2023-09-14T12:34:06,129 Created temporary directory: /tmp/pip-build-tracker-5791rbam 2023-09-14T12:34:06,130 Initialized build tracking at /tmp/pip-build-tracker-5791rbam 2023-09-14T12:34:06,130 Created build tracker: /tmp/pip-build-tracker-5791rbam 2023-09-14T12:34:06,131 Entered build tracker: /tmp/pip-build-tracker-5791rbam 2023-09-14T12:34:06,132 Created temporary directory: /tmp/pip-wheel-1lxaib_k 2023-09-14T12:34:06,135 Created temporary directory: /tmp/pip-ephem-wheel-cache-qsawm2_5 2023-09-14T12:34:06,157 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-14T12:34:06,161 2 location(s) to search for versions of ont-bonito-cuda111: 2023-09-14T12:34:06,161 * https://pypi.org/simple/ont-bonito-cuda111/ 2023-09-14T12:34:06,161 * https://www.piwheels.org/simple/ont-bonito-cuda111/ 2023-09-14T12:34:06,161 Fetching project page and analyzing links: https://pypi.org/simple/ont-bonito-cuda111/ 2023-09-14T12:34:06,162 Getting page https://pypi.org/simple/ont-bonito-cuda111/ 2023-09-14T12:34:06,164 Found index url https://pypi.org/simple/ 2023-09-14T12:34:06,303 Fetched page https://pypi.org/simple/ont-bonito-cuda111/ as application/vnd.pypi.simple.v1+json 2023-09-14T12:34:06,306 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 2023-09-14T12:34:06,307 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 2023-09-14T12:34:06,308 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 2023-09-14T12:34:06,308 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 2023-09-14T12:34:06,309 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 2023-09-14T12:34:06,310 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 2023-09-14T12:34:06,311 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 2023-09-14T12:34:06,312 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 2023-09-14T12:34:06,313 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 2023-09-14T12:34:06,313 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 2023-09-14T12:34:06,314 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 2023-09-14T12:34:06,315 Fetching project page and analyzing links: https://www.piwheels.org/simple/ont-bonito-cuda111/ 2023-09-14T12:34:06,316 Getting page https://www.piwheels.org/simple/ont-bonito-cuda111/ 2023-09-14T12:34:06,317 Found index url https://www.piwheels.org/simple/ 2023-09-14T12:34:06,610 Fetched page https://www.piwheels.org/simple/ont-bonito-cuda111/ as text/html 2023-09-14T12:34:06,612 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/) 2023-09-14T12:34:06,613 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/) 2023-09-14T12:34:06,613 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/) 2023-09-14T12:34:06,614 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/) 2023-09-14T12:34:06,614 Skipping link: not a file: https://www.piwheels.org/simple/ont-bonito-cuda111/ 2023-09-14T12:34:06,615 Skipping link: not a file: https://pypi.org/simple/ont-bonito-cuda111/ 2023-09-14T12:34:06,634 Given no hashes to check 1 links for project 'ont-bonito-cuda111': discarding no candidates 2023-09-14T12:34:06,652 Collecting ont-bonito-cuda111==0.4.0a4 2023-09-14T12:34:06,654 Created temporary directory: /tmp/pip-unpack-61xsqo0v 2023-09-14T12:34:07,253 Downloading ont-bonito-cuda111-0.4.0a4.tar.gz (43 kB) 2023-09-14T12:34:07,394 Added ont-bonito-cuda111==0.4.0a4 from https://files.pythonhosted.org/packages/b4/03/d3afcda7d932e31137dd77b3e7cdf4ddfee7e207ebe455410f65be8ad79a/ont-bonito-cuda111-0.4.0a4.tar.gz to build tracker '/tmp/pip-build-tracker-5791rbam' 2023-09-14T12:34:07,395 Running setup.py (path:/tmp/pip-wheel-1lxaib_k/ont-bonito-cuda111_f43ea0ef96d44acc8f8419ff170acd0c/setup.py) egg_info for package ont-bonito-cuda111 2023-09-14T12:34:07,396 Created temporary directory: /tmp/pip-pip-egg-info-va83w9uw 2023-09-14T12:34:07,397 Preparing metadata (setup.py): started 2023-09-14T12:34:07,398 Running command python setup.py egg_info 2023-09-14T12:34:08,629 Building with CUDA 11.1 2023-09-14T12:34:08,629 running egg_info 2023-09-14T12:34:08,630 creating /tmp/pip-pip-egg-info-va83w9uw/ont_bonito_cuda111.egg-info 2023-09-14T12:34:08,655 writing /tmp/pip-pip-egg-info-va83w9uw/ont_bonito_cuda111.egg-info/PKG-INFO 2023-09-14T12:34:08,658 writing dependency_links to /tmp/pip-pip-egg-info-va83w9uw/ont_bonito_cuda111.egg-info/dependency_links.txt 2023-09-14T12:34:08,659 writing entry points to /tmp/pip-pip-egg-info-va83w9uw/ont_bonito_cuda111.egg-info/entry_points.txt 2023-09-14T12:34:08,661 writing requirements to /tmp/pip-pip-egg-info-va83w9uw/ont_bonito_cuda111.egg-info/requires.txt 2023-09-14T12:34:08,662 writing top-level names to /tmp/pip-pip-egg-info-va83w9uw/ont_bonito_cuda111.egg-info/top_level.txt 2023-09-14T12:34:08,663 writing manifest file '/tmp/pip-pip-egg-info-va83w9uw/ont_bonito_cuda111.egg-info/SOURCES.txt' 2023-09-14T12:34:08,741 reading manifest file '/tmp/pip-pip-egg-info-va83w9uw/ont_bonito_cuda111.egg-info/SOURCES.txt' 2023-09-14T12:34:08,742 reading manifest template 'MANIFEST.in' 2023-09-14T12:34:08,745 adding license file 'LICENCE.txt' 2023-09-14T12:34:08,748 writing manifest file '/tmp/pip-pip-egg-info-va83w9uw/ont_bonito_cuda111.egg-info/SOURCES.txt' 2023-09-14T12:34:08,855 Preparing metadata (setup.py): finished with status 'done' 2023-09-14T12:34:08,860 Source in /tmp/pip-wheel-1lxaib_k/ont-bonito-cuda111_f43ea0ef96d44acc8f8419ff170acd0c has version 0.4.0a4, which satisfies requirement ont-bonito-cuda111==0.4.0a4 from https://files.pythonhosted.org/packages/b4/03/d3afcda7d932e31137dd77b3e7cdf4ddfee7e207ebe455410f65be8ad79a/ont-bonito-cuda111-0.4.0a4.tar.gz 2023-09-14T12:34:08,861 Removed ont-bonito-cuda111==0.4.0a4 from https://files.pythonhosted.org/packages/b4/03/d3afcda7d932e31137dd77b3e7cdf4ddfee7e207ebe455410f65be8ad79a/ont-bonito-cuda111-0.4.0a4.tar.gz from build tracker '/tmp/pip-build-tracker-5791rbam' 2023-09-14T12:34:08,866 Created temporary directory: /tmp/pip-unpack-il35a7uo 2023-09-14T12:34:08,867 Created temporary directory: /tmp/pip-unpack-yadlej2d 2023-09-14T12:34:08,889 Building wheels for collected packages: ont-bonito-cuda111 2023-09-14T12:34:08,893 Created temporary directory: /tmp/pip-wheel-elcstvhi 2023-09-14T12:34:08,893 Building wheel for ont-bonito-cuda111 (setup.py): started 2023-09-14T12:34:08,894 Destination directory: /tmp/pip-wheel-elcstvhi 2023-09-14T12:34:08,895 Running command python setup.py bdist_wheel 2023-09-14T12:34:09,294 Building with CUDA 11.1 2023-09-14T12:34:09,877 running bdist_wheel 2023-09-14T12:34:09,968 running build 2023-09-14T12:34:09,969 running build_py 2023-09-14T12:34:09,995 creating build 2023-09-14T12:34:09,995 creating build/lib 2023-09-14T12:34:09,996 creating build/lib/bonito 2023-09-14T12:34:09,997 copying bonito/io.py -> build/lib/bonito 2023-09-14T12:34:09,999 copying bonito/multiprocessing.py -> build/lib/bonito 2023-09-14T12:34:10,001 copying bonito/training.py -> build/lib/bonito 2023-09-14T12:34:10,003 copying bonito/util.py -> build/lib/bonito 2023-09-14T12:34:10,005 copying bonito/__init__.py -> build/lib/bonito 2023-09-14T12:34:10,007 copying bonito/nn.py -> build/lib/bonito 2023-09-14T12:34:10,009 copying bonito/fast5.py -> build/lib/bonito 2023-09-14T12:34:10,011 copying bonito/aligner.py -> build/lib/bonito 2023-09-14T12:34:10,013 creating build/lib/bonito/crf 2023-09-14T12:34:10,013 copying bonito/crf/__init__.py -> build/lib/bonito/crf 2023-09-14T12:34:10,015 copying bonito/crf/basecall.py -> build/lib/bonito/crf 2023-09-14T12:34:10,017 copying bonito/crf/model.py -> build/lib/bonito/crf 2023-09-14T12:34:10,020 creating build/lib/bonito/cli 2023-09-14T12:34:10,021 copying bonito/cli/view.py -> build/lib/bonito/cli 2023-09-14T12:34:10,022 copying bonito/cli/train.py -> build/lib/bonito/cli 2023-09-14T12:34:10,024 copying bonito/cli/evaluate.py -> build/lib/bonito/cli 2023-09-14T12:34:10,026 copying bonito/cli/download.py -> build/lib/bonito/cli 2023-09-14T12:34:10,028 copying bonito/cli/duplex.py -> build/lib/bonito/cli 2023-09-14T12:34:10,030 copying bonito/cli/convert.py -> build/lib/bonito/cli 2023-09-14T12:34:10,032 copying bonito/cli/basecaller.py -> build/lib/bonito/cli 2023-09-14T12:34:10,033 copying bonito/cli/__init__.py -> build/lib/bonito/cli 2023-09-14T12:34:10,035 copying bonito/cli/export.py -> build/lib/bonito/cli 2023-09-14T12:34:10,037 creating build/lib/bonito/ctc 2023-09-14T12:34:10,038 copying bonito/ctc/__init__.py -> build/lib/bonito/ctc 2023-09-14T12:34:10,039 copying bonito/ctc/basecall.py -> build/lib/bonito/ctc 2023-09-14T12:34:10,041 copying bonito/ctc/model.py -> build/lib/bonito/ctc 2023-09-14T12:34:10,043 running egg_info 2023-09-14T12:34:10,098 writing ont_bonito_cuda111.egg-info/PKG-INFO 2023-09-14T12:34:10,100 writing dependency_links to ont_bonito_cuda111.egg-info/dependency_links.txt 2023-09-14T12:34:10,102 writing entry points to ont_bonito_cuda111.egg-info/entry_points.txt 2023-09-14T12:34:10,103 writing requirements to ont_bonito_cuda111.egg-info/requires.txt 2023-09-14T12:34:10,105 writing top-level names to ont_bonito_cuda111.egg-info/top_level.txt 2023-09-14T12:34:10,132 reading manifest file 'ont_bonito_cuda111.egg-info/SOURCES.txt' 2023-09-14T12:34:10,135 reading manifest template 'MANIFEST.in' 2023-09-14T12:34:10,137 adding license file 'LICENCE.txt' 2023-09-14T12:34:10,140 writing manifest file 'ont_bonito_cuda111.egg-info/SOURCES.txt' 2023-09-14T12:34:10,142 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'bonito.data' is absent from the `packages` configuration. 2023-09-14T12:34:10,143 !! 2023-09-14T12:34:10,144 ******************************************************************************** 2023-09-14T12:34:10,144 ############################ 2023-09-14T12:34:10,145 # Package would be ignored # 2023-09-14T12:34:10,145 ############################ 2023-09-14T12:34:10,146 Python recognizes 'bonito.data' as an importable package[^1], 2023-09-14T12:34:10,146 but it is absent from setuptools' `packages` configuration. 2023-09-14T12:34:10,147 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-14T12:34:10,148 package, please make sure that 'bonito.data' is explicitly added 2023-09-14T12:34:10,148 to the `packages` configuration field. 2023-09-14T12:34:10,149 Alternatively, you can also rely on setuptools' discovery methods 2023-09-14T12:34:10,150 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-14T12:34:10,150 instead of `find_packages(...)`/`find:`). 2023-09-14T12:34:10,151 You can read more about "package discovery" on setuptools documentation page: 2023-09-14T12:34:10,152 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-14T12:34:10,153 If you don't want 'bonito.data' to be distributed and are 2023-09-14T12:34:10,154 already explicitly excluding 'bonito.data' via 2023-09-14T12:34:10,154 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-14T12:34:10,155 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-14T12:34:10,155 combination with a more fine grained `package-data` configuration. 2023-09-14T12:34:10,156 You can read more about "package data files" on setuptools documentation page: 2023-09-14T12:34:10,157 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-14T12:34:10,159 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-14T12:34:10,160 even if it does not contain any `.py` files. 2023-09-14T12:34:10,160 On the other hand, currently there is no concept of package data 2023-09-14T12:34:10,161 directory, all directories are treated like packages. 2023-09-14T12:34:10,161 ******************************************************************************** 2023-09-14T12:34:10,163 !! 2023-09-14T12:34:10,163 check.warn(importable) 2023-09-14T12:34:10,164 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'bonito.models' is absent from the `packages` configuration. 2023-09-14T12:34:10,165 !! 2023-09-14T12:34:10,166 ******************************************************************************** 2023-09-14T12:34:10,167 ############################ 2023-09-14T12:34:10,167 # Package would be ignored # 2023-09-14T12:34:10,168 ############################ 2023-09-14T12:34:10,168 Python recognizes 'bonito.models' as an importable package[^1], 2023-09-14T12:34:10,169 but it is absent from setuptools' `packages` configuration. 2023-09-14T12:34:10,170 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-14T12:34:10,170 package, please make sure that 'bonito.models' is explicitly added 2023-09-14T12:34:10,171 to the `packages` configuration field. 2023-09-14T12:34:10,172 Alternatively, you can also rely on setuptools' discovery methods 2023-09-14T12:34:10,173 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-14T12:34:10,173 instead of `find_packages(...)`/`find:`). 2023-09-14T12:34:10,174 You can read more about "package discovery" on setuptools documentation page: 2023-09-14T12:34:10,176 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-14T12:34:10,177 If you don't want 'bonito.models' to be distributed and are 2023-09-14T12:34:10,177 already explicitly excluding 'bonito.models' via 2023-09-14T12:34:10,178 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-14T12:34:10,178 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-14T12:34:10,179 combination with a more fine grained `package-data` configuration. 2023-09-14T12:34:10,180 You can read more about "package data files" on setuptools documentation page: 2023-09-14T12:34:10,181 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-14T12:34:10,182 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-14T12:34:10,183 even if it does not contain any `.py` files. 2023-09-14T12:34:10,183 On the other hand, currently there is no concept of package data 2023-09-14T12:34:10,184 directory, all directories are treated like packages. 2023-09-14T12:34:10,184 ******************************************************************************** 2023-09-14T12:34:10,185 !! 2023-09-14T12:34:10,186 check.warn(importable) 2023-09-14T12:34:10,186 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'bonito.models.configs' is absent from the `packages` configuration. 2023-09-14T12:34:10,187 !! 2023-09-14T12:34:10,188 ******************************************************************************** 2023-09-14T12:34:10,189 ############################ 2023-09-14T12:34:10,189 # Package would be ignored # 2023-09-14T12:34:10,190 ############################ 2023-09-14T12:34:10,191 Python recognizes 'bonito.models.configs' as an importable package[^1], 2023-09-14T12:34:10,191 but it is absent from setuptools' `packages` configuration. 2023-09-14T12:34:10,193 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-14T12:34:10,193 package, please make sure that 'bonito.models.configs' is explicitly added 2023-09-14T12:34:10,194 to the `packages` configuration field. 2023-09-14T12:34:10,195 Alternatively, you can also rely on setuptools' discovery methods 2023-09-14T12:34:10,196 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-14T12:34:10,197 instead of `find_packages(...)`/`find:`). 2023-09-14T12:34:10,198 You can read more about "package discovery" on setuptools documentation page: 2023-09-14T12:34:10,199 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-14T12:34:10,200 If you don't want 'bonito.models.configs' to be distributed and are 2023-09-14T12:34:10,201 already explicitly excluding 'bonito.models.configs' via 2023-09-14T12:34:10,201 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-14T12:34:10,202 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-14T12:34:10,202 combination with a more fine grained `package-data` configuration. 2023-09-14T12:34:10,203 You can read more about "package data files" on setuptools documentation page: 2023-09-14T12:34:10,204 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-14T12:34:10,206 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-14T12:34:10,207 even if it does not contain any `.py` files. 2023-09-14T12:34:10,207 On the other hand, currently there is no concept of package data 2023-09-14T12:34:10,208 directory, all directories are treated like packages. 2023-09-14T12:34:10,209 ******************************************************************************** 2023-09-14T12:34:10,210 !! 2023-09-14T12:34:10,210 check.warn(importable) 2023-09-14T12:34:10,211 creating build/lib/bonito/data 2023-09-14T12:34:10,211 copying bonito/data/README.md -> build/lib/bonito/data 2023-09-14T12:34:10,211 creating build/lib/bonito/models 2023-09-14T12:34:10,212 copying bonito/models/README.md -> build/lib/bonito/models 2023-09-14T12:34:10,212 creating build/lib/bonito/models/configs 2023-09-14T12:34:10,212 copying bonito/models/configs/dna_r9.4.1@v1.toml -> build/lib/bonito/models/configs 2023-09-14T12:34:10,213 copying bonito/models/configs/dna_r9.4.1@v2.toml -> build/lib/bonito/models/configs 2023-09-14T12:34:10,213 copying bonito/models/configs/dna_r9.4.1@v3.toml -> build/lib/bonito/models/configs 2023-09-14T12:34:10,214 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-09-14T12:34:10,214 !! 2023-09-14T12:34:10,215 ******************************************************************************** 2023-09-14T12:34:10,215 Please avoid running ``setup.py`` directly. 2023-09-14T12:34:10,216 Instead, use pypa/build, pypa/installer or other 2023-09-14T12:34:10,216 standards-based tools. 2023-09-14T12:34:10,217 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-09-14T12:34:10,218 ******************************************************************************** 2023-09-14T12:34:10,219 !! 2023-09-14T12:34:10,219 self.initialize_options() 2023-09-14T12:34:10,220 installing to build/bdist.linux-armv7l/wheel 2023-09-14T12:34:10,221 running install 2023-09-14T12:34:10,221 running install_lib 2023-09-14T12:34:10,239 creating build/bdist.linux-armv7l 2023-09-14T12:34:10,240 creating build/bdist.linux-armv7l/wheel 2023-09-14T12:34:10,241 creating build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:34:10,243 creating build/bdist.linux-armv7l/wheel/bonito/crf 2023-09-14T12:34:10,244 copying build/lib/bonito/crf/__init__.py -> build/bdist.linux-armv7l/wheel/bonito/crf 2023-09-14T12:34:10,245 copying build/lib/bonito/crf/basecall.py -> build/bdist.linux-armv7l/wheel/bonito/crf 2023-09-14T12:34:10,247 copying build/lib/bonito/crf/model.py -> build/bdist.linux-armv7l/wheel/bonito/crf 2023-09-14T12:34:10,249 copying build/lib/bonito/io.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:34:10,252 creating build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:10,253 copying build/lib/bonito/cli/view.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:10,255 copying build/lib/bonito/cli/train.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:10,257 copying build/lib/bonito/cli/evaluate.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:10,259 copying build/lib/bonito/cli/download.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:10,261 copying build/lib/bonito/cli/duplex.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:10,263 copying build/lib/bonito/cli/convert.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:10,265 copying build/lib/bonito/cli/basecaller.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:10,267 copying build/lib/bonito/cli/__init__.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:10,268 copying build/lib/bonito/cli/export.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:10,271 creating build/bdist.linux-armv7l/wheel/bonito/models 2023-09-14T12:34:10,272 copying build/lib/bonito/models/README.md -> build/bdist.linux-armv7l/wheel/bonito/models 2023-09-14T12:34:10,274 creating build/bdist.linux-armv7l/wheel/bonito/models/configs 2023-09-14T12:34:10,275 copying build/lib/bonito/models/configs/dna_r9.4.1@v3.toml -> build/bdist.linux-armv7l/wheel/bonito/models/configs 2023-09-14T12:34:10,277 copying build/lib/bonito/models/configs/dna_r9.4.1@v2.toml -> build/bdist.linux-armv7l/wheel/bonito/models/configs 2023-09-14T12:34:10,279 copying build/lib/bonito/models/configs/dna_r9.4.1@v1.toml -> build/bdist.linux-armv7l/wheel/bonito/models/configs 2023-09-14T12:34:10,280 copying build/lib/bonito/multiprocessing.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:34:10,282 copying build/lib/bonito/training.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:34:10,284 copying build/lib/bonito/util.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:34:10,287 creating build/bdist.linux-armv7l/wheel/bonito/data 2023-09-14T12:34:10,287 copying build/lib/bonito/data/README.md -> build/bdist.linux-armv7l/wheel/bonito/data 2023-09-14T12:34:10,289 copying build/lib/bonito/__init__.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:34:10,291 creating build/bdist.linux-armv7l/wheel/bonito/ctc 2023-09-14T12:34:10,292 copying build/lib/bonito/ctc/__init__.py -> build/bdist.linux-armv7l/wheel/bonito/ctc 2023-09-14T12:34:10,294 copying build/lib/bonito/ctc/basecall.py -> build/bdist.linux-armv7l/wheel/bonito/ctc 2023-09-14T12:34:10,295 copying build/lib/bonito/ctc/model.py -> build/bdist.linux-armv7l/wheel/bonito/ctc 2023-09-14T12:34:10,298 copying build/lib/bonito/nn.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:34:10,300 copying build/lib/bonito/fast5.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:34:10,302 copying build/lib/bonito/aligner.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:34:10,304 running install_egg_info 2023-09-14T12:34:10,333 Copying ont_bonito_cuda111.egg-info to build/bdist.linux-armv7l/wheel/ont_bonito_cuda111-0.4.0a4-py3.11.egg-info 2023-09-14T12:34:10,344 running install_scripts 2023-09-14T12:34:10,346 error: [Errno 2] No such file or directory: 'bonito' 2023-09-14T12:34:10,457 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-14T12:34:10,470 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-14T12:34:10,470 exec(compile('"'"''"'"''"'"' 2023-09-14T12:34:10,470 # This is -- a caller that pip uses to run setup.py 2023-09-14T12:34:10,470 # 2023-09-14T12:34:10,470 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-14T12:34:10,470 # import from `distutils.core` to work with newer packaging standards. 2023-09-14T12:34:10,470 # - It provides a clear error message when setuptools is not installed. 2023-09-14T12:34:10,470 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-14T12:34:10,470 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-14T12:34:10,470 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-14T12:34:10,470 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-14T12:34:10,470 import os, sys, tokenize 2023-09-14T12:34:10,470 2023-09-14T12:34:10,470 try: 2023-09-14T12:34:10,470 import setuptools 2023-09-14T12:34:10,470 except ImportError as error: 2023-09-14T12:34:10,470 print( 2023-09-14T12:34:10,470 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-14T12:34:10,470 "the build environment.", 2023-09-14T12:34:10,470 file=sys.stderr, 2023-09-14T12:34:10,470 ) 2023-09-14T12:34:10,470 sys.exit(1) 2023-09-14T12:34:10,470 2023-09-14T12:34:10,470 __file__ = %r 2023-09-14T12:34:10,470 sys.argv[0] = __file__ 2023-09-14T12:34:10,470 2023-09-14T12:34:10,470 if os.path.exists(__file__): 2023-09-14T12:34:10,470 filename = __file__ 2023-09-14T12:34:10,470 with tokenize.open(__file__) as f: 2023-09-14T12:34:10,470 setup_py_code = f.read() 2023-09-14T12:34:10,470 else: 2023-09-14T12:34:10,470 filename = "" 2023-09-14T12:34:10,470 setup_py_code = "from setuptools import setup; setup()" 2023-09-14T12:34:10,470 2023-09-14T12:34:10,470 exec(compile(setup_py_code, filename, "exec")) 2023-09-14T12:34:10,470 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-1lxaib_k/ont-bonito-cuda111_f43ea0ef96d44acc8f8419ff170acd0c/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-elcstvhi[/] 2023-09-14T12:34:10,471 [bold magenta]cwd[/]: /tmp/pip-wheel-1lxaib_k/ont-bonito-cuda111_f43ea0ef96d44acc8f8419ff170acd0c/ 2023-09-14T12:34:10,472 Building wheel for ont-bonito-cuda111 (setup.py): finished with status 'error' 2023-09-14T12:34:10,473 ERROR: Failed building wheel for ont-bonito-cuda111 2023-09-14T12:34:10,474 Running setup.py clean for ont-bonito-cuda111 2023-09-14T12:34:10,475 Running command python setup.py clean 2023-09-14T12:34:10,874 Building with CUDA 11.1 2023-09-14T12:34:11,459 running clean 2023-09-14T12:34:11,505 removing 'build/lib' (and everything under it) 2023-09-14T12:34:11,514 removing 'build/bdist.linux-armv7l' (and everything under it) 2023-09-14T12:34:11,528 'build/scripts-3.11' does not exist -- can't clean it 2023-09-14T12:34:11,528 removing 'build' 2023-09-14T12:34:11,634 Failed to build ont-bonito-cuda111 2023-09-14T12:34:11,636 ERROR: Failed to build one or more wheels 2023-09-14T12:34:11,637 Exception information: 2023-09-14T12:34:11,637 Traceback (most recent call last): 2023-09-14T12:34:11,637 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-14T12:34:11,637 status = run_func(*args) 2023-09-14T12:34:11,637 ^^^^^^^^^^^^^^^ 2023-09-14T12:34:11,637 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-14T12:34:11,637 return func(self, options, args) 2023-09-14T12:34:11,637 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-14T12:34:11,637 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-14T12:34:11,637 raise CommandError("Failed to build one or more wheels") 2023-09-14T12:34:11,637 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-14T12:34:11,640 Removed build tracker: '/tmp/pip-build-tracker-5791rbam'