2024-01-22T00:30:18,064 Created temporary directory: /tmp/pip-build-tracker-5cakwmwq 2024-01-22T00:30:18,065 Initialized build tracking at /tmp/pip-build-tracker-5cakwmwq 2024-01-22T00:30:18,066 Created build tracker: /tmp/pip-build-tracker-5cakwmwq 2024-01-22T00:30:18,066 Entered build tracker: /tmp/pip-build-tracker-5cakwmwq 2024-01-22T00:30:18,067 Created temporary directory: /tmp/pip-wheel-s125gggm 2024-01-22T00:30:18,070 Created temporary directory: /tmp/pip-ephem-wheel-cache-yjwaqgyz 2024-01-22T00:30:18,092 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-01-22T00:30:18,096 2 location(s) to search for versions of mitywgs: 2024-01-22T00:30:18,096 * https://pypi.org/simple/mitywgs/ 2024-01-22T00:30:18,096 * https://www.piwheels.org/simple/mitywgs/ 2024-01-22T00:30:18,097 Fetching project page and analyzing links: https://pypi.org/simple/mitywgs/ 2024-01-22T00:30:18,097 Getting page https://pypi.org/simple/mitywgs/ 2024-01-22T00:30:18,099 Found index url https://pypi.org/simple/ 2024-01-22T00:30:18,312 Fetched page https://pypi.org/simple/mitywgs/ as application/vnd.pypi.simple.v1+json 2024-01-22T00:30:18,316 Skipping link: No binaries permitted for mitywgs: https://files.pythonhosted.org/packages/95/5f/0fba9bf0dc8952226a3f354f63799ffc90c6316bd29655a65af24a4eb38a/mitywgs-0.1.0-py3-none-any.whl (from https://pypi.org/simple/mitywgs/) (requires-python:>=3.5.3) 2024-01-22T00:30:18,317 Found link https://files.pythonhosted.org/packages/86/fc/4260dd9cae80420e003f605e31b54e73af7fb685625664d1ccf0435ac64e/mitywgs-0.1.0.tar.gz (from https://pypi.org/simple/mitywgs/) (requires-python:>=3.5.3), version: 0.1.0 2024-01-22T00:30:18,318 Skipping link: No binaries permitted for mitywgs: https://files.pythonhosted.org/packages/4f/5e/b43206082ca61da3e83d9e5c1e143c3de55f32c04146c81a70281726522a/mitywgs-0.1.1-py3-none-any.whl (from https://pypi.org/simple/mitywgs/) (requires-python:>=3.5.3) 2024-01-22T00:30:18,319 Found link https://files.pythonhosted.org/packages/9b/c5/77f664847f6788589008debb792b3c5436e4b496a030cb90e2062aaa1086/mitywgs-0.1.1.tar.gz (from https://pypi.org/simple/mitywgs/) (requires-python:>=3.5.3), version: 0.1.1 2024-01-22T00:30:18,320 Skipping link: No binaries permitted for mitywgs: https://files.pythonhosted.org/packages/e5/b4/1512000bcbc0c4187fb9078309af272f45133fd51123b493a487b4712d3d/mitywgs-0.1.2-py3-none-any.whl (from https://pypi.org/simple/mitywgs/) (requires-python:>=3.5.3) 2024-01-22T00:30:18,321 Found link https://files.pythonhosted.org/packages/9a/17/bd154ed0992c1dfe18326afd02587f9acc83c7f06d0d10c7b1953b4dbd26/mitywgs-0.1.2.tar.gz (from https://pypi.org/simple/mitywgs/) (requires-python:>=3.5.3), version: 0.1.2 2024-01-22T00:30:18,322 Skipping link: No binaries permitted for mitywgs: https://files.pythonhosted.org/packages/40/b3/d2199c137c3893b5935b31a46b771ca9cb02e01ea169646a124bc8b19bde/mitywgs-0.1.3-py3-none-any.whl (from https://pypi.org/simple/mitywgs/) (requires-python:>=3.5.3) 2024-01-22T00:30:18,323 Found link https://files.pythonhosted.org/packages/09/89/ec808bf6dd1fb7095eda564ef732a03d2146981fa599f862b3d0ed07a687/mitywgs-0.1.3.tar.gz (from https://pypi.org/simple/mitywgs/) (requires-python:>=3.5.3), version: 0.1.3 2024-01-22T00:30:18,323 Skipping link: No binaries permitted for mitywgs: https://files.pythonhosted.org/packages/c7/ab/17446e81990597f0ede16c0426ba76037f02b440dc5d51a6b8dc9a208881/mitywgs-0.2.0-py3-none-any.whl (from https://pypi.org/simple/mitywgs/) (requires-python:>=3.5.3) 2024-01-22T00:30:18,324 Found link https://files.pythonhosted.org/packages/c9/ab/7de2568d5ed11e067b0390fd31fa1d30eb099bce133b55cb0afed11c1986/mitywgs-0.2.0.tar.gz (from https://pypi.org/simple/mitywgs/) (requires-python:>=3.5.3), version: 0.2.0 2024-01-22T00:30:18,325 Found link https://files.pythonhosted.org/packages/1d/42/c1c72c18c8e20c698dde0e058896655b177d48e46693afd5f25a4820a8d0/mitywgs-0.2.1.tar.gz (from https://pypi.org/simple/mitywgs/) (requires-python:>=3.5.4), version: 0.2.1 2024-01-22T00:30:18,326 Skipping link: No binaries permitted for mitywgs: https://files.pythonhosted.org/packages/70/65/149da0fc3c6b39d585afe30be8e565acd57c30ab061098b91d24e4bf3b28/mitywgs-0.3.0-py3-none-any.whl (from https://pypi.org/simple/mitywgs/) (requires-python:>=3.5.4) 2024-01-22T00:30:18,327 Found link https://files.pythonhosted.org/packages/85/f2/da170c825d1453e9c350e288bd19018b54d9df4dc1c1d1fcb7332bbc67d2/mitywgs-0.3.0.tar.gz (from https://pypi.org/simple/mitywgs/) (requires-python:>=3.5.4), version: 0.3.0 2024-01-22T00:30:18,328 Skipping link: No binaries permitted for mitywgs: https://files.pythonhosted.org/packages/29/f0/3e335d7958a5d6d3dcf1dfba93594eec77bcf0aa9adde9d0978c0ff444bb/mitywgs-0.3.1-py3-none-any.whl (from https://pypi.org/simple/mitywgs/) (requires-python:>=3.5.4) 2024-01-22T00:30:18,329 Found link https://files.pythonhosted.org/packages/93/a8/845e11c50e4bf8459685b1fe4a3123c2495d573056c3e56a17c6e84d35c5/mitywgs-0.3.1.tar.gz (from https://pypi.org/simple/mitywgs/) (requires-python:>=3.5.4), version: 0.3.1 2024-01-22T00:30:18,329 Skipping link: No binaries permitted for mitywgs: https://files.pythonhosted.org/packages/1b/9e/ca91734f30aaf35c1b27ac388e8b333de771694b23c20559ab3c7469abe3/mitywgs-0.4.0-py3-none-any.whl (from https://pypi.org/simple/mitywgs/) (requires-python:>=3.5.4) 2024-01-22T00:30:18,330 Found link https://files.pythonhosted.org/packages/11/3e/0afdf01d6c7065637962c87ace18a33bfdd4c33a0685f255459a73c29662/mitywgs-0.4.0.tar.gz (from https://pypi.org/simple/mitywgs/) (requires-python:>=3.5.4), version: 0.4.0 2024-01-22T00:30:18,331 Found link https://files.pythonhosted.org/packages/27/00/b37d3d18ec330c45f5922187afc37eaa805a6182d8fa29954c29652068a7/mitywgs-1.0.0.tar.gz (from https://pypi.org/simple/mitywgs/) (requires-python:>=3.5.4), version: 1.0.0 2024-01-22T00:30:18,332 Fetching project page and analyzing links: https://www.piwheels.org/simple/mitywgs/ 2024-01-22T00:30:18,332 Getting page https://www.piwheels.org/simple/mitywgs/ 2024-01-22T00:30:18,334 Found index url https://www.piwheels.org/simple/ 2024-01-22T00:30:18,483 Fetched page https://www.piwheels.org/simple/mitywgs/ as text/html 2024-01-22T00:30:18,487 Skipping link: No binaries permitted for mitywgs: https://www.piwheels.org/simple/mitywgs/mitywgs-0.4.0-py3-none-any.whl#sha256=f8865542ccd554aba04ac95d9728beee6034f5c1de378ccf783d530a0d4db8f9 (from https://www.piwheels.org/simple/mitywgs/) (requires-python:>=3.5.4) 2024-01-22T00:30:18,487 Skipping link: No binaries permitted for mitywgs: https://www.piwheels.org/simple/mitywgs/mitywgs-0.3.1-py3-none-any.whl#sha256=bd4183a43f9f7e27c073f03cb6d76dbb1e81448b2712bf4d2247c205bd0a5572 (from https://www.piwheels.org/simple/mitywgs/) (requires-python:>=3.5.4) 2024-01-22T00:30:18,488 Skipping link: No binaries permitted for mitywgs: https://www.piwheels.org/simple/mitywgs/mitywgs-0.3.0-py3-none-any.whl#sha256=0e8c010b09481b6c8a42d1cc2a56d0406491b1b3bd937d4b122d905315bb968f (from https://www.piwheels.org/simple/mitywgs/) (requires-python:>=3.5.4) 2024-01-22T00:30:18,489 Skipping link: No binaries permitted for mitywgs: https://www.piwheels.org/simple/mitywgs/mitywgs-0.2.1-py3-none-any.whl#sha256=b0e58845f593a26d29938af561d632fa6174a7428a90b1f2b49cf5cd8e1a3950 (from https://www.piwheels.org/simple/mitywgs/) (requires-python:>=3.5.4) 2024-01-22T00:30:18,489 Skipping link: No binaries permitted for mitywgs: https://www.piwheels.org/simple/mitywgs/mitywgs-0.2.0-py3-none-any.whl#sha256=59db3a95242366e4220ca17e0d453c893e0e0ac128f0ce98c494ad7ce76cf7d7 (from https://www.piwheels.org/simple/mitywgs/) (requires-python:>=3.5.3) 2024-01-22T00:30:18,490 Skipping link: No binaries permitted for mitywgs: https://www.piwheels.org/simple/mitywgs/mitywgs-0.1.3-py3-none-any.whl#sha256=0a374d9c6a2f3332d7807769be46d2afa345326c4820f6bc0997ca0aeb6f5f36 (from https://www.piwheels.org/simple/mitywgs/) (requires-python:>=3.5.3) 2024-01-22T00:30:18,490 Skipping link: No binaries permitted for mitywgs: https://www.piwheels.org/simple/mitywgs/mitywgs-0.1.2-py3-none-any.whl#sha256=a69913d9779386126f0b05545efd39978dfab19c637cd2a9536c436bd0b54d51 (from https://www.piwheels.org/simple/mitywgs/) (requires-python:>=3.5.3) 2024-01-22T00:30:18,491 Skipping link: No binaries permitted for mitywgs: https://www.piwheels.org/simple/mitywgs/mitywgs-0.1.1-py3-none-any.whl#sha256=a48d78fdf8a9fb6409720d417602a7e690c2b28aeff99462182df4d6fb9acf27 (from https://www.piwheels.org/simple/mitywgs/) (requires-python:>=3.5.3) 2024-01-22T00:30:18,492 Skipping link: No binaries permitted for mitywgs: https://www.piwheels.org/simple/mitywgs/mitywgs-0.1.0-py3-none-any.whl#sha256=90e433721fea608ae7c7843812b355412ebe36937935f260e72a87ab21f6aefd (from https://www.piwheels.org/simple/mitywgs/) (requires-python:>=3.5.3) 2024-01-22T00:30:18,492 Skipping link: not a file: https://www.piwheels.org/simple/mitywgs/ 2024-01-22T00:30:18,493 Skipping link: not a file: https://pypi.org/simple/mitywgs/ 2024-01-22T00:30:18,512 Given no hashes to check 1 links for project 'mitywgs': discarding no candidates 2024-01-22T00:30:18,530 Collecting mitywgs==1.0.0 2024-01-22T00:30:18,532 Created temporary directory: /tmp/pip-unpack-65srqpir 2024-01-22T00:30:19,194 Downloading mitywgs-1.0.0.tar.gz (535 kB) 2024-01-22T00:30:19,450 Added mitywgs==1.0.0 from https://files.pythonhosted.org/packages/27/00/b37d3d18ec330c45f5922187afc37eaa805a6182d8fa29954c29652068a7/mitywgs-1.0.0.tar.gz to build tracker '/tmp/pip-build-tracker-5cakwmwq' 2024-01-22T00:30:19,452 Running setup.py (path:/tmp/pip-wheel-s125gggm/mitywgs_3a2a5d58557843c3b10dcac1cab67791/setup.py) egg_info for package mitywgs 2024-01-22T00:30:19,453 Created temporary directory: /tmp/pip-pip-egg-info-7lvdza1b 2024-01-22T00:30:19,453 Preparing metadata (setup.py): started 2024-01-22T00:30:19,455 Running command python setup.py egg_info 2024-01-22T00:30:20,456 running egg_info 2024-01-22T00:30:20,458 creating /tmp/pip-pip-egg-info-7lvdza1b/mitywgs.egg-info 2024-01-22T00:30:20,482 writing /tmp/pip-pip-egg-info-7lvdza1b/mitywgs.egg-info/PKG-INFO 2024-01-22T00:30:20,486 writing dependency_links to /tmp/pip-pip-egg-info-7lvdza1b/mitywgs.egg-info/dependency_links.txt 2024-01-22T00:30:20,487 writing requirements to /tmp/pip-pip-egg-info-7lvdza1b/mitywgs.egg-info/requires.txt 2024-01-22T00:30:20,488 writing top-level names to /tmp/pip-pip-egg-info-7lvdza1b/mitywgs.egg-info/top_level.txt 2024-01-22T00:30:20,490 writing manifest file '/tmp/pip-pip-egg-info-7lvdza1b/mitywgs.egg-info/SOURCES.txt' 2024-01-22T00:30:20,593 reading manifest file '/tmp/pip-pip-egg-info-7lvdza1b/mitywgs.egg-info/SOURCES.txt' 2024-01-22T00:30:20,594 adding license file 'LICENSE.txt' 2024-01-22T00:30:20,597 writing manifest file '/tmp/pip-pip-egg-info-7lvdza1b/mitywgs.egg-info/SOURCES.txt' 2024-01-22T00:30:20,704 Preparing metadata (setup.py): finished with status 'done' 2024-01-22T00:30:20,708 Source in /tmp/pip-wheel-s125gggm/mitywgs_3a2a5d58557843c3b10dcac1cab67791 has version 1.0.0, which satisfies requirement mitywgs==1.0.0 from https://files.pythonhosted.org/packages/27/00/b37d3d18ec330c45f5922187afc37eaa805a6182d8fa29954c29652068a7/mitywgs-1.0.0.tar.gz 2024-01-22T00:30:20,709 Removed mitywgs==1.0.0 from https://files.pythonhosted.org/packages/27/00/b37d3d18ec330c45f5922187afc37eaa805a6182d8fa29954c29652068a7/mitywgs-1.0.0.tar.gz from build tracker '/tmp/pip-build-tracker-5cakwmwq' 2024-01-22T00:30:20,716 Created temporary directory: /tmp/pip-unpack-rgv707ae 2024-01-22T00:30:20,724 Created temporary directory: /tmp/pip-unpack-qiyfmrpr 2024-01-22T00:30:20,732 Building wheels for collected packages: mitywgs 2024-01-22T00:30:20,736 Created temporary directory: /tmp/pip-wheel-tpkqjhr6 2024-01-22T00:30:20,737 Building wheel for mitywgs (setup.py): started 2024-01-22T00:30:20,738 Destination directory: /tmp/pip-wheel-tpkqjhr6 2024-01-22T00:30:20,739 Running command python setup.py bdist_wheel 2024-01-22T00:30:21,747 running bdist_wheel 2024-01-22T00:30:21,840 running build 2024-01-22T00:30:21,841 running build_py 2024-01-22T00:30:21,867 creating build 2024-01-22T00:30:21,868 creating build/lib 2024-01-22T00:30:21,869 creating build/lib/mitylib 2024-01-22T00:30:21,870 copying mitylib/merge.py -> build/lib/mitylib 2024-01-22T00:30:21,872 copying mitylib/util.py -> build/lib/mitylib 2024-01-22T00:30:21,874 copying mitylib/normalise.py -> build/lib/mitylib 2024-01-22T00:30:21,876 copying mitylib/_version.py -> build/lib/mitylib 2024-01-22T00:30:21,878 copying mitylib/report.py -> build/lib/mitylib 2024-01-22T00:30:21,880 copying mitylib/commands.py -> build/lib/mitylib 2024-01-22T00:30:21,882 copying mitylib/call.py -> build/lib/mitylib 2024-01-22T00:30:21,884 copying mitylib/__init__.py -> build/lib/mitylib 2024-01-22T00:30:21,885 running egg_info 2024-01-22T00:30:21,939 writing mitywgs.egg-info/PKG-INFO 2024-01-22T00:30:21,942 writing dependency_links to mitywgs.egg-info/dependency_links.txt 2024-01-22T00:30:21,944 writing requirements to mitywgs.egg-info/requires.txt 2024-01-22T00:30:21,945 writing top-level names to mitywgs.egg-info/top_level.txt 2024-01-22T00:30:21,974 reading manifest file 'mitywgs.egg-info/SOURCES.txt' 2024-01-22T00:30:21,976 adding license file 'LICENSE.txt' 2024-01-22T00:30:21,979 writing manifest file 'mitywgs.egg-info/SOURCES.txt' 2024-01-22T00:30:21,981 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'mitylib.annot' is absent from the `packages` configuration. 2024-01-22T00:30:21,982 !! 2024-01-22T00:30:21,983 ******************************************************************************** 2024-01-22T00:30:21,983 ############################ 2024-01-22T00:30:21,984 # Package would be ignored # 2024-01-22T00:30:21,984 ############################ 2024-01-22T00:30:21,985 Python recognizes 'mitylib.annot' as an importable package[^1], 2024-01-22T00:30:21,985 but it is absent from setuptools' `packages` configuration. 2024-01-22T00:30:21,986 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-22T00:30:21,987 package, please make sure that 'mitylib.annot' is explicitly added 2024-01-22T00:30:21,988 to the `packages` configuration field. 2024-01-22T00:30:21,989 Alternatively, you can also rely on setuptools' discovery methods 2024-01-22T00:30:21,989 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-22T00:30:21,990 instead of `find_packages(...)`/`find:`). 2024-01-22T00:30:21,991 You can read more about "package discovery" on setuptools documentation page: 2024-01-22T00:30:21,992 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-22T00:30:21,993 If you don't want 'mitylib.annot' to be distributed and are 2024-01-22T00:30:21,993 already explicitly excluding 'mitylib.annot' via 2024-01-22T00:30:21,994 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-22T00:30:21,994 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-22T00:30:21,995 combination with a more fine grained `package-data` configuration. 2024-01-22T00:30:21,996 You can read more about "package data files" on setuptools documentation page: 2024-01-22T00:30:21,997 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-22T00:30:21,999 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-22T00:30:22,000 even if it does not contain any `.py` files. 2024-01-22T00:30:22,000 On the other hand, currently there is no concept of package data 2024-01-22T00:30:22,001 directory, all directories are treated like packages. 2024-01-22T00:30:22,002 ******************************************************************************** 2024-01-22T00:30:22,002 !! 2024-01-22T00:30:22,003 check.warn(importable) 2024-01-22T00:30:22,003 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'mitylib.reference' is absent from the `packages` configuration. 2024-01-22T00:30:22,004 !! 2024-01-22T00:30:22,006 ******************************************************************************** 2024-01-22T00:30:22,006 ############################ 2024-01-22T00:30:22,006 # Package would be ignored # 2024-01-22T00:30:22,007 ############################ 2024-01-22T00:30:22,007 Python recognizes 'mitylib.reference' as an importable package[^1], 2024-01-22T00:30:22,008 but it is absent from setuptools' `packages` configuration. 2024-01-22T00:30:22,008 This leads to an ambiguous overall configuration. If you want to distribute this 2024-01-22T00:30:22,009 package, please make sure that 'mitylib.reference' is explicitly added 2024-01-22T00:30:22,010 to the `packages` configuration field. 2024-01-22T00:30:22,011 Alternatively, you can also rely on setuptools' discovery methods 2024-01-22T00:30:22,011 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-01-22T00:30:22,012 instead of `find_packages(...)`/`find:`). 2024-01-22T00:30:22,013 You can read more about "package discovery" on setuptools documentation page: 2024-01-22T00:30:22,014 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-01-22T00:30:22,015 If you don't want 'mitylib.reference' to be distributed and are 2024-01-22T00:30:22,016 already explicitly excluding 'mitylib.reference' via 2024-01-22T00:30:22,017 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-01-22T00:30:22,017 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-01-22T00:30:22,018 combination with a more fine grained `package-data` configuration. 2024-01-22T00:30:22,019 You can read more about "package data files" on setuptools documentation page: 2024-01-22T00:30:22,020 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-01-22T00:30:22,021 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-01-22T00:30:22,022 even if it does not contain any `.py` files. 2024-01-22T00:30:22,022 On the other hand, currently there is no concept of package data 2024-01-22T00:30:22,024 directory, all directories are treated like packages. 2024-01-22T00:30:22,025 ******************************************************************************** 2024-01-22T00:30:22,026 !! 2024-01-22T00:30:22,026 check.warn(importable) 2024-01-22T00:30:22,027 copying mitylib/mity -> build/lib/mitylib 2024-01-22T00:30:22,027 creating build/lib/mitylib/annot 2024-01-22T00:30:22,027 copying mitylib/annot/anticodon_positions.bed.gz -> build/lib/mitylib/annot 2024-01-22T00:30:22,028 copying mitylib/annot/anticodon_positions.bed.gz.tbi -> build/lib/mitylib/annot 2024-01-22T00:30:22,028 copying mitylib/annot/gtf_annotations.bed.gz -> build/lib/mitylib/annot 2024-01-22T00:30:22,029 copying mitylib/annot/gtf_annotations.bed.gz.tbi -> build/lib/mitylib/annot 2024-01-22T00:30:22,029 copying mitylib/annot/haplotype_data.vcf.gz -> build/lib/mitylib/annot 2024-01-22T00:30:22,030 copying mitylib/annot/haplotype_data.vcf.gz.tbi -> build/lib/mitylib/annot 2024-01-22T00:30:22,030 copying mitylib/annot/mgrb_variants.vcf.gz -> build/lib/mitylib/annot 2024-01-22T00:30:22,032 copying mitylib/annot/mgrb_variants.vcf.gz.tbi -> build/lib/mitylib/annot 2024-01-22T00:30:22,032 copying mitylib/annot/mito_dna_func_loc.bed.gz -> build/lib/mitylib/annot 2024-01-22T00:30:22,032 copying mitylib/annot/mito_dna_func_loc.bed.gz.tbi -> build/lib/mitylib/annot 2024-01-22T00:30:22,033 copying mitylib/annot/mitomap_panel_annotations.vcf.gz -> build/lib/mitylib/annot 2024-01-22T00:30:22,034 copying mitylib/annot/mitomap_panel_annotations.vcf.gz.tbi -> build/lib/mitylib/annot 2024-01-22T00:30:22,034 copying mitylib/annot/mitotip_score_fixed_del.vcf.gz -> build/lib/mitylib/annot 2024-01-22T00:30:22,035 copying mitylib/annot/mitotip_score_fixed_del.vcf.gz.tbi -> build/lib/mitylib/annot 2024-01-22T00:30:22,036 creating build/lib/mitylib/reference 2024-01-22T00:30:22,036 copying mitylib/reference/hg19.chrM.fa -> build/lib/mitylib/reference 2024-01-22T00:30:22,039 copying mitylib/reference/hg19.chrM.fa.fai -> build/lib/mitylib/reference 2024-01-22T00:30:22,041 copying mitylib/reference/hg19.dict -> build/lib/mitylib/reference 2024-01-22T00:30:22,044 copying mitylib/reference/hg19.genome -> build/lib/mitylib/reference 2024-01-22T00:30:22,046 copying mitylib/reference/hg38.chrM.fa -> build/lib/mitylib/reference 2024-01-22T00:30:22,048 copying mitylib/reference/hg38.chrM.fa.fai -> build/lib/mitylib/reference 2024-01-22T00:30:22,050 copying mitylib/reference/hg38.dict -> build/lib/mitylib/reference 2024-01-22T00:30:22,061 copying mitylib/reference/hg38.genome -> build/lib/mitylib/reference 2024-01-22T00:30:22,064 copying mitylib/reference/hs37d5.MT.fa -> build/lib/mitylib/reference 2024-01-22T00:30:22,067 copying mitylib/reference/hs37d5.MT.fa.fai -> build/lib/mitylib/reference 2024-01-22T00:30:22,068 copying mitylib/reference/hs37d5.dict -> build/lib/mitylib/reference 2024-01-22T00:30:22,071 copying mitylib/reference/hs37d5.genome -> build/lib/mitylib/reference 2024-01-22T00:30:22,073 copying mitylib/reference/mm10.chrM.fa -> build/lib/mitylib/reference 2024-01-22T00:30:22,075 copying mitylib/reference/mm10.chrM.fa.fai -> build/lib/mitylib/reference 2024-01-22T00:30:22,078 copying mitylib/reference/mm10.genome -> build/lib/mitylib/reference 2024-01-22T00:30:22,081 running build_scripts 2024-01-22T00:30:22,081 creating build/scripts-3.11 2024-01-22T00:30:22,082 copying and adjusting mitylib/mity -> build/scripts-3.11 2024-01-22T00:30:22,083 changing mode of build/scripts-3.11/mity from 644 to 755 2024-01-22T00:30:22,107 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-01-22T00:30:22,108 !! 2024-01-22T00:30:22,109 ******************************************************************************** 2024-01-22T00:30:22,109 Please avoid running ``setup.py`` directly. 2024-01-22T00:30:22,110 Instead, use pypa/build, pypa/installer or other 2024-01-22T00:30:22,111 standards-based tools. 2024-01-22T00:30:22,112 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-01-22T00:30:22,112 ******************************************************************************** 2024-01-22T00:30:22,113 !! 2024-01-22T00:30:22,114 self.initialize_options() 2024-01-22T00:30:22,133 installing to build/bdist.linux-armv7l/wheel 2024-01-22T00:30:22,133 running install 2024-01-22T00:30:22,157 running install_lib 2024-01-22T00:30:22,181 creating build/bdist.linux-armv7l 2024-01-22T00:30:22,182 creating build/bdist.linux-armv7l/wheel 2024-01-22T00:30:22,183 creating build/bdist.linux-armv7l/wheel/mitylib 2024-01-22T00:30:22,184 copying build/lib/mitylib/merge.py -> build/bdist.linux-armv7l/wheel/mitylib 2024-01-22T00:30:22,186 copying build/lib/mitylib/util.py -> build/bdist.linux-armv7l/wheel/mitylib 2024-01-22T00:30:22,189 copying build/lib/mitylib/mity -> build/bdist.linux-armv7l/wheel/mitylib 2024-01-22T00:30:22,191 creating build/bdist.linux-armv7l/wheel/mitylib/reference 2024-01-22T00:30:22,192 copying build/lib/mitylib/reference/hs37d5.genome -> build/bdist.linux-armv7l/wheel/mitylib/reference 2024-01-22T00:30:22,193 copying build/lib/mitylib/reference/hg19.chrM.fa.fai -> build/bdist.linux-armv7l/wheel/mitylib/reference 2024-01-22T00:30:22,195 copying build/lib/mitylib/reference/hg38.genome -> build/bdist.linux-armv7l/wheel/mitylib/reference 2024-01-22T00:30:22,198 copying build/lib/mitylib/reference/hs37d5.dict -> build/bdist.linux-armv7l/wheel/mitylib/reference 2024-01-22T00:30:22,201 copying build/lib/mitylib/reference/hg38.chrM.fa -> build/bdist.linux-armv7l/wheel/mitylib/reference 2024-01-22T00:30:22,203 copying build/lib/mitylib/reference/mm10.chrM.fa -> build/bdist.linux-armv7l/wheel/mitylib/reference 2024-01-22T00:30:22,206 copying build/lib/mitylib/reference/mm10.genome -> build/bdist.linux-armv7l/wheel/mitylib/reference 2024-01-22T00:30:22,208 copying build/lib/mitylib/reference/hg19.genome -> build/bdist.linux-armv7l/wheel/mitylib/reference 2024-01-22T00:30:22,209 copying build/lib/mitylib/reference/hs37d5.MT.fa -> build/bdist.linux-armv7l/wheel/mitylib/reference 2024-01-22T00:30:22,212 copying build/lib/mitylib/reference/mm10.chrM.fa.fai -> build/bdist.linux-armv7l/wheel/mitylib/reference 2024-01-22T00:30:22,214 copying build/lib/mitylib/reference/hg38.chrM.fa.fai -> build/bdist.linux-armv7l/wheel/mitylib/reference 2024-01-22T00:30:22,216 copying build/lib/mitylib/reference/hg19.dict -> build/bdist.linux-armv7l/wheel/mitylib/reference 2024-01-22T00:30:22,218 copying build/lib/mitylib/reference/hs37d5.MT.fa.fai -> build/bdist.linux-armv7l/wheel/mitylib/reference 2024-01-22T00:30:22,220 copying build/lib/mitylib/reference/hg19.chrM.fa -> build/bdist.linux-armv7l/wheel/mitylib/reference 2024-01-22T00:30:22,222 copying build/lib/mitylib/reference/hg38.dict -> build/bdist.linux-armv7l/wheel/mitylib/reference 2024-01-22T00:30:22,234 copying build/lib/mitylib/normalise.py -> build/bdist.linux-armv7l/wheel/mitylib 2024-01-22T00:30:22,237 copying build/lib/mitylib/_version.py -> build/bdist.linux-armv7l/wheel/mitylib 2024-01-22T00:30:22,239 creating build/bdist.linux-armv7l/wheel/mitylib/annot 2024-01-22T00:30:22,240 copying build/lib/mitylib/annot/gtf_annotations.bed.gz -> build/bdist.linux-armv7l/wheel/mitylib/annot 2024-01-22T00:30:22,243 copying build/lib/mitylib/annot/mitotip_score_fixed_del.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/mitylib/annot 2024-01-22T00:30:22,245 copying build/lib/mitylib/annot/haplotype_data.vcf.gz -> build/bdist.linux-armv7l/wheel/mitylib/annot 2024-01-22T00:30:22,248 copying build/lib/mitylib/annot/anticodon_positions.bed.gz.tbi -> build/bdist.linux-armv7l/wheel/mitylib/annot 2024-01-22T00:30:22,249 copying build/lib/mitylib/annot/mitomap_panel_annotations.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/mitylib/annot 2024-01-22T00:30:22,251 copying build/lib/mitylib/annot/mito_dna_func_loc.bed.gz -> build/bdist.linux-armv7l/wheel/mitylib/annot 2024-01-22T00:30:22,254 copying build/lib/mitylib/annot/mgrb_variants.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/mitylib/annot 2024-01-22T00:30:22,256 copying build/lib/mitylib/annot/mitotip_score_fixed_del.vcf.gz -> build/bdist.linux-armv7l/wheel/mitylib/annot 2024-01-22T00:30:22,259 copying build/lib/mitylib/annot/mitomap_panel_annotations.vcf.gz -> build/bdist.linux-armv7l/wheel/mitylib/annot 2024-01-22T00:30:22,264 copying build/lib/mitylib/annot/mgrb_variants.vcf.gz -> build/bdist.linux-armv7l/wheel/mitylib/annot 2024-01-22T00:30:22,266 copying build/lib/mitylib/annot/mito_dna_func_loc.bed.gz.tbi -> build/bdist.linux-armv7l/wheel/mitylib/annot 2024-01-22T00:30:22,268 copying build/lib/mitylib/annot/anticodon_positions.bed.gz -> build/bdist.linux-armv7l/wheel/mitylib/annot 2024-01-22T00:30:22,270 copying build/lib/mitylib/annot/haplotype_data.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/mitylib/annot 2024-01-22T00:30:22,272 copying build/lib/mitylib/annot/gtf_annotations.bed.gz.tbi -> build/bdist.linux-armv7l/wheel/mitylib/annot 2024-01-22T00:30:22,273 copying build/lib/mitylib/report.py -> build/bdist.linux-armv7l/wheel/mitylib 2024-01-22T00:30:22,276 copying build/lib/mitylib/commands.py -> build/bdist.linux-armv7l/wheel/mitylib 2024-01-22T00:30:22,278 copying build/lib/mitylib/call.py -> build/bdist.linux-armv7l/wheel/mitylib 2024-01-22T00:30:22,280 copying build/lib/mitylib/__init__.py -> build/bdist.linux-armv7l/wheel/mitylib 2024-01-22T00:30:22,281 running install_egg_info 2024-01-22T00:30:22,310 Copying mitywgs.egg-info to build/bdist.linux-armv7l/wheel/mitywgs-1.0.0-py3.11.egg-info 2024-01-22T00:30:22,319 running install_scripts 2024-01-22T00:30:22,320 creating build/bdist.linux-armv7l/wheel/mitywgs-1.0.0.data 2024-01-22T00:30:22,321 creating build/bdist.linux-armv7l/wheel/mitywgs-1.0.0.data/scripts 2024-01-22T00:30:22,322 copying build/scripts-3.11/mity -> build/bdist.linux-armv7l/wheel/mitywgs-1.0.0.data/scripts 2024-01-22T00:30:22,323 changing mode of build/bdist.linux-armv7l/wheel/mitywgs-1.0.0.data/scripts/mity to 755 2024-01-22T00:30:22,337 creating build/bdist.linux-armv7l/wheel/mitywgs-1.0.0.dist-info/WHEEL 2024-01-22T00:30:22,339 creating '/tmp/pip-wheel-tpkqjhr6/mitywgs-1.0.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-01-22T00:30:22,341 adding 'mitylib/__init__.py' 2024-01-22T00:30:22,342 adding 'mitylib/_version.py' 2024-01-22T00:30:22,344 adding 'mitylib/call.py' 2024-01-22T00:30:22,346 adding 'mitylib/commands.py' 2024-01-22T00:30:22,348 adding 'mitylib/merge.py' 2024-01-22T00:30:22,349 adding 'mitylib/mity' 2024-01-22T00:30:22,351 adding 'mitylib/normalise.py' 2024-01-22T00:30:22,353 adding 'mitylib/report.py' 2024-01-22T00:30:22,355 adding 'mitylib/util.py' 2024-01-22T00:30:22,357 adding 'mitylib/annot/anticodon_positions.bed.gz' 2024-01-22T00:30:22,358 adding 'mitylib/annot/anticodon_positions.bed.gz.tbi' 2024-01-22T00:30:22,362 adding 'mitylib/annot/gtf_annotations.bed.gz' 2024-01-22T00:30:22,364 adding 'mitylib/annot/gtf_annotations.bed.gz.tbi' 2024-01-22T00:30:22,369 adding 'mitylib/annot/haplotype_data.vcf.gz' 2024-01-22T00:30:22,370 adding 'mitylib/annot/haplotype_data.vcf.gz.tbi' 2024-01-22T00:30:22,373 adding 'mitylib/annot/mgrb_variants.vcf.gz' 2024-01-22T00:30:22,375 adding 'mitylib/annot/mgrb_variants.vcf.gz.tbi' 2024-01-22T00:30:22,380 adding 'mitylib/annot/mito_dna_func_loc.bed.gz' 2024-01-22T00:30:22,382 adding 'mitylib/annot/mito_dna_func_loc.bed.gz.tbi' 2024-01-22T00:30:22,404 adding 'mitylib/annot/mitomap_panel_annotations.vcf.gz' 2024-01-22T00:30:22,406 adding 'mitylib/annot/mitomap_panel_annotations.vcf.gz.tbi' 2024-01-22T00:30:22,412 adding 'mitylib/annot/mitotip_score_fixed_del.vcf.gz' 2024-01-22T00:30:22,414 adding 'mitylib/annot/mitotip_score_fixed_del.vcf.gz.tbi' 2024-01-22T00:30:22,422 adding 'mitylib/reference/hg19.chrM.fa' 2024-01-22T00:30:22,423 adding 'mitylib/reference/hg19.chrM.fa.fai' 2024-01-22T00:30:22,425 adding 'mitylib/reference/hg19.dict' 2024-01-22T00:30:22,426 adding 'mitylib/reference/hg19.genome' 2024-01-22T00:30:22,435 adding 'mitylib/reference/hg38.chrM.fa' 2024-01-22T00:30:22,436 adding 'mitylib/reference/hg38.chrM.fa.fai' 2024-01-22T00:30:22,471 adding 'mitylib/reference/hg38.dict' 2024-01-22T00:30:22,485 adding 'mitylib/reference/hg38.genome' 2024-01-22T00:30:22,493 adding 'mitylib/reference/hs37d5.MT.fa' 2024-01-22T00:30:22,494 adding 'mitylib/reference/hs37d5.MT.fa.fai' 2024-01-22T00:30:22,496 adding 'mitylib/reference/hs37d5.dict' 2024-01-22T00:30:22,497 adding 'mitylib/reference/hs37d5.genome' 2024-01-22T00:30:22,505 adding 'mitylib/reference/mm10.chrM.fa' 2024-01-22T00:30:22,513 adding 'mitylib/reference/mm10.chrM.fa.fai' 2024-01-22T00:30:22,515 adding 'mitylib/reference/mm10.genome' 2024-01-22T00:30:22,517 adding 'mitywgs-1.0.0.data/scripts/mity' 2024-01-22T00:30:22,519 adding 'mitywgs-1.0.0.dist-info/LICENSE.txt' 2024-01-22T00:30:22,521 adding 'mitywgs-1.0.0.dist-info/METADATA' 2024-01-22T00:30:22,522 adding 'mitywgs-1.0.0.dist-info/WHEEL' 2024-01-22T00:30:22,523 adding 'mitywgs-1.0.0.dist-info/top_level.txt' 2024-01-22T00:30:22,524 adding 'mitywgs-1.0.0.dist-info/RECORD' 2024-01-22T00:30:22,531 removing build/bdist.linux-armv7l/wheel 2024-01-22T00:30:22,651 Building wheel for mitywgs (setup.py): finished with status 'done' 2024-01-22T00:30:22,658 Created wheel for mitywgs: filename=mitywgs-1.0.0-py3-none-any.whl size=538940 sha256=b347af79edf93d63124288c6875a3f9b20eb1e9c0386a990c7222166f8af2461 2024-01-22T00:30:22,660 Stored in directory: /tmp/pip-ephem-wheel-cache-yjwaqgyz/wheels/fb/66/9e/65d8213934cec98aff47220abdbb8315cb769b7f2dff3d219e 2024-01-22T00:30:22,672 Successfully built mitywgs 2024-01-22T00:30:22,696 Removed build tracker: '/tmp/pip-build-tracker-5cakwmwq'