2025-08-31T18:17:39,204 Created temporary directory: /tmp/pip-build-tracker-shy3jo8n 2025-08-31T18:17:39,205 Initialized build tracking at /tmp/pip-build-tracker-shy3jo8n 2025-08-31T18:17:39,206 Created build tracker: /tmp/pip-build-tracker-shy3jo8n 2025-08-31T18:17:39,206 Entered build tracker: /tmp/pip-build-tracker-shy3jo8n 2025-08-31T18:17:39,207 Created temporary directory: /tmp/pip-wheel-43_gjhd1 2025-08-31T18:17:39,211 Created temporary directory: /tmp/pip-ephem-wheel-cache-xj0rvz96 2025-08-31T18:17:39,258 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-08-31T18:17:39,260 2 location(s) to search for versions of clasv: 2025-08-31T18:17:39,260 * https://pypi.org/simple/clasv/ 2025-08-31T18:17:39,260 * https://www.piwheels.org/simple/clasv/ 2025-08-31T18:17:39,261 Fetching project page and analyzing links: https://pypi.org/simple/clasv/ 2025-08-31T18:17:39,262 Getting page https://pypi.org/simple/clasv/ 2025-08-31T18:17:39,263 Found index url https://pypi.org/simple/ 2025-08-31T18:17:39,408 Fetched page https://pypi.org/simple/clasv/ as application/vnd.pypi.simple.v1+json 2025-08-31T18:17:39,411 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) 2025-08-31T18:17:39,413 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 2025-08-31T18:17:39,413 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) 2025-08-31T18:17:39,414 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 2025-08-31T18:17:39,414 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) 2025-08-31T18:17:39,415 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 2025-08-31T18:17:39,416 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) 2025-08-31T18:17:39,416 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 2025-08-31T18:17:39,417 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) 2025-08-31T18:17:39,418 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 2025-08-31T18:17:39,418 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) 2025-08-31T18:17:39,419 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 2025-08-31T18:17:39,420 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) 2025-08-31T18:17:39,421 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 2025-08-31T18:17:39,422 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) 2025-08-31T18:17:39,422 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 2025-08-31T18:17:39,423 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) 2025-08-31T18:17:39,423 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 2025-08-31T18:17:39,424 Fetching project page and analyzing links: https://www.piwheels.org/simple/clasv/ 2025-08-31T18:17:39,424 Getting page https://www.piwheels.org/simple/clasv/ 2025-08-31T18:17:39,426 Found index url https://www.piwheels.org/simple/ 2025-08-31T18:17:39,592 Fetched page https://www.piwheels.org/simple/clasv/ as text/html 2025-08-31T18:17:39,595 Skipping link: No binaries permitted for clasv: https://www.piwheels.org/simple/clasv/clasv-1.0.4-py3-none-any.whl#sha256=03db5788c67d9f72aae0d57f4608cf4481b337adf8087a0d69e8de2449863da6 (from https://www.piwheels.org/simple/clasv/) (requires-python:>=3.7,<3.14) 2025-08-31T18:17:39,596 Skipping link: No binaries permitted for clasv: https://archive1.piwheels.org/simple/clasv/clasv-1.0.1-py3-none-any.whl#sha256=e9390e4b39429a31e3b2ee578bb0e1342144a82b447a3601b3e16b3e7bf89380 (from https://www.piwheels.org/simple/clasv/) (requires-python:>=3.6) 2025-08-31T18:17:39,596 Skipping link: No binaries permitted for clasv: https://archive1.piwheels.org/simple/clasv/clasv-1.0.0-py3-none-any.whl#sha256=57259d69e3ed26589c32ec59cad8baf578af19cc69c1743475c5814f0cc3164e (from https://www.piwheels.org/simple/clasv/) (requires-python:>=3.6) 2025-08-31T18:17:39,597 Skipping link: No binaries permitted for clasv: https://archive1.piwheels.org/simple/clasv/CLASV-0.1.16-py3-none-any.whl#sha256=da2929fcce2e7f68ca008ca3afe547bb1bca0da33b6d3b5f31dc93559d323c2f (from https://www.piwheels.org/simple/clasv/) (requires-python:>=3.6) 2025-08-31T18:17:39,598 Skipping link: No binaries permitted for clasv: https://archive1.piwheels.org/simple/clasv/CLASV-0.1.15-py3-none-any.whl#sha256=e0e432f07cc0268e603ea2fc23ee116450d1514e6a74a467526a515fd1ed177d (from https://www.piwheels.org/simple/clasv/) (requires-python:>=3.6) 2025-08-31T18:17:39,598 Skipping link: No binaries permitted for clasv: https://archive1.piwheels.org/simple/clasv/CLASV-0.1.14-py3-none-any.whl#sha256=df7ac2bc8947ae60805237e722746c632985fb9714d7ad952d4b300baed27f86 (from https://www.piwheels.org/simple/clasv/) (requires-python:>=3.6) 2025-08-31T18:17:39,599 Skipping link: not a file: https://www.piwheels.org/simple/clasv/ 2025-08-31T18:17:39,599 Skipping link: not a file: https://pypi.org/simple/clasv/ 2025-08-31T18:17:39,618 Given no hashes to check 1 links for project 'clasv': discarding no candidates 2025-08-31T18:17:39,619 Collecting clasv==1.0.5 2025-08-31T18:17:39,622 Created temporary directory: /tmp/pip-unpack-jd2dzqyo 2025-08-31T18:17:39,844 Downloading clasv-1.0.5.tar.gz (2.3 MB) 2025-08-31T18:17:40,835 Added clasv==1.0.5 from https://files.pythonhosted.org/packages/de/b0/ce608a6857fc6753be849706d938c7252569ac46235997cb33b83cdcff18/clasv-1.0.5.tar.gz to build tracker '/tmp/pip-build-tracker-shy3jo8n' 2025-08-31T18:17:40,837 Running setup.py (path:/tmp/pip-wheel-43_gjhd1/clasv_8a4c695c916e4cc7888b0b395e3303db/setup.py) egg_info for package clasv 2025-08-31T18:17:40,838 Created temporary directory: /tmp/pip-pip-egg-info-61nb3s2n 2025-08-31T18:17:40,839 Preparing metadata (setup.py): started 2025-08-31T18:17:40,840 Running command python setup.py egg_info 2025-08-31T18:17:41,941 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-08-31T18:17:41,941 !! 2025-08-31T18:17:41,942 ******************************************************************************** 2025-08-31T18:17:41,942 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-08-31T18:17:41,943 License :: OSI Approved :: MIT License 2025-08-31T18:17:41,945 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-08-31T18:17:41,945 ******************************************************************************** 2025-08-31T18:17:41,946 !! 2025-08-31T18:17:41,947 self._finalize_license_expression() 2025-08-31T18:17:41,971 Running setup... 2025-08-31T18:17:41,971 running egg_info 2025-08-31T18:17:41,998 creating /tmp/pip-pip-egg-info-61nb3s2n/CLASV.egg-info 2025-08-31T18:17:41,999 writing /tmp/pip-pip-egg-info-61nb3s2n/CLASV.egg-info/PKG-INFO 2025-08-31T18:17:42,004 writing dependency_links to /tmp/pip-pip-egg-info-61nb3s2n/CLASV.egg-info/dependency_links.txt 2025-08-31T18:17:42,005 writing entry points to /tmp/pip-pip-egg-info-61nb3s2n/CLASV.egg-info/entry_points.txt 2025-08-31T18:17:42,022 writing requirements to /tmp/pip-pip-egg-info-61nb3s2n/CLASV.egg-info/requires.txt 2025-08-31T18:17:42,023 writing top-level names to /tmp/pip-pip-egg-info-61nb3s2n/CLASV.egg-info/top_level.txt 2025-08-31T18:17:42,025 writing manifest file '/tmp/pip-pip-egg-info-61nb3s2n/CLASV.egg-info/SOURCES.txt' 2025-08-31T18:17:42,130 reading manifest file '/tmp/pip-pip-egg-info-61nb3s2n/CLASV.egg-info/SOURCES.txt' 2025-08-31T18:17:42,131 reading manifest template 'MANIFEST.in' 2025-08-31T18:17:42,308 warning: no files found matching 'config' under directory 'CLASV' 2025-08-31T18:17:42,526 warning: no files found matching 'predictions' under directory 'CLASV' 2025-08-31T18:17:42,599 warning: no files found matching 'raw_data' under directory 'CLASV' 2025-08-31T18:17:42,637 warning: no files found matching 'results' under directory 'CLASV' 2025-08-31T18:17:42,675 warning: no files found matching 'visuals' under directory 'CLASV' 2025-08-31T18:17:42,701 adding license file 'LICENSE' 2025-08-31T18:17:42,709 writing manifest file '/tmp/pip-pip-egg-info-61nb3s2n/CLASV.egg-info/SOURCES.txt' 2025-08-31T18:17:42,814 Preparing metadata (setup.py): finished with status 'done' 2025-08-31T18:17:42,821 Source in /tmp/pip-wheel-43_gjhd1/clasv_8a4c695c916e4cc7888b0b395e3303db has version 1.0.5, which satisfies requirement clasv==1.0.5 from https://files.pythonhosted.org/packages/de/b0/ce608a6857fc6753be849706d938c7252569ac46235997cb33b83cdcff18/clasv-1.0.5.tar.gz 2025-08-31T18:17:42,824 Removed clasv==1.0.5 from https://files.pythonhosted.org/packages/de/b0/ce608a6857fc6753be849706d938c7252569ac46235997cb33b83cdcff18/clasv-1.0.5.tar.gz from build tracker '/tmp/pip-build-tracker-shy3jo8n' 2025-08-31T18:17:42,876 Created temporary directory: /tmp/pip-unpack-bq1fr_p3 2025-08-31T18:17:42,879 Created temporary directory: /tmp/pip-unpack-253h3b_c 2025-08-31T18:17:42,880 Building wheels for collected packages: clasv 2025-08-31T18:17:42,887 Created temporary directory: /tmp/pip-wheel-8kcvfdtx 2025-08-31T18:17:42,888 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 2025-08-31T18:17:42,891 Building wheel for clasv (setup.py): started 2025-08-31T18:17:42,892 Destination directory: /tmp/pip-wheel-8kcvfdtx 2025-08-31T18:17:42,893 Running command python setup.py bdist_wheel 2025-08-31T18:17:43,383 Running setup... 2025-08-31T18:17:44,024 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-08-31T18:17:44,025 !! 2025-08-31T18:17:44,025 ******************************************************************************** 2025-08-31T18:17:44,026 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-08-31T18:17:44,027 License :: OSI Approved :: MIT License 2025-08-31T18:17:44,028 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-08-31T18:17:44,029 ******************************************************************************** 2025-08-31T18:17:44,030 !! 2025-08-31T18:17:44,030 self._finalize_license_expression() 2025-08-31T18:17:44,031 running bdist_wheel 2025-08-31T18:17:44,156 running build 2025-08-31T18:17:44,156 running build_py 2025-08-31T18:17:44,186 creating build/lib/CLASV 2025-08-31T18:17:44,188 copying CLASV/core.py -> build/lib/CLASV 2025-08-31T18:17:44,190 copying CLASV/__init__.py -> build/lib/CLASV 2025-08-31T18:17:44,192 copying CLASV/install_nextclade.py -> build/lib/CLASV 2025-08-31T18:17:44,195 copying CLASV/setup.py -> build/lib/CLASV 2025-08-31T18:17:44,197 copying CLASV/install_seqkit.py -> build/lib/CLASV 2025-08-31T18:17:44,199 copying CLASV/pipeline.py -> build/lib/CLASV 2025-08-31T18:17:44,202 copying CLASV/cli.py -> build/lib/CLASV 2025-08-31T18:17:44,203 copying CLASV/benchmark_clasv.py -> build/lib/CLASV 2025-08-31T18:17:44,206 creating build/lib/CLASV/tools 2025-08-31T18:17:44,207 copying CLASV/tools/__init__.py -> build/lib/CLASV/tools 2025-08-31T18:17:44,208 copying CLASV/tools/benchmark_clasv.py -> build/lib/CLASV/tools 2025-08-31T18:17:44,211 running egg_info 2025-08-31T18:17:44,239 writing CLASV.egg-info/PKG-INFO 2025-08-31T18:17:44,243 writing dependency_links to CLASV.egg-info/dependency_links.txt 2025-08-31T18:17:44,245 writing entry points to CLASV.egg-info/entry_points.txt 2025-08-31T18:17:44,262 writing requirements to CLASV.egg-info/requires.txt 2025-08-31T18:17:44,263 writing top-level names to CLASV.egg-info/top_level.txt 2025-08-31T18:17:44,296 reading manifest file 'CLASV.egg-info/SOURCES.txt' 2025-08-31T18:17:44,302 reading manifest template 'MANIFEST.in' 2025-08-31T18:17:44,394 warning: no files found matching 'config' under directory 'CLASV' 2025-08-31T18:17:44,435 warning: no files found matching 'predictions' under directory 'CLASV' 2025-08-31T18:17:44,472 warning: no files found matching 'raw_data' under directory 'CLASV' 2025-08-31T18:17:44,509 warning: no files found matching 'results' under directory 'CLASV' 2025-08-31T18:17:44,547 warning: no files found matching 'visuals' under directory 'CLASV' 2025-08-31T18:17:44,571 adding license file 'LICENSE' 2025-08-31T18:17:44,580 writing manifest file 'CLASV.egg-info/SOURCES.txt' 2025-08-31T18:17:44,583 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'CLASV.__pycache__' is absent from the `packages` configuration. 2025-08-31T18:17:44,584 !! 2025-08-31T18:17:44,585 ******************************************************************************** 2025-08-31T18:17:44,585 ############################ 2025-08-31T18:17:44,586 # Package would be ignored # 2025-08-31T18:17:44,587 ############################ 2025-08-31T18:17:44,587 Python recognizes 'CLASV.__pycache__' as an importable package[^1], 2025-08-31T18:17:44,588 but it is absent from setuptools' `packages` configuration. 2025-08-31T18:17:44,589 This leads to an ambiguous overall configuration. If you want to distribute this 2025-08-31T18:17:44,589 package, please make sure that 'CLASV.__pycache__' is explicitly added 2025-08-31T18:17:44,590 to the `packages` configuration field. 2025-08-31T18:17:44,590 Alternatively, you can also rely on setuptools' discovery methods 2025-08-31T18:17:44,591 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-08-31T18:17:44,591 instead of `find_packages(...)`/`find:`). 2025-08-31T18:17:44,592 You can read more about "package discovery" on setuptools documentation page: 2025-08-31T18:17:44,593 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-08-31T18:17:44,594 If you don't want 'CLASV.__pycache__' to be distributed and are 2025-08-31T18:17:44,594 already explicitly excluding 'CLASV.__pycache__' via 2025-08-31T18:17:44,595 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-08-31T18:17:44,595 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-08-31T18:17:44,595 combination with a more fine grained `package-data` configuration. 2025-08-31T18:17:44,596 You can read more about "package data files" on setuptools documentation page: 2025-08-31T18:17:44,597 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-08-31T18:17:44,599 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-08-31T18:17:44,599 even if it does not contain any `.py` files. 2025-08-31T18:17:44,600 On the other hand, currently there is no concept of package data 2025-08-31T18:17:44,600 directory, all directories are treated like packages. 2025-08-31T18:17:44,601 ******************************************************************************** 2025-08-31T18:17:44,602 !! 2025-08-31T18:17:44,602 check.warn(importable) 2025-08-31T18:17:44,603 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'CLASV.config' is absent from the `packages` configuration. 2025-08-31T18:17:44,603 !! 2025-08-31T18:17:44,604 ******************************************************************************** 2025-08-31T18:17:44,605 ############################ 2025-08-31T18:17:44,607 # Package would be ignored # 2025-08-31T18:17:44,610 ############################ 2025-08-31T18:17:44,610 Python recognizes 'CLASV.config' as an importable package[^1], 2025-08-31T18:17:44,611 but it is absent from setuptools' `packages` configuration. 2025-08-31T18:17:44,612 This leads to an ambiguous overall configuration. If you want to distribute this 2025-08-31T18:17:44,612 package, please make sure that 'CLASV.config' is explicitly added 2025-08-31T18:17:44,613 to the `packages` configuration field. 2025-08-31T18:17:44,614 Alternatively, you can also rely on setuptools' discovery methods 2025-08-31T18:17:44,614 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-08-31T18:17:44,615 instead of `find_packages(...)`/`find:`). 2025-08-31T18:17:44,616 You can read more about "package discovery" on setuptools documentation page: 2025-08-31T18:17:44,617 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-08-31T18:17:44,618 If you don't want 'CLASV.config' to be distributed and are 2025-08-31T18:17:44,618 already explicitly excluding 'CLASV.config' via 2025-08-31T18:17:44,619 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-08-31T18:17:44,620 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-08-31T18:17:44,620 combination with a more fine grained `package-data` configuration. 2025-08-31T18:17:44,621 You can read more about "package data files" on setuptools documentation page: 2025-08-31T18:17:44,622 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-08-31T18:17:44,623 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-08-31T18:17:44,623 even if it does not contain any `.py` files. 2025-08-31T18:17:44,624 On the other hand, currently there is no concept of package data 2025-08-31T18:17:44,624 directory, all directories are treated like packages. 2025-08-31T18:17:44,624 ******************************************************************************** 2025-08-31T18:17:44,625 !! 2025-08-31T18:17:44,626 check.warn(importable) 2025-08-31T18:17:44,626 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'CLASV.raw_data' is absent from the `packages` configuration. 2025-08-31T18:17:44,627 !! 2025-08-31T18:17:44,628 ******************************************************************************** 2025-08-31T18:17:44,628 ############################ 2025-08-31T18:17:44,628 # Package would be ignored # 2025-08-31T18:17:44,629 ############################ 2025-08-31T18:17:44,629 Python recognizes 'CLASV.raw_data' as an importable package[^1], 2025-08-31T18:17:44,630 but it is absent from setuptools' `packages` configuration. 2025-08-31T18:17:44,631 This leads to an ambiguous overall configuration. If you want to distribute this 2025-08-31T18:17:44,631 package, please make sure that 'CLASV.raw_data' is explicitly added 2025-08-31T18:17:44,632 to the `packages` configuration field. 2025-08-31T18:17:44,633 Alternatively, you can also rely on setuptools' discovery methods 2025-08-31T18:17:44,633 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-08-31T18:17:44,634 instead of `find_packages(...)`/`find:`). 2025-08-31T18:17:44,634 You can read more about "package discovery" on setuptools documentation page: 2025-08-31T18:17:44,635 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-08-31T18:17:44,636 If you don't want 'CLASV.raw_data' to be distributed and are 2025-08-31T18:17:44,637 already explicitly excluding 'CLASV.raw_data' via 2025-08-31T18:17:44,637 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-08-31T18:17:44,638 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-08-31T18:17:44,638 combination with a more fine grained `package-data` configuration. 2025-08-31T18:17:44,639 You can read more about "package data files" on setuptools documentation page: 2025-08-31T18:17:44,640 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-08-31T18:17:44,642 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-08-31T18:17:44,642 even if it does not contain any `.py` files. 2025-08-31T18:17:44,643 On the other hand, currently there is no concept of package data 2025-08-31T18:17:44,643 directory, all directories are treated like packages. 2025-08-31T18:17:44,643 ******************************************************************************** 2025-08-31T18:17:44,644 !! 2025-08-31T18:17:44,645 check.warn(importable) 2025-08-31T18:17:44,645 copying CLASV/MANIFEST.in -> build/lib/CLASV 2025-08-31T18:17:44,646 copying CLASV/README.md -> build/lib/CLASV 2025-08-31T18:17:44,646 copying CLASV/VERSION -> build/lib/CLASV 2025-08-31T18:17:44,647 copying CLASV/predflow_updated.png -> build/lib/CLASV 2025-08-31T18:17:44,648 copying CLASV/predict_lineage.smk -> build/lib/CLASV 2025-08-31T18:17:44,648 copying CLASV/requirements.txt -> build/lib/CLASV 2025-08-31T18:17:44,649 creating build/lib/CLASV/CLASV.egg-info 2025-08-31T18:17:44,649 copying CLASV/CLASV.egg-info/PKG-INFO -> build/lib/CLASV/CLASV.egg-info 2025-08-31T18:17:44,649 copying CLASV/CLASV.egg-info/SOURCES.txt -> build/lib/CLASV/CLASV.egg-info 2025-08-31T18:17:44,650 copying CLASV/CLASV.egg-info/dependency_links.txt -> build/lib/CLASV/CLASV.egg-info 2025-08-31T18:17:44,650 copying CLASV/CLASV.egg-info/entry_points.txt -> build/lib/CLASV/CLASV.egg-info 2025-08-31T18:17:44,651 copying CLASV/CLASV.egg-info/requires.txt -> build/lib/CLASV/CLASV.egg-info 2025-08-31T18:17:44,651 copying CLASV/CLASV.egg-info/top_level.txt -> build/lib/CLASV/CLASV.egg-info 2025-08-31T18:17:44,651 creating build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,652 copying CLASV/__pycache__/__init__.cpython-310.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,652 copying CLASV/__pycache__/__init__.cpython-311.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,653 copying CLASV/__pycache__/__init__.cpython-312.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,653 copying CLASV/__pycache__/__init__.cpython-313.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,654 copying CLASV/__pycache__/__init__.cpython-38.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,654 copying CLASV/__pycache__/__init__.cpython-39.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,655 copying CLASV/__pycache__/cli.cpython-310.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,655 copying CLASV/__pycache__/cli.cpython-311.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,656 copying CLASV/__pycache__/cli.cpython-312.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,656 copying CLASV/__pycache__/cli.cpython-313.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,658 copying CLASV/__pycache__/cli.cpython-38.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,660 copying CLASV/__pycache__/cli.cpython-39.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,662 copying CLASV/__pycache__/core.cpython-310.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,665 copying CLASV/__pycache__/core.cpython-311.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,668 copying CLASV/__pycache__/core.cpython-312.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,670 copying CLASV/__pycache__/core.cpython-313.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,673 copying CLASV/__pycache__/core.cpython-38.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,675 copying CLASV/__pycache__/core.cpython-39.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,678 copying CLASV/__pycache__/install_nextclade.cpython-310.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,681 copying CLASV/__pycache__/install_nextclade.cpython-311.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,683 copying CLASV/__pycache__/install_nextclade.cpython-312.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,686 copying CLASV/__pycache__/install_nextclade.cpython-313.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,689 copying CLASV/__pycache__/install_nextclade.cpython-38.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,691 copying CLASV/__pycache__/install_nextclade.cpython-39.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,694 copying CLASV/__pycache__/install_seqkit.cpython-310.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,696 copying CLASV/__pycache__/install_seqkit.cpython-311.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,699 copying CLASV/__pycache__/install_seqkit.cpython-312.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,701 copying CLASV/__pycache__/install_seqkit.cpython-313.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,704 copying CLASV/__pycache__/install_seqkit.cpython-38.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,707 copying CLASV/__pycache__/install_seqkit.cpython-39.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,709 copying CLASV/__pycache__/pipeline.cpython-310.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,711 copying CLASV/__pycache__/pipeline.cpython-311.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,713 copying CLASV/__pycache__/pipeline.cpython-312.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,716 copying CLASV/__pycache__/pipeline.cpython-313.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,718 copying CLASV/__pycache__/pipeline.cpython-38.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,720 copying CLASV/__pycache__/pipeline.cpython-39.pyc -> build/lib/CLASV/__pycache__ 2025-08-31T18:17:44,722 creating build/lib/CLASV/config 2025-08-31T18:17:44,723 copying CLASV/config/NC_004296.fasta -> build/lib/CLASV/config 2025-08-31T18:17:44,725 copying CLASV/config/RF_LASV_lineage_n100_aa.joblib -> build/lib/CLASV/config 2025-08-31T18:17:44,740 copying CLASV/config/config.yaml -> build/lib/CLASV/config 2025-08-31T18:17:44,742 creating build/lib/CLASV/raw_data 2025-08-31T18:17:44,742 copying CLASV/raw_data/Adesina_et_al_2023_EMI.csv -> build/lib/CLASV/raw_data 2025-08-31T18:17:44,747 copying CLASV/raw_data/Adesina_et_al_2023_EMI.fasta -> build/lib/CLASV/raw_data 2025-08-31T18:17:44,751 copying CLASV/raw_data/All_LASV_06_07_24.csv -> build/lib/CLASV/raw_data 2025-08-31T18:17:44,775 copying CLASV/raw_data/All_LASV_06_07_24.fasta -> build/lib/CLASV/raw_data 2025-08-31T18:17:44,926 copying CLASV/raw_data/Bangura_et_al_2024_EMI.csv -> build/lib/CLASV/raw_data 2025-08-31T18:17:44,929 copying CLASV/raw_data/Bangura_et_al_2024_EMI.fasta -> build/lib/CLASV/raw_data 2025-08-31T18:17:44,934 copying CLASV/tools/README-benchmark.md -> build/lib/CLASV/tools 2025-08-31T18:17:44,938 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-08-31T18:17:44,939 !! 2025-08-31T18:17:44,940 ******************************************************************************** 2025-08-31T18:17:44,941 Please avoid running ``setup.py`` directly. 2025-08-31T18:17:44,941 Instead, use pypa/build, pypa/installer or other 2025-08-31T18:17:44,942 standards-based tools. 2025-08-31T18:17:44,943 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-08-31T18:17:44,943 or your builds will no longer be supported. 2025-08-31T18:17:44,945 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-08-31T18:17:44,945 ******************************************************************************** 2025-08-31T18:17:44,947 !! 2025-08-31T18:17:44,947 self.initialize_options() 2025-08-31T18:17:44,967 installing to build/bdist.linux-armv7l/wheel 2025-08-31T18:17:44,967 running install 2025-08-31T18:17:44,990 running install_lib 2025-08-31T18:17:45,017 creating build/bdist.linux-armv7l/wheel 2025-08-31T18:17:45,020 creating build/bdist.linux-armv7l/wheel/CLASV 2025-08-31T18:17:45,021 copying build/lib/CLASV/predict_lineage.smk -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:45,024 creating build/bdist.linux-armv7l/wheel/CLASV/CLASV.egg-info 2025-08-31T18:17:45,025 copying build/lib/CLASV/CLASV.egg-info/dependency_links.txt -> build/bdist.linux-armv7l/wheel/./CLASV/CLASV.egg-info 2025-08-31T18:17:45,026 copying build/lib/CLASV/CLASV.egg-info/requires.txt -> build/bdist.linux-armv7l/wheel/./CLASV/CLASV.egg-info 2025-08-31T18:17:45,029 copying build/lib/CLASV/CLASV.egg-info/top_level.txt -> build/bdist.linux-armv7l/wheel/./CLASV/CLASV.egg-info 2025-08-31T18:17:45,030 copying build/lib/CLASV/CLASV.egg-info/PKG-INFO -> build/bdist.linux-armv7l/wheel/./CLASV/CLASV.egg-info 2025-08-31T18:17:45,033 copying build/lib/CLASV/CLASV.egg-info/SOURCES.txt -> build/bdist.linux-armv7l/wheel/./CLASV/CLASV.egg-info 2025-08-31T18:17:45,035 copying build/lib/CLASV/CLASV.egg-info/entry_points.txt -> build/bdist.linux-armv7l/wheel/./CLASV/CLASV.egg-info 2025-08-31T18:17:45,036 copying build/lib/CLASV/MANIFEST.in -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:45,038 copying build/lib/CLASV/VERSION -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:45,040 copying build/lib/CLASV/core.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:45,042 copying build/lib/CLASV/README.md -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:45,044 copying build/lib/CLASV/__init__.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:45,046 creating build/bdist.linux-armv7l/wheel/CLASV/config 2025-08-31T18:17:45,047 copying build/lib/CLASV/config/config.yaml -> build/bdist.linux-armv7l/wheel/./CLASV/config 2025-08-31T18:17:45,049 copying build/lib/CLASV/config/NC_004296.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/config 2025-08-31T18:17:45,051 copying build/lib/CLASV/config/RF_LASV_lineage_n100_aa.joblib -> build/bdist.linux-armv7l/wheel/./CLASV/config 2025-08-31T18:17:45,071 creating build/bdist.linux-armv7l/wheel/CLASV/raw_data 2025-08-31T18:17:45,072 copying build/lib/CLASV/raw_data/Adesina_et_al_2023_EMI.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data 2025-08-31T18:17:45,079 copying build/lib/CLASV/raw_data/All_LASV_06_07_24.csv -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data 2025-08-31T18:17:45,110 copying build/lib/CLASV/raw_data/Bangura_et_al_2024_EMI.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data 2025-08-31T18:17:45,117 copying build/lib/CLASV/raw_data/Bangura_et_al_2024_EMI.csv -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data 2025-08-31T18:17:45,120 copying build/lib/CLASV/raw_data/Adesina_et_al_2023_EMI.csv -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data 2025-08-31T18:17:45,125 copying build/lib/CLASV/raw_data/All_LASV_06_07_24.fasta -> build/bdist.linux-armv7l/wheel/./CLASV/raw_data 2025-08-31T18:17:45,272 copying build/lib/CLASV/install_nextclade.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:45,274 copying build/lib/CLASV/setup.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:45,276 copying build/lib/CLASV/requirements.txt -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:45,279 creating build/bdist.linux-armv7l/wheel/CLASV/__pycache__ 2025-08-31T18:17:45,280 copying build/lib/CLASV/__pycache__/cli.cpython-313.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,282 copying build/lib/CLASV/__pycache__/__init__.cpython-39.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,284 copying build/lib/CLASV/__pycache__/core.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,286 copying build/lib/CLASV/__pycache__/core.cpython-313.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,289 copying build/lib/CLASV/__pycache__/core.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,291 copying build/lib/CLASV/__pycache__/__init__.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,293 copying build/lib/CLASV/__pycache__/pipeline.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,295 copying build/lib/CLASV/__pycache__/__init__.cpython-313.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,297 copying build/lib/CLASV/__pycache__/core.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,299 copying build/lib/CLASV/__pycache__/cli.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,301 copying build/lib/CLASV/__pycache__/install_nextclade.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,303 copying build/lib/CLASV/__pycache__/install_seqkit.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,306 copying build/lib/CLASV/__pycache__/install_nextclade.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,308 copying build/lib/CLASV/__pycache__/pipeline.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,310 copying build/lib/CLASV/__pycache__/cli.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,312 copying build/lib/CLASV/__pycache__/__init__.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,313 copying build/lib/CLASV/__pycache__/core.cpython-39.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,316 copying build/lib/CLASV/__pycache__/install_seqkit.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,318 copying build/lib/CLASV/__pycache__/install_nextclade.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,320 copying build/lib/CLASV/__pycache__/install_seqkit.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,322 copying build/lib/CLASV/__pycache__/__init__.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,324 copying build/lib/CLASV/__pycache__/install_nextclade.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,326 copying build/lib/CLASV/__pycache__/cli.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,328 copying build/lib/CLASV/__pycache__/pipeline.cpython-39.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,330 copying build/lib/CLASV/__pycache__/pipeline.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,332 copying build/lib/CLASV/__pycache__/__init__.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,334 copying build/lib/CLASV/__pycache__/install_nextclade.cpython-313.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,336 copying build/lib/CLASV/__pycache__/core.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,339 copying build/lib/CLASV/__pycache__/pipeline.cpython-313.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,341 copying build/lib/CLASV/__pycache__/pipeline.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,343 copying build/lib/CLASV/__pycache__/install_seqkit.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,345 copying build/lib/CLASV/__pycache__/install_nextclade.cpython-39.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,348 copying build/lib/CLASV/__pycache__/cli.cpython-39.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,349 copying build/lib/CLASV/__pycache__/install_seqkit.cpython-313.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,352 copying build/lib/CLASV/__pycache__/install_seqkit.cpython-39.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,354 copying build/lib/CLASV/__pycache__/cli.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./CLASV/__pycache__ 2025-08-31T18:17:45,356 copying build/lib/CLASV/install_seqkit.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:45,359 copying build/lib/CLASV/pipeline.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:45,361 copying build/lib/CLASV/cli.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:45,364 copying build/lib/CLASV/benchmark_clasv.py -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:45,366 copying build/lib/CLASV/predflow_updated.png -> build/bdist.linux-armv7l/wheel/./CLASV 2025-08-31T18:17:45,375 creating build/bdist.linux-armv7l/wheel/CLASV/tools 2025-08-31T18:17:45,376 copying build/lib/CLASV/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./CLASV/tools 2025-08-31T18:17:45,379 copying build/lib/CLASV/tools/README-benchmark.md -> build/bdist.linux-armv7l/wheel/./CLASV/tools 2025-08-31T18:17:45,381 copying build/lib/CLASV/tools/benchmark_clasv.py -> build/bdist.linux-armv7l/wheel/./CLASV/tools 2025-08-31T18:17:45,383 running install_egg_info 2025-08-31T18:17:45,420 Copying CLASV.egg-info to build/bdist.linux-armv7l/wheel/./CLASV-1.0.5-py3.11.egg-info 2025-08-31T18:17:45,431 running install_scripts 2025-08-31T18:17:45,432 Installing Nextclade... 2025-08-31T18:17:45,433 Failed to install Nextclade: [Errno 2] No such file or directory: 'python' 2025-08-31T18:17:45,434 Installing Seqkit... 2025-08-31T18:17:45,434 Failed to install Seqkit: [Errno 2] No such file or directory: 'python' 2025-08-31T18:17:45,447 creating build/bdist.linux-armv7l/wheel/clasv-1.0.5.dist-info/WHEEL 2025-08-31T18:17:45,450 creating '/tmp/pip-wheel-8kcvfdtx/clasv-1.0.5-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-08-31T18:17:45,452 adding 'CLASV/MANIFEST.in' 2025-08-31T18:17:45,454 adding 'CLASV/README.md' 2025-08-31T18:17:45,455 adding 'CLASV/VERSION' 2025-08-31T18:17:45,457 adding 'CLASV/__init__.py' 2025-08-31T18:17:45,458 adding 'CLASV/benchmark_clasv.py' 2025-08-31T18:17:45,459 adding 'CLASV/cli.py' 2025-08-31T18:17:45,462 adding 'CLASV/core.py' 2025-08-31T18:17:45,463 adding 'CLASV/install_nextclade.py' 2025-08-31T18:17:45,465 adding 'CLASV/install_seqkit.py' 2025-08-31T18:17:45,467 adding 'CLASV/pipeline.py' 2025-08-31T18:17:45,513 adding 'CLASV/predflow_updated.png' 2025-08-31T18:17:45,517 adding 'CLASV/predict_lineage.smk' 2025-08-31T18:17:45,519 adding 'CLASV/requirements.txt' 2025-08-31T18:17:45,520 adding 'CLASV/setup.py' 2025-08-31T18:17:45,523 adding 'CLASV/CLASV.egg-info/PKG-INFO' 2025-08-31T18:17:45,524 adding 'CLASV/CLASV.egg-info/SOURCES.txt' 2025-08-31T18:17:45,525 adding 'CLASV/CLASV.egg-info/dependency_links.txt' 2025-08-31T18:17:45,526 adding 'CLASV/CLASV.egg-info/entry_points.txt' 2025-08-31T18:17:45,527 adding 'CLASV/CLASV.egg-info/requires.txt' 2025-08-31T18:17:45,528 adding 'CLASV/CLASV.egg-info/top_level.txt' 2025-08-31T18:17:45,530 adding 'CLASV/__pycache__/__init__.cpython-310.pyc' 2025-08-31T18:17:45,532 adding 'CLASV/__pycache__/__init__.cpython-311.pyc' 2025-08-31T18:17:45,533 adding 'CLASV/__pycache__/__init__.cpython-312.pyc' 2025-08-31T18:17:45,534 adding 'CLASV/__pycache__/__init__.cpython-313.pyc' 2025-08-31T18:17:45,536 adding 'CLASV/__pycache__/__init__.cpython-38.pyc' 2025-08-31T18:17:45,537 adding 'CLASV/__pycache__/__init__.cpython-39.pyc' 2025-08-31T18:17:45,538 adding 'CLASV/__pycache__/cli.cpython-310.pyc' 2025-08-31T18:17:45,540 adding 'CLASV/__pycache__/cli.cpython-311.pyc' 2025-08-31T18:17:45,541 adding 'CLASV/__pycache__/cli.cpython-312.pyc' 2025-08-31T18:17:45,543 adding 'CLASV/__pycache__/cli.cpython-313.pyc' 2025-08-31T18:17:45,544 adding 'CLASV/__pycache__/cli.cpython-38.pyc' 2025-08-31T18:17:45,546 adding 'CLASV/__pycache__/cli.cpython-39.pyc' 2025-08-31T18:17:45,548 adding 'CLASV/__pycache__/core.cpython-310.pyc' 2025-08-31T18:17:45,551 adding 'CLASV/__pycache__/core.cpython-311.pyc' 2025-08-31T18:17:45,553 adding 'CLASV/__pycache__/core.cpython-312.pyc' 2025-08-31T18:17:45,556 adding 'CLASV/__pycache__/core.cpython-313.pyc' 2025-08-31T18:17:45,558 adding 'CLASV/__pycache__/core.cpython-38.pyc' 2025-08-31T18:17:45,560 adding 'CLASV/__pycache__/core.cpython-39.pyc' 2025-08-31T18:17:45,562 adding 'CLASV/__pycache__/install_nextclade.cpython-310.pyc' 2025-08-31T18:17:45,564 adding 'CLASV/__pycache__/install_nextclade.cpython-311.pyc' 2025-08-31T18:17:45,566 adding 'CLASV/__pycache__/install_nextclade.cpython-312.pyc' 2025-08-31T18:17:45,568 adding 'CLASV/__pycache__/install_nextclade.cpython-313.pyc' 2025-08-31T18:17:45,569 adding 'CLASV/__pycache__/install_nextclade.cpython-38.pyc' 2025-08-31T18:17:45,571 adding 'CLASV/__pycache__/install_nextclade.cpython-39.pyc' 2025-08-31T18:17:45,573 adding 'CLASV/__pycache__/install_seqkit.cpython-310.pyc' 2025-08-31T18:17:45,575 adding 'CLASV/__pycache__/install_seqkit.cpython-311.pyc' 2025-08-31T18:17:45,577 adding 'CLASV/__pycache__/install_seqkit.cpython-312.pyc' 2025-08-31T18:17:45,579 adding 'CLASV/__pycache__/install_seqkit.cpython-313.pyc' 2025-08-31T18:17:45,580 adding 'CLASV/__pycache__/install_seqkit.cpython-38.pyc' 2025-08-31T18:17:45,582 adding 'CLASV/__pycache__/install_seqkit.cpython-39.pyc' 2025-08-31T18:17:45,583 adding 'CLASV/__pycache__/pipeline.cpython-310.pyc' 2025-08-31T18:17:45,585 adding 'CLASV/__pycache__/pipeline.cpython-311.pyc' 2025-08-31T18:17:45,586 adding 'CLASV/__pycache__/pipeline.cpython-312.pyc' 2025-08-31T18:17:45,588 adding 'CLASV/__pycache__/pipeline.cpython-313.pyc' 2025-08-31T18:17:45,590 adding 'CLASV/__pycache__/pipeline.cpython-38.pyc' 2025-08-31T18:17:45,591 adding 'CLASV/__pycache__/pipeline.cpython-39.pyc' 2025-08-31T18:17:45,593 adding 'CLASV/config/NC_004296.fasta' 2025-08-31T18:17:45,650 adding 'CLASV/config/RF_LASV_lineage_n100_aa.joblib' 2025-08-31T18:17:45,656 adding 'CLASV/config/config.yaml' 2025-08-31T18:17:45,659 adding 'CLASV/raw_data/Adesina_et_al_2023_EMI.csv' 2025-08-31T18:17:45,670 adding 'CLASV/raw_data/Adesina_et_al_2023_EMI.fasta' 2025-08-31T18:17:45,714 adding 'CLASV/raw_data/All_LASV_06_07_24.csv' 2025-08-31T18:17:49,029 adding 'CLASV/raw_data/All_LASV_06_07_24.fasta' 2025-08-31T18:17:49,090 adding 'CLASV/raw_data/Bangura_et_al_2024_EMI.csv' 2025-08-31T18:17:49,149 adding 'CLASV/raw_data/Bangura_et_al_2024_EMI.fasta' 2025-08-31T18:17:49,152 adding 'CLASV/tools/README-benchmark.md' 2025-08-31T18:17:49,153 adding 'CLASV/tools/__init__.py' 2025-08-31T18:17:49,156 adding 'CLASV/tools/benchmark_clasv.py' 2025-08-31T18:17:49,158 adding 'clasv-1.0.5.dist-info/licenses/LICENSE' 2025-08-31T18:17:49,160 adding 'clasv-1.0.5.dist-info/METADATA' 2025-08-31T18:17:49,161 adding 'clasv-1.0.5.dist-info/WHEEL' 2025-08-31T18:17:49,162 adding 'clasv-1.0.5.dist-info/entry_points.txt' 2025-08-31T18:17:49,163 adding 'clasv-1.0.5.dist-info/top_level.txt' 2025-08-31T18:17:49,165 adding 'clasv-1.0.5.dist-info/RECORD' 2025-08-31T18:17:49,199 removing build/bdist.linux-armv7l/wheel 2025-08-31T18:17:49,335 Building wheel for clasv (setup.py): finished with status 'done' 2025-08-31T18:17:49,365 Created wheel for clasv: filename=clasv-1.0.5-py3-none-any.whl size=2819045 sha256=a29890945aad27d2a5f9bb9c63b937850e953e6f83ce8164cca7ac408bc7fec8 2025-08-31T18:17:49,366 Stored in directory: /tmp/pip-ephem-wheel-cache-xj0rvz96/wheels/01/dc/53/719fc894afbbce0ff7a7d7a7609120ab1e48580302369be6de 2025-08-31T18:17:49,382 Successfully built clasv 2025-08-31T18:17:49,462 Removed build tracker: '/tmp/pip-build-tracker-shy3jo8n'