2023-09-14T12:33:24,790 Created temporary directory: /tmp/pip-build-tracker-p2msiroo 2023-09-14T12:33:24,791 Initialized build tracking at /tmp/pip-build-tracker-p2msiroo 2023-09-14T12:33:24,792 Created build tracker: /tmp/pip-build-tracker-p2msiroo 2023-09-14T12:33:24,792 Entered build tracker: /tmp/pip-build-tracker-p2msiroo 2023-09-14T12:33:24,793 Created temporary directory: /tmp/pip-wheel-qdk6crxh 2023-09-14T12:33:24,797 Created temporary directory: /tmp/pip-ephem-wheel-cache-zoumrn6e 2023-09-14T12:33:24,818 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-14T12:33:24,822 2 location(s) to search for versions of ont-bonito-cuda111: 2023-09-14T12:33:24,822 * https://pypi.org/simple/ont-bonito-cuda111/ 2023-09-14T12:33:24,822 * https://www.piwheels.org/simple/ont-bonito-cuda111/ 2023-09-14T12:33:24,823 Fetching project page and analyzing links: https://pypi.org/simple/ont-bonito-cuda111/ 2023-09-14T12:33:24,823 Getting page https://pypi.org/simple/ont-bonito-cuda111/ 2023-09-14T12:33:24,825 Found index url https://pypi.org/simple/ 2023-09-14T12:33:24,966 Fetched page https://pypi.org/simple/ont-bonito-cuda111/ as application/vnd.pypi.simple.v1+json 2023-09-14T12:33:24,970 Found link https://files.pythonhosted.org/packages/4b/e9/326d358ab1d32037c760b9f7b1010edf4eb9de07b68af8e0fdd8bdc5c0c7/ont-bonito-cuda111-0.4.0a0.tar.gz (from https://pypi.org/simple/ont-bonito-cuda111/), version: 0.4.0a0 2023-09-14T12:33:24,970 Found link https://files.pythonhosted.org/packages/a1/9f/19c6571eb24457fa6ed8cf7699f2586a4b376cf875c58f0c26ced182f6a1/ont-bonito-cuda111-0.4.0a1.tar.gz (from https://pypi.org/simple/ont-bonito-cuda111/), version: 0.4.0a1 2023-09-14T12:33:24,971 Found link https://files.pythonhosted.org/packages/25/8c/28c43178094cb5cdae8df6c80d47e232a3e3013fba61f0bcdc02c5ca42f2/ont-bonito-cuda111-0.4.0a2.tar.gz (from https://pypi.org/simple/ont-bonito-cuda111/), version: 0.4.0a2 2023-09-14T12:33:24,972 Found link https://files.pythonhosted.org/packages/b4/03/d3afcda7d932e31137dd77b3e7cdf4ddfee7e207ebe455410f65be8ad79a/ont-bonito-cuda111-0.4.0a4.tar.gz (from https://pypi.org/simple/ont-bonito-cuda111/), version: 0.4.0a4 2023-09-14T12:33:24,972 Found link https://files.pythonhosted.org/packages/2e/c0/01dfa9cd140ab87acd038089bf3c9719a7e2794ef50c17c9796a719f2fb7/ont-bonito-cuda111-0.4.0.tar.gz (from https://pypi.org/simple/ont-bonito-cuda111/), version: 0.4.0 2023-09-14T12:33:24,973 Found link https://files.pythonhosted.org/packages/79/bf/17eb8226b121bc06d06717d650351a8527a5bd40e91786b3761a79249bf8/ont-bonito-cuda111-0.5.0a0.tar.gz (from https://pypi.org/simple/ont-bonito-cuda111/), version: 0.5.0a0 2023-09-14T12:33:24,974 Found link https://files.pythonhosted.org/packages/25/1b/673484db9eb7a3885b6267e4e40c45caf4a99dd8cfa7d9a132a7c9bbe3d2/ont-bonito-cuda111-0.5.0.tar.gz (from https://pypi.org/simple/ont-bonito-cuda111/), version: 0.5.0 2023-09-14T12:33:24,974 Found link https://files.pythonhosted.org/packages/e3/6d/9d71c39319000bfc7e764fc202d3ba660b47fdaa94184386c65914850b5b/ont-bonito-cuda111-0.5.1a0.tar.gz (from https://pypi.org/simple/ont-bonito-cuda111/), version: 0.5.1a0 2023-09-14T12:33:24,975 Found link https://files.pythonhosted.org/packages/73/91/2f55f4b660b61e68bfd934f7c35e57c26ca59c2412af9052811fc0ddd979/ont-bonito-cuda111-0.5.1.tar.gz (from https://pypi.org/simple/ont-bonito-cuda111/), version: 0.5.1 2023-09-14T12:33:24,976 Found link https://files.pythonhosted.org/packages/32/9f/cef7b19d5dfe469bedf51472750ab0f06bbd701f27fc4a5b9637c0d779d5/ont-bonito-cuda111-0.5.2.tar.gz (from https://pypi.org/simple/ont-bonito-cuda111/), version: 0.5.2 2023-09-14T12:33:24,976 Found link https://files.pythonhosted.org/packages/d2/3d/474532af41c93290f8799ecbe17a4febd2a3fe4c6c5f6a1ec284c318b825/ont-bonito-cuda111-0.5.3.tar.gz (from https://pypi.org/simple/ont-bonito-cuda111/), version: 0.5.3 2023-09-14T12:33:24,977 Fetching project page and analyzing links: https://www.piwheels.org/simple/ont-bonito-cuda111/ 2023-09-14T12:33:24,978 Getting page https://www.piwheels.org/simple/ont-bonito-cuda111/ 2023-09-14T12:33:24,979 Found index url https://www.piwheels.org/simple/ 2023-09-14T12:33:25,460 Fetched page https://www.piwheels.org/simple/ont-bonito-cuda111/ as text/html 2023-09-14T12:33:25,465 Skipping link: No binaries permitted for ont-bonito-cuda111: https://www.piwheels.org/simple/ont-bonito-cuda111/ont_bonito_cuda111-0.5.3-py3-none-any.whl#sha256=aff35ee488b8fa61eaa75e378eb8b71d2a6444d344084464708443dc2b52ef6c (from https://www.piwheels.org/simple/ont-bonito-cuda111/) 2023-09-14T12:33:25,466 Skipping link: No binaries permitted for ont-bonito-cuda111: https://www.piwheels.org/simple/ont-bonito-cuda111/ont_bonito_cuda111-0.5.2-py3-none-any.whl#sha256=95173382e2e9216de065cc03dc107316c20726d578a55e1e637ec6d79bc4fdbd (from https://www.piwheels.org/simple/ont-bonito-cuda111/) 2023-09-14T12:33:25,467 Skipping link: No binaries permitted for ont-bonito-cuda111: https://www.piwheels.org/simple/ont-bonito-cuda111/ont_bonito_cuda111-0.5.1-py3-none-any.whl#sha256=afddc1337c8bc21fd69ae9479da2c8b0cef796a55a0a405d944c23c8e3b390e9 (from https://www.piwheels.org/simple/ont-bonito-cuda111/) 2023-09-14T12:33:25,468 Skipping link: No binaries permitted for ont-bonito-cuda111: https://www.piwheels.org/simple/ont-bonito-cuda111/ont_bonito_cuda111-0.5.1a0-py3-none-any.whl#sha256=796864665c170e8c36a9b804a3191312afaebe72a8dd563d9f583ea5b8f75ccf (from https://www.piwheels.org/simple/ont-bonito-cuda111/) 2023-09-14T12:33:25,469 Skipping link: not a file: https://www.piwheels.org/simple/ont-bonito-cuda111/ 2023-09-14T12:33:25,469 Skipping link: not a file: https://pypi.org/simple/ont-bonito-cuda111/ 2023-09-14T12:33:25,505 Given no hashes to check 1 links for project 'ont-bonito-cuda111': discarding no candidates 2023-09-14T12:33:25,531 Collecting ont-bonito-cuda111==0.4.0a2 2023-09-14T12:33:25,534 Created temporary directory: /tmp/pip-unpack-yknlj38v 2023-09-14T12:33:26,105 Downloading ont-bonito-cuda111-0.4.0a2.tar.gz (43 kB) 2023-09-14T12:33:26,230 Added ont-bonito-cuda111==0.4.0a2 from https://files.pythonhosted.org/packages/25/8c/28c43178094cb5cdae8df6c80d47e232a3e3013fba61f0bcdc02c5ca42f2/ont-bonito-cuda111-0.4.0a2.tar.gz to build tracker '/tmp/pip-build-tracker-p2msiroo' 2023-09-14T12:33:26,231 Running setup.py (path:/tmp/pip-wheel-qdk6crxh/ont-bonito-cuda111_beedfaab95a54390a6a576d44b7af67a/setup.py) egg_info for package ont-bonito-cuda111 2023-09-14T12:33:26,232 Created temporary directory: /tmp/pip-pip-egg-info-19zxzfl7 2023-09-14T12:33:26,233 Preparing metadata (setup.py): started 2023-09-14T12:33:26,234 Running command python setup.py egg_info 2023-09-14T12:33:27,285 Building with CUDA 11.1 2023-09-14T12:33:27,286 running egg_info 2023-09-14T12:33:27,287 creating /tmp/pip-pip-egg-info-19zxzfl7/ont_bonito_cuda111.egg-info 2023-09-14T12:33:27,311 writing /tmp/pip-pip-egg-info-19zxzfl7/ont_bonito_cuda111.egg-info/PKG-INFO 2023-09-14T12:33:27,314 writing dependency_links to /tmp/pip-pip-egg-info-19zxzfl7/ont_bonito_cuda111.egg-info/dependency_links.txt 2023-09-14T12:33:27,316 writing entry points to /tmp/pip-pip-egg-info-19zxzfl7/ont_bonito_cuda111.egg-info/entry_points.txt 2023-09-14T12:33:27,317 writing requirements to /tmp/pip-pip-egg-info-19zxzfl7/ont_bonito_cuda111.egg-info/requires.txt 2023-09-14T12:33:27,319 writing top-level names to /tmp/pip-pip-egg-info-19zxzfl7/ont_bonito_cuda111.egg-info/top_level.txt 2023-09-14T12:33:27,320 writing manifest file '/tmp/pip-pip-egg-info-19zxzfl7/ont_bonito_cuda111.egg-info/SOURCES.txt' 2023-09-14T12:33:27,396 reading manifest file '/tmp/pip-pip-egg-info-19zxzfl7/ont_bonito_cuda111.egg-info/SOURCES.txt' 2023-09-14T12:33:27,398 reading manifest template 'MANIFEST.in' 2023-09-14T12:33:27,401 adding license file 'LICENCE.txt' 2023-09-14T12:33:27,403 writing manifest file '/tmp/pip-pip-egg-info-19zxzfl7/ont_bonito_cuda111.egg-info/SOURCES.txt' 2023-09-14T12:33:27,516 Preparing metadata (setup.py): finished with status 'done' 2023-09-14T12:33:27,520 Source in /tmp/pip-wheel-qdk6crxh/ont-bonito-cuda111_beedfaab95a54390a6a576d44b7af67a has version 0.4.0a2, which satisfies requirement ont-bonito-cuda111==0.4.0a2 from https://files.pythonhosted.org/packages/25/8c/28c43178094cb5cdae8df6c80d47e232a3e3013fba61f0bcdc02c5ca42f2/ont-bonito-cuda111-0.4.0a2.tar.gz 2023-09-14T12:33:27,521 Removed ont-bonito-cuda111==0.4.0a2 from https://files.pythonhosted.org/packages/25/8c/28c43178094cb5cdae8df6c80d47e232a3e3013fba61f0bcdc02c5ca42f2/ont-bonito-cuda111-0.4.0a2.tar.gz from build tracker '/tmp/pip-build-tracker-p2msiroo' 2023-09-14T12:33:27,526 Created temporary directory: /tmp/pip-unpack-wfb_d3yi 2023-09-14T12:33:27,527 Created temporary directory: /tmp/pip-unpack-yz4s6fyb 2023-09-14T12:33:27,549 Building wheels for collected packages: ont-bonito-cuda111 2023-09-14T12:33:27,553 Created temporary directory: /tmp/pip-wheel-hodicd71 2023-09-14T12:33:27,553 Building wheel for ont-bonito-cuda111 (setup.py): started 2023-09-14T12:33:27,555 Destination directory: /tmp/pip-wheel-hodicd71 2023-09-14T12:33:27,555 Running command python setup.py bdist_wheel 2023-09-14T12:33:27,956 Building with CUDA 11.1 2023-09-14T12:33:28,534 running bdist_wheel 2023-09-14T12:33:28,629 running build 2023-09-14T12:33:28,630 running build_py 2023-09-14T12:33:28,656 creating build 2023-09-14T12:33:28,657 creating build/lib 2023-09-14T12:33:28,658 creating build/lib/bonito 2023-09-14T12:33:28,659 copying bonito/__init__.py -> build/lib/bonito 2023-09-14T12:33:28,661 copying bonito/training.py -> build/lib/bonito 2023-09-14T12:33:28,663 copying bonito/nn.py -> build/lib/bonito 2023-09-14T12:33:28,665 copying bonito/multiprocessing.py -> build/lib/bonito 2023-09-14T12:33:28,667 copying bonito/io.py -> build/lib/bonito 2023-09-14T12:33:28,669 copying bonito/aligner.py -> build/lib/bonito 2023-09-14T12:33:28,671 copying bonito/util.py -> build/lib/bonito 2023-09-14T12:33:28,673 copying bonito/fast5.py -> build/lib/bonito 2023-09-14T12:33:28,676 creating build/lib/bonito/cli 2023-09-14T12:33:28,677 copying bonito/cli/basecaller.py -> build/lib/bonito/cli 2023-09-14T12:33:28,680 copying bonito/cli/convert.py -> build/lib/bonito/cli 2023-09-14T12:33:28,682 copying bonito/cli/__init__.py -> build/lib/bonito/cli 2023-09-14T12:33:28,683 copying bonito/cli/train.py -> build/lib/bonito/cli 2023-09-14T12:33:28,686 copying bonito/cli/duplex.py -> build/lib/bonito/cli 2023-09-14T12:33:28,688 copying bonito/cli/view.py -> build/lib/bonito/cli 2023-09-14T12:33:28,690 copying bonito/cli/evaluate.py -> build/lib/bonito/cli 2023-09-14T12:33:28,692 copying bonito/cli/export.py -> build/lib/bonito/cli 2023-09-14T12:33:28,694 copying bonito/cli/download.py -> build/lib/bonito/cli 2023-09-14T12:33:28,697 creating build/lib/bonito/ctc 2023-09-14T12:33:28,698 copying bonito/ctc/__init__.py -> build/lib/bonito/ctc 2023-09-14T12:33:28,700 copying bonito/ctc/basecall.py -> build/lib/bonito/ctc 2023-09-14T12:33:28,702 copying bonito/ctc/model.py -> build/lib/bonito/ctc 2023-09-14T12:33:28,705 creating build/lib/bonito/crf 2023-09-14T12:33:28,706 copying bonito/crf/__init__.py -> build/lib/bonito/crf 2023-09-14T12:33:28,709 copying bonito/crf/basecall.py -> build/lib/bonito/crf 2023-09-14T12:33:28,711 copying bonito/crf/model.py -> build/lib/bonito/crf 2023-09-14T12:33:28,713 running egg_info 2023-09-14T12:33:28,768 writing ont_bonito_cuda111.egg-info/PKG-INFO 2023-09-14T12:33:28,772 writing dependency_links to ont_bonito_cuda111.egg-info/dependency_links.txt 2023-09-14T12:33:28,774 writing entry points to ont_bonito_cuda111.egg-info/entry_points.txt 2023-09-14T12:33:28,775 writing requirements to ont_bonito_cuda111.egg-info/requires.txt 2023-09-14T12:33:28,777 writing top-level names to ont_bonito_cuda111.egg-info/top_level.txt 2023-09-14T12:33:28,804 reading manifest file 'ont_bonito_cuda111.egg-info/SOURCES.txt' 2023-09-14T12:33:28,807 reading manifest template 'MANIFEST.in' 2023-09-14T12:33:28,810 adding license file 'LICENCE.txt' 2023-09-14T12:33:28,813 writing manifest file 'ont_bonito_cuda111.egg-info/SOURCES.txt' 2023-09-14T12:33:28,816 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'bonito.data' is absent from the `packages` configuration. 2023-09-14T12:33:28,817 !! 2023-09-14T12:33:28,818 ******************************************************************************** 2023-09-14T12:33:28,818 ############################ 2023-09-14T12:33:28,818 # Package would be ignored # 2023-09-14T12:33:28,819 ############################ 2023-09-14T12:33:28,819 Python recognizes 'bonito.data' as an importable package[^1], 2023-09-14T12:33:28,820 but it is absent from setuptools' `packages` configuration. 2023-09-14T12:33:28,820 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-14T12:33:28,821 package, please make sure that 'bonito.data' is explicitly added 2023-09-14T12:33:28,821 to the `packages` configuration field. 2023-09-14T12:33:28,822 Alternatively, you can also rely on setuptools' discovery methods 2023-09-14T12:33:28,822 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-14T12:33:28,823 instead of `find_packages(...)`/`find:`). 2023-09-14T12:33:28,824 You can read more about "package discovery" on setuptools documentation page: 2023-09-14T12:33:28,825 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-14T12:33:28,826 If you don't want 'bonito.data' to be distributed and are 2023-09-14T12:33:28,826 already explicitly excluding 'bonito.data' via 2023-09-14T12:33:28,827 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-14T12:33:28,827 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-14T12:33:28,828 combination with a more fine grained `package-data` configuration. 2023-09-14T12:33:28,829 You can read more about "package data files" on setuptools documentation page: 2023-09-14T12:33:28,830 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-14T12:33:28,831 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-14T12:33:28,832 even if it does not contain any `.py` files. 2023-09-14T12:33:28,832 On the other hand, currently there is no concept of package data 2023-09-14T12:33:28,832 directory, all directories are treated like packages. 2023-09-14T12:33:28,833 ******************************************************************************** 2023-09-14T12:33:28,834 !! 2023-09-14T12:33:28,835 check.warn(importable) 2023-09-14T12:33:28,835 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'bonito.models' is absent from the `packages` configuration. 2023-09-14T12:33:28,836 !! 2023-09-14T12:33:28,836 ******************************************************************************** 2023-09-14T12:33:28,837 ############################ 2023-09-14T12:33:28,837 # Package would be ignored # 2023-09-14T12:33:28,838 ############################ 2023-09-14T12:33:28,839 Python recognizes 'bonito.models' as an importable package[^1], 2023-09-14T12:33:28,839 but it is absent from setuptools' `packages` configuration. 2023-09-14T12:33:28,840 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-14T12:33:28,841 package, please make sure that 'bonito.models' is explicitly added 2023-09-14T12:33:28,841 to the `packages` configuration field. 2023-09-14T12:33:28,842 Alternatively, you can also rely on setuptools' discovery methods 2023-09-14T12:33:28,843 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-14T12:33:28,843 instead of `find_packages(...)`/`find:`). 2023-09-14T12:33:28,844 You can read more about "package discovery" on setuptools documentation page: 2023-09-14T12:33:28,846 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-14T12:33:28,846 If you don't want 'bonito.models' to be distributed and are 2023-09-14T12:33:28,847 already explicitly excluding 'bonito.models' via 2023-09-14T12:33:28,847 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-14T12:33:28,847 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-14T12:33:28,848 combination with a more fine grained `package-data` configuration. 2023-09-14T12:33:28,849 You can read more about "package data files" on setuptools documentation page: 2023-09-14T12:33:28,850 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-14T12:33:28,851 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-14T12:33:28,851 even if it does not contain any `.py` files. 2023-09-14T12:33:28,852 On the other hand, currently there is no concept of package data 2023-09-14T12:33:28,852 directory, all directories are treated like packages. 2023-09-14T12:33:28,853 ******************************************************************************** 2023-09-14T12:33:28,854 !! 2023-09-14T12:33:28,854 check.warn(importable) 2023-09-14T12:33:28,854 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'bonito.models.configs' is absent from the `packages` configuration. 2023-09-14T12:33:28,855 !! 2023-09-14T12:33:28,856 ******************************************************************************** 2023-09-14T12:33:28,857 ############################ 2023-09-14T12:33:28,857 # Package would be ignored # 2023-09-14T12:33:28,858 ############################ 2023-09-14T12:33:28,858 Python recognizes 'bonito.models.configs' as an importable package[^1], 2023-09-14T12:33:28,859 but it is absent from setuptools' `packages` configuration. 2023-09-14T12:33:28,860 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-14T12:33:28,861 package, please make sure that 'bonito.models.configs' is explicitly added 2023-09-14T12:33:28,861 to the `packages` configuration field. 2023-09-14T12:33:28,862 Alternatively, you can also rely on setuptools' discovery methods 2023-09-14T12:33:28,863 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-14T12:33:28,863 instead of `find_packages(...)`/`find:`). 2023-09-14T12:33:28,865 You can read more about "package discovery" on setuptools documentation page: 2023-09-14T12:33:28,866 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-14T12:33:28,867 If you don't want 'bonito.models.configs' to be distributed and are 2023-09-14T12:33:28,867 already explicitly excluding 'bonito.models.configs' via 2023-09-14T12:33:28,868 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-14T12:33:28,868 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-14T12:33:28,869 combination with a more fine grained `package-data` configuration. 2023-09-14T12:33:28,870 You can read more about "package data files" on setuptools documentation page: 2023-09-14T12:33:28,871 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-14T12:33:28,873 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-14T12:33:28,874 even if it does not contain any `.py` files. 2023-09-14T12:33:28,875 On the other hand, currently there is no concept of package data 2023-09-14T12:33:28,875 directory, all directories are treated like packages. 2023-09-14T12:33:28,876 ******************************************************************************** 2023-09-14T12:33:28,877 !! 2023-09-14T12:33:28,877 check.warn(importable) 2023-09-14T12:33:28,878 creating build/lib/bonito/data 2023-09-14T12:33:28,878 copying bonito/data/README.md -> build/lib/bonito/data 2023-09-14T12:33:28,879 creating build/lib/bonito/models 2023-09-14T12:33:28,879 copying bonito/models/README.md -> build/lib/bonito/models 2023-09-14T12:33:28,880 creating build/lib/bonito/models/configs 2023-09-14T12:33:28,880 copying bonito/models/configs/dna_r9.4.1@v1.toml -> build/lib/bonito/models/configs 2023-09-14T12:33:28,880 copying bonito/models/configs/dna_r9.4.1@v2.toml -> build/lib/bonito/models/configs 2023-09-14T12:33:28,881 copying bonito/models/configs/dna_r9.4.1@v3.toml -> build/lib/bonito/models/configs 2023-09-14T12:33:28,881 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-09-14T12:33:28,882 !! 2023-09-14T12:33:28,883 ******************************************************************************** 2023-09-14T12:33:28,883 Please avoid running ``setup.py`` directly. 2023-09-14T12:33:28,884 Instead, use pypa/build, pypa/installer or other 2023-09-14T12:33:28,884 standards-based tools. 2023-09-14T12:33:28,885 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-09-14T12:33:28,885 ******************************************************************************** 2023-09-14T12:33:28,886 !! 2023-09-14T12:33:28,887 self.initialize_options() 2023-09-14T12:33:28,888 installing to build/bdist.linux-armv7l/wheel 2023-09-14T12:33:28,888 running install 2023-09-14T12:33:28,909 running install_lib 2023-09-14T12:33:28,933 creating build/bdist.linux-armv7l 2023-09-14T12:33:28,933 creating build/bdist.linux-armv7l/wheel 2023-09-14T12:33:28,935 creating build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:33:28,936 creating build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:33:28,937 copying build/lib/bonito/cli/basecaller.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:33:28,939 copying build/lib/bonito/cli/convert.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:33:28,942 copying build/lib/bonito/cli/__init__.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:33:28,943 copying build/lib/bonito/cli/train.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:33:28,945 copying build/lib/bonito/cli/duplex.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:33:28,947 copying build/lib/bonito/cli/view.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:33:28,949 copying build/lib/bonito/cli/evaluate.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:33:28,951 copying build/lib/bonito/cli/export.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:33:28,953 copying build/lib/bonito/cli/download.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:33:28,955 copying build/lib/bonito/__init__.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:33:28,957 copying build/lib/bonito/training.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:33:28,959 copying build/lib/bonito/nn.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:33:28,961 copying build/lib/bonito/multiprocessing.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:33:28,963 copying build/lib/bonito/io.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:33:28,965 creating build/bdist.linux-armv7l/wheel/bonito/data 2023-09-14T12:33:28,966 copying build/lib/bonito/data/README.md -> build/bdist.linux-armv7l/wheel/bonito/data 2023-09-14T12:33:28,969 creating build/bdist.linux-armv7l/wheel/bonito/ctc 2023-09-14T12:33:28,970 copying build/lib/bonito/ctc/__init__.py -> build/bdist.linux-armv7l/wheel/bonito/ctc 2023-09-14T12:33:28,971 copying build/lib/bonito/ctc/basecall.py -> build/bdist.linux-armv7l/wheel/bonito/ctc 2023-09-14T12:33:28,973 copying build/lib/bonito/ctc/model.py -> build/bdist.linux-armv7l/wheel/bonito/ctc 2023-09-14T12:33:28,976 copying build/lib/bonito/aligner.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:33:28,977 copying build/lib/bonito/util.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:33:28,979 copying build/lib/bonito/fast5.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:33:28,982 creating build/bdist.linux-armv7l/wheel/bonito/models 2023-09-14T12:33:28,982 copying build/lib/bonito/models/README.md -> build/bdist.linux-armv7l/wheel/bonito/models 2023-09-14T12:33:28,984 creating build/bdist.linux-armv7l/wheel/bonito/models/configs 2023-09-14T12:33:28,985 copying build/lib/bonito/models/configs/dna_r9.4.1@v2.toml -> build/bdist.linux-armv7l/wheel/bonito/models/configs 2023-09-14T12:33:28,987 copying build/lib/bonito/models/configs/dna_r9.4.1@v3.toml -> build/bdist.linux-armv7l/wheel/bonito/models/configs 2023-09-14T12:33:28,989 copying build/lib/bonito/models/configs/dna_r9.4.1@v1.toml -> build/bdist.linux-armv7l/wheel/bonito/models/configs 2023-09-14T12:33:28,991 creating build/bdist.linux-armv7l/wheel/bonito/crf 2023-09-14T12:33:28,991 copying build/lib/bonito/crf/__init__.py -> build/bdist.linux-armv7l/wheel/bonito/crf 2023-09-14T12:33:28,993 copying build/lib/bonito/crf/basecall.py -> build/bdist.linux-armv7l/wheel/bonito/crf 2023-09-14T12:33:28,995 copying build/lib/bonito/crf/model.py -> build/bdist.linux-armv7l/wheel/bonito/crf 2023-09-14T12:33:28,997 running install_egg_info 2023-09-14T12:33:29,030 Copying ont_bonito_cuda111.egg-info to build/bdist.linux-armv7l/wheel/ont_bonito_cuda111-0.4.0a2-py3.11.egg-info 2023-09-14T12:33:29,041 running install_scripts 2023-09-14T12:33:29,043 error: [Errno 2] No such file or directory: 'bonito' 2023-09-14T12:33:29,165 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-14T12:33:29,178 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-14T12:33:29,178 exec(compile('"'"''"'"''"'"' 2023-09-14T12:33:29,178 # This is -- a caller that pip uses to run setup.py 2023-09-14T12:33:29,178 # 2023-09-14T12:33:29,178 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-14T12:33:29,178 # import from `distutils.core` to work with newer packaging standards. 2023-09-14T12:33:29,178 # - It provides a clear error message when setuptools is not installed. 2023-09-14T12:33:29,178 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-14T12:33:29,178 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-14T12:33:29,178 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-14T12:33:29,178 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-14T12:33:29,178 import os, sys, tokenize 2023-09-14T12:33:29,178 2023-09-14T12:33:29,178 try: 2023-09-14T12:33:29,178 import setuptools 2023-09-14T12:33:29,178 except ImportError as error: 2023-09-14T12:33:29,178 print( 2023-09-14T12:33:29,178 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-14T12:33:29,178 "the build environment.", 2023-09-14T12:33:29,178 file=sys.stderr, 2023-09-14T12:33:29,178 ) 2023-09-14T12:33:29,178 sys.exit(1) 2023-09-14T12:33:29,178 2023-09-14T12:33:29,178 __file__ = %r 2023-09-14T12:33:29,178 sys.argv[0] = __file__ 2023-09-14T12:33:29,178 2023-09-14T12:33:29,178 if os.path.exists(__file__): 2023-09-14T12:33:29,178 filename = __file__ 2023-09-14T12:33:29,178 with tokenize.open(__file__) as f: 2023-09-14T12:33:29,178 setup_py_code = f.read() 2023-09-14T12:33:29,178 else: 2023-09-14T12:33:29,178 filename = "" 2023-09-14T12:33:29,178 setup_py_code = "from setuptools import setup; setup()" 2023-09-14T12:33:29,178 2023-09-14T12:33:29,178 exec(compile(setup_py_code, filename, "exec")) 2023-09-14T12:33:29,178 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-qdk6crxh/ont-bonito-cuda111_beedfaab95a54390a6a576d44b7af67a/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-hodicd71[/] 2023-09-14T12:33:29,178 [bold magenta]cwd[/]: /tmp/pip-wheel-qdk6crxh/ont-bonito-cuda111_beedfaab95a54390a6a576d44b7af67a/ 2023-09-14T12:33:29,179 Building wheel for ont-bonito-cuda111 (setup.py): finished with status 'error' 2023-09-14T12:33:29,180 ERROR: Failed building wheel for ont-bonito-cuda111 2023-09-14T12:33:29,181 Running setup.py clean for ont-bonito-cuda111 2023-09-14T12:33:29,182 Running command python setup.py clean 2023-09-14T12:33:29,612 Building with CUDA 11.1 2023-09-14T12:33:30,196 running clean 2023-09-14T12:33:30,242 removing 'build/lib' (and everything under it) 2023-09-14T12:33:30,251 removing 'build/bdist.linux-armv7l' (and everything under it) 2023-09-14T12:33:30,264 'build/scripts-3.11' does not exist -- can't clean it 2023-09-14T12:33:30,264 removing 'build' 2023-09-14T12:33:30,375 Failed to build ont-bonito-cuda111 2023-09-14T12:33:30,376 ERROR: Failed to build one or more wheels 2023-09-14T12:33:30,378 Exception information: 2023-09-14T12:33:30,378 Traceback (most recent call last): 2023-09-14T12:33:30,378 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-14T12:33:30,378 status = run_func(*args) 2023-09-14T12:33:30,378 ^^^^^^^^^^^^^^^ 2023-09-14T12:33:30,378 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-14T12:33:30,378 return func(self, options, args) 2023-09-14T12:33:30,378 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-14T12:33:30,378 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-14T12:33:30,378 raise CommandError("Failed to build one or more wheels") 2023-09-14T12:33:30,378 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-14T12:33:30,381 Removed build tracker: '/tmp/pip-build-tracker-p2msiroo'