copying CLASV/install_seqkit.py -> build/lib/CLASV
2025-06-09T21:13:09,492   copying CLASV/pipeline.py -> build/lib/CLASV
2025-06-09T21:13:09,494   copying CLASV/core.py -> build/lib/CLASV
2025-06-09T21:13:09,497   copying CLASV/benchmark_clasv.py -> build/lib/CLASV
2025-06-09T21:13:09,499   copying CLASV/setup.py -> build/lib/CLASV
2025-06-09T21:13:09,501   copying CLASV/install_nextclade.py -> build/lib/CLASV
2025-06-09T21:13:09,504   creating build/lib/CLASV/tools
2025-06-09T21:13:09,506   copying CLASV/tools/__init__.py -> build/lib/CLASV/tools
2025-06-09T21:13:09,508   copying CLASV/tools/benchmark_clasv.py -> build/lib/CLASV/tools
2025-06-09T21:13:09,510   running egg_info
2025-06-09T21:13:09,541   writing CLASV.egg-info/PKG-INFO
2025-06-09T21:13:09,546   writing dependency_links to CLASV.egg-info/dependency_links.txt
2025-06-09T21:13:09,548   writing entry points to CLASV.egg-info/entry_points.txt
2025-06-09T21:13:09,551   writing requirements to CLASV.egg-info/requires.txt
2025-06-09T21:13:09,552   writing top-level names to CLASV.egg-info/top_level.txt
2025-06-09T21:13:09,588   reading manifest file 'CLASV.egg-info/SOURCES.txt'
2025-06-09T21:13:09,592   reading manifest template 'MANIFEST.in'
2025-06-09T21:13:09,594   warning: no files found matching 'CLASV/config/config.yaml'
2025-06-09T21:13:09,631   warning: no files found matching '*.png' under directory 'CLASV'
2025-06-09T21:13:09,639   warning: no files found matching 'config' under directory 'CLASV'
2025-06-09T21:13:09,659   warning: no files found matching 'predictions' under directory 'CLASV'
2025-06-09T21:13:09,680   warning: no files found matching 'raw_data' under directory 'CLASV'
2025-06-09T21:13:09,700   warning: no files found matching 'results' under directory 'CLASV'
2025-06-09T21:13:09,722   warning: no files found matching 'visuals' under directory 'CLASV'
2025-06-09T21:13:09,736   adding license file 'LICENSE'
2025-06-09T21:13:09,741   writing manifest file 'CLASV.egg-info/SOURCES.txt'
2025-06-09T21:13:09,744   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'CLASV.__pycache__' is absent from the `packages` configuration.
2025-06-09T21:13:09,744   !!

2025-06-09T21:13:09,746           ********************************************************************************
2025-06-09T21:13:09,746           ############################
2025-06-09T21:13:09,747           # Package would be ignored #
2025-06-09T21:13:09,747           ############################
2025-06-09T21:13:09,748           Python recognizes 'CLASV.__pycache__' as an importable package[^1],
2025-06-09T21:13:09,748           but it is absent from setuptools' `packages` configuration.

2025-06-09T21:13:09,749           This leads to an ambiguous overall configuration. If you want to distribute this
2025-06-09T21:13:09,750           package, please make sure that 'CLASV.__pycache__' is explicitly added
2025-06-09T21:13:09,750           to the `packages` configuration field.

2025-06-09T21:13:09,751           Alternatively, you can also rely on setuptools' discovery methods
2025-06-09T21:13:09,752           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-06-09T21:13:09,752           instead of `find_packages(...)`/`find:`).

2025-06-09T21:13:09,753           You can read more about "package discovery" on setuptools documentation page:

2025-06-09T21:13:09,754           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-06-09T21:13:09,756           If you don't want 'CLASV.__pycache__' to be distributed and are
2025-06-09T21:13:09,756           already explicitly excluding 'CLASV.__pycache__' via
2025-06-09T21:13:09,756           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-06-09T21:13:09,757           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-06-09T21:13:09,758           combination with a more fine grained `package-data` configuration.

2025-06-09T21:13:09,759           You can read more about "package data files" on setuptools documentation page:

2025-06-09T21:13:09,760           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-06-09T21:13:09,761           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-06-09T21:13:09,762                 even if it does not contain any `.py` files.
2025-06-09T21:13:09,763                 On the other hand, currently there is no concept of package data
2025-06-09T21:13:09,763                 directory, all directories are treated like packages.
2025-06-09T21:13:09,764           ********************************************************************************

2025-06-09T21:13:09,765   !!
2025-06-09T21:13:09,765     check.warn(importable)
2025-06-09T21:13:09,766   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'CLASV.config' is absent from the `packages` configuration.
2025-06-09T21:13:09,767   !!

2025-06-09T21:13:09,768           ********************************************************************************
2025-06-09T21:13:09,768           ############################
2025-06-09T21:13:09,769           # Package would be ignored #
2025-06-09T21:13:09,770           ############################
2025-06-09T21:13:09,770           Python recognizes 'CLASV.config' as an importable package[^1],
2025-06-09T21:13:09,771           but it is absent from setuptools' `packages` configuration.

2025-06-09T21:13:09,772           This leads to an ambiguous overall configuration. If you want to distribute this
2025-06-09T21:13:09,772           package, please make sure that 'CLASV.config' is explicitly added
2025-06-09T21:13:09,773           to the `packages` configuration field.

2025-06-09T21:13:09,774           Alternatively, you can also rely on setuptools' discovery methods
2025-06-09T21:13:09,775           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-06-09T21:13:09,775           instead of `find_packages(...)`/`find:`).

2025-06-09T21:13:09,777           You can read more about "package discovery" on setuptools documentation page:

2025-06-09T21:13:09,778           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-06-09T21:13:09,779           If you don't want 'CLASV.config' to be distributed and are
2025-06-09T21:13:09,779           already explicitly excluding 'CLASV.config' via
2025-06-09T21:13:09,780           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-06-09T21:13:09,780           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-06-09T21:13:09,781           combination with a more fine grained `package-data` configuration.

2025-06-09T21:13:09,782           You can read more about "package data files" on setuptools documentation page:

2025-06-09T21:13:09,783           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-06-09T21:13:09,785           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-06-09T21:13:09,785                 even if it does not contain any `.py` files.
2025-06-09T21:13:09,786                 On the other hand, currently there is no concept of package data
2025-06-09T21:13:09,787                 directory, all directories are treated like packages.
2025-06-09T21:13:09,787           ********************************************************************************

2025-06-09T21:13:09,788   !!
2025-06-09T21:13:09,789     check.warn(importable)
2025-06-09T21:13:09,789   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'CLASV.raw_data' is absent from the `packages` configuration.
2025-06-09T21:13:09,790   !!

2025-06-09T21:13:09,791           ********************************************************************************
2025-06-09T21:13:09,791           ############################
2025-06-09T21:13:09,792           # Package would be ignored #
2025-06-09T21:13:09,793           ############################
2025-06-09T21:13:09,793           Python recognizes 'CLASV.raw_data' as an importable package[^1],
2025-06-09T21:13:09,794           but it is absent from setuptools' `packages` configuration.

2025-06-09T21:13:09,795           This leads to an ambiguous overall configuration. If you want to distribute this
2025-06-09T21:13:09,796           package, please make sure that 'CLASV.raw_data' is explicitly added
2025-06-09T21:13:09,809           to the `packages` configuration field.

2025-06-09T21:13:09,810           Alternatively, you can also rely on setuptools' discovery methods
2025-06-09T21:13:09,812           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-06-09T21:13:09,812           instead of `find_packages(...)`/`find:`).

2025-06-09T21:13:09,815           You can read more about "package discovery" on setuptools documentation page:

2025-06-09T21:13:09,816           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-06-09T21:13:09,817           If you don't want 'CLASV.raw_data' to be distributed and are
2025-06-09T21:13:09,818           already explicitly excluding 'CLASV.raw_data' via
2025-06-09T21:13:09,818           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-06-09T21:13:09,819           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-06-09T21:13:09,820           combination with a more fine grained `package-data` configuration.

2025-06-09T21:13:09,821           You can read more about "package data files" on setuptools documentation page:

2025-06-09T21:13:09,823           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-06-09T21:13:09,824           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-06-09T21:13:09,825                 even if it does not contain any `.py` files.
2025-06-09T21:13:09,826                 On the other hand, currently there is no concept of package data
2025-06-09T21:13:09,826                 directory, all directories are treated like packages.
2025-06-09T21:13:09,827           ********************************************************************************

2025-06-09T21:13:09,829   !!
2025-06-09T21:13:09,829     check.warn(importable)
2025-06-09T21:13:09,830   copying CLASV/.DS_Store -> build/lib/CLASV
2025-06-09T21:13:09,830   copying CLASV/MANIFEST.in -> build/lib/CLASV
2025-06-09T21:13:09,831   copying CLASV/README.md -> build/lib/CLASV
2025-06-09T21:13:09,831   copying CLASV/VERSION -> build/lib/CLASV
2025-06-09T21:13:09,832   copying CLASV/predict_lineage.smk -> build/lib/CLASV
2025-06-09T21:13:09,832   copying CLASV/requirements.txt -> build/lib/CLASV
2025-06-09T21:13:09,833   creating build/lib/CLASV/__pycache__
2025-06-09T21:13:09,834   copying CLASV/__pycache__/__init__.cpython-311.pyc -> build/lib/CLASV/__pycache__
2025-06-09T21:13:09,834   copying CLASV/__pycache__/cli.cpython-311.pyc -> build/lib/CLASV/__pycache__
2025-06-09T21:13:09,835   copying CLASV/__pycache__/core.cpython-311.pyc -> build/lib/CLASV/__pycache__
2025-06-09T21:13:09,835   copying CLASV/__pycache__/install_nextclade.cpython-311.pyc -> build/lib/CLASV/__pycache__
2025-06-09T21:13:09,836   copying CLASV/__pycache__/install_seqkit.cpython-311.pyc -> build/lib/CLASV/__pycache__
2025-06-09T21:13:09,837   copying CLASV/__pycache__/pipeline.cpython-311.pyc -> build/lib/CLASV/__pycache__
2025-06-09T21:13:09,837   creating build/lib/CLASV/config
2025-06-09T21:13:09,838   copying CLASV/config/NC_004296.fasta -> build/lib/CLASV/config
2025-06-09T21:13:09,839   copying CLASV/config/RF_LASV_lineage_n100_aa.joblib -> build/lib/CLASV/config
2025-06-09T21:13:09,839   creating build/lib/CLASV/raw_data
2025-06-09T21:13:09,840   copying CLASV/raw_data/Adesina_et_al_2023_EMI.csv -> build/lib/CLASV/raw_data
2025-06-09T21:13:09,840   copying CLASV/raw_data/Adesina_et_al_2023_EMI.fasta -> build/lib/CLASV/raw_data
2025-06-09T21:13:09,841   copying CLASV/raw_data/All_LASV_06_07_24.csv -> build/lib/CLASV/raw_data
2025-06-09T21:13:09,873   copying CLASV/raw_data/All_LASV_06_07_24.fasta -> build/lib/CLASV/raw_data
2025-06-09T21:13:10,017   copying CLASV/raw_data/Bangura_et_al_2024_EMI.csv -> build/lib/CLASV/raw_data
2025-06-09T21:13:10,020   copying CLASV/raw_data/Bangura_et_al_2024_EMI.fasta -> build/lib/CLASV/raw_data
2025-06-09T21:13:10,027   copying CLASV/tools/README-benchmark.md -> build/lib/CLASV/tools
2025-06-09T21:13:10,032   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-06-09T21:13:10,032   !!

2025-06-09T21:13:10,033           ********************************************************************************
2025-06-09T21:13:10,034           Please avoid running ``setup.py`` directly.
2025-06-09T21:13:10,035           Instead, use pypa/build, pypa/installer or other
2025-06-09T21:13:10,035           standards-based tools.

2025-06-09T21:13:10,036           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-06-09T21:13:10,037           or your builds will no longer be supported.

2025-06-09T21:13:10,038           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-06-09T21:13:10,039           ********************************************************************************

2025-06-09T21:13:10,040   !!
2025-06-09T21:13:10,040     self.initialize_options()
2025-06-09T21:13:10,078   installing to build/bdist.linux-armv7l/wheel
2025-06-09T21:13:10,079   running install
2025-06-09T21:13:10,103   running install_lib
2025-06-09T21:13:10,132   creating build/bdist.linux-armv7l/wheel
2025-06-09T21:13:10,135   creating build/bdist.linux-armv7l/wheel/CLASV
2025-06-09T21:13:10,137   copying build/lib/CLASV/requirements.txt -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-09T21:13:10,139   copying build/lib/CLASV/cli.py -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-09T21:13:10,142   copying build/lib/CLASV/__init__.py -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-09T21:13:10,144   copying build/lib/CLASV/README.md -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-09T21:13:10,147   copying build/lib/CLASV/install_seqkit.py -> build/bdist.linux-armv7l/wheel/./CLASV
2025-06-09T21:13:10,150   creating build/bdist.linux-armv7l/wheel/CLASV/raw_data
2025-06-09T21:13:10,151   copying build/lib/CLASV/raw_data/Adesina_et_al_2023_EMI.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data
2025-06-09T21:13:10,157   copying build/lib/CLASV/raw_data/Adesina_et_al_2023_EMI.csv -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data
2025-06-09T21:13:10,161   copying build/lib/CLASV/raw_data/Bangura_et_al_2024_EMI.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data
2025-06-09T21:13:10,169   copying build/lib/CLASV/raw_data/Bangura_et_al_2024_EMI.csv -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data
2025-06-09T21:13:10,172   copying build/lib/CLASV/raw_data/All_LASV_06_07_24.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data
2025-06-09T21:13:10,318   error: [Errno 28] No space left on device
2025-06-09T21:13:10,434   ERROR: python setup.py bdist_wheel exited with 1
2025-06-09T21:13:10,448   [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c '
2025-06-09T21:13:10,448   exec(compile('"'"''"'"''"'"'
2025-06-09T21:13:10,448   # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
2025-06-09T21:13:10,448   #
2025-06-09T21:13:10,448   # - It imports setuptools before invoking setup.py, to enable projects that directly
2025-06-09T21:13:10,448   #   import from `distutils.core` to work with newer packaging standards.
2025-06-09T21:13:10,448   # - It provides a clear error message when setuptools is not installed.
2025-06-09T21:13:10,448   # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
2025-06-09T21:13:10,448   #   setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
2025-06-09T21:13:10,448   #     manifest_maker: standard file '"'"'-c'"'"' not found".
2025-06-09T21:13:10,448   # - It generates a shim setup.py, for handling setup.cfg-only projects.
2025-06-09T21:13:10,448   import os, sys, tokenize, traceback
2025-06-09T21:13:10,448   
2025-06-09T21:13:10,448   try:
2025-06-09T21:13:10,448       import setuptools
2025-06-09T21:13:10,448   except ImportError:
2025-06-09T21:13:10,448       print(
2025-06-09T21:13:10,448           "ERROR: Can not execute `setup.py` since setuptools failed to import in "
2025-06-09T21:13:10,448           "the build environment with exception:",
2025-06-09T21:13:10,448           file=sys.stderr,
2025-06-09T21:13:10,448       )
2025-06-09T21:13:10,448       traceback.print_exc()
2025-06-09T21:13:10,448       sys.exit(1)
2025-06-09T21:13:10,448   
2025-06-09T21:13:10,448   __file__ = %r
2025-06-09T21:13:10,448   sys.argv[0] = __file__
2025-06-09T21:13:10,448   
2025-06-09T21:13:10,448   if os.path.exists(__file__):
2025-06-09T21:13:10,448       filename = __file__
2025-06-09T21:13:10,448       with tokenize.open(__file__) as f:
2025-06-09T21:13:10,448           setup_py_code = f.read()
2025-06-09T21:13:10,448   else:
2025-06-09T21:13:10,448       filename = "<auto-generated setuptools caller>"
2025-06-09T21:13:10,448       setup_py_code = "from setuptools import setup; setup()"
2025-06-09T21:13:10,448   
2025-06-09T21:13:10,448   exec(compile(setup_py_code, filename, "exec"))
2025-06-09T21:13:10,448   '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-lepxfftg/clasv_7975b303a7a745ed9dc6e1bbebf37d31/setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' bdist_wheel -d /tmp/pip-wheel-wmhr2j40[/]
2025-06-09T21:13:10,448   [bold magenta]cwd[/]: /tmp/pip-wheel-lepxfftg/clasv_7975b303a7a745ed9dc6e1bbebf37d31/
2025-06-09T21:13:10,449   Building wheel for clasv (setup.py): finished with status 'error'
2025-06-09T21:13:10,450   ERROR: Failed building wheel for clasv
2025-06-09T21:13:10,452   Running setup.py clean for clasv
2025-06-09T21:13:10,453   Running command python setup.py clean
2025-06-09T21:13:10,945   Running setup...
2025-06-09T21:13:11,32025-06-09T21:13:11,365   running clean
2025-06-09T21:13:11,422   removing 'build/lib' (and everything under it)
2025-06-09T21:13:11,434   removing 'build/bdist.linux-armv7l' (and everything under it)
2025-06-09T21:13:11,496   'build/scripts-3.11' does not exist -- can't clean it
2025-06-09T21:13:11,496   removing 'build'
2025-06-09T21:13:11,610 Failed to build clasv
2025-06-09T21:13:11,611 ERROR: Failed to build one or more wheels
2025-06-09T21:13:11,613 Exception information:
2025-06-09T21:13:11,613 Traceback (most recent call last):
2025-06-09T21:13:11,613   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 107, in _run_wrapper
2025-06-09T21:13:11,613     status = _inner_run()
2025-06-09T21:13:11,613              ^^^^^^^^^^^^
2025-06-09T21:13:11,613   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 98, in _inner_run
2025-06-09T21:13:11,613     return self.run(options, args)
2025-06-09T21:13:11,613            ^^^^^^^^^^^^^^^^^^^^^^^
2025-06-09T21:13:11,613   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 71, in wrapper
2025-06-09T21:13:11,613     return func(self, options, args)
2025-06-09T21:13:11,613            ^^^^^^^^^^^^^^^^^^^^^^^^^
2025-06-09T21:13:11,613   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 179, in run
2025-06-09T21:13:11,613     raise CommandError("Failed to build one or more wheels")
2025-06-09T21:13:11,613 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2025-06-09T21:13:11,614 Removed build tracker: '/tmp/pip-build-tracker-8_2bivv_'