2024-11-28T14:05:15,765 Created temporary directory: /tmp/pip-build-tracker-x5sjnmzz
2024-11-28T14:05:15,767 Initialized build tracking at /tmp/pip-build-tracker-x5sjnmzz
2024-11-28T14:05:15,768 Created build tracker: /tmp/pip-build-tracker-x5sjnmzz
2024-11-28T14:05:15,768 Entered build tracker: /tmp/pip-build-tracker-x5sjnmzz
2024-11-28T14:05:15,770 Created temporary directory: /tmp/pip-wheel-5tvkqgzu
2024-11-28T14:05:15,774 Created temporary directory: /tmp/pip-ephem-wheel-cache-0735xli6
2024-11-28T14:05:15,818 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2024-11-28T14:05:15,820 2 location(s) to search for versions of homi-pipeline:
2024-11-28T14:05:15,820 * https://pypi.org/simple/homi-pipeline/
2024-11-28T14:05:15,820 * https://www.piwheels.org/simple/homi-pipeline/
2024-11-28T14:05:15,821 Fetching project page and analyzing links: https://pypi.org/simple/homi-pipeline/
2024-11-28T14:05:15,822 Getting page https://pypi.org/simple/homi-pipeline/
2024-11-28T14:05:15,823 Found index url https://pypi.org/simple/
2024-11-28T14:05:16,043 Fetched page https://pypi.org/simple/homi-pipeline/ as application/vnd.pypi.simple.v1+json
2024-11-28T14:05:16,047   Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/2b/2f/d7f737bbbcf5acdb21caad36381ddf833f3ae20a98eb9f38a60d630f8b19/HoMi_pipeline-1.0.4-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-11-28T14:05:16,048   Found link https://files.pythonhosted.org/packages/56/81/2de14d31804045b5b7a0c582de19188c01a8de5ad3f953841f01aef86419/homi_pipeline-1.0.4.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.4
2024-11-28T14:05:16,049   Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/14/73/530144aadf2b945ecb5d635e333dfc6038a5ce1a1ea03a1d54f1cf4a40a5/HoMi_pipeline-1.0.5-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-11-28T14:05:16,050   Found link https://files.pythonhosted.org/packages/81/4c/0bfa30002f2c33ff1bb90392ccdf509e1f38a472e5807bc4238fb1842d7c/homi_pipeline-1.0.5.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.5
2024-11-28T14:05:16,050   Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/1e/5f/eaa4752e3474d13c00c1e7a1e6e797c898bb925f2b3bcb39fd57474bbf72/HoMi_pipeline-1.0.6-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-11-28T14:05:16,051   Found link https://files.pythonhosted.org/packages/96/1c/d8cf18b86b78600bbd4b771fd8c2c1965c2397e162575c65e4e1d081a12e/homi_pipeline-1.0.6.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.6
2024-11-28T14:05:16,052   Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/e7/82/b5cf93b605bb58cf43d5086e05573f7b960410768cfd10c9212c884356fe/HoMi_pipeline-1.0.7-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-11-28T14:05:16,053   Found link https://files.pythonhosted.org/packages/8c/ce/d1098487cb2f77ab95dab26bd6fdb548572494e84034a9ce6deb2f986b0b/homi_pipeline-1.0.7.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.7
2024-11-28T14:05:16,054   Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/67/28/51f5cc23bbf4b5db0b1afb91dc058649b690bf64beaea710305f5014b2c1/HoMi_pipeline-1.0.8-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-11-28T14:05:16,055   Found link https://files.pythonhosted.org/packages/58/bf/fa627d33c0c8a77ef1f2bf3ad69560a790a8b2c8cce78041b3723fa24a8d/homi_pipeline-1.0.8.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.8
2024-11-28T14:05:16,055   Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/b3/f4/88f0f43ae830bcde620a8013bf0385035eb78e6ae8dd5ef66e9499e417cd/homi_pipeline-1.0.9-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-11-28T14:05:16,056   Found link https://files.pythonhosted.org/packages/5e/66/35b815aa9f646b0adaa5a6b98ead6067515c76903ca272eb913d78f2c379/homi_pipeline-1.0.9.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.9
2024-11-28T14:05:16,057   Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/31/eb/3763821c57a80520685fcc7c95c3665d5b1060a84b505f7ebadad54a3b7c/homi_pipeline-1.0.10-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-11-28T14:05:16,058   Found link https://files.pythonhosted.org/packages/d1/5f/828957918f33fbed6588f625aaf9384a9d7569e21606e2f7560f1249b70e/homi_pipeline-1.0.10.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.10
2024-11-28T14:05:16,059   Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/ee/b7/5c8fd935b67baff8e1c27b43911a490ffe7310e210e95e541acb66663f2d/homi_pipeline-1.0.11-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-11-28T14:05:16,059   Found link https://files.pythonhosted.org/packages/77/41/ca735a610bd9f7998c347c3d498e65bef1dabc02f42a217adad1d4cd19dd/homi_pipeline-1.0.11.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.11
2024-11-28T14:05:16,060   Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/8b/27/5f3915836722d13033a603ff16a9f608869cf1b8ce4b9bc00a29536c0b17/homi_pipeline-1.0.12-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-11-28T14:05:16,061   Found link https://files.pythonhosted.org/packages/6b/5a/bcf2cb296114b08c23319bac9bf748c0978f63d2e24dd0e7c66305192ec8/homi_pipeline-1.0.12.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.12
2024-11-28T14:05:16,061 Fetching project page and analyzing links: https://www.piwheels.org/simple/homi-pipeline/
2024-11-28T14:05:16,062 Getting page https://www.piwheels.org/simple/homi-pipeline/
2024-11-28T14:05:16,064 Found index url https://www.piwheels.org/simple/
2024-11-28T14:05:16,253 Fetched page https://www.piwheels.org/simple/homi-pipeline/ as text/html
2024-11-28T14:05:16,256   Skipping link: No binaries permitted for homi-pipeline: https://www.piwheels.org/simple/homi-pipeline/homi_pipeline-1.0.11-py3-none-any.whl#sha256=f38d6f322e26b94c4b6d87ace732c953b2d93a6a5f5004b6cd68d53aeff65eb6 (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-11-28T14:05:16,257   Skipping link: No binaries permitted for homi-pipeline: https://www.piwheels.org/simple/homi-pipeline/homi_pipeline-1.0.10-py3-none-any.whl#sha256=47782d893da5b163f47b447ce6624f07704ace41e7e743841962d5c074b4e366 (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-11-28T14:05:16,258   Skipping link: No binaries permitted for homi-pipeline: https://www.piwheels.org/simple/homi-pipeline/homi_pipeline-1.0.9-py3-none-any.whl#sha256=7e6216111167f6a7190da3e0cde77f73360b79a8177fb09035bd1ae650c1e507 (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-11-28T14:05:16,258   Skipping link: No binaries permitted for homi-pipeline: https://www.piwheels.org/simple/homi-pipeline/HoMi_pipeline-1.0.8-py3-none-any.whl#sha256=51b4b72a1a7278e9e56e84f3c6747b186a3e4745ad6ab68800b30a50bc914f86 (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-11-28T14:05:16,259   Skipping link: No binaries permitted for homi-pipeline: https://www.piwheels.org/simple/homi-pipeline/HoMi_pipeline-1.0.7-py3-none-any.whl#sha256=f0dc342ef3431deb1fe0119908dfaf6639c2172a72f2e024cd0ed49f2835183a (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-11-28T14:05:16,260   Skipping link: No binaries permitted for homi-pipeline: https://www.piwheels.org/simple/homi-pipeline/HoMi_pipeline-1.0.6-py3-none-any.whl#sha256=db11d135158a25a6e0c26125df20efe6c4215670508e11b243dc26bde8fa475d (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-11-28T14:05:16,260   Skipping link: No binaries permitted for homi-pipeline: https://www.piwheels.org/simple/homi-pipeline/HoMi_pipeline-1.0.5-py3-none-any.whl#sha256=e3d12dbe9433bef87e816014c345a09af2f99a91d543497606b0105bf3c73421 (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-11-28T14:05:16,261   Skipping link: No binaries permitted for homi-pipeline: https://www.piwheels.org/simple/homi-pipeline/HoMi_pipeline-1.0.4-py3-none-any.whl#sha256=a28da3efa0ab27e400f13a9e67038b54c72121a15fcebb90b87e2520fb85756f (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-11-28T14:05:16,262 Skipping link: not a file: https://www.piwheels.org/simple/homi-pipeline/
2024-11-28T14:05:16,262 Skipping link: not a file: https://pypi.org/simple/homi-pipeline/
2024-11-28T14:05:16,282 Given no hashes to check 1 links for project 'homi-pipeline': discarding no candidates
2024-11-28T14:05:16,284 Collecting homi-pipeline==1.0.12
2024-11-28T14:05:16,287   Created temporary directory: /tmp/pip-unpack-tjdgf00m
2024-11-28T14:05:16,500   Downloading homi_pipeline-1.0.12.tar.gz (50 kB)
2024-11-28T14:05:16,645   Added homi-pipeline==1.0.12 from https://files.pythonhosted.org/packages/6b/5a/bcf2cb296114b08c23319bac9bf748c0978f63d2e24dd0e7c66305192ec8/homi_pipeline-1.0.12.tar.gz to build tracker '/tmp/pip-build-tracker-x5sjnmzz'
2024-11-28T14:05:16,646   Running setup.py (path:/tmp/pip-wheel-5tvkqgzu/homi-pipeline_c56a432f4b364fbbaa9f7d3b86bd6abe/setup.py) egg_info for package homi-pipeline
2024-11-28T14:05:16,647   Created temporary directory: /tmp/pip-pip-egg-info-417ce40w
2024-11-28T14:05:16,648   Preparing metadata (setup.py): started
2024-11-28T14:05:16,649   Running command python setup.py egg_info
2024-11-28T14:05:17,400   /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
2024-11-28T14:05:17,400   !!

2024-11-28T14:05:17,401           ********************************************************************************
2024-11-28T14:05:17,402           Requirements should be satisfied by a PEP 517 installer.
2024-11-28T14:05:17,403           If you are using pip, you can try `pip install --use-pep517`.
2024-11-28T14:05:17,403           ********************************************************************************

2024-11-28T14:05:17,404   !!
2024-11-28T14:05:17,405     dist.fetch_build_eggs(dist.setup_requires)
2024-11-28T14:05:20,223   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
2024-11-28T14:05:20,224     warnings.warn(msg)
2024-11-28T14:05:20,319   running egg_info
2024-11-28T14:05:20,348   creating /tmp/pip-pip-egg-info-417ce40w/homi_pipeline.egg-info
2024-11-28T14:05:20,350   writing /tmp/pip-pip-egg-info-417ce40w/homi_pipeline.egg-info/PKG-INFO
2024-11-28T14:05:20,353   writing dependency_links to /tmp/pip-pip-egg-info-417ce40w/homi_pipeline.egg-info/dependency_links.txt
2024-11-28T14:05:20,355   writing requirements to /tmp/pip-pip-egg-info-417ce40w/homi_pipeline.egg-info/requires.txt
2024-11-28T14:05:20,356   writing top-level names to /tmp/pip-pip-egg-info-417ce40w/homi_pipeline.egg-info/top_level.txt
2024-11-28T14:05:20,358   writing manifest file '/tmp/pip-pip-egg-info-417ce40w/homi_pipeline.egg-info/SOURCES.txt'
2024-11-28T14:05:20,483   reading manifest file '/tmp/pip-pip-egg-info-417ce40w/homi_pipeline.egg-info/SOURCES.txt'
2024-11-28T14:05:20,485   adding license file 'LICENSE'
2024-11-28T14:05:20,489   writing manifest file '/tmp/pip-pip-egg-info-417ce40w/homi_pipeline.egg-info/SOURCES.txt'
2024-11-28T14:05:20,601   Preparing metadata (setup.py): finished with status 'done'
2024-11-28T14:05:20,605   Source in /tmp/pip-wheel-5tvkqgzu/homi-pipeline_c56a432f4b364fbbaa9f7d3b86bd6abe has version 1.0.12, which satisfies requirement homi-pipeline==1.0.12 from https://files.pythonhosted.org/packages/6b/5a/bcf2cb296114b08c23319bac9bf748c0978f63d2e24dd0e7c66305192ec8/homi_pipeline-1.0.12.tar.gz
2024-11-28T14:05:20,606   Removed homi-pipeline==1.0.12 from https://files.pythonhosted.org/packages/6b/5a/bcf2cb296114b08c23319bac9bf748c0978f63d2e24dd0e7c66305192ec8/homi_pipeline-1.0.12.tar.gz from build tracker '/tmp/pip-build-tracker-x5sjnmzz'
2024-11-28T14:05:20,614 Created temporary directory: /tmp/pip-unpack-kn5pri52
2024-11-28T14:05:20,615 Created temporary directory: /tmp/pip-unpack-fzy0hcbt
2024-11-28T14:05:20,615 Building wheels for collected packages: homi-pipeline
2024-11-28T14:05:20,619   Created temporary directory: /tmp/pip-wheel-ddfpyamf
2024-11-28T14:05:20,619   Building wheel for homi-pipeline (setup.py): started
2024-11-28T14:05:20,621   Destination directory: /tmp/pip-wheel-ddfpyamf
2024-11-28T14:05:20,621   Running command python setup.py bdist_wheel
2024-11-28T14:05:21,336   /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
2024-11-28T14:05:21,336   !!

2024-11-28T14:05:21,337           ********************************************************************************
2024-11-28T14:05:21,338           Requirements should be satisfied by a PEP 517 installer.
2024-11-28T14:05:21,338           If you are using pip, you can try `pip install --use-pep517`.
2024-11-28T14:05:21,339           ********************************************************************************

2024-11-28T14:05:21,340   !!
2024-11-28T14:05:21,340     dist.fetch_build_eggs(dist.setup_requires)
2024-11-28T14:05:21,549   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
2024-11-28T14:05:21,550     warnings.warn(msg)
2024-11-28T14:05:21,839   running bdist_wheel
2024-11-28T14:05:21,979   running build
2024-11-28T14:05:21,980   running build_py
2024-11-28T14:05:22,012   creating build/lib/homi_pipeline
2024-11-28T14:05:22,014   copying src/homi_pipeline/check_config.py -> build/lib/homi_pipeline
2024-11-28T14:05:22,016   copying src/homi_pipeline/profile_setup.py -> build/lib/homi_pipeline
2024-11-28T14:05:22,019   copying src/homi_pipeline/HoMi_cleanup.py -> build/lib/homi_pipeline
2024-11-28T14:05:22,021   copying src/homi_pipeline/snake_utils.py -> build/lib/homi_pipeline
2024-11-28T14:05:22,023   copying src/homi_pipeline/HoMi.py -> build/lib/homi_pipeline
2024-11-28T14:05:22,025   copying src/homi_pipeline/__init__.py -> build/lib/homi_pipeline
2024-11-28T14:05:22,027   running egg_info
2024-11-28T14:05:22,056   writing src/homi_pipeline.egg-info/PKG-INFO
2024-11-28T14:05:22,060   writing dependency_links to src/homi_pipeline.egg-info/dependency_links.txt
2024-11-28T14:05:22,062   writing requirements to src/homi_pipeline.egg-info/requires.txt
2024-11-28T14:05:22,063   writing top-level names to src/homi_pipeline.egg-info/top_level.txt
2024-11-28T14:05:22,099   reading manifest file 'src/homi_pipeline.egg-info/SOURCES.txt'
2024-11-28T14:05:22,103   adding license file 'LICENSE'
2024-11-28T14:05:22,107   writing manifest file 'src/homi_pipeline.egg-info/SOURCES.txt'
2024-11-28T14:05:22,110   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'homi_pipeline.conda_envs' is absent from the `packages` configuration.
2024-11-28T14:05:22,110   !!

2024-11-28T14:05:22,112           ********************************************************************************
2024-11-28T14:05:22,113           ############################
2024-11-28T14:05:22,113           # Package would be ignored #
2024-11-28T14:05:22,114           ############################
2024-11-28T14:05:22,114           Python recognizes 'homi_pipeline.conda_envs' as an importable package[^1],
2024-11-28T14:05:22,115           but it is absent from setuptools' `packages` configuration.

2024-11-28T14:05:22,117           This leads to an ambiguous overall configuration. If you want to distribute this
2024-11-28T14:05:22,117           package, please make sure that 'homi_pipeline.conda_envs' is explicitly added
2024-11-28T14:05:22,117           to the `packages` configuration field.

2024-11-28T14:05:22,119           Alternatively, you can also rely on setuptools' discovery methods
2024-11-28T14:05:22,120           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-11-28T14:05:22,121           instead of `find_packages(...)`/`find:`).

2024-11-28T14:05:22,122           You can read more about "package discovery" on setuptools documentation page:

2024-11-28T14:05:22,123           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-11-28T14:05:22,124           If you don't want 'homi_pipeline.conda_envs' to be distributed and are
2024-11-28T14:05:22,125           already explicitly excluding 'homi_pipeline.conda_envs' via
2024-11-28T14:05:22,125           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-11-28T14:05:22,126           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-11-28T14:05:22,127           combination with a more fine grained `package-data` configuration.

2024-11-28T14:05:22,128           You can read more about "package data files" on setuptools documentation page:

2024-11-28T14:05:22,129           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-11-28T14:05:22,131           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-11-28T14:05:22,132                 even if it does not contain any `.py` files.
2024-11-28T14:05:22,133                 On the other hand, currently there is no concept of package data
2024-11-28T14:05:22,133                 directory, all directories are treated like packages.
2024-11-28T14:05:22,134           ********************************************************************************

2024-11-28T14:05:22,135   !!
2024-11-28T14:05:22,135     check.warn(importable)
2024-11-28T14:05:22,136   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'homi_pipeline.data' is absent from the `packages` configuration.
2024-11-28T14:05:22,137   !!

2024-11-28T14:05:22,138           ********************************************************************************
2024-11-28T14:05:22,138           ############################
2024-11-28T14:05:22,139           # Package would be ignored #
2024-11-28T14:05:22,139           ############################
2024-11-28T14:05:22,140           Python recognizes 'homi_pipeline.data' as an importable package[^1],
2024-11-28T14:05:22,141           but it is absent from setuptools' `packages` configuration.

2024-11-28T14:05:22,142           This leads to an ambiguous overall configuration. If you want to distribute this
2024-11-28T14:05:22,142           package, please make sure that 'homi_pipeline.data' is explicitly added
2024-11-28T14:05:22,143           to the `packages` configuration field.

2024-11-28T14:05:22,144           Alternatively, you can also rely on setuptools' discovery methods
2024-11-28T14:05:22,145           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-11-28T14:05:22,146           instead of `find_packages(...)`/`find:`).

2024-11-28T14:05:22,147           You can read more about "package discovery" on setuptools documentation page:

2024-11-28T14:05:22,148           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-11-28T14:05:22,149           If you don't want 'homi_pipeline.data' to be distributed and are
2024-11-28T14:05:22,150           already explicitly excluding 'homi_pipeline.data' via
2024-11-28T14:05:22,150           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-11-28T14:05:22,151           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-11-28T14:05:22,151           combination with a more fine grained `package-data` configuration.

2024-11-28T14:05:22,153           You can read more about "package data files" on setuptools documentation page:

2024-11-28T14:05:22,154           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-11-28T14:05:22,156           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-11-28T14:05:22,156                 even if it does not contain any `.py` files.
2024-11-28T14:05:22,157                 On the other hand, currently there is no concept of package data
2024-11-28T14:05:22,157                 directory, all directories are treated like packages.
2024-11-28T14:05:22,158           ********************************************************************************

2024-11-28T14:05:22,159   !!
2024-11-28T14:05:22,159     check.warn(importable)
2024-11-28T14:05:22,160   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'homi_pipeline.rule_utils' is absent from the `packages` configuration.
2024-11-28T14:05:22,160   !!

2024-11-28T14:05:22,161           ********************************************************************************
2024-11-28T14:05:22,162           ############################
2024-11-28T14:05:22,162           # Package would be ignored #
2024-11-28T14:05:22,163           ############################
2024-11-28T14:05:22,163           Python recognizes 'homi_pipeline.rule_utils' as an importable package[^1],
2024-11-28T14:05:22,164           but it is absent from setuptools' `packages` configuration.

2024-11-28T14:05:22,165           This leads to an ambiguous overall configuration. If you want to distribute this
2024-11-28T14:05:22,165           package, please make sure that 'homi_pipeline.rule_utils' is explicitly added
2024-11-28T14:05:22,166           to the `packages` configuration field.

2024-11-28T14:05:22,167           Alternatively, you can also rely on setuptools' discovery methods
2024-11-28T14:05:22,168           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-11-28T14:05:22,168           instead of `find_packages(...)`/`find:`).

2024-11-28T14:05:22,169           You can read more about "package discovery" on setuptools documentation page:

2024-11-28T14:05:22,170           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-11-28T14:05:22,171           If you don't want 'homi_pipeline.rule_utils' to be distributed and are
2024-11-28T14:05:22,172           already explicitly excluding 'homi_pipeline.rule_utils' via
2024-11-28T14:05:22,172           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-11-28T14:05:22,173           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-11-28T14:05:22,173           combination with a more fine grained `package-data` configuration.

2024-11-28T14:05:22,175           You can read more about "package data files" on setuptools documentation page:

2024-11-28T14:05:22,176           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-11-28T14:05:22,177           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-11-28T14:05:22,178                 even if it does not contain any `.py` files.
2024-11-28T14:05:22,178                 On the other hand, currently there is no concept of package data
2024-11-28T14:05:22,179                 directory, all directories are treated like packages.
2024-11-28T14:05:22,180           ********************************************************************************

2024-11-28T14:05:22,181   !!
2024-11-28T14:05:22,181     check.warn(importable)
2024-11-28T14:05:22,182   copying src/homi_pipeline/snakefile -> build/lib/homi_pipeline
2024-11-28T14:05:22,182   creating build/lib/homi_pipeline/conda_envs
2024-11-28T14:05:22,183   copying src/homi_pipeline/conda_envs/bbmap.yaml -> build/lib/homi_pipeline/conda_envs
2024-11-28T14:05:22,183   copying src/homi_pipeline/conda_envs/fastqc.yaml -> build/lib/homi_pipeline/conda_envs
2024-11-28T14:05:22,184   copying src/homi_pipeline/conda_envs/featureCounts.yaml -> build/lib/homi_pipeline/conda_envs
2024-11-28T14:05:22,185   copying src/homi_pipeline/conda_envs/hisat2.yaml -> build/lib/homi_pipeline/conda_envs
2024-11-28T14:05:22,185   copying src/homi_pipeline/conda_envs/hostile.yaml -> build/lib/homi_pipeline/conda_envs
2024-11-28T14:05:22,185   copying src/homi_pipeline/conda_envs/humann.yaml -> build/lib/homi_pipeline/conda_envs
2024-11-28T14:05:22,186   copying src/homi_pipeline/conda_envs/kraken.yaml -> build/lib/homi_pipeline/conda_envs
2024-11-28T14:05:22,186   copying src/homi_pipeline/conda_envs/nonpareil.yaml -> build/lib/homi_pipeline/conda_envs
2024-11-28T14:05:22,187   copying src/homi_pipeline/conda_envs/r_env.yaml -> build/lib/homi_pipeline/conda_envs
2024-11-28T14:05:22,187   copying src/homi_pipeline/conda_envs/seqtk.yaml -> build/lib/homi_pipeline/conda_envs
2024-11-28T14:05:22,188   copying src/homi_pipeline/conda_envs/trimmomatic.yaml -> build/lib/homi_pipeline/conda_envs
2024-11-28T14:05:22,188   creating build/lib/homi_pipeline/data
2024-11-28T14:05:22,189   copying src/homi_pipeline/data/adapters.fa -> build/lib/homi_pipeline/data
2024-11-28T14:05:22,189   creating build/lib/homi_pipeline/rule_utils
2024-11-28T14:05:22,190   copying src/homi_pipeline/rule_utils/Gut_metabolic_modules.Rmd -> build/lib/homi_pipeline/rule_utils
2024-11-28T14:05:22,190   copying src/homi_pipeline/rule_utils/HUMAnN_microshades.Rmd -> build/lib/homi_pipeline/rule_utils
2024-11-28T14:05:22,191   copying src/homi_pipeline/rule_utils/HUMAnN_to_phyloseq_helper.R -> build/lib/homi_pipeline/rule_utils
2024-11-28T14:05:22,191   copying src/homi_pipeline/rule_utils/Kraken_microshades.Rmd -> build/lib/homi_pipeline/rule_utils
2024-11-28T14:05:22,192   copying src/homi_pipeline/rule_utils/Metaphlan_microshades.Rmd -> build/lib/homi_pipeline/rule_utils
2024-11-28T14:05:22,192   copying src/homi_pipeline/rule_utils/R_packages.R -> build/lib/homi_pipeline/rule_utils
2024-11-28T14:05:22,193   copying src/homi_pipeline/rule_utils/aggregate_metaphlan_bugslists.py -> build/lib/homi_pipeline/rule_utils
2024-11-28T14:05:22,193   copying src/homi_pipeline/rule_utils/bracken_to_phyloseq_helper.R -> build/lib/homi_pipeline/rule_utils
2024-11-28T14:05:22,194   copying src/homi_pipeline/rule_utils/combine_kreports.py -> build/lib/homi_pipeline/rule_utils
2024-11-28T14:05:22,194   copying src/homi_pipeline/rule_utils/convert_mphlan_v4_to_v3.py -> build/lib/homi_pipeline/rule_utils
2024-11-28T14:05:22,195   copying src/homi_pipeline/rule_utils/counts_to_tpm.py -> build/lib/homi_pipeline/rule_utils
2024-11-28T14:05:22,195   copying src/homi_pipeline/rule_utils/metaphlan_to_phyloseq_helper.R -> build/lib/homi_pipeline/rule_utils
2024-11-28T14:05:22,196   copying src/homi_pipeline/rule_utils/nonpareil_curves.Rmd -> build/lib/homi_pipeline/rule_utils
2024-11-28T14:05:22,197   copying src/homi_pipeline/rule_utils/read_reports.py -> build/lib/homi_pipeline/rule_utils
2024-11-28T14:05:22,197   copying src/homi_pipeline/rule_utils/sam2bam.sh -> build/lib/homi_pipeline/rule_utils
2024-11-28T14:05:22,198   running build_scripts
2024-11-28T14:05:22,199   creating build/scripts-3.11
2024-11-28T14:05:22,199   copying and adjusting src/homi_pipeline/HoMi.py -> build/scripts-3.11
2024-11-28T14:05:22,201   copying src/homi_pipeline/snake_utils.py -> build/scripts-3.11
2024-11-28T14:05:22,203   copying and adjusting src/homi_pipeline/HoMi_cleanup.py -> build/scripts-3.11
2024-11-28T14:05:22,205   copying and adjusting src/homi_pipeline/profile_setup.py -> build/scripts-3.11
2024-11-28T14:05:22,207   copying and adjusting src/homi_pipeline/check_config.py -> build/scripts-3.11
2024-11-28T14:05:22,209   copying and adjusting src/homi_pipeline/rule_utils/combine_kreports.py -> build/scripts-3.11
2024-11-28T14:05:22,211   copying and adjusting src/homi_pipeline/rule_utils/aggregate_metaphlan_bugslists.py -> build/scripts-3.11
2024-11-28T14:05:22,213   copying and adjusting src/homi_pipeline/rule_utils/convert_mphlan_v4_to_v3.py -> build/scripts-3.11
2024-11-28T14:05:22,214   copying and adjusting src/homi_pipeline/rule_utils/counts_to_tpm.py -> build/scripts-3.11
2024-11-28T14:05:22,216   copying and adjusting src/homi_pipeline/rule_utils/read_reports.py -> build/scripts-3.11
2024-11-28T14:05:22,218   changing mode of build/scripts-3.11/HoMi.py from 644 to 755
2024-11-28T14:05:22,218   changing mode of build/scripts-3.11/snake_utils.py from 644 to 755
2024-11-28T14:05:22,218   changing mode of build/scripts-3.11/HoMi_cleanup.py from 644 to 755
2024-11-28T14:05:22,219   changing mode of build/scripts-3.11/profile_setup.py from 644 to 755
2024-11-28T14:05:22,219   changing mode of build/scripts-3.11/check_config.py from 644 to 755
2024-11-28T14:05:22,220   changing mode of build/scripts-3.11/combine_kreports.py from 644 to 755
2024-11-28T14:05:22,220   changing mode of build/scripts-3.11/aggregate_metaphlan_bugslists.py from 644 to 755
2024-11-28T14:05:22,221   changing mode of build/scripts-3.11/convert_mphlan_v4_to_v3.py from 644 to 755
2024-11-28T14:05:22,221   changing mode of build/scripts-3.11/counts_to_tpm.py from 644 to 755
2024-11-28T14:05:22,222   changing mode of build/scripts-3.11/read_reports.py from 644 to 755
2024-11-28T14:05:22,249   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2024-11-28T14:05:22,250   !!

2024-11-28T14:05:22,250           ********************************************************************************
2024-11-28T14:05:22,251           Please avoid running ``setup.py`` directly.
2024-11-28T14:05:22,252           Instead, use pypa/build, pypa/installer or other
2024-11-28T14:05:22,252           standards-based tools.

2024-11-28T14:05:22,253           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2024-11-28T14:05:22,254           ********************************************************************************

2024-11-28T14:05:22,255   !!
2024-11-28T14:05:22,256     self.initialize_options()
2024-11-28T14:05:22,278   installing to build/bdist.linux-armv7l/wheel
2024-11-28T14:05:22,278   running install
2024-11-28T14:05:22,303   running install_lib
2024-11-28T14:05:22,332   creating build/bdist.linux-armv7l/wheel
2024-11-28T14:05:22,335   creating build/bdist.linux-armv7l/wheel/homi_pipeline
2024-11-28T14:05:22,336   copying build/lib/homi_pipeline/check_config.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline
2024-11-28T14:05:22,338   copying build/lib/homi_pipeline/snakefile -> build/bdist.linux-armv7l/wheel/./homi_pipeline
2024-11-28T14:05:22,341   copying build/lib/homi_pipeline/profile_setup.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline
2024-11-28T14:05:22,343   copying build/lib/homi_pipeline/HoMi_cleanup.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline
2024-11-28T14:05:22,345   copying build/lib/homi_pipeline/snake_utils.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline
2024-11-28T14:05:22,348   creating build/bdist.linux-armv7l/wheel/homi_pipeline/rule_utils
2024-11-28T14:05:22,349   copying build/lib/homi_pipeline/rule_utils/counts_to_tpm.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-11-28T14:05:22,351   copying build/lib/homi_pipeline/rule_utils/metaphlan_to_phyloseq_helper.R -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-11-28T14:05:22,353   copying build/lib/homi_pipeline/rule_utils/Gut_metabolic_modules.Rmd -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-11-28T14:05:22,355   copying build/lib/homi_pipeline/rule_utils/convert_mphlan_v4_to_v3.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-11-28T14:05:22,357   copying build/lib/homi_pipeline/rule_utils/HUMAnN_microshades.Rmd -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-11-28T14:05:22,359   copying build/lib/homi_pipeline/rule_utils/nonpareil_curves.Rmd -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-11-28T14:05:22,361   copying build/lib/homi_pipeline/rule_utils/combine_kreports.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-11-28T14:05:22,364   copying build/lib/homi_pipeline/rule_utils/Kraken_microshades.Rmd -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-11-28T14:05:22,366   copying build/lib/homi_pipeline/rule_utils/Metaphlan_microshades.Rmd -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-11-28T14:05:22,369   copying build/lib/homi_pipeline/rule_utils/sam2bam.sh -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-11-28T14:05:22,370   copying build/lib/homi_pipeline/rule_utils/read_reports.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-11-28T14:05:22,373   copying build/lib/homi_pipeline/rule_utils/aggregate_metaphlan_bugslists.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-11-28T14:05:22,374   copying build/lib/homi_pipeline/rule_utils/R_packages.R -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-11-28T14:05:22,376   copying build/lib/homi_pipeline/rule_utils/HUMAnN_to_phyloseq_helper.R -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-11-28T14:05:22,378   copying build/lib/homi_pipeline/rule_utils/bracken_to_phyloseq_helper.R -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-11-28T14:05:22,380   creating build/bdist.linux-armv7l/wheel/homi_pipeline/data
2024-11-28T14:05:22,381   copying build/lib/homi_pipeline/data/adapters.fa -> build/bdist.linux-armv7l/wheel/./homi_pipeline/data
2024-11-28T14:05:22,384   copying build/lib/homi_pipeline/HoMi.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline
2024-11-28T14:05:22,386   copying build/lib/homi_pipeline/__init__.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline
2024-11-28T14:05:22,389   creating build/bdist.linux-armv7l/wheel/homi_pipeline/conda_envs
2024-11-28T14:05:22,390   copying build/lib/homi_pipeline/conda_envs/nonpareil.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-11-28T14:05:22,392   copying build/lib/homi_pipeline/conda_envs/trimmomatic.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-11-28T14:05:22,393   copying build/lib/homi_pipeline/conda_envs/r_env.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-11-28T14:05:22,395   copying build/lib/homi_pipeline/conda_envs/featureCounts.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-11-28T14:05:22,397   copying build/lib/homi_pipeline/conda_envs/hisat2.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-11-28T14:05:22,399   copying build/lib/homi_pipeline/conda_envs/seqtk.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-11-28T14:05:22,401   copying build/lib/homi_pipeline/conda_envs/humann.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-11-28T14:05:22,402   copying build/lib/homi_pipeline/conda_envs/bbmap.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-11-28T14:05:22,404   copying build/lib/homi_pipeline/conda_envs/fastqc.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-11-28T14:05:22,406   copying build/lib/homi_pipeline/conda_envs/kraken.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-11-28T14:05:22,408   copying build/lib/homi_pipeline/conda_envs/hostile.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-11-28T14:05:22,409   running install_egg_info
2024-11-28T14:05:22,440   Copying src/homi_pipeline.egg-info to build/bdist.linux-armv7l/wheel/./homi_pipeline-1.0.12-py3.11.egg-info
2024-11-28T14:05:22,450   running install_scripts
2024-11-28T14:05:22,451   creating build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts
2024-11-28T14:05:22,453   copying build/scripts-3.11/counts_to_tpm.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts
2024-11-28T14:05:22,455   copying build/scripts-3.11/check_config.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts
2024-11-28T14:05:22,457   copying build/scripts-3.11/convert_mphlan_v4_to_v3.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts
2024-11-28T14:05:22,459   copying build/scripts-3.11/profile_setup.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts
2024-11-28T14:05:22,461   copying build/scripts-3.11/HoMi_cleanup.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts
2024-11-28T14:05:22,463   copying build/scripts-3.11/snake_utils.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts
2024-11-28T14:05:22,465   copying build/scripts-3.11/combine_kreports.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts
2024-11-28T14:05:22,468   copying build/scripts-3.11/read_reports.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts
2024-11-28T14:05:22,470   copying build/scripts-3.11/HoMi.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts
2024-11-28T14:05:22,472   copying build/scripts-3.11/aggregate_metaphlan_bugslists.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts
2024-11-28T14:05:22,473   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts/counts_to_tpm.py to 755
2024-11-28T14:05:22,474   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts/check_config.py to 755
2024-11-28T14:05:22,474   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts/convert_mphlan_v4_to_v3.py to 755
2024-11-28T14:05:22,475   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts/profile_setup.py to 755
2024-11-28T14:05:22,475   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts/HoMi_cleanup.py to 755
2024-11-28T14:05:22,476   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts/snake_utils.py to 755
2024-11-28T14:05:22,476   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts/combine_kreports.py to 755
2024-11-28T14:05:22,477   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts/read_reports.py to 755
2024-11-28T14:05:22,477   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts/HoMi.py to 755
2024-11-28T14:05:22,478   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.data/scripts/aggregate_metaphlan_bugslists.py to 755
2024-11-28T14:05:22,493   creating build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.12.dist-info/WHEEL
2024-11-28T14:05:22,495   creating '/tmp/pip-wheel-ddfpyamf/homi_pipeline-1.0.12-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2024-11-28T14:05:22,497   adding 'homi_pipeline/HoMi.py'
2024-11-28T14:05:22,499   adding 'homi_pipeline/HoMi_cleanup.py'
2024-11-28T14:05:22,500   adding 'homi_pipeline/__init__.py'
2024-11-28T14:05:22,502   adding 'homi_pipeline/check_config.py'
2024-11-28T14:05:22,503   adding 'homi_pipeline/profile_setup.py'
2024-11-28T14:05:22,505   adding 'homi_pipeline/snake_utils.py'
2024-11-28T14:05:22,510   adding 'homi_pipeline/snakefile'
2024-11-28T14:05:22,512   adding 'homi_pipeline/conda_envs/bbmap.yaml'
2024-11-28T14:05:22,513   adding 'homi_pipeline/conda_envs/fastqc.yaml'
2024-11-28T14:05:22,514   adding 'homi_pipeline/conda_envs/featureCounts.yaml'
2024-11-28T14:05:22,515   adding 'homi_pipeline/conda_envs/hisat2.yaml'
2024-11-28T14:05:22,516   adding 'homi_pipeline/conda_envs/hostile.yaml'
2024-11-28T14:05:22,517   adding 'homi_pipeline/conda_envs/humann.yaml'
2024-11-28T14:05:22,519   adding 'homi_pipeline/conda_envs/kraken.yaml'
2024-11-28T14:05:22,520   adding 'homi_pipeline/conda_envs/nonpareil.yaml'
2024-11-28T14:05:22,521   adding 'homi_pipeline/conda_envs/r_env.yaml'
2024-11-28T14:05:22,522   adding 'homi_pipeline/conda_envs/seqtk.yaml'
2024-11-28T14:05:22,523   adding 'homi_pipeline/conda_envs/trimmomatic.yaml'
2024-11-28T14:05:22,526   adding 'homi_pipeline/data/adapters.fa'
2024-11-28T14:05:22,528   adding 'homi_pipeline/rule_utils/Gut_metabolic_modules.Rmd'
2024-11-28T14:05:22,529   adding 'homi_pipeline/rule_utils/HUMAnN_microshades.Rmd'
2024-11-28T14:05:22,531   adding 'homi_pipeline/rule_utils/HUMAnN_to_phyloseq_helper.R'
2024-11-28T14:05:22,532   adding 'homi_pipeline/rule_utils/Kraken_microshades.Rmd'
2024-11-28T14:05:22,535   adding 'homi_pipeline/rule_utils/Metaphlan_microshades.Rmd'
2024-11-28T14:05:22,536   adding 'homi_pipeline/rule_utils/R_packages.R'
2024-11-28T14:05:22,537   adding 'homi_pipeline/rule_utils/aggregate_metaphlan_bugslists.py'
2024-11-28T14:05:22,538   adding 'homi_pipeline/rule_utils/bracken_to_phyloseq_helper.R'
2024-11-28T14:05:22,540   adding 'homi_pipeline/rule_utils/combine_kreports.py'
2024-11-28T14:05:22,541   adding 'homi_pipeline/rule_utils/convert_mphlan_v4_to_v3.py'
2024-11-28T14:05:22,543   adding 'homi_pipeline/rule_utils/counts_to_tpm.py'
2024-11-28T14:05:22,544   adding 'homi_pipeline/rule_utils/metaphlan_to_phyloseq_helper.R'
2024-11-28T14:05:22,546   adding 'homi_pipeline/rule_utils/nonpareil_curves.Rmd'
2024-11-28T14:05:22,547   adding 'homi_pipeline/rule_utils/read_reports.py'
2024-11-28T14:05:22,548   adding 'homi_pipeline/rule_utils/sam2bam.sh'
2024-11-28T14:05:22,551   adding 'homi_pipeline-1.0.12.data/scripts/HoMi.py'
2024-11-28T14:05:22,552   adding 'homi_pipeline-1.0.12.data/scripts/HoMi_cleanup.py'
2024-11-28T14:05:22,554   adding 'homi_pipeline-1.0.12.data/scripts/aggregate_metaphlan_bugslists.py'
2024-11-28T14:05:22,555   adding 'homi_pipeline-1.0.12.data/scripts/check_config.py'
2024-11-28T14:05:22,557   adding 'homi_pipeline-1.0.12.data/scripts/combine_kreports.py'
2024-11-28T14:05:22,559   adding 'homi_pipeline-1.0.12.data/scripts/convert_mphlan_v4_to_v3.py'
2024-11-28T14:05:22,560   adding 'homi_pipeline-1.0.12.data/scripts/counts_to_tpm.py'
2024-11-28T14:05:22,562   adding 'homi_pipeline-1.0.12.data/scripts/profile_setup.py'
2024-11-28T14:05:22,563   adding 'homi_pipeline-1.0.12.data/scripts/read_reports.py'
2024-11-28T14:05:22,565   adding 'homi_pipeline-1.0.12.data/scripts/snake_utils.py'
2024-11-28T14:05:22,568   adding 'homi_pipeline-1.0.12.dist-info/LICENSE'
2024-11-28T14:05:22,570   adding 'homi_pipeline-1.0.12.dist-info/METADATA'
2024-11-28T14:05:22,571   adding 'homi_pipeline-1.0.12.dist-info/WHEEL'
2024-11-28T14:05:22,572   adding 'homi_pipeline-1.0.12.dist-info/top_level.txt'
2024-11-28T14:05:22,573   adding 'homi_pipeline-1.0.12.dist-info/RECORD'
2024-11-28T14:05:22,577   removing build/bdist.linux-armv7l/wheel
2024-11-28T14:05:22,702   Building wheel for homi-pipeline (setup.py): finished with status 'done'
2024-11-28T14:05:22,705   Created wheel for homi-pipeline: filename=homi_pipeline-1.0.12-py3-none-any.whl size=72849 sha256=9e996678bebe3b97072ad16e50c5b8953a6fb84c7e7ec6311e6fb27d3e5fade7
2024-11-28T14:05:22,706   Stored in directory: /tmp/pip-ephem-wheel-cache-0735xli6/wheels/a7/7e/bb/622df513630d186688a7579cfa88c02dd7502d638840b16d79
2024-11-28T14:05:22,719 Successfully built homi-pipeline
2024-11-28T14:05:22,724 Removed build tracker: '/tmp/pip-build-tracker-x5sjnmzz'