2024-03-04T01:20:17,262 Created temporary directory: /tmp/pip-build-tracker-qgqkgojv 2024-03-04T01:20:17,263 Initialized build tracking at /tmp/pip-build-tracker-qgqkgojv 2024-03-04T01:20:17,263 Created build tracker: /tmp/pip-build-tracker-qgqkgojv 2024-03-04T01:20:17,264 Entered build tracker: /tmp/pip-build-tracker-qgqkgojv 2024-03-04T01:20:17,264 Created temporary directory: /tmp/pip-wheel-3los7v14 2024-03-04T01:20:17,268 Created temporary directory: /tmp/pip-ephem-wheel-cache-q8oxfc8c 2024-03-04T01:20:17,295 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-03-04T01:20:17,299 2 location(s) to search for versions of uncalled4: 2024-03-04T01:20:17,299 * https://pypi.org/simple/uncalled4/ 2024-03-04T01:20:17,299 * https://www.piwheels.org/simple/uncalled4/ 2024-03-04T01:20:17,299 Fetching project page and analyzing links: https://pypi.org/simple/uncalled4/ 2024-03-04T01:20:17,300 Getting page https://pypi.org/simple/uncalled4/ 2024-03-04T01:20:17,301 Found index url https://pypi.org/simple/ 2024-03-04T01:20:17,353 Fetched page https://pypi.org/simple/uncalled4/ as application/vnd.pypi.simple.v1+json 2024-03-04T01:20:17,354 Found link https://files.pythonhosted.org/packages/84/34/b2d0e57215e66cb04e9185ad6f858f3ded32b197dee61328b96d3dddd47a/uncalled4-3.5.1.tar.gz (from https://pypi.org/simple/uncalled4/) (requires-python:>=3.8), version: 3.5.1 2024-03-04T01:20:17,354 Fetching project page and analyzing links: https://www.piwheels.org/simple/uncalled4/ 2024-03-04T01:20:17,355 Getting page https://www.piwheels.org/simple/uncalled4/ 2024-03-04T01:20:17,356 Found index url https://www.piwheels.org/simple/ 2024-03-04T01:20:17,418 Fetched page https://www.piwheels.org/simple/uncalled4/ as text/html 2024-03-04T01:20:17,419 Skipping link: not a file: https://www.piwheels.org/simple/uncalled4/ 2024-03-04T01:20:17,419 Skipping link: not a file: https://pypi.org/simple/uncalled4/ 2024-03-04T01:20:17,436 Given no hashes to check 1 links for project 'uncalled4': discarding no candidates 2024-03-04T01:20:17,453 Collecting uncalled4==3.5.1 2024-03-04T01:20:17,455 Created temporary directory: /tmp/pip-unpack-v_106hgx 2024-03-04T01:20:17,499 Downloading uncalled4-3.5.1.tar.gz (15.3 MB) 2024-03-04T01:20:20,831 Added uncalled4==3.5.1 from https://files.pythonhosted.org/packages/84/34/b2d0e57215e66cb04e9185ad6f858f3ded32b197dee61328b96d3dddd47a/uncalled4-3.5.1.tar.gz to build tracker '/tmp/pip-build-tracker-qgqkgojv' 2024-03-04T01:20:20,833 Running setup.py (path:/tmp/pip-wheel-3los7v14/uncalled4_0021919ebf9c40a2bfb7ffddc0e248b0/setup.py) egg_info for package uncalled4 2024-03-04T01:20:20,833 Created temporary directory: /tmp/pip-pip-egg-info-v7u82czy 2024-03-04T01:20:20,834 Preparing metadata (setup.py): started 2024-03-04T01:20:20,835 Running command python setup.py egg_info 2024-03-04T01:20:21,723 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-03-04T01:20:21,723 !! 2024-03-04T01:20:21,723 ******************************************************************************** 2024-03-04T01:20:21,724 Requirements should be satisfied by a PEP 517 installer. 2024-03-04T01:20:21,724 If you are using pip, you can try `pip install --use-pep517`. 2024-03-04T01:20:21,724 ******************************************************************************** 2024-03-04T01:20:21,724 !! 2024-03-04T01:20:21,724 dist.fetch_build_eggs(dist.setup_requires) 2024-03-04T01:20:21,797 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'build_backend' 2024-03-04T01:20:21,798 warnings.warn(msg) 2024-03-04T01:20:21,962 running egg_info 2024-03-04T01:20:21,964 creating /tmp/pip-pip-egg-info-v7u82czy/uncalled4.egg-info 2024-03-04T01:20:21,989 writing /tmp/pip-pip-egg-info-v7u82czy/uncalled4.egg-info/PKG-INFO 2024-03-04T01:20:21,993 writing dependency_links to /tmp/pip-pip-egg-info-v7u82czy/uncalled4.egg-info/dependency_links.txt 2024-03-04T01:20:21,994 writing entry points to /tmp/pip-pip-egg-info-v7u82czy/uncalled4.egg-info/entry_points.txt 2024-03-04T01:20:21,996 writing requirements to /tmp/pip-pip-egg-info-v7u82czy/uncalled4.egg-info/requires.txt 2024-03-04T01:20:21,997 writing top-level names to /tmp/pip-pip-egg-info-v7u82czy/uncalled4.egg-info/top_level.txt 2024-03-04T01:20:21,998 writing manifest file '/tmp/pip-pip-egg-info-v7u82czy/uncalled4.egg-info/SOURCES.txt' 2024-03-04T01:20:22,107 reading manifest file '/tmp/pip-pip-egg-info-v7u82czy/uncalled4.egg-info/SOURCES.txt' 2024-03-04T01:20:22,108 reading manifest template 'MANIFEST.in' 2024-03-04T01:20:22,158 adding license file 'LICENSE' 2024-03-04T01:20:22,165 writing manifest file '/tmp/pip-pip-egg-info-v7u82czy/uncalled4.egg-info/SOURCES.txt' 2024-03-04T01:20:22,258 Preparing metadata (setup.py): finished with status 'done' 2024-03-04T01:20:22,262 Source in /tmp/pip-wheel-3los7v14/uncalled4_0021919ebf9c40a2bfb7ffddc0e248b0 has version 3.5.1, which satisfies requirement uncalled4==3.5.1 from https://files.pythonhosted.org/packages/84/34/b2d0e57215e66cb04e9185ad6f858f3ded32b197dee61328b96d3dddd47a/uncalled4-3.5.1.tar.gz 2024-03-04T01:20:22,263 Removed uncalled4==3.5.1 from https://files.pythonhosted.org/packages/84/34/b2d0e57215e66cb04e9185ad6f858f3ded32b197dee61328b96d3dddd47a/uncalled4-3.5.1.tar.gz from build tracker '/tmp/pip-build-tracker-qgqkgojv' 2024-03-04T01:20:22,269 Created temporary directory: /tmp/pip-unpack-dwu6pot8 2024-03-04T01:20:22,270 Created temporary directory: /tmp/pip-unpack-9_mg4onm 2024-03-04T01:20:22,286 Building wheels for collected packages: uncalled4 2024-03-04T01:20:22,290 Created temporary directory: /tmp/pip-wheel-h5wbi_qo 2024-03-04T01:20:22,290 Building wheel for uncalled4 (setup.py): started 2024-03-04T01:20:22,291 Destination directory: /tmp/pip-wheel-h5wbi_qo 2024-03-04T01:20:22,291 Running command python setup.py bdist_wheel 2024-03-04T01:20:23,242 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-03-04T01:20:23,243 !! 2024-03-04T01:20:23,243 ******************************************************************************** 2024-03-04T01:20:23,243 Requirements should be satisfied by a PEP 517 installer. 2024-03-04T01:20:23,243 If you are using pip, you can try `pip install --use-pep517`. 2024-03-04T01:20:23,244 ******************************************************************************** 2024-03-04T01:20:23,244 !! 2024-03-04T01:20:23,244 dist.fetch_build_eggs(dist.setup_requires) 2024-03-04T01:20:23,320 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'build_backend' 2024-03-04T01:20:23,320 warnings.warn(msg) 2024-03-04T01:20:23,477 running bdist_wheel 2024-03-04T01:20:23,576 running build 2024-03-04T01:20:23,576 running build_py 2024-03-04T01:20:23,604 creating build 2024-03-04T01:20:23,605 creating build/lib.linux-armv7l-cpython-39 2024-03-04T01:20:23,606 creating build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-04T01:20:23,607 copying src/uncalled4/params.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-04T01:20:23,610 copying src/uncalled4/signal_processor.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-04T01:20:23,612 copying src/uncalled4/align.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-04T01:20:23,615 copying src/uncalled4/__main__.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-04T01:20:23,617 copying src/uncalled4/ref_index.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-04T01:20:23,619 copying src/uncalled4/argparse.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-04T01:20:23,621 copying src/uncalled4/__init__.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-04T01:20:23,623 copying src/uncalled4/__about__.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-04T01:20:23,625 copying src/uncalled4/moves.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-04T01:20:23,626 copying src/uncalled4/config.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-04T01:20:23,628 copying src/uncalled4/pore_model.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-04T01:20:23,631 copying src/uncalled4/train.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-04T01:20:23,633 copying src/uncalled4/read_index.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-04T01:20:23,635 copying src/uncalled4/tracks.py -> build/lib.linux-armv7l-cpython-39/uncalled4 2024-03-04T01:20:23,640 creating build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-04T01:20:23,641 copying src/uncalled4/vis/dotplot.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-04T01:20:23,643 copying src/uncalled4/vis/__init__.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-04T01:20:23,645 copying src/uncalled4/vis/refplot.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-04T01:20:23,647 copying src/uncalled4/vis/sigplot.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-04T01:20:23,650 copying src/uncalled4/vis/browser.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-04T01:20:23,652 copying src/uncalled4/vis/trackplot.py -> build/lib.linux-armv7l-cpython-39/uncalled4/vis 2024-03-04T01:20:23,656 creating build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-03-04T01:20:23,657 copying src/uncalled4/stats/layerstats.py -> build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-03-04T01:20:23,659 copying src/uncalled4/stats/readstats.py -> build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-03-04T01:20:23,661 copying src/uncalled4/stats/refstats.py -> build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-03-04T01:20:23,663 copying src/uncalled4/stats/__init__.py -> build/lib.linux-armv7l-cpython-39/uncalled4/stats 2024-03-04T01:20:23,665 creating build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-04T01:20:23,666 copying src/uncalled4/io/m6anet.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-04T01:20:23,669 copying src/uncalled4/io/model_trainer.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-04T01:20:23,671 copying src/uncalled4/io/tombo.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-04T01:20:23,673 copying src/uncalled4/io/bam.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-04T01:20:23,676 copying src/uncalled4/io/eventalign.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-04T01:20:23,679 copying src/uncalled4/io/__init__.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-04T01:20:23,681 copying src/uncalled4/io/tsv.py -> build/lib.linux-armv7l-cpython-39/uncalled4/io 2024-03-04T01:20:23,682 running egg_info 2024-03-04T01:20:23,733 writing src/uncalled4.egg-info/PKG-INFO 2024-03-04T01:20:23,736 writing dependency_links to src/uncalled4.egg-info/dependency_links.txt 2024-03-04T01:20:23,738 writing entry points to src/uncalled4.egg-info/entry_points.txt 2024-03-04T01:20:23,740 writing requirements to src/uncalled4.egg-info/requires.txt 2024-03-04T01:20:23,741 writing top-level names to src/uncalled4.egg-info/top_level.txt 2024-03-04T01:20:24,014 reading manifest file 'src/uncalled4.egg-info/SOURCES.txt' 2024-03-04T01:20:24,019 reading manifest template 'MANIFEST.in' 2024-03-04T01:20:24,108 adding license file 'LICENSE' 2024-03-04T01:20:24,117 writing manifest file 'src/uncalled4.egg-info/SOURCES.txt' 2024-03-04T01:20:24,121 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'uncalled4.__pycache__' is absent from the `packages` configuration. 2024-03-04T01:20:24,122 !! 2024-03-04T01:20:24,122 ******************************************************************************** 2024-03-04T01:20:24,122 ############################ 2024-03-04T01:20:24,122 # Package would be ignored # 2024-03-04T01:20:24,122 ############################ 2024-03-04T01:20:24,122 Python recognizes 'uncalled4.__pycache__' as an importable package[^1], 2024-03-04T01:20:24,123 but it is absent from setuptools' `packages` configuration. 2024-03-04T01:20:24,123 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-04T01:20:24,123 package, please make sure that 'uncalled4.__pycache__' is explicitly added 2024-03-04T01:20:24,123 to the `packages` configuration field. 2024-03-04T01:20:24,123 Alternatively, you can also rely on setuptools' discovery methods 2024-03-04T01:20:24,123 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-04T01:20:24,123 instead of `find_packages(...)`/`find:`). 2024-03-04T01:20:24,124 You can read more about "package discovery" on setuptools documentation page: 2024-03-04T01:20:24,124 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-04T01:20:24,124 If you don't want 'uncalled4.__pycache__' to be distributed and are 2024-03-04T01:20:24,124 already explicitly excluding 'uncalled4.__pycache__' via 2024-03-04T01:20:24,124 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-04T01:20:24,125 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-04T01:20:24,125 combination with a more fine grained `package-data` configuration. 2024-03-04T01:20:24,125 You can read more about "package data files" on setuptools documentation page: 2024-03-04T01:20:24,125 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-04T01:20:24,125 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-04T01:20:24,126 even if it does not contain any `.py` files. 2024-03-04T01:20:24,126 On the other hand, currently there is no concept of package data 2024-03-04T01:20:24,126 directory, all directories are treated like packages. 2024-03-04T01:20:24,126 ******************************************************************************** 2024-03-04T01:20:24,126 !! 2024-03-04T01:20:24,126 check.warn(importable) 2024-03-04T01:20:24,126 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'uncalled4.io.__pycache__' is absent from the `packages` configuration. 2024-03-04T01:20:24,127 !! 2024-03-04T01:20:24,127 ******************************************************************************** 2024-03-04T01:20:24,127 ############################ 2024-03-04T01:20:24,127 # Package would be ignored # 2024-03-04T01:20:24,127 ############################ 2024-03-04T01:20:24,127 Python recognizes 'uncalled4.io.__pycache__' as an importable package[^1], 2024-03-04T01:20:24,127 but it is absent from setuptools' `packages` configuration. 2024-03-04T01:20:24,128 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-04T01:20:24,128 package, please make sure that 'uncalled4.io.__pycache__' is explicitly added 2024-03-04T01:20:24,128 to the `packages` configuration field. 2024-03-04T01:20:24,128 Alternatively, you can also rely on setuptools' discovery methods 2024-03-04T01:20:24,128 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-04T01:20:24,128 instead of `find_packages(...)`/`find:`). 2024-03-04T01:20:24,129 You can read more about "package discovery" on setuptools documentation page: 2024-03-04T01:20:24,129 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-04T01:20:24,129 If you don't want 'uncalled4.io.__pycache__' to be distributed and are 2024-03-04T01:20:24,129 already explicitly excluding 'uncalled4.io.__pycache__' via 2024-03-04T01:20:24,129 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-04T01:20:24,129 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-04T01:20:24,129 combination with a more fine grained `package-data` configuration. 2024-03-04T01:20:24,130 You can read more about "package data files" on setuptools documentation page: 2024-03-04T01:20:24,130 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-04T01:20:24,130 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-04T01:20:24,130 even if it does not contain any `.py` files. 2024-03-04T01:20:24,131 On the other hand, currently there is no concept of package data 2024-03-04T01:20:24,131 directory, all directories are treated like packages. 2024-03-04T01:20:24,131 ******************************************************************************** 2024-03-04T01:20:24,131 !! 2024-03-04T01:20:24,131 check.warn(importable) 2024-03-04T01:20:24,131 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'uncalled4.models' is absent from the `packages` configuration. 2024-03-04T01:20:24,131 !! 2024-03-04T01:20:24,132 ******************************************************************************** 2024-03-04T01:20:24,132 ############################ 2024-03-04T01:20:24,132 # Package would be ignored # 2024-03-04T01:20:24,132 ############################ 2024-03-04T01:20:24,132 Python recognizes 'uncalled4.models' as an importable package[^1], 2024-03-04T01:20:24,132 but it is absent from setuptools' `packages` configuration. 2024-03-04T01:20:24,132 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-04T01:20:24,132 package, please make sure that 'uncalled4.models' is explicitly added 2024-03-04T01:20:24,133 to the `packages` configuration field. 2024-03-04T01:20:24,133 Alternatively, you can also rely on setuptools' discovery methods 2024-03-04T01:20:24,133 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-04T01:20:24,133 instead of `find_packages(...)`/`find:`). 2024-03-04T01:20:24,133 You can read more about "package discovery" on setuptools documentation page: 2024-03-04T01:20:24,133 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-04T01:20:24,134 If you don't want 'uncalled4.models' to be distributed and are 2024-03-04T01:20:24,134 already explicitly excluding 'uncalled4.models' via 2024-03-04T01:20:24,134 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-04T01:20:24,134 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-04T01:20:24,134 combination with a more fine grained `package-data` configuration. 2024-03-04T01:20:24,134 You can read more about "package data files" on setuptools documentation page: 2024-03-04T01:20:24,135 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-04T01:20:24,135 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-04T01:20:24,135 even if it does not contain any `.py` files. 2024-03-04T01:20:24,135 On the other hand, currently there is no concept of package data 2024-03-04T01:20:24,135 directory, all directories are treated like packages. 2024-03-04T01:20:24,136 ******************************************************************************** 2024-03-04T01:20:24,136 !! 2024-03-04T01:20:24,136 check.warn(importable) 2024-03-04T01:20:24,136 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'uncalled4.models.tombo' is absent from the `packages` configuration. 2024-03-04T01:20:24,136 !! 2024-03-04T01:20:24,137 ******************************************************************************** 2024-03-04T01:20:24,137 ############################ 2024-03-04T01:20:24,137 # Package would be ignored # 2024-03-04T01:20:24,137 ############################ 2024-03-04T01:20:24,137 Python recognizes 'uncalled4.models.tombo' as an importable package[^1], 2024-03-04T01:20:24,137 but it is absent from setuptools' `packages` configuration. 2024-03-04T01:20:24,137 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-04T01:20:24,138 package, please make sure that 'uncalled4.models.tombo' is explicitly added 2024-03-04T01:20:24,138 to the `packages` configuration field. 2024-03-04T01:20:24,138 Alternatively, you can also rely on setuptools' discovery methods 2024-03-04T01:20:24,138 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-04T01:20:24,138 instead of `find_packages(...)`/`find:`). 2024-03-04T01:20:24,138 You can read more about "package discovery" on setuptools documentation page: 2024-03-04T01:20:24,139 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-04T01:20:24,139 If you don't want 'uncalled4.models.tombo' to be distributed and are 2024-03-04T01:20:24,139 already explicitly excluding 'uncalled4.models.tombo' via 2024-03-04T01:20:24,139 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-04T01:20:24,139 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-04T01:20:24,139 combination with a more fine grained `package-data` configuration. 2024-03-04T01:20:24,140 You can read more about "package data files" on setuptools documentation page: 2024-03-04T01:20:24,140 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-04T01:20:24,140 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-04T01:20:24,140 even if it does not contain any `.py` files. 2024-03-04T01:20:24,141 On the other hand, currently there is no concept of package data 2024-03-04T01:20:24,141 directory, all directories are treated like packages. 2024-03-04T01:20:24,141 ******************************************************************************** 2024-03-04T01:20:24,141 !! 2024-03-04T01:20:24,141 check.warn(importable) 2024-03-04T01:20:24,141 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'uncalled4.stats.__pycache__' is absent from the `packages` configuration. 2024-03-04T01:20:24,142 !! 2024-03-04T01:20:24,142 ******************************************************************************** 2024-03-04T01:20:24,142 ############################ 2024-03-04T01:20:24,142 # Package would be ignored # 2024-03-04T01:20:24,142 ############################ 2024-03-04T01:20:24,142 Python recognizes 'uncalled4.stats.__pycache__' as an importable package[^1], 2024-03-04T01:20:24,142 but it is absent from setuptools' `packages` configuration. 2024-03-04T01:20:24,143 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-04T01:20:24,143 package, please make sure that 'uncalled4.stats.__pycache__' is explicitly added 2024-03-04T01:20:24,143 to the `packages` configuration field. 2024-03-04T01:20:24,144 Alternatively, you can also rely on setuptools' discovery methods 2024-03-04T01:20:24,144 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-04T01:20:24,144 instead of `find_packages(...)`/`find:`). 2024-03-04T01:20:24,144 You can read more about "package discovery" on setuptools documentation page: 2024-03-04T01:20:24,145 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-04T01:20:24,145 If you don't want 'uncalled4.stats.__pycache__' to be distributed and are 2024-03-04T01:20:24,145 already explicitly excluding 'uncalled4.stats.__pycache__' via 2024-03-04T01:20:24,145 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-04T01:20:24,146 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-04T01:20:24,146 combination with a more fine grained `package-data` configuration. 2024-03-04T01:20:24,146 You can read more about "package data files" on setuptools documentation page: 2024-03-04T01:20:24,147 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-04T01:20:24,147 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-04T01:20:24,147 even if it does not contain any `.py` files. 2024-03-04T01:20:24,148 On the other hand, currently there is no concept of package data 2024-03-04T01:20:24,148 directory, all directories are treated like packages. 2024-03-04T01:20:24,148 ******************************************************************************** 2024-03-04T01:20:24,148 !! 2024-03-04T01:20:24,149 check.warn(importable) 2024-03-04T01:20:24,149 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'uncalled4.vis.__pycache__' is absent from the `packages` configuration. 2024-03-04T01:20:24,149 !! 2024-03-04T01:20:24,149 ******************************************************************************** 2024-03-04T01:20:24,150 ############################ 2024-03-04T01:20:24,150 # Package would be ignored # 2024-03-04T01:20:24,150 ############################ 2024-03-04T01:20:24,150 Python recognizes 'uncalled4.vis.__pycache__' as an importable package[^1], 2024-03-04T01:20:24,150 but it is absent from setuptools' `packages` configuration. 2024-03-04T01:20:24,151 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-04T01:20:24,151 package, please make sure that 'uncalled4.vis.__pycache__' is explicitly added 2024-03-04T01:20:24,151 to the `packages` configuration field. 2024-03-04T01:20:24,151 Alternatively, you can also rely on setuptools' discovery methods 2024-03-04T01:20:24,152 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-04T01:20:24,152 instead of `find_packages(...)`/`find:`). 2024-03-04T01:20:24,152 You can read more about "package discovery" on setuptools documentation page: 2024-03-04T01:20:24,152 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-04T01:20:24,153 If you don't want 'uncalled4.vis.__pycache__' to be distributed and are 2024-03-04T01:20:24,153 already explicitly excluding 'uncalled4.vis.__pycache__' via 2024-03-04T01:20:24,153 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-04T01:20:24,153 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-04T01:20:24,154 combination with a more fine grained `package-data` configuration. 2024-03-04T01:20:24,154 You can read more about "package data files" on setuptools documentation page: 2024-03-04T01:20:24,154 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-04T01:20:24,155 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-04T01:20:24,155 even if it does not contain any `.py` files. 2024-03-04T01:20:24,155 On the other hand, currently there is no concept of package data 2024-03-04T01:20:24,155 directory, all directories are treated like packages. 2024-03-04T01:20:24,156 ******************************************************************************** 2024-03-04T01:20:24,156 !! 2024-03-04T01:20:24,156 check.warn(importable) 2024-03-04T01:20:24,156 /usr/local/lib/python3.9/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'uncalled4.vis.assets' is absent from the `packages` configuration. 2024-03-04T01:20:24,156 !! 2024-03-04T01:20:24,157 ******************************************************************************** 2024-03-04T01:20:24,157 ############################ 2024-03-04T01:20:24,157 # Package would be ignored # 2024-03-04T01:20:24,157 ############################ 2024-03-04T01:20:24,158 Python recognizes 'uncalled4.vis.assets' as an importable package[^1], 2024-03-04T01:20:24,158 but it is absent from setuptools' `packages` configuration. 2024-03-04T01:20:24,158 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-04T01:20:24,158 package, please make sure that 'uncalled4.vis.assets' is explicitly added 2024-03-04T01:20:24,158 to the `packages` configuration field. 2024-03-04T01:20:24,159 Alternatively, you can also rely on setuptools' discovery methods 2024-03-04T01:20:24,159 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-04T01:20:24,159 instead of `find_packages(...)`/`find:`). 2024-03-04T01:20:24,160 You can read more about "package discovery" on setuptools documentation page: 2024-03-04T01:20:24,160 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-04T01:20:24,160 If you don't want 'uncalled4.vis.assets' to be distributed and are 2024-03-04T01:20:24,161 already explicitly excluding 'uncalled4.vis.assets' via 2024-03-04T01:20:24,161 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-04T01:20:24,161 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-04T01:20:24,161 combination with a more fine grained `package-data` configuration. 2024-03-04T01:20:24,162 You can read more about "package data files" on setuptools documentation page: 2024-03-04T01:20:24,162 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-04T01:20:24,162 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-04T01:20:24,163 even if it does not contain any `.py` files. 2024-03-04T01:20:24,163 On the other hand, currently there is no concept of package data 2024-03-04T01:20:24,163 directory, all directories are treated like packages. 2024-03-04T01:20:24,163 ******************************************************************************** 2024-03-04T01:20:24,164 !! 2024-03-04T01:20:24,164 check.warn(importable) 2024-03-04T01:20:24,164 creating build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-04T01:20:24,164 copying src/uncalled4/__pycache__/__about__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-04T01:20:24,164 copying src/uncalled4/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-04T01:20:24,164 copying src/uncalled4/__pycache__/__main__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-04T01:20:24,165 copying src/uncalled4/__pycache__/align.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-04T01:20:24,165 copying src/uncalled4/__pycache__/aln.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-04T01:20:24,165 copying src/uncalled4/__pycache__/aln_track.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-04T01:20:24,165 copying src/uncalled4/__pycache__/argparse.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-04T01:20:24,166 copying src/uncalled4/__pycache__/config.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-04T01:20:24,166 copying src/uncalled4/__pycache__/dtw.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-04T01:20:24,166 copying src/uncalled4/__pycache__/index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-04T01:20:24,166 copying src/uncalled4/__pycache__/layers.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-04T01:20:24,167 copying src/uncalled4/__pycache__/moves.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-04T01:20:24,170 copying src/uncalled4/__pycache__/params.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-04T01:20:24,173 copying src/uncalled4/__pycache__/pore_model.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-04T01:20:24,176 copying src/uncalled4/__pycache__/read_index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-04T01:20:24,179 copying src/uncalled4/__pycache__/ref_index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-04T01:20:24,182 copying src/uncalled4/__pycache__/signal_processor.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-04T01:20:24,184 copying src/uncalled4/__pycache__/tracks.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/__pycache__ 2024-03-04T01:20:24,189 creating build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-03-04T01:20:24,190 copying src/uncalled4/models/README.txt -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-03-04T01:20:24,192 copying src/uncalled4/models/dna_r10.4.1_400bps_9mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-03-04T01:20:24,230 copying src/uncalled4/models/dna_r9.4.1_400bps_6mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-03-04T01:20:24,234 copying src/uncalled4/models/presets.tsv -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-03-04T01:20:24,238 copying src/uncalled4/models/rna_r9.4.1_70bps_5mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models 2024-03-04T01:20:24,241 creating build/lib.linux-armv7l-cpython-39/uncalled4/models/tombo 2024-03-04T01:20:24,242 copying src/uncalled4/models/tombo/dna_r9.4.1_400bps_6mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models/tombo 2024-03-04T01:20:24,245 copying src/uncalled4/models/tombo/rna_r9.4.1_70bps_5mer.npz -> build/lib.linux-armv7l-cpython-39/uncalled4/models/tombo 2024-03-04T01:20:24,248 creating build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-04T01:20:24,249 copying src/uncalled4/vis/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-04T01:20:24,251 copying src/uncalled4/vis/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-04T01:20:24,253 copying src/uncalled4/vis/__pycache__/__init__.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-04T01:20:24,255 copying src/uncalled4/vis/__pycache__/browser.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-04T01:20:24,257 copying src/uncalled4/vis/__pycache__/browser.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-04T01:20:24,259 copying src/uncalled4/vis/__pycache__/browser.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-04T01:20:24,262 copying src/uncalled4/vis/__pycache__/dotplot.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-04T01:20:24,265 copying src/uncalled4/vis/__pycache__/dotplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-04T01:20:24,267 copying src/uncalled4/vis/__pycache__/dotplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-04T01:20:24,270 copying src/uncalled4/vis/__pycache__/refplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-04T01:20:24,272 copying src/uncalled4/vis/__pycache__/sigplot.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-04T01:20:24,274 copying src/uncalled4/vis/__pycache__/sigplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-04T01:20:24,276 copying src/uncalled4/vis/__pycache__/sigplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-04T01:20:24,279 copying src/uncalled4/vis/__pycache__/trackplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-04T01:20:24,281 copying src/uncalled4/vis/__pycache__/trackplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/__pycache__ 2024-03-04T01:20:24,284 creating build/lib.linux-armv7l-cpython-39/uncalled4/vis/assets 2024-03-04T01:20:24,285 copying src/uncalled4/vis/assets/.browser.js.swp -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/assets 2024-03-04T01:20:24,287 copying src/uncalled4/vis/assets/browser.css -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/assets 2024-03-04T01:20:24,289 copying src/uncalled4/vis/assets/browser.js -> build/lib.linux-armv7l-cpython-39/uncalled4/vis/assets 2024-03-04T01:20:24,291 creating build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-04T01:20:24,292 copying src/uncalled4/stats/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-04T01:20:24,294 copying src/uncalled4/stats/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-04T01:20:24,296 copying src/uncalled4/stats/__pycache__/__init__.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-04T01:20:24,298 copying src/uncalled4/stats/__pycache__/_dtwstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-04T01:20:24,301 copying src/uncalled4/stats/__pycache__/_dtwstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-04T01:20:24,303 copying src/uncalled4/stats/__pycache__/_readstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-04T01:20:24,305 copying src/uncalled4/stats/__pycache__/_readstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-04T01:20:24,307 copying src/uncalled4/stats/__pycache__/_refstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-04T01:20:24,309 copying src/uncalled4/stats/__pycache__/_refstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-04T01:20:24,311 copying src/uncalled4/stats/__pycache__/dtwstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-04T01:20:24,313 copying src/uncalled4/stats/__pycache__/layerstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-04T01:20:24,315 copying src/uncalled4/stats/__pycache__/layerstats.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-04T01:20:24,317 copying src/uncalled4/stats/__pycache__/refstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-04T01:20:24,320 copying src/uncalled4/stats/__pycache__/refstats.cpython-39.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/stats/__pycache__ 2024-03-04T01:20:24,322 creating build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-04T01:20:24,322 copying src/uncalled4/io/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-04T01:20:24,325 copying src/uncalled4/io/__pycache__/bam.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-04T01:20:24,327 copying src/uncalled4/io/__pycache__/eventalign.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-04T01:20:24,330 copying src/uncalled4/io/__pycache__/guppy.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-04T01:20:24,332 copying src/uncalled4/io/__pycache__/m6anet.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-04T01:20:24,334 copying src/uncalled4/io/__pycache__/model.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-04T01:20:24,336 copying src/uncalled4/io/__pycache__/model_trainer.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-04T01:20:24,338 copying src/uncalled4/io/__pycache__/sqlite.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-04T01:20:24,341 copying src/uncalled4/io/__pycache__/tombo.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-04T01:20:24,343 copying src/uncalled4/io/__pycache__/tsv.cpython-38.pyc -> build/lib.linux-armv7l-cpython-39/uncalled4/io/__pycache__ 2024-03-04T01:20:24,348 running build_ext 2024-03-04T01:20:24,902 building '_uncalled4' extension 2024-03-04T01:20:24,902 creating build/temp.linux-armv7l-cpython-39 2024-03-04T01:20:24,903 creating build/temp.linux-armv7l-cpython-39/src 2024-03-04T01:20:24,904 creating build/temp.linux-armv7l-cpython-39/src/cpp 2024-03-04T01:20:24,940 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I./src/cpp/ -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c src/cpp/event_detector.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/event_detector.o -fvisibility=hidden -g0 -std=c++11 -O3 -g 2024-03-04T01:20:24,941 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I./src/cpp/ -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c src/cpp/config.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/config.o -fvisibility=hidden -g0 -std=c++11 -O3 -g 2024-03-04T01:20:24,942 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I./src/cpp/ -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c src/cpp/dtw.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/dtw.o -fvisibility=hidden -g0 -std=c++11 -O3 -g 2024-03-04T01:20:24,942 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I./src/cpp/ -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c src/cpp/intervals.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/intervals.o -fvisibility=hidden -g0 -std=c++11 -O3 -g 2024-03-04T01:20:31,933 In file included from src/cpp/event_detector.cpp:15: 2024-03-04T01:20:31,933 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-04T01:20:31,934 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-04T01:20:31,934 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-04T01:20:31,935 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-04T01:20:31,935 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-04T01:20:31,935 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-04T01:20:31,973 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-04T01:20:31,974 src/cpp/event_detector.hpp:147:39: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘i32’ {aka ‘int’} [-Wsign-compare] 2024-03-04T01:20:31,974 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-04T01:20:31,974 | ~~^~~~~~~~~~ 2024-03-04T01:20:31,975 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-04T01:20:31,975 src/cpp/event_detector.hpp:158:34: warning: narrowing conversion of ‘((ProcessedRead*)this)->ProcessedRead::events.std::vector::size()’ from ‘std::vector::size_type’ {aka ‘unsigned int’} to ‘i32’ {aka ‘int’} [-Wnarrowing] 2024-03-04T01:20:31,975 158 | normalize({0, events.size(), scale, shift}); 2024-03-04T01:20:31,976 | ~~~~~~~~~~~^~ 2024-03-04T01:20:32,077 In file included from src/cpp/aln.hpp:11, 2024-03-04T01:20:32,078 from src/cpp/dtw.hpp:9, 2024-03-04T01:20:32,078 from src/cpp/dtw.cpp:1: 2024-03-04T01:20:32,078 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-04T01:20:32,079 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-04T01:20:32,079 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-04T01:20:32,079 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-04T01:20:32,080 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-04T01:20:32,080 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-04T01:20:32,138 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-04T01:20:32,138 src/cpp/event_detector.hpp:147:39: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘i32’ {aka ‘int’} [-Wsign-compare] 2024-03-04T01:20:32,139 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-04T01:20:32,139 | ~~^~~~~~~~~~ 2024-03-04T01:20:32,141 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-04T01:20:32,141 src/cpp/event_detector.hpp:158:34: warning: narrowing conversion of ‘((ProcessedRead*)this)->ProcessedRead::events.std::vector::size()’ from ‘std::vector::size_type’ {aka ‘unsigned int’} to ‘i32’ {aka ‘int’} [-Wnarrowing] 2024-03-04T01:20:32,141 158 | normalize({0, events.size(), scale, shift}); 2024-03-04T01:20:32,142 | ~~~~~~~~~~~^~ 2024-03-04T01:20:32,197 In file included from src/cpp/aln.hpp:11, 2024-03-04T01:20:32,198 from src/cpp/dtw.hpp:9, 2024-03-04T01:20:32,198 from src/cpp/config.hpp:30, 2024-03-04T01:20:32,198 from src/cpp/config.cpp:1: 2024-03-04T01:20:32,198 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-04T01:20:32,199 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-04T01:20:32,199 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-04T01:20:32,199 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-04T01:20:32,200 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-04T01:20:32,200 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-04T01:20:32,254 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-04T01:20:32,255 src/cpp/event_detector.hpp:147:39: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘i32’ {aka ‘int’} [-Wsign-compare] 2024-03-04T01:20:32,255 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-04T01:20:32,255 | ~~^~~~~~~~~~ 2024-03-04T01:20:32,256 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-04T01:20:32,256 src/cpp/event_detector.hpp:158:34: warning: narrowing conversion of ‘((ProcessedRead*)this)->ProcessedRead::events.std::vector::size()’ from ‘std::vector::size_type’ {aka ‘unsigned int’} to ‘i32’ {aka ‘int’} [-Wnarrowing] 2024-03-04T01:20:32,256 158 | normalize({0, events.size(), scale, shift}); 2024-03-04T01:20:32,257 | ~~~~~~~~~~~^~ 2024-03-04T01:20:32,322 In file included from src/cpp/dtw.hpp:9, 2024-03-04T01:20:32,322 from src/cpp/dtw.cpp:1: 2024-03-04T01:20:32,323 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-03-04T01:20:32,323 src/cpp/aln.hpp:187:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-03-04T01:20:32,323 187 | i64 ref; 2024-03-04T01:20:32,324 | ^~~ 2024-03-04T01:20:32,329 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-03-04T01:20:32,330 src/cpp/aln.hpp:279:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-03-04T01:20:32,330 279 | int len,dist; 2024-03-04T01:20:32,330 | ^~~~ 2024-03-04T01:20:32,432 In file included from src/cpp/dtw.hpp:9, 2024-03-04T01:20:32,433 from src/cpp/config.hpp:30, 2024-03-04T01:20:32,433 from src/cpp/config.cpp:1: 2024-03-04T01:20:32,433 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-03-04T01:20:32,434 src/cpp/aln.hpp:187:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-03-04T01:20:32,434 187 | i64 ref; 2024-03-04T01:20:32,434 | ^~~ 2024-03-04T01:20:32,438 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-03-04T01:20:32,439 src/cpp/aln.hpp:279:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-03-04T01:20:32,439 279 | int len,dist; 2024-03-04T01:20:32,439 | ^~~~ 2024-03-04T01:20:32,493 src/cpp/dtw.cpp: In function ‘pybind11::array_t get_guided_bands(pybind11::array_t&, pybind11::array_t&, pybind11::array_t&, size_t, i32)’: 2024-03-04T01:20:32,494 src/cpp/dtw.cpp:21:26: warning: unused variable ‘b’ [-Wunused-variable] 2024-03-04T01:20:32,494 21 | size_t i = 0, j = 0, b = 0; 2024-03-04T01:20:32,494 | ^ 2024-03-04T01:20:32,508 src/cpp/dtw.cpp: In function ‘AlnDF read_to_ref_moves(const AlnDF&, pybind11::array_t, pybind11::array_t, i32, i32, bool)’: 2024-03-04T01:20:32,509 src/cpp/dtw.cpp:98:18: warning: variable ‘fill’ set but not used [-Wunused-but-set-variable] 2024-03-04T01:20:32,509 98 | auto fill = backfill_na ? samps : Interval(); 2024-03-04T01:20:32,509 | ^~~~ 2024-03-04T01:20:34,401 In file included from src/cpp/intervals.cpp:2: 2024-03-04T01:20:34,401 src/cpp/intervals.hpp: In instantiation of ‘ValArray IntervalIndex::to_runlen() const [with T = int]’: 2024-03-04T01:20:34,401 src/cpp/intervals.hpp:467:31: required from ‘static void IntervalIndex::pybind(pybind11::module_&, const string&) [with T = int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:20:34,402 src/cpp/intervals.cpp:7:25: required from here 2024-03-04T01:20:34,402 src/cpp/intervals.hpp:348:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const unsigned int’} [-Wsign-compare] 2024-03-04T01:20:34,402 348 | while (gap >= MAX_LEN_I16) { 2024-03-04T01:20:34,403 | ~~~~^~~~~~~~~~~~~~ 2024-03-04T01:20:55,489 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I./src/cpp/ -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c src/cpp/normalizer.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/normalizer.o -fvisibility=hidden -g0 -std=c++11 -O3 -g 2024-03-04T01:21:05,388 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I./src/cpp/ -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c src/cpp/pore_model.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/pore_model.o -fvisibility=hidden -g0 -std=c++11 -O3 -g 2024-03-04T01:21:12,757 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I./src/cpp/ -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c src/cpp/pybinder.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/pybinder.o -fvisibility=hidden -g0 -std=c++11 -O3 -g 2024-03-04T01:21:18,911 In file included from /usr/include/c++/10/vector:72, 2024-03-04T01:21:18,912 from src/cpp/intervals.hpp:6, 2024-03-04T01:21:18,912 from src/cpp/intervals.cpp:2: 2024-03-04T01:21:18,912 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Interval&}; _Tp = Interval; _Alloc = std::allocator >]’: 2024-03-04T01:21:18,913 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ changed in GCC 7.1 2024-03-04T01:21:18,913 426 | vector<_Tp, _Alloc>:: 2024-03-04T01:21:18,913 | ^~~~~~~~~~~~~~~~~~~ 2024-03-04T01:21:19,025 In file included from /usr/include/c++/10/vector:67, 2024-03-04T01:21:19,025 from src/cpp/intervals.hpp:6, 2024-03-04T01:21:19,025 from src/cpp/intervals.cpp:2: 2024-03-04T01:21:19,026 /usr/include/c++/10/bits/stl_vector.h: In member function ‘IntervalIndex IntervalIndex::mirror() const [with T = long long int]’: 2024-03-04T01:21:19,026 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-04T01:21:19,026 1198 | _M_realloc_insert(end(), __x); 2024-03-04T01:21:19,027 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-04T01:21:19,123 /usr/include/c++/10/bits/stl_vector.h: In member function ‘IntervalIndex IntervalIndex::get_union(IntervalIndex) const [with T = long long int]’: 2024-03-04T01:21:19,124 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-04T01:21:19,124 1198 | _M_realloc_insert(end(), __x); 2024-03-04T01:21:19,125 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-04T01:21:19,125 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-04T01:21:19,125 1198 | _M_realloc_insert(end(), __x); 2024-03-04T01:21:19,126 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-04T01:21:19,271 /usr/include/c++/10/bits/stl_vector.h: In member function ‘IntervalIndex IntervalIndex::intersect(IntervalIndex) const [with T = long long int]’: 2024-03-04T01:21:19,271 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-04T01:21:19,271 1198 | _M_realloc_insert(end(), __x); 2024-03-04T01:21:19,272 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-04T01:21:19,409 /usr/include/c++/10/bits/stl_vector.h: In member function ‘IntervalIndex IntervalIndex::islice(size_t, size_t) const [with T = long long int]’: 2024-03-04T01:21:19,409 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-04T01:21:19,409 1198 | _M_realloc_insert(end(), __x); 2024-03-04T01:21:19,410 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-04T01:21:19,410 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-04T01:21:19,411 1198 | _M_realloc_insert(end(), __x); 2024-03-04T01:21:19,411 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-04T01:21:19,411 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-04T01:21:19,412 1198 | _M_realloc_insert(end(), __x); 2024-03-04T01:21:19,412 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-04T01:21:20,111 In file included from src/cpp/signal_processor.hpp:7, 2024-03-04T01:21:20,111 from src/cpp/pybinder.cpp:6: 2024-03-04T01:21:20,112 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-04T01:21:20,112 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-04T01:21:20,113 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-04T01:21:20,113 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-04T01:21:20,113 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-04T01:21:20,114 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-04T01:21:20,157 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-04T01:21:20,157 src/cpp/event_detector.hpp:147:39: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘i32’ {aka ‘int’} [-Wsign-compare] 2024-03-04T01:21:20,157 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-04T01:21:20,158 | ~~^~~~~~~~~~ 2024-03-04T01:21:20,158 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-04T01:21:20,158 src/cpp/event_detector.hpp:158:34: warning: narrowing conversion of ‘((ProcessedRead*)this)->ProcessedRead::events.std::vector::size()’ from ‘std::vector::size_type’ {aka ‘unsigned int’} to ‘i32’ {aka ‘int’} [-Wnarrowing] 2024-03-04T01:21:20,159 158 | normalize({0, events.size(), scale, shift}); 2024-03-04T01:21:20,159 | ~~~~~~~~~~~^~ 2024-03-04T01:21:20,632 In file included from src/cpp/dtw.hpp:9, 2024-03-04T01:21:20,633 from src/cpp/pybinder.cpp:8: 2024-03-04T01:21:20,633 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-03-04T01:21:20,633 src/cpp/aln.hpp:187:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-03-04T01:21:20,634 187 | i64 ref; 2024-03-04T01:21:20,634 | ^~~ 2024-03-04T01:21:20,639 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-03-04T01:21:20,639 src/cpp/aln.hpp:279:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-03-04T01:21:20,639 279 | int len,dist; 2024-03-04T01:21:20,640 | ^~~~ 2024-03-04T01:21:26,978 In file included from src/cpp/pybinder.cpp:10: 2024-03-04T01:21:26,978 src/cpp/eventalign.hpp: In instantiation of ‘std::string write_eventalign_new(Alignment&, bool, bool, pybind11::array_t) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’: 2024-03-04T01:21:26,979 src/cpp/pybinder.cpp:34:10: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = short unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:21:26,979 src/cpp/pybinder.cpp:66:31: required from here 2024-03-04T01:21:26,979 src/cpp/eventalign.hpp:76:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-04T01:21:26,980 76 | for (size_t j = samps.start+1; j < samps.end; j++) { 2024-03-04T01:21:26,980 | ~~^~~~~~~~~~~ 2024-03-04T01:21:27,274 src/cpp/eventalign.hpp: In instantiation of ‘std::string write_eventalign_new(Alignment&, bool, bool, pybind11::array_t) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’: 2024-03-04T01:21:27,274 src/cpp/pybinder.cpp:34:10: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:21:27,275 src/cpp/pybinder.cpp:67:31: required from here 2024-03-04T01:21:27,275 src/cpp/eventalign.hpp:76:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-04T01:21:34,368 In file included from /usr/include/c++/10/vector:72, 2024-03-04T01:21:34,368 from src/cpp/intervals.hpp:6, 2024-03-04T01:21:34,368 from src/cpp/intervals.cpp:2: 2024-03-04T01:21:34,369 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: 2024-03-04T01:21:34,369 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ changed in GCC 7.1 2024-03-04T01:21:34,369 426 | vector<_Tp, _Alloc>:: 2024-03-04T01:21:34,369 | ^~~~~~~~~~~~~~~~~~~ 2024-03-04T01:21:34,474 /usr/include/c++/10/bits/vector.tcc: In member function ‘bool pybind11::detail::list_caster::load(pybind11::handle, bool) [with Type = std::vector, std::allocator > >; Value = std::pair]’: 2024-03-04T01:21:34,475 /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-04T01:21:34,475 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2024-03-04T01:21:34,476 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-04T01:21:34,766 In file included from /usr/include/c++/10/vector:67, 2024-03-04T01:21:34,766 from src/cpp/intervals.hpp:6, 2024-03-04T01:21:34,767 from src/cpp/intervals.cpp:2: 2024-03-04T01:21:34,767 /usr/include/c++/10/bits/stl_vector.h: In static member function ‘static pybind11::handle pybind11::cpp_function::initialize::execute >, {}, 0>::, std::allocator > >)>, void, {pybind11::detail::value_and_holder&, std::vector, std::allocator > >}, {pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::detail::is_new_style_constructor}>::::_FUN(pybind11::detail::function_call&)’: 2024-03-04T01:21:34,767 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-04T01:21:34,768 1198 | _M_realloc_insert(end(), __x); 2024-03-04T01:21:34,768 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-04T01:21:34,768 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-04T01:21:34,769 1198 | _M_realloc_insert(end(), __x); 2024-03-04T01:21:34,769 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-04T01:21:38,297 In file included from src/cpp/pybinder.cpp:8: 2024-03-04T01:21:38,297 src/cpp/dtw.hpp: In instantiation of ‘std::vector BandedDTW::get_flat_mat() const [with ModelType = PoreModel]’: 2024-03-04T01:21:38,298 src/cpp/dtw.hpp:734:9: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:21:38,299 src/cpp/pybinder.cpp:23:34: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = short unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:21:38,299 src/cpp/pybinder.cpp:66:31: required from here 2024-03-04T01:21:38,300 src/cpp/dtw.hpp:644:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-04T01:21:38,300 644 | if (q0 >= qry_size()) { 2024-03-04T01:21:38,301 | ~~~^~~~~~~~~~~~~ 2024-03-04T01:21:38,301 src/cpp/dtw.hpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-04T01:21:38,302 651 | if (r1 > ref_size()) { 2024-03-04T01:21:38,302 | ~~~^~~~~~~~~~~~ 2024-03-04T01:21:39,339 src/cpp/dtw.hpp: In instantiation of ‘std::vector BandedDTW::get_flat_mat() const [with ModelType = PoreModel]’: 2024-03-04T01:21:39,339 src/cpp/dtw.hpp:734:9: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:21:39,340 src/cpp/pybinder.cpp:23:34: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:21:39,340 src/cpp/pybinder.cpp:67:31: required from here 2024-03-04T01:21:39,340 src/cpp/dtw.hpp:644:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-04T01:21:39,340 644 | if (q0 >= qry_size()) { 2024-03-04T01:21:39,341 | ~~~^~~~~~~~~~~~~ 2024-03-04T01:21:39,341 src/cpp/dtw.hpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-04T01:21:39,341 651 | if (r1 > ref_size()) { 2024-03-04T01:21:39,341 | ~~~^~~~~~~~~~~~ 2024-03-04T01:21:48,408 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I./src/cpp/ -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c src/cpp/read_buffer.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/read_buffer.o -fvisibility=hidden -g0 -std=c++11 -O3 -g 2024-03-04T01:21:53,104 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I./src/cpp/ -I/home/piwheels/.local/lib/python3.9/site-packages/pybind11/include -I/usr/include/python3.9 -c src/cpp/util.cpp -o build/temp.linux-armv7l-cpython-39/src/cpp/util.o -fvisibility=hidden -g0 -std=c++11 -O3 -g 2024-03-04T01:21:56,049 In file included from src/cpp/seq.hpp:32, 2024-03-04T01:21:56,049 from src/cpp/pybinder.cpp:7: 2024-03-04T01:21:56,050 src/cpp/pore_model.hpp: In instantiation of ‘DestIter PoreModel::str_to_kmers(StrIter, DestIter, size_t, KmerType, bool) const [with StrIter = __gnu_cxx::__normal_iterator >; DestIter = short unsigned int*; KmerType = short unsigned int; size_t = unsigned int]’: 2024-03-04T01:21:56,050 src/cpp/pore_model.hpp:496:32: required from ‘DestIter PoreModel::str_to_kmers(const string&, DestIter, bool, bool) const [with DestIter = short unsigned int*; KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:21:56,051 src/cpp/pore_model.hpp:480:21: required from ‘ValArray PoreModel::str_to_kmers(const string&, bool, bool) const [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:21:56,051 src/cpp/pore_model.hpp:672:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:21:56,051 src/cpp/pybinder.cpp:21:18: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = short unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:21:56,052 src/cpp/pybinder.cpp:66:31: required from here 2024-03-04T01:21:56,052 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-04T01:21:56,052 507 | kmer = kmer_neighbor(kmer, BASE_BYTES[*iseq]); 2024-03-04T01:21:56,052 | ~~~~~~~~~~^ 2024-03-04T01:21:56,056 src/cpp/pore_model.hpp: In instantiation of ‘DestIter PoreModel::str_to_kmers(StrIter, DestIter, size_t, KmerType, bool) const [with StrIter = std::reverse_iterator<__gnu_cxx::__normal_iterator > >; DestIter = short unsigned int*; KmerType = short unsigned int; size_t = unsigned int]’: 2024-03-04T01:21:56,056 src/cpp/pore_model.hpp:498:32: required from ‘DestIter PoreModel::str_to_kmers(const string&, DestIter, bool, bool) const [with DestIter = short unsigned int*; KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:21:56,057 src/cpp/pore_model.hpp:480:21: required from ‘ValArray PoreModel::str_to_kmers(const string&, bool, bool) const [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:21:56,057 src/cpp/pore_model.hpp:672:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:21:56,058 src/cpp/pybinder.cpp:21:18: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = short unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:21:56,058 src/cpp/pybinder.cpp:66:31: required from here 2024-03-04T01:21:56,058 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-04T01:22:02,030 src/cpp/pore_model.hpp: In instantiation of ‘DestIter PoreModel::str_to_kmers(StrIter, DestIter, size_t, KmerType, bool) const [with StrIter = __gnu_cxx::__normal_iterator >; DestIter = unsigned int*; KmerType = unsigned int; size_t = unsigned int]’: 2024-03-04T01:22:02,030 src/cpp/pore_model.hpp:496:32: required from ‘DestIter PoreModel::str_to_kmers(const string&, DestIter, bool, bool) const [with DestIter = unsigned int*; KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:02,030 src/cpp/pore_model.hpp:480:21: required from ‘ValArray PoreModel::str_to_kmers(const string&, bool, bool) const [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:02,031 src/cpp/pore_model.hpp:672:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:02,031 src/cpp/pybinder.cpp:21:18: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:02,031 src/cpp/pybinder.cpp:67:31: required from here 2024-03-04T01:22:02,031 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-04T01:22:02,033 src/cpp/pore_model.hpp: In instantiation of ‘DestIter PoreModel::str_to_kmers(StrIter, DestIter, size_t, KmerType, bool) const [with StrIter = std::reverse_iterator<__gnu_cxx::__normal_iterator > >; DestIter = unsigned int*; KmerType = unsigned int; size_t = unsigned int]’: 2024-03-04T01:22:02,033 src/cpp/pore_model.hpp:498:32: required from ‘DestIter PoreModel::str_to_kmers(const string&, DestIter, bool, bool) const [with DestIter = unsigned int*; KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:02,033 src/cpp/pore_model.hpp:480:21: required from ‘ValArray PoreModel::str_to_kmers(const string&, bool, bool) const [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:02,034 src/cpp/pore_model.hpp:672:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:02,034 src/cpp/pybinder.cpp:21:18: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:02,034 src/cpp/pybinder.cpp:67:31: required from here 2024-03-04T01:22:02,034 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-04T01:22:07,812 src/cpp/pore_model.hpp: In instantiation of ‘void PoreModel::init_current(const Container&, const Container&, const Container&, const Container&, bool) [with Container = PyArray; KmerType = short unsigned int]’: 2024-03-04T01:22:07,812 src/cpp/pore_model.hpp:339:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = short unsigned int]’ 2024-03-04T01:22:07,813 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = PoreModel; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; typename std::enable_if::value, int>::type = 0]’ 2024-03-04T01:22:07,813 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}]’ 2024-03-04T01:22:07,813 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; Extra = {}; type_ = PoreModel; options = {}]’ 2024-03-04T01:22:07,814 src/cpp/pore_model.hpp:646:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:07,814 src/cpp/pybinder.cpp:21:18: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = short unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:07,814 src/cpp/pybinder.cpp:66:31: required from here 2024-03-04T01:22:07,814 src/cpp/pore_model.hpp:354:14: warning: variable ‘get_kmer’ set but not used [-Wunused-but-set-variable] 2024-03-04T01:22:07,814 354 | auto get_kmer = [&](size_t i) {return i;}; 2024-03-04T01:22:07,814 | ^~~~~~~~ 2024-03-04T01:22:08,719 In file included from src/cpp/pybinder.cpp:8: 2024-03-04T01:22:08,719 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::fill_mat() [with ModelType = PoreModel]’: 2024-03-04T01:22:08,719 src/cpp/dtw.hpp:356:9: required from ‘BandedDTW::BandedDTW(const DtwParams&, const ProcessedRead&, size_t, size_t, const std::vector&, const ModelType&, const PyArray&) [with ModelType = PoreModel; size_t = unsigned int; typename ModelType::kmer_t = short unsigned int]’ 2024-03-04T01:22:08,720 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = BandedDTW >; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; typename std::enable_if::value, int>::type = 0]’ 2024-03-04T01:22:08,720 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ > >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}]’ 2024-03-04T01:22:08,720 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; Extra = {}; type_ = BandedDTW >; options = {}]’ 2024-03-04T01:22:08,720 src/cpp/dtw.hpp:714:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:08,721 src/cpp/pybinder.cpp:23:34: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = short unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:08,721 src/cpp/pybinder.cpp:66:31: required from here 2024-03-04T01:22:08,721 src/cpp/dtw.hpp:443:33: warning: comparison of integer expressions of different signedness: ‘i32’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-04T01:22:08,722 443 | if (q >= 0 && q < qry_size() && in_range(r, ref_vals_)) { 2024-03-04T01:22:08,722 | ~~^~~~~~~~~~~~ 2024-03-04T01:22:08,724 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::traceback() [with ModelType = PoreModel]’: 2024-03-04T01:22:08,725 src/cpp/dtw.hpp:357:9: required from ‘BandedDTW::BandedDTW(const DtwParams&, const ProcessedRead&, size_t, size_t, const std::vector&, const ModelType&, const PyArray&) [with ModelType = PoreModel; size_t = unsigned int; typename ModelType::kmer_t = short unsigned int]’ 2024-03-04T01:22:08,725 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = BandedDTW >; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; typename std::enable_if::value, int>::type = 0]’ 2024-03-04T01:22:08,725 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ > >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}]’ 2024-03-04T01:22:08,726 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; Extra = {}; type_ = BandedDTW >; options = {}]’ 2024-03-04T01:22:08,726 src/cpp/dtw.hpp:714:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:08,726 src/cpp/pybinder.cpp:23:34: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = short unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:08,727 src/cpp/pybinder.cpp:66:31: required from here 2024-03-04T01:22:08,727 src/cpp/dtw.hpp:507:46: warning: narrowing conversion of ‘(((size_t)(path_ll.Coord::qry - offs)) + ((BandedDTW >*)this)->BandedDTW >::event_start_)’ from ‘size_t’ {aka ‘unsigned int’} to ‘i32’ {aka ‘int’} [-Wnarrowing] 2024-03-04T01:22:08,727 507 | path_.push_back({path_ll.qry-offs+event_start_, path_ll.ref+offs}); 2024-03-04T01:22:08,728 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2024-03-04T01:22:09,812 In file included from src/cpp/seq.hpp:32, 2024-03-04T01:22:09,812 from src/cpp/pybinder.cpp:7: 2024-03-04T01:22:09,812 src/cpp/pore_model.hpp: In instantiation of ‘void PoreModel::init_current(const Container&, const Container&, const Container&, const Container&, bool) [with Container = PyArray; KmerType = unsigned int]’: 2024-03-04T01:22:09,813 src/cpp/pore_model.hpp:339:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = unsigned int]’ 2024-03-04T01:22:09,813 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = PoreModel; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; typename std::enable_if::value, int>::type = 0]’ 2024-03-04T01:22:09,813 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}]’ 2024-03-04T01:22:09,814 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; Extra = {}; type_ = PoreModel; options = {}]’ 2024-03-04T01:22:09,814 src/cpp/pore_model.hpp:646:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:09,815 src/cpp/pybinder.cpp:21:18: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:09,815 src/cpp/pybinder.cpp:67:31: required from here 2024-03-04T01:22:09,815 src/cpp/pore_model.hpp:354:14: warning: variable ‘get_kmer’ set but not used [-Wunused-but-set-variable] 2024-03-04T01:22:09,816 354 | auto get_kmer = [&](size_t i) {return i;}; 2024-03-04T01:22:09,816 | ^~~~~~~~ 2024-03-04T01:22:10,019 In file included from src/cpp/pybinder.cpp:8: 2024-03-04T01:22:10,020 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::fill_mat() [with ModelType = PoreModel]’: 2024-03-04T01:22:10,020 src/cpp/dtw.hpp:356:9: required from ‘BandedDTW::BandedDTW(const DtwParams&, const ProcessedRead&, size_t, size_t, const std::vector&, const ModelType&, const PyArray&) [with ModelType = PoreModel; size_t = unsigned int; typename ModelType::kmer_t = unsigned int]’ 2024-03-04T01:22:10,020 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = BandedDTW >; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; typename std::enable_if::value, int>::type = 0]’ 2024-03-04T01:22:10,021 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ > >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}]’ 2024-03-04T01:22:10,021 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; Extra = {}; type_ = BandedDTW >; options = {}]’ 2024-03-04T01:22:10,021 src/cpp/dtw.hpp:714:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:10,022 src/cpp/pybinder.cpp:23:34: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:10,022 src/cpp/pybinder.cpp:67:31: required from here 2024-03-04T01:22:10,022 src/cpp/dtw.hpp:443:33: warning: comparison of integer expressions of different signedness: ‘i32’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-04T01:22:10,023 443 | if (q >= 0 && q < qry_size() && in_range(r, ref_vals_)) { 2024-03-04T01:22:10,023 | ~~^~~~~~~~~~~~ 2024-03-04T01:22:10,023 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::traceback() [with ModelType = PoreModel]’: 2024-03-04T01:22:10,024 src/cpp/dtw.hpp:357:9: required from ‘BandedDTW::BandedDTW(const DtwParams&, const ProcessedRead&, size_t, size_t, const std::vector&, const ModelType&, const PyArray&) [with ModelType = PoreModel; size_t = unsigned int; typename ModelType::kmer_t = unsigned int]’ 2024-03-04T01:22:10,024 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = BandedDTW >; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; typename std::enable_if::value, int>::type = 0]’ 2024-03-04T01:22:10,025 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ > >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}]’ 2024-03-04T01:22:10,025 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {const DtwParams&, const ProcessedRead&, unsigned int, unsigned int, const std::vector >&, const PoreModel&, const PyArray&}; Extra = {}; type_ = BandedDTW >; options = {}]’ 2024-03-04T01:22:10,025 src/cpp/dtw.hpp:714:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:10,026 src/cpp/pybinder.cpp:23:34: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:10,026 src/cpp/pybinder.cpp:67:31: required from here 2024-03-04T01:22:10,027 src/cpp/dtw.hpp:507:46: warning: narrowing conversion of ‘(((size_t)(path_ll.Coord::qry - offs)) + ((BandedDTW >*)this)->BandedDTW >::event_start_)’ from ‘size_t’ {aka ‘unsigned int’} to ‘i32’ {aka ‘int’} [-Wnarrowing] 2024-03-04T01:22:10,027 507 | path_.push_back({path_ll.qry-offs+event_start_, path_ll.ref+offs}); 2024-03-04T01:22:10,027 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2024-03-04T01:22:11,965 In file included from src/cpp/read_buffer.hpp:30, 2024-03-04T01:22:11,966 from src/cpp/pybinder.cpp:5: 2024-03-04T01:22:11,966 src/cpp/util.hpp: In instantiation of ‘T ValArray::mean() const [with T = float]’: 2024-03-04T01:22:11,966 src/cpp/pore_model.hpp:369:45: required from ‘void PoreModel::init_current(const Container&, const Container&, const Container&, const Container&, bool) [with Container = PyArray; KmerType = short unsigned int]’ 2024-03-04T01:22:11,967 src/cpp/pore_model.hpp:339:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = short unsigned int]’ 2024-03-04T01:22:11,967 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:76:12: required from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = PoreModel; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; typename std::enable_if::value, int>::type = 0]’ 2024-03-04T01:22:11,968 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/detail/init.h:206:70: required from ‘static void pybind11::detail::initimpl::constructor::execute(Class&, const Extra& ...) [with Class = pybind11::class_ >; Extra = {}; typename std::enable_if<(! Class::has_alias), int>::type = 0; Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}]’ 2024-03-04T01:22:11,968 /home/piwheels/.local/lib/python3.9/site-packages/pybind11/include/pybind11/pybind11.h:1613:21: required from ‘pybind11::class_& pybind11::class_::def(const pybind11::detail::initimpl::constructor&, const Extra& ...) [with Args = {PoreModelParams, pybind11::array_t, pybind11::array_t, bool}; Extra = {}; type_ = PoreModel; options = {}]’ 2024-03-04T01:22:11,969 src/cpp/pore_model.hpp:646:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:11,969 src/cpp/pybinder.cpp:21:18: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = short unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-04T01:22:11,969 src/cpp/pybinder.cpp:66:31: required from here 2024-03-04T01:22:11,970 src/cpp/util.hpp:144:14: warning: unused variable ‘sum’ [-Wunused-variable] 2024-03-04T01:22:11,970 144 | auto sum = super::sum(); 2024-03-04T01:22:11,970 | ^~~ 2024-03-04T01:22:11,971 src/cpp/util.hpp:145:14: warning: unused variable ‘len’ [-Wunused-variable] 2024-03-04T01:22:11,971 145 | auto len = super::size(); 2024-03-04T01:22:11,971 | ^~~ 2024-03-04T01:22:30,976 virtual memory exhausted: Cannot allocate memory 2024-03-04T01:22:31,113 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2024-03-04T01:23:20,379 ERROR: python setup.py bdist_wheel exited with 1 2024-03-04T01:23:20,397 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2024-03-04T01:23:20,397 exec(compile('"'"''"'"''"'"' 2024-03-04T01:23:20,397 # This is -- a caller that pip uses to run setup.py 2024-03-04T01:23:20,397 # 2024-03-04T01:23:20,397 # - It imports setuptools before invoking setup.py, to enable projects that directly 2024-03-04T01:23:20,397 # import from `distutils.core` to work with newer packaging standards. 2024-03-04T01:23:20,397 # - It provides a clear error message when setuptools is not installed. 2024-03-04T01:23:20,397 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2024-03-04T01:23:20,397 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2024-03-04T01:23:20,397 # manifest_maker: standard file '"'"'-c'"'"' not found". 2024-03-04T01:23:20,397 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2024-03-04T01:23:20,397 import os, sys, tokenize 2024-03-04T01:23:20,397 2024-03-04T01:23:20,397 try: 2024-03-04T01:23:20,397 import setuptools 2024-03-04T01:23:20,397 except ImportError as error: 2024-03-04T01:23:20,397 print( 2024-03-04T01:23:20,397 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2024-03-04T01:23:20,397 "the build environment.", 2024-03-04T01:23:20,397 file=sys.stderr, 2024-03-04T01:23:20,397 ) 2024-03-04T01:23:20,397 sys.exit(1) 2024-03-04T01:23:20,397 2024-03-04T01:23:20,397 __file__ = %r 2024-03-04T01:23:20,397 sys.argv[0] = __file__ 2024-03-04T01:23:20,397 2024-03-04T01:23:20,397 if os.path.exists(__file__): 2024-03-04T01:23:20,397 filename = __file__ 2024-03-04T01:23:20,397 with tokenize.open(__file__) as f: 2024-03-04T01:23:20,397 setup_py_code = f.read() 2024-03-04T01:23:20,397 else: 2024-03-04T01:23:20,397 filename = "" 2024-03-04T01:23:20,397 setup_py_code = "from setuptools import setup; setup()" 2024-03-04T01:23:20,397 2024-03-04T01:23:20,397 exec(compile(setup_py_code, filename, "exec")) 2024-03-04T01:23:20,397 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-3los7v14/uncalled4_0021919ebf9c40a2bfb7ffddc0e248b0/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-h5wbi_qo[/] 2024-03-04T01:23:20,397 [bold magenta]cwd[/]: /tmp/pip-wheel-3los7v14/uncalled4_0021919ebf9c40a2bfb7ffddc0e248b0/ 2024-03-04T01:23:20,397 Building wheel for uncalled4 (setup.py): finished with status 'error' 2024-03-04T01:23:20,398 ERROR: Failed building wheel for uncalled4 2024-03-04T01:23:20,399 Running setup.py clean for uncalled4 2024-03-04T01:23:20,400 Running command python setup.py clean 2024-03-04T01:23:21,340 /usr/local/lib/python3.9/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-03-04T01:23:21,341 !! 2024-03-04T01:23:21,341 ******************************************************************************** 2024-03-04T01:23:21,341 Requirements should be satisfied by a PEP 517 installer. 2024-03-04T01:23:21,341 If you are using pip, you can try `pip install --use-pep517`. 2024-03-04T01:23:21,341 ******************************************************************************** 2024-03-04T01:23:21,342 !! 2024-03-04T01:23:21,342 dist.fetch_build_eggs(dist.setup_requires) 2024-03-04T01:23:21,415 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'build_backend' 2024-03-04T01:23:21,415 warnings.warn(msg) 2024-03-04T01:23:21,588 running clean 2024-03-04T01:23:21,637 removing 'build/temp.linux-armv7l-cpython-39' (and everything under it) 2024-03-04T01:23:21,659 removing 'build/lib.linux-armv7l-cpython-39' (and everything under it) 2024-03-04T01:23:21,705 'build/bdist.linux-armv7l' does not exist -- can't clean it 2024-03-04T01:23:21,705 'build/scripts-3.9' does not exist -- can't clean it 2024-03-04T01:23:21,705 removing 'build' 2024-03-04T01:23:21,798 Failed to build uncalled4 2024-03-04T01:23:21,799 ERROR: Failed to build one or more wheels 2024-03-04T01:23:21,801 Exception information: 2024-03-04T01:23:21,801 Traceback (most recent call last): 2024-03-04T01:23:21,801 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2024-03-04T01:23:21,801 status = run_func(*args) 2024-03-04T01:23:21,801 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper 2024-03-04T01:23:21,801 return func(self, options, args) 2024-03-04T01:23:21,801 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/commands/wheel.py", line 181, in run 2024-03-04T01:23:21,801 raise CommandError("Failed to build one or more wheels") 2024-03-04T01:23:21,801 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2024-03-04T01:23:21,804 Removed build tracker: '/tmp/pip-build-tracker-qgqkgojv'