2021-08-24T20:41:00,794 Created temporary directory: /tmp/pip-ephem-wheel-cache-eb7gpwyq
2021-08-24T20:41:00,797 Created temporary directory: /tmp/pip-req-tracker-jm57tvxg
2021-08-24T20:41:00,798 Initialized build tracking at /tmp/pip-req-tracker-jm57tvxg
2021-08-24T20:41:00,798 Created build tracker: /tmp/pip-req-tracker-jm57tvxg
2021-08-24T20:41:00,798 Entered build tracker: /tmp/pip-req-tracker-jm57tvxg
2021-08-24T20:41:00,799 Created temporary directory: /tmp/pip-wheel-h4qijbk_
2021-08-24T20:41:00,830 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2021-08-24T20:41:00,833 2 location(s) to search for versions of ont-bonito-cuda111:
2021-08-24T20:41:00,833 * https://pypi.org/simple/ont-bonito-cuda111/
2021-08-24T20:41:00,833 * https://www.piwheels.org/simple/ont-bonito-cuda111/
2021-08-24T20:41:00,833 Fetching project page and analyzing links: https://pypi.org/simple/ont-bonito-cuda111/
2021-08-24T20:41:00,834 Getting page https://pypi.org/simple/ont-bonito-cuda111/
2021-08-24T20:41:00,835 Found index url https://pypi.org/simple
2021-08-24T20:41:00,922   Found link https://files.pythonhosted.org/packages/4b/e9/326d358ab1d32037c760b9f7b1010edf4eb9de07b68af8e0fdd8bdc5c0c7/ont-bonito-cuda111-0.4.0a0.tar.gz#sha256=ed1d55117b8295e2bce313b195623d2a3ae111242e7e74dd0daaabfc348eb02e (from https://pypi.org/simple/ont-bonito-cuda111/), version: 0.4.0a0
2021-08-24T20:41:00,923   Found link https://files.pythonhosted.org/packages/a1/9f/19c6571eb24457fa6ed8cf7699f2586a4b376cf875c58f0c26ced182f6a1/ont-bonito-cuda111-0.4.0a1.tar.gz#sha256=7d920614f050aba11b20ccfa082e290c24b79c963445c64a6f5691cb98004e4e (from https://pypi.org/simple/ont-bonito-cuda111/), version: 0.4.0a1
2021-08-24T20:41:00,923   Found link https://files.pythonhosted.org/packages/25/8c/28c43178094cb5cdae8df6c80d47e232a3e3013fba61f0bcdc02c5ca42f2/ont-bonito-cuda111-0.4.0a2.tar.gz#sha256=87a95bb62b6e1c5abe647d56732842d7fd7e84c2bdc0a96e427acba969d6879d (from https://pypi.org/simple/ont-bonito-cuda111/), version: 0.4.0a2
2021-08-24T20:41:00,924 Fetching project page and analyzing links: https://www.piwheels.org/simple/ont-bonito-cuda111/
2021-08-24T20:41:00,924 Getting page https://www.piwheels.org/simple/ont-bonito-cuda111/
2021-08-24T20:41:00,925 Found index url https://www.piwheels.org/simple
2021-08-24T20:41:01,038 Skipping link: not a file: https://www.piwheels.org/simple/ont-bonito-cuda111/
2021-08-24T20:41:01,038 Skipping link: not a file: https://pypi.org/simple/ont-bonito-cuda111/
2021-08-24T20:41:01,057 Given no hashes to check 1 links for project 'ont-bonito-cuda111': discarding no candidates
2021-08-24T20:41:01,071 Collecting ont-bonito-cuda111==0.4.0a2
2021-08-24T20:41:01,073   Created temporary directory: /tmp/pip-unpack-azqvrrib
2021-08-24T20:41:01,113   Downloading ont-bonito-cuda111-0.4.0a2.tar.gz (43 kB)
2021-08-24T20:41:01,233   Added ont-bonito-cuda111==0.4.0a2 from https://files.pythonhosted.org/packages/25/8c/28c43178094cb5cdae8df6c80d47e232a3e3013fba61f0bcdc02c5ca42f2/ont-bonito-cuda111-0.4.0a2.tar.gz#sha256=87a95bb62b6e1c5abe647d56732842d7fd7e84c2bdc0a96e427acba969d6879d to build tracker '/tmp/pip-req-tracker-jm57tvxg'
2021-08-24T20:41:01,235     Running setup.py (path:/tmp/pip-wheel-h4qijbk_/ont-bonito-cuda111_44d9081ca61d48b482b5b85321bb1d1e/setup.py) egg_info for package ont-bonito-cuda111
2021-08-24T20:41:01,235     Created temporary directory: /tmp/pip-pip-egg-info-io3trrq8
2021-08-24T20:41:01,236     Running command python setup.py egg_info
2021-08-24T20:41:02,176     Building with CUDA 11.1
2021-08-24T20:41:02,177     running egg_info
2021-08-24T20:41:02,179     creating /tmp/pip-pip-egg-info-io3trrq8/ont_bonito_cuda111.egg-info
2021-08-24T20:41:02,179     writing /tmp/pip-pip-egg-info-io3trrq8/ont_bonito_cuda111.egg-info/PKG-INFO
2021-08-24T20:41:02,182     writing dependency_links to /tmp/pip-pip-egg-info-io3trrq8/ont_bonito_cuda111.egg-info/dependency_links.txt
2021-08-24T20:41:02,183     writing entry points to /tmp/pip-pip-egg-info-io3trrq8/ont_bonito_cuda111.egg-info/entry_points.txt
2021-08-24T20:41:02,184     writing requirements to /tmp/pip-pip-egg-info-io3trrq8/ont_bonito_cuda111.egg-info/requires.txt
2021-08-24T20:41:02,185     writing top-level names to /tmp/pip-pip-egg-info-io3trrq8/ont_bonito_cuda111.egg-info/top_level.txt
2021-08-24T20:41:02,187     writing manifest file '/tmp/pip-pip-egg-info-io3trrq8/ont_bonito_cuda111.egg-info/SOURCES.txt'
2021-08-24T20:41:02,328     reading manifest file '/tmp/pip-pip-egg-info-io3trrq8/ont_bonito_cuda111.egg-info/SOURCES.txt'
2021-08-24T20:41:02,329     reading manifest template 'MANIFEST.in'
2021-08-24T20:41:02,333     adding license file 'LICENCE.txt'
2021-08-24T20:41:02,336     writing manifest file '/tmp/pip-pip-egg-info-io3trrq8/ont_bonito_cuda111.egg-info/SOURCES.txt'
2021-08-24T20:41:02,399   Source in /tmp/pip-wheel-h4qijbk_/ont-bonito-cuda111_44d9081ca61d48b482b5b85321bb1d1e 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#sha256=87a95bb62b6e1c5abe647d56732842d7fd7e84c2bdc0a96e427acba969d6879d
2021-08-24T20:41:02,400   Removed ont-bonito-cuda111==0.4.0a2 from https://files.pythonhosted.org/packages/25/8c/28c43178094cb5cdae8df6c80d47e232a3e3013fba61f0bcdc02c5ca42f2/ont-bonito-cuda111-0.4.0a2.tar.gz#sha256=87a95bb62b6e1c5abe647d56732842d7fd7e84c2bdc0a96e427acba969d6879d from build tracker '/tmp/pip-req-tracker-jm57tvxg'
2021-08-24T20:41:02,405 Created temporary directory: /tmp/pip-unpack-mfvhxk_m
2021-08-24T20:41:02,405 Building wheels for collected packages: ont-bonito-cuda111
2021-08-24T20:41:02,410   Created temporary directory: /tmp/pip-wheel-vv76_oww
2021-08-24T20:41:02,411   Building wheel for ont-bonito-cuda111 (setup.py): started
2021-08-24T20:41:02,411   Destination directory: /tmp/pip-wheel-vv76_oww
2021-08-24T20:41:02,411   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-h4qijbk_/ont-bonito-cuda111_44d9081ca61d48b482b5b85321bb1d1e/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-h4qijbk_/ont-bonito-cuda111_44d9081ca61d48b482b5b85321bb1d1e/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-vv76_oww
2021-08-24T20:41:03,101   Building with CUDA 11.1
2021-08-24T20:41:03,318   running bdist_wheel
2021-08-24T20:41:03,322   running build
2021-08-24T20:41:03,323   running build_py
2021-08-24T20:41:03,448   creating build
2021-08-24T20:41:03,449   creating build/lib
2021-08-24T20:41:03,450   creating build/lib/bonito
2021-08-24T20:41:03,451   copying bonito/__init__.py -> build/lib/bonito
2021-08-24T20:41:03,453   copying bonito/fast5.py -> build/lib/bonito
2021-08-24T20:41:03,456   copying bonito/multiprocessing.py -> build/lib/bonito
2021-08-24T20:41:03,458   copying bonito/util.py -> build/lib/bonito
2021-08-24T20:41:03,461   copying bonito/io.py -> build/lib/bonito
2021-08-24T20:41:03,464   copying bonito/aligner.py -> build/lib/bonito
2021-08-24T20:41:03,466   copying bonito/nn.py -> build/lib/bonito
2021-08-24T20:41:03,469   copying bonito/training.py -> build/lib/bonito
2021-08-24T20:41:03,472   creating build/lib/bonito/cli
2021-08-24T20:41:03,473   copying bonito/cli/view.py -> build/lib/bonito/cli
2021-08-24T20:41:03,476   copying bonito/cli/__init__.py -> build/lib/bonito/cli
2021-08-24T20:41:03,477   copying bonito/cli/evaluate.py -> build/lib/bonito/cli
2021-08-24T20:41:03,480   copying bonito/cli/train.py -> build/lib/bonito/cli
2021-08-24T20:41:03,482   copying bonito/cli/basecaller.py -> build/lib/bonito/cli
2021-08-24T20:41:03,485   copying bonito/cli/export.py -> build/lib/bonito/cli
2021-08-24T20:41:03,487   copying bonito/cli/download.py -> build/lib/bonito/cli
2021-08-24T20:41:03,490   copying bonito/cli/convert.py -> build/lib/bonito/cli
2021-08-24T20:41:03,493   copying bonito/cli/duplex.py -> build/lib/bonito/cli
2021-08-24T20:41:03,497   creating build/lib/bonito/crf
2021-08-24T20:41:03,498   copying bonito/crf/__init__.py -> build/lib/bonito/crf
2021-08-24T20:41:03,501   copying bonito/crf/model.py -> build/lib/bonito/crf
2021-08-24T20:41:03,503   copying bonito/crf/basecall.py -> build/lib/bonito/crf
2021-08-24T20:41:03,507   creating build/lib/bonito/ctc
2021-08-24T20:41:03,508   copying bonito/ctc/__init__.py -> build/lib/bonito/ctc
2021-08-24T20:41:03,510   copying bonito/ctc/model.py -> build/lib/bonito/ctc
2021-08-24T20:41:03,513   copying bonito/ctc/basecall.py -> build/lib/bonito/ctc
2021-08-24T20:41:03,515   running egg_info
2021-08-24T20:41:03,531   writing ont_bonito_cuda111.egg-info/PKG-INFO
2021-08-24T20:41:03,533   writing dependency_links to ont_bonito_cuda111.egg-info/dependency_links.txt
2021-08-24T20:41:03,536   writing entry points to ont_bonito_cuda111.egg-info/entry_points.txt
2021-08-24T20:41:03,537   writing requirements to ont_bonito_cuda111.egg-info/requires.txt
2021-08-24T20:41:03,539   writing top-level names to ont_bonito_cuda111.egg-info/top_level.txt
2021-08-24T20:41:03,546   reading manifest file 'ont_bonito_cuda111.egg-info/SOURCES.txt'
2021-08-24T20:41:03,549   reading manifest template 'MANIFEST.in'
2021-08-24T20:41:03,553   adding license file 'LICENCE.txt'
2021-08-24T20:41:03,557   writing manifest file 'ont_bonito_cuda111.egg-info/SOURCES.txt'
2021-08-24T20:41:03,561   creating build/lib/bonito/data
2021-08-24T20:41:03,562   copying bonito/data/README.md -> build/lib/bonito/data
2021-08-24T20:41:03,565   creating build/lib/bonito/models
2021-08-24T20:41:03,566   copying bonito/models/README.md -> build/lib/bonito/models
2021-08-24T20:41:03,568   creating build/lib/bonito/models/configs
2021-08-24T20:41:03,569   copying bonito/models/configs/dna_r9.4.1@v1.toml -> build/lib/bonito/models/configs
2021-08-24T20:41:03,572   copying bonito/models/configs/dna_r9.4.1@v2.toml -> build/lib/bonito/models/configs
2021-08-24T20:41:03,574   copying bonito/models/configs/dna_r9.4.1@v3.toml -> build/lib/bonito/models/configs
2021-08-24T20:41:03,581   installing to build/bdist.linux-armv7l/wheel
2021-08-24T20:41:03,582   running install
2021-08-24T20:41:03,583   running install_lib
2021-08-24T20:41:03,588   creating build/bdist.linux-armv7l
2021-08-24T20:41:03,589   creating build/bdist.linux-armv7l/wheel
2021-08-24T20:41:03,591   creating build/bdist.linux-armv7l/wheel/bonito
2021-08-24T20:41:03,592   copying build/lib/bonito/__init__.py -> build/bdist.linux-armv7l/wheel/bonito
2021-08-24T20:41:03,595   creating build/bdist.linux-armv7l/wheel/bonito/cli
2021-08-24T20:41:03,597   copying build/lib/bonito/cli/view.py -> build/bdist.linux-armv7l/wheel/bonito/cli
2021-08-24T20:41:03,599   copying build/lib/bonito/cli/__init__.py -> build/bdist.linux-armv7l/wheel/bonito/cli
2021-08-24T20:41:03,601   copying build/lib/bonito/cli/evaluate.py -> build/bdist.linux-armv7l/wheel/bonito/cli
2021-08-24T20:41:03,603   copying build/lib/bonito/cli/train.py -> build/bdist.linux-armv7l/wheel/bonito/cli
2021-08-24T20:41:03,606   copying build/lib/bonito/cli/basecaller.py -> build/bdist.linux-armv7l/wheel/bonito/cli
2021-08-24T20:41:03,609   copying build/lib/bonito/cli/export.py -> build/bdist.linux-armv7l/wheel/bonito/cli
2021-08-24T20:41:03,612   copying build/lib/bonito/cli/download.py -> build/bdist.linux-armv7l/wheel/bonito/cli
2021-08-24T20:41:03,615   copying build/lib/bonito/cli/convert.py -> build/bdist.linux-armv7l/wheel/bonito/cli
2021-08-24T20:41:03,617   copying build/lib/bonito/cli/duplex.py -> build/bdist.linux-armv7l/wheel/bonito/cli
2021-08-24T20:41:03,621   copying build/lib/bonito/fast5.py -> build/bdist.linux-armv7l/wheel/bonito
2021-08-24T20:41:03,623   copying build/lib/bonito/multiprocessing.py -> build/bdist.linux-armv7l/wheel/bonito
2021-08-24T20:41:03,627   creating build/bdist.linux-armv7l/wheel/bonito/crf
2021-08-24T20:41:03,628   copying build/lib/bonito/crf/__init__.py -> build/bdist.linux-armv7l/wheel/bonito/crf
2021-08-24T20:41:03,631   copying build/lib/bonito/crf/model.py -> build/bdist.linux-armv7l/wheel/bonito/crf
2021-08-24T20:41:03,634   copying build/lib/bonito/crf/basecall.py -> build/bdist.linux-armv7l/wheel/bonito/crf
2021-08-24T20:41:03,637   copying build/lib/bonito/util.py -> build/bdist.linux-armv7l/wheel/bonito
2021-08-24T20:41:03,641   copying build/lib/bonito/io.py -> build/bdist.linux-armv7l/wheel/bonito
2021-08-24T20:41:03,645   creating build/bdist.linux-armv7l/wheel/bonito/models
2021-08-24T20:41:03,647   creating build/bdist.linux-armv7l/wheel/bonito/models/configs
2021-08-24T20:41:03,649   copying build/lib/bonito/models/configs/dna_r9.4.1@v2.toml -> build/bdist.linux-armv7l/wheel/bonito/models/configs
2021-08-24T20:41:03,651   copying build/lib/bonito/models/configs/dna_r9.4.1@v1.toml -> build/bdist.linux-armv7l/wheel/bonito/models/configs
2021-08-24T20:41:03,654   copying build/lib/bonito/models/configs/dna_r9.4.1@v3.toml -> build/bdist.linux-armv7l/wheel/bonito/models/configs
2021-08-24T20:41:03,656   copying build/lib/bonito/models/README.md -> build/bdist.linux-armv7l/wheel/bonito/models
2021-08-24T20:41:03,659   creating build/bdist.linux-armv7l/wheel/bonito/ctc
2021-08-24T20:41:03,660   copying build/lib/bonito/ctc/__init__.py -> build/bdist.linux-armv7l/wheel/bonito/ctc
2021-08-24T20:41:03,663   copying build/lib/bonito/ctc/model.py -> build/bdist.linux-armv7l/wheel/bonito/ctc
2021-08-24T20:41:03,666   copying build/lib/bonito/ctc/basecall.py -> build/bdist.linux-armv7l/wheel/bonito/ctc
2021-08-24T20:41:03,669   creating build/bdist.linux-armv7l/wheel/bonito/data
2021-08-24T20:41:03,670   copying build/lib/bonito/data/README.md -> build/bdist.linux-armv7l/wheel/bonito/data
2021-08-24T20:41:03,672   copying build/lib/bonito/aligner.py -> build/bdist.linux-armv7l/wheel/bonito
2021-08-24T20:41:03,675   copying build/lib/bonito/nn.py -> build/bdist.linux-armv7l/wheel/bonito
2021-08-24T20:41:03,677   copying build/lib/bonito/training.py -> build/bdist.linux-armv7l/wheel/bonito
2021-08-24T20:41:03,680   running install_egg_info
2021-08-24T20:41:03,689   Copying ont_bonito_cuda111.egg-info to build/bdist.linux-armv7l/wheel/ont_bonito_cuda111-0.4.0a2-py3.7.egg-info
2021-08-24T20:41:03,702   running install_scripts
2021-08-24T20:41:03,766   error: [Errno 2] No such file or directory: 'bonito': 'bonito'
2021-08-24T20:41:03,841   Building wheel for ont-bonito-cuda111 (setup.py): finished with status 'error'
2021-08-24T20:41:03,842   ERROR: Failed building wheel for ont-bonito-cuda111
2021-08-24T20:41:03,843   Running setup.py clean for ont-bonito-cuda111
2021-08-24T20:41:03,843   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-h4qijbk_/ont-bonito-cuda111_44d9081ca61d48b482b5b85321bb1d1e/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-h4qijbk_/ont-bonito-cuda111_44d9081ca61d48b482b5b85321bb1d1e/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
2021-08-24T20:41:04,515   Building with CUDA 11.1
2021-08-24T20:41:04,707   running clean
2021-08-24T20:41:04,709   removing 'build/lib' (and everything under it)
2021-08-24T20:41:04,722   removing 'build/bdist.linux-armv7l' (and everything under it)
2021-08-24T20:41:04,741   'build/scripts-3.7' does not exist -- can't clean it
2021-08-24T20:41:04,741   removing 'build'
2021-08-24T20:41:04,800 Failed to build ont-bonito-cuda111
2021-08-24T20:41:04,800 ERROR: Failed to build one or more wheels
2021-08-24T20:41:04,801 Exception information:
2021-08-24T20:41:04,801 Traceback (most recent call last):
2021-08-24T20:41:04,801   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main
2021-08-24T20:41:04,801     status = self.run(options, args)
2021-08-24T20:41:04,801   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper
2021-08-24T20:41:04,801     return func(self, options, args)
2021-08-24T20:41:04,801   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/commands/wheel.py", line 175, in run
2021-08-24T20:41:04,801     "Failed to build one or more wheels"
2021-08-24T20:41:04,801 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2021-08-24T20:41:04,804 Removed build tracker: '/tmp/pip-req-tracker-jm57tvxg'