2023-09-14T12:34:13,515 Created temporary directory: /tmp/pip-build-tracker-n9avgfpt 2023-09-14T12:34:13,516 Initialized build tracking at /tmp/pip-build-tracker-n9avgfpt 2023-09-14T12:34:13,516 Created build tracker: /tmp/pip-build-tracker-n9avgfpt 2023-09-14T12:34:13,517 Entered build tracker: /tmp/pip-build-tracker-n9avgfpt 2023-09-14T12:34:13,517 Created temporary directory: /tmp/pip-wheel-gwmsb_5x 2023-09-14T12:34:13,520 Created temporary directory: /tmp/pip-ephem-wheel-cache-vk0czmim 2023-09-14T12:34:13,542 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-14T12:34:13,546 2 location(s) to search for versions of ont-bonito-cuda111: 2023-09-14T12:34:13,546 * https://pypi.org/simple/ont-bonito-cuda111/ 2023-09-14T12:34:13,546 * https://www.piwheels.org/simple/ont-bonito-cuda111/ 2023-09-14T12:34:13,547 Fetching project page and analyzing links: https://pypi.org/simple/ont-bonito-cuda111/ 2023-09-14T12:34:13,548 Getting page https://pypi.org/simple/ont-bonito-cuda111/ 2023-09-14T12:34:13,549 Found index url https://pypi.org/simple/ 2023-09-14T12:34:13,689 Fetched page https://pypi.org/simple/ont-bonito-cuda111/ as application/vnd.pypi.simple.v1+json 2023-09-14T12:34:13,692 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 2023-09-14T12:34:13,693 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 2023-09-14T12:34:13,693 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 2023-09-14T12:34:13,694 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 2023-09-14T12:34:13,695 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 2023-09-14T12:34:13,696 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 2023-09-14T12:34:13,696 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 2023-09-14T12:34:13,697 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 2023-09-14T12:34:13,698 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 2023-09-14T12:34:13,699 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 2023-09-14T12:34:13,700 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 2023-09-14T12:34:13,700 Fetching project page and analyzing links: https://www.piwheels.org/simple/ont-bonito-cuda111/ 2023-09-14T12:34:13,701 Getting page https://www.piwheels.org/simple/ont-bonito-cuda111/ 2023-09-14T12:34:13,702 Found index url https://www.piwheels.org/simple/ 2023-09-14T12:34:13,981 Fetched page https://www.piwheels.org/simple/ont-bonito-cuda111/ as text/html 2023-09-14T12:34:13,983 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/) 2023-09-14T12:34:13,984 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/) 2023-09-14T12:34:13,984 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/) 2023-09-14T12:34:13,985 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/) 2023-09-14T12:34:13,985 Skipping link: not a file: https://www.piwheels.org/simple/ont-bonito-cuda111/ 2023-09-14T12:34:13,986 Skipping link: not a file: https://pypi.org/simple/ont-bonito-cuda111/ 2023-09-14T12:34:14,005 Given no hashes to check 1 links for project 'ont-bonito-cuda111': discarding no candidates 2023-09-14T12:34:14,023 Collecting ont-bonito-cuda111==0.4.0 2023-09-14T12:34:14,025 Created temporary directory: /tmp/pip-unpack-rtb0kj26 2023-09-14T12:34:14,530 Downloading ont-bonito-cuda111-0.4.0.tar.gz (43 kB) 2023-09-14T12:34:14,693 Added ont-bonito-cuda111==0.4.0 from https://files.pythonhosted.org/packages/2e/c0/01dfa9cd140ab87acd038089bf3c9719a7e2794ef50c17c9796a719f2fb7/ont-bonito-cuda111-0.4.0.tar.gz to build tracker '/tmp/pip-build-tracker-n9avgfpt' 2023-09-14T12:34:14,694 Running setup.py (path:/tmp/pip-wheel-gwmsb_5x/ont-bonito-cuda111_bb852733fb014ff38031275be76c96ec/setup.py) egg_info for package ont-bonito-cuda111 2023-09-14T12:34:14,695 Created temporary directory: /tmp/pip-pip-egg-info-a73j9om2 2023-09-14T12:34:14,696 Preparing metadata (setup.py): started 2023-09-14T12:34:14,697 Running command python setup.py egg_info 2023-09-14T12:34:15,710 Building with CUDA 11.1 2023-09-14T12:34:15,710 running egg_info 2023-09-14T12:34:15,712 creating /tmp/pip-pip-egg-info-a73j9om2/ont_bonito_cuda111.egg-info 2023-09-14T12:34:15,736 writing /tmp/pip-pip-egg-info-a73j9om2/ont_bonito_cuda111.egg-info/PKG-INFO 2023-09-14T12:34:15,739 writing dependency_links to /tmp/pip-pip-egg-info-a73j9om2/ont_bonito_cuda111.egg-info/dependency_links.txt 2023-09-14T12:34:15,740 writing entry points to /tmp/pip-pip-egg-info-a73j9om2/ont_bonito_cuda111.egg-info/entry_points.txt 2023-09-14T12:34:15,742 writing requirements to /tmp/pip-pip-egg-info-a73j9om2/ont_bonito_cuda111.egg-info/requires.txt 2023-09-14T12:34:15,743 writing top-level names to /tmp/pip-pip-egg-info-a73j9om2/ont_bonito_cuda111.egg-info/top_level.txt 2023-09-14T12:34:15,744 writing manifest file '/tmp/pip-pip-egg-info-a73j9om2/ont_bonito_cuda111.egg-info/SOURCES.txt' 2023-09-14T12:34:15,821 reading manifest file '/tmp/pip-pip-egg-info-a73j9om2/ont_bonito_cuda111.egg-info/SOURCES.txt' 2023-09-14T12:34:15,823 reading manifest template 'MANIFEST.in' 2023-09-14T12:34:15,826 adding license file 'LICENCE.txt' 2023-09-14T12:34:15,828 writing manifest file '/tmp/pip-pip-egg-info-a73j9om2/ont_bonito_cuda111.egg-info/SOURCES.txt' 2023-09-14T12:34:15,936 Preparing metadata (setup.py): finished with status 'done' 2023-09-14T12:34:15,941 Source in /tmp/pip-wheel-gwmsb_5x/ont-bonito-cuda111_bb852733fb014ff38031275be76c96ec has version 0.4.0, which satisfies requirement ont-bonito-cuda111==0.4.0 from https://files.pythonhosted.org/packages/2e/c0/01dfa9cd140ab87acd038089bf3c9719a7e2794ef50c17c9796a719f2fb7/ont-bonito-cuda111-0.4.0.tar.gz 2023-09-14T12:34:15,942 Removed ont-bonito-cuda111==0.4.0 from https://files.pythonhosted.org/packages/2e/c0/01dfa9cd140ab87acd038089bf3c9719a7e2794ef50c17c9796a719f2fb7/ont-bonito-cuda111-0.4.0.tar.gz from build tracker '/tmp/pip-build-tracker-n9avgfpt' 2023-09-14T12:34:15,948 Created temporary directory: /tmp/pip-unpack-29chzdkw 2023-09-14T12:34:15,949 Created temporary directory: /tmp/pip-unpack-1x3_px21 2023-09-14T12:34:15,971 Building wheels for collected packages: ont-bonito-cuda111 2023-09-14T12:34:15,975 Created temporary directory: /tmp/pip-wheel-gf69gyur 2023-09-14T12:34:15,975 Building wheel for ont-bonito-cuda111 (setup.py): started 2023-09-14T12:34:15,977 Destination directory: /tmp/pip-wheel-gf69gyur 2023-09-14T12:34:15,977 Running command python setup.py bdist_wheel 2023-09-14T12:34:16,410 Building with CUDA 11.1 2023-09-14T12:34:16,998 running bdist_wheel 2023-09-14T12:34:17,090 running build 2023-09-14T12:34:17,091 running build_py 2023-09-14T12:34:17,117 creating build 2023-09-14T12:34:17,118 creating build/lib 2023-09-14T12:34:17,118 creating build/lib/bonito 2023-09-14T12:34:17,119 copying bonito/io.py -> build/lib/bonito 2023-09-14T12:34:17,122 copying bonito/multiprocessing.py -> build/lib/bonito 2023-09-14T12:34:17,124 copying bonito/training.py -> build/lib/bonito 2023-09-14T12:34:17,127 copying bonito/util.py -> build/lib/bonito 2023-09-14T12:34:17,129 copying bonito/__init__.py -> build/lib/bonito 2023-09-14T12:34:17,130 copying bonito/nn.py -> build/lib/bonito 2023-09-14T12:34:17,133 copying bonito/fast5.py -> build/lib/bonito 2023-09-14T12:34:17,135 copying bonito/aligner.py -> build/lib/bonito 2023-09-14T12:34:17,137 creating build/lib/bonito/crf 2023-09-14T12:34:17,138 copying bonito/crf/__init__.py -> build/lib/bonito/crf 2023-09-14T12:34:17,139 copying bonito/crf/basecall.py -> build/lib/bonito/crf 2023-09-14T12:34:17,141 copying bonito/crf/model.py -> build/lib/bonito/crf 2023-09-14T12:34:17,144 creating build/lib/bonito/cli 2023-09-14T12:34:17,145 copying bonito/cli/view.py -> build/lib/bonito/cli 2023-09-14T12:34:17,147 copying bonito/cli/train.py -> build/lib/bonito/cli 2023-09-14T12:34:17,149 copying bonito/cli/evaluate.py -> build/lib/bonito/cli 2023-09-14T12:34:17,151 copying bonito/cli/download.py -> build/lib/bonito/cli 2023-09-14T12:34:17,153 copying bonito/cli/duplex.py -> build/lib/bonito/cli 2023-09-14T12:34:17,155 copying bonito/cli/convert.py -> build/lib/bonito/cli 2023-09-14T12:34:17,158 copying bonito/cli/basecaller.py -> build/lib/bonito/cli 2023-09-14T12:34:17,159 copying bonito/cli/__init__.py -> build/lib/bonito/cli 2023-09-14T12:34:17,161 copying bonito/cli/export.py -> build/lib/bonito/cli 2023-09-14T12:34:17,163 creating build/lib/bonito/ctc 2023-09-14T12:34:17,164 copying bonito/ctc/__init__.py -> build/lib/bonito/ctc 2023-09-14T12:34:17,166 copying bonito/ctc/basecall.py -> build/lib/bonito/ctc 2023-09-14T12:34:17,168 copying bonito/ctc/model.py -> build/lib/bonito/ctc 2023-09-14T12:34:17,169 running egg_info 2023-09-14T12:34:17,223 writing ont_bonito_cuda111.egg-info/PKG-INFO 2023-09-14T12:34:17,227 writing dependency_links to ont_bonito_cuda111.egg-info/dependency_links.txt 2023-09-14T12:34:17,228 writing entry points to ont_bonito_cuda111.egg-info/entry_points.txt 2023-09-14T12:34:17,229 writing requirements to ont_bonito_cuda111.egg-info/requires.txt 2023-09-14T12:34:17,231 writing top-level names to ont_bonito_cuda111.egg-info/top_level.txt 2023-09-14T12:34:17,257 reading manifest file 'ont_bonito_cuda111.egg-info/SOURCES.txt' 2023-09-14T12:34:17,260 reading manifest template 'MANIFEST.in' 2023-09-14T12:34:17,262 adding license file 'LICENCE.txt' 2023-09-14T12:34:17,265 writing manifest file 'ont_bonito_cuda111.egg-info/SOURCES.txt' 2023-09-14T12:34:17,268 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'bonito.data' is absent from the `packages` configuration. 2023-09-14T12:34:17,269 !! 2023-09-14T12:34:17,272 ******************************************************************************** 2023-09-14T12:34:17,272 ############################ 2023-09-14T12:34:17,273 # Package would be ignored # 2023-09-14T12:34:17,274 ############################ 2023-09-14T12:34:17,274 Python recognizes 'bonito.data' as an importable package[^1], 2023-09-14T12:34:17,274 but it is absent from setuptools' `packages` configuration. 2023-09-14T12:34:17,275 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-14T12:34:17,276 package, please make sure that 'bonito.data' is explicitly added 2023-09-14T12:34:17,276 to the `packages` configuration field. 2023-09-14T12:34:17,277 Alternatively, you can also rely on setuptools' discovery methods 2023-09-14T12:34:17,277 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-14T12:34:17,278 instead of `find_packages(...)`/`find:`). 2023-09-14T12:34:17,278 You can read more about "package discovery" on setuptools documentation page: 2023-09-14T12:34:17,279 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-14T12:34:17,280 If you don't want 'bonito.data' to be distributed and are 2023-09-14T12:34:17,281 already explicitly excluding 'bonito.data' via 2023-09-14T12:34:17,281 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-14T12:34:17,282 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-14T12:34:17,282 combination with a more fine grained `package-data` configuration. 2023-09-14T12:34:17,283 You can read more about "package data files" on setuptools documentation page: 2023-09-14T12:34:17,284 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-14T12:34:17,285 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-14T12:34:17,286 even if it does not contain any `.py` files. 2023-09-14T12:34:17,286 On the other hand, currently there is no concept of package data 2023-09-14T12:34:17,287 directory, all directories are treated like packages. 2023-09-14T12:34:17,287 ******************************************************************************** 2023-09-14T12:34:17,288 !! 2023-09-14T12:34:17,289 check.warn(importable) 2023-09-14T12:34:17,289 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'bonito.models' is absent from the `packages` configuration. 2023-09-14T12:34:17,290 !! 2023-09-14T12:34:17,291 ******************************************************************************** 2023-09-14T12:34:17,291 ############################ 2023-09-14T12:34:17,292 # Package would be ignored # 2023-09-14T12:34:17,292 ############################ 2023-09-14T12:34:17,293 Python recognizes 'bonito.models' as an importable package[^1], 2023-09-14T12:34:17,293 but it is absent from setuptools' `packages` configuration. 2023-09-14T12:34:17,295 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-14T12:34:17,295 package, please make sure that 'bonito.models' is explicitly added 2023-09-14T12:34:17,296 to the `packages` configuration field. 2023-09-14T12:34:17,297 Alternatively, you can also rely on setuptools' discovery methods 2023-09-14T12:34:17,297 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-14T12:34:17,298 instead of `find_packages(...)`/`find:`). 2023-09-14T12:34:17,299 You can read more about "package discovery" on setuptools documentation page: 2023-09-14T12:34:17,300 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-14T12:34:17,301 If you don't want 'bonito.models' to be distributed and are 2023-09-14T12:34:17,301 already explicitly excluding 'bonito.models' via 2023-09-14T12:34:17,302 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-14T12:34:17,302 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-14T12:34:17,303 combination with a more fine grained `package-data` configuration. 2023-09-14T12:34:17,303 You can read more about "package data files" on setuptools documentation page: 2023-09-14T12:34:17,304 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-14T12:34:17,306 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-14T12:34:17,306 even if it does not contain any `.py` files. 2023-09-14T12:34:17,306 On the other hand, currently there is no concept of package data 2023-09-14T12:34:17,307 directory, all directories are treated like packages. 2023-09-14T12:34:17,307 ******************************************************************************** 2023-09-14T12:34:17,308 !! 2023-09-14T12:34:17,309 check.warn(importable) 2023-09-14T12:34:17,309 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'bonito.models.configs' is absent from the `packages` configuration. 2023-09-14T12:34:17,309 !! 2023-09-14T12:34:17,310 ******************************************************************************** 2023-09-14T12:34:17,311 ############################ 2023-09-14T12:34:17,311 # Package would be ignored # 2023-09-14T12:34:17,312 ############################ 2023-09-14T12:34:17,313 Python recognizes 'bonito.models.configs' as an importable package[^1], 2023-09-14T12:34:17,313 but it is absent from setuptools' `packages` configuration. 2023-09-14T12:34:17,314 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-14T12:34:17,315 package, please make sure that 'bonito.models.configs' is explicitly added 2023-09-14T12:34:17,315 to the `packages` configuration field. 2023-09-14T12:34:17,317 Alternatively, you can also rely on setuptools' discovery methods 2023-09-14T12:34:17,317 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-14T12:34:17,318 instead of `find_packages(...)`/`find:`). 2023-09-14T12:34:17,319 You can read more about "package discovery" on setuptools documentation page: 2023-09-14T12:34:17,320 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-14T12:34:17,321 If you don't want 'bonito.models.configs' to be distributed and are 2023-09-14T12:34:17,322 already explicitly excluding 'bonito.models.configs' via 2023-09-14T12:34:17,322 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-14T12:34:17,323 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-14T12:34:17,323 combination with a more fine grained `package-data` configuration. 2023-09-14T12:34:17,324 You can read more about "package data files" on setuptools documentation page: 2023-09-14T12:34:17,325 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-14T12:34:17,327 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-14T12:34:17,328 even if it does not contain any `.py` files. 2023-09-14T12:34:17,328 On the other hand, currently there is no concept of package data 2023-09-14T12:34:17,329 directory, all directories are treated like packages. 2023-09-14T12:34:17,329 ******************************************************************************** 2023-09-14T12:34:17,330 !! 2023-09-14T12:34:17,331 check.warn(importable) 2023-09-14T12:34:17,331 creating build/lib/bonito/data 2023-09-14T12:34:17,332 copying bonito/data/README.md -> build/lib/bonito/data 2023-09-14T12:34:17,332 creating build/lib/bonito/models 2023-09-14T12:34:17,332 copying bonito/models/README.md -> build/lib/bonito/models 2023-09-14T12:34:17,333 creating build/lib/bonito/models/configs 2023-09-14T12:34:17,333 copying bonito/models/configs/dna_r9.4.1@v1.toml -> build/lib/bonito/models/configs 2023-09-14T12:34:17,333 copying bonito/models/configs/dna_r9.4.1@v2.toml -> build/lib/bonito/models/configs 2023-09-14T12:34:17,334 copying bonito/models/configs/dna_r9.4.1@v3.toml -> build/lib/bonito/models/configs 2023-09-14T12:34:17,334 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-09-14T12:34:17,335 !! 2023-09-14T12:34:17,335 ******************************************************************************** 2023-09-14T12:34:17,336 Please avoid running ``setup.py`` directly. 2023-09-14T12:34:17,336 Instead, use pypa/build, pypa/installer or other 2023-09-14T12:34:17,337 standards-based tools. 2023-09-14T12:34:17,337 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-09-14T12:34:17,338 ******************************************************************************** 2023-09-14T12:34:17,339 !! 2023-09-14T12:34:17,339 self.initialize_options() 2023-09-14T12:34:17,340 installing to build/bdist.linux-armv7l/wheel 2023-09-14T12:34:17,340 running install 2023-09-14T12:34:17,350 running install_lib 2023-09-14T12:34:17,374 creating build/bdist.linux-armv7l 2023-09-14T12:34:17,375 creating build/bdist.linux-armv7l/wheel 2023-09-14T12:34:17,377 creating build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:34:17,381 creating build/bdist.linux-armv7l/wheel/bonito/crf 2023-09-14T12:34:17,382 copying build/lib/bonito/crf/__init__.py -> build/bdist.linux-armv7l/wheel/bonito/crf 2023-09-14T12:34:17,384 copying build/lib/bonito/crf/basecall.py -> build/bdist.linux-armv7l/wheel/bonito/crf 2023-09-14T12:34:17,386 copying build/lib/bonito/crf/model.py -> build/bdist.linux-armv7l/wheel/bonito/crf 2023-09-14T12:34:17,388 copying build/lib/bonito/io.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:34:17,392 creating build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:17,392 copying build/lib/bonito/cli/view.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:17,394 copying build/lib/bonito/cli/train.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:17,396 copying build/lib/bonito/cli/evaluate.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:17,398 copying build/lib/bonito/cli/download.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:17,400 copying build/lib/bonito/cli/duplex.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:17,403 copying build/lib/bonito/cli/convert.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:17,405 copying build/lib/bonito/cli/basecaller.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:17,406 copying build/lib/bonito/cli/__init__.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:17,408 copying build/lib/bonito/cli/export.py -> build/bdist.linux-armv7l/wheel/bonito/cli 2023-09-14T12:34:17,410 creating build/bdist.linux-armv7l/wheel/bonito/models 2023-09-14T12:34:17,411 copying build/lib/bonito/models/README.md -> build/bdist.linux-armv7l/wheel/bonito/models 2023-09-14T12:34:17,413 creating build/bdist.linux-armv7l/wheel/bonito/models/configs 2023-09-14T12:34:17,414 copying build/lib/bonito/models/configs/dna_r9.4.1@v3.toml -> build/bdist.linux-armv7l/wheel/bonito/models/configs 2023-09-14T12:34:17,416 copying build/lib/bonito/models/configs/dna_r9.4.1@v2.toml -> build/bdist.linux-armv7l/wheel/bonito/models/configs 2023-09-14T12:34:17,418 copying build/lib/bonito/models/configs/dna_r9.4.1@v1.toml -> build/bdist.linux-armv7l/wheel/bonito/models/configs 2023-09-14T12:34:17,420 copying build/lib/bonito/multiprocessing.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:34:17,422 copying build/lib/bonito/training.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:34:17,424 copying build/lib/bonito/util.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:34:17,426 creating build/bdist.linux-armv7l/wheel/bonito/data 2023-09-14T12:34:17,427 copying build/lib/bonito/data/README.md -> build/bdist.linux-armv7l/wheel/bonito/data 2023-09-14T12:34:17,429 copying build/lib/bonito/__init__.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:34:17,431 creating build/bdist.linux-armv7l/wheel/bonito/ctc 2023-09-14T12:34:17,432 copying build/lib/bonito/ctc/__init__.py -> build/bdist.linux-armv7l/wheel/bonito/ctc 2023-09-14T12:34:17,434 copying build/lib/bonito/ctc/basecall.py -> build/bdist.linux-armv7l/wheel/bonito/ctc 2023-09-14T12:34:17,436 copying build/lib/bonito/ctc/model.py -> build/bdist.linux-armv7l/wheel/bonito/ctc 2023-09-14T12:34:17,438 copying build/lib/bonito/nn.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:34:17,440 copying build/lib/bonito/fast5.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:34:17,442 copying build/lib/bonito/aligner.py -> build/bdist.linux-armv7l/wheel/bonito 2023-09-14T12:34:17,444 running install_egg_info 2023-09-14T12:34:17,474 Copying ont_bonito_cuda111.egg-info to build/bdist.linux-armv7l/wheel/ont_bonito_cuda111-0.4.0-py3.11.egg-info 2023-09-14T12:34:17,487 running install_scripts 2023-09-14T12:34:17,489 error: [Errno 2] No such file or directory: 'bonito' 2023-09-14T12:34:17,600 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-14T12:34:17,613 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-14T12:34:17,613 exec(compile('"'"''"'"''"'"' 2023-09-14T12:34:17,613 # This is -- a caller that pip uses to run setup.py 2023-09-14T12:34:17,613 # 2023-09-14T12:34:17,613 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-14T12:34:17,613 # import from `distutils.core` to work with newer packaging standards. 2023-09-14T12:34:17,613 # - It provides a clear error message when setuptools is not installed. 2023-09-14T12:34:17,613 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-14T12:34:17,613 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-14T12:34:17,613 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-14T12:34:17,613 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-14T12:34:17,613 import os, sys, tokenize 2023-09-14T12:34:17,613 2023-09-14T12:34:17,613 try: 2023-09-14T12:34:17,613 import setuptools 2023-09-14T12:34:17,613 except ImportError as error: 2023-09-14T12:34:17,613 print( 2023-09-14T12:34:17,613 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-14T12:34:17,613 "the build environment.", 2023-09-14T12:34:17,613 file=sys.stderr, 2023-09-14T12:34:17,613 ) 2023-09-14T12:34:17,613 sys.exit(1) 2023-09-14T12:34:17,613 2023-09-14T12:34:17,613 __file__ = %r 2023-09-14T12:34:17,613 sys.argv[0] = __file__ 2023-09-14T12:34:17,613 2023-09-14T12:34:17,613 if os.path.exists(__file__): 2023-09-14T12:34:17,613 filename = __file__ 2023-09-14T12:34:17,613 with tokenize.open(__file__) as f: 2023-09-14T12:34:17,613 setup_py_code = f.read() 2023-09-14T12:34:17,613 else: 2023-09-14T12:34:17,613 filename = "" 2023-09-14T12:34:17,613 setup_py_code = "from setuptools import setup; setup()" 2023-09-14T12:34:17,613 2023-09-14T12:34:17,613 exec(compile(setup_py_code, filename, "exec")) 2023-09-14T12:34:17,613 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-gwmsb_5x/ont-bonito-cuda111_bb852733fb014ff38031275be76c96ec/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-gf69gyur[/] 2023-09-14T12:34:17,613 [bold magenta]cwd[/]: /tmp/pip-wheel-gwmsb_5x/ont-bonito-cuda111_bb852733fb014ff38031275be76c96ec/ 2023-09-14T12:34:17,614 Building wheel for ont-bonito-cuda111 (setup.py): finished with status 'error' 2023-09-14T12:34:17,615 ERROR: Failed building wheel for ont-bonito-cuda111 2023-09-14T12:34:17,617 Running setup.py clean for ont-bonito-cuda111 2023-09-14T12:34:17,618 Running command python setup.py clean 2023-09-14T12:34:18,024 Building with CUDA 11.1 2023-09-14T12:34:18,627 running clean 2023-09-14T12:34:18,674 removing 'build/lib' (and everything under it) 2023-09-14T12:34:18,694 removing 'build/bdist.linux-armv7l' (and everything under it) 2023-09-14T12:34:18,707 'build/scripts-3.11' does not exist -- can't clean it 2023-09-14T12:34:18,707 removing 'build' 2023-09-14T12:34:18,814 Failed to build ont-bonito-cuda111 2023-09-14T12:34:18,815 ERROR: Failed to build one or more wheels 2023-09-14T12:34:18,816 Exception information: 2023-09-14T12:34:18,816 Traceback (most recent call last): 2023-09-14T12:34:18,816 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-14T12:34:18,816 status = run_func(*args) 2023-09-14T12:34:18,816 ^^^^^^^^^^^^^^^ 2023-09-14T12:34:18,816 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-14T12:34:18,816 return func(self, options, args) 2023-09-14T12:34:18,816 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-14T12:34:18,816 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-14T12:34:18,816 raise CommandError("Failed to build one or more wheels") 2023-09-14T12:34:18,816 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-14T12:34:18,819 Removed build tracker: '/tmp/pip-build-tracker-n9avgfpt'