2024-03-21T19:01:12,637 Created temporary directory: /tmp/pip-build-tracker-7nbra8ty 2024-03-21T19:01:12,638 Initialized build tracking at /tmp/pip-build-tracker-7nbra8ty 2024-03-21T19:01:12,639 Created build tracker: /tmp/pip-build-tracker-7nbra8ty 2024-03-21T19:01:12,639 Entered build tracker: /tmp/pip-build-tracker-7nbra8ty 2024-03-21T19:01:12,640 Created temporary directory: /tmp/pip-wheel-mxbmlf6w 2024-03-21T19:01:12,643 Created temporary directory: /tmp/pip-ephem-wheel-cache-ifzhkxgz 2024-03-21T19:01:12,665 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-03-21T19:01:12,668 2 location(s) to search for versions of uncalled4: 2024-03-21T19:01:12,668 * https://pypi.org/simple/uncalled4/ 2024-03-21T19:01:12,668 * https://www.piwheels.org/simple/uncalled4/ 2024-03-21T19:01:12,669 Fetching project page and analyzing links: https://pypi.org/simple/uncalled4/ 2024-03-21T19:01:12,670 Getting page https://pypi.org/simple/uncalled4/ 2024-03-21T19:01:12,671 Found index url https://pypi.org/simple/ 2024-03-21T19:01:17,925 Fetched page https://pypi.org/simple/uncalled4/ as application/vnd.pypi.simple.v1+json 2024-03-21T19:01:17,927 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 2024-03-21T19:01:17,928 Found link https://files.pythonhosted.org/packages/bc/fd/a714f3b65dee9941ca73910515fd77bda3b6813c5832df5d4392221ad64b/uncalled4-4.0.0.tar.gz (from https://pypi.org/simple/uncalled4/) (requires-python:>=3.8), version: 4.0.0 2024-03-21T19:01:17,929 Found link https://files.pythonhosted.org/packages/47/e3/f549652974d8e10f90214041a747af1d93d6b7be9e61720234b5c082eef8/uncalled4-4.0.1.tar.gz (from https://pypi.org/simple/uncalled4/) (requires-python:>=3.8), version: 4.0.1 2024-03-21T19:01:17,930 Fetching project page and analyzing links: https://www.piwheels.org/simple/uncalled4/ 2024-03-21T19:01:17,930 Getting page https://www.piwheels.org/simple/uncalled4/ 2024-03-21T19:01:17,932 Found index url https://www.piwheels.org/simple/ 2024-03-21T19:01:18,415 Fetched page https://www.piwheels.org/simple/uncalled4/ as text/html 2024-03-21T19:01:18,416 Skipping link: not a file: https://www.piwheels.org/simple/uncalled4/ 2024-03-21T19:01:18,417 Skipping link: not a file: https://pypi.org/simple/uncalled4/ 2024-03-21T19:01:18,435 Given no hashes to check 1 links for project 'uncalled4': discarding no candidates 2024-03-21T19:01:18,457 Collecting uncalled4==4.0.1 2024-03-21T19:01:18,461 Created temporary directory: /tmp/pip-unpack-uvwzkchp 2024-03-21T19:01:18,714 Downloading uncalled4-4.0.1.tar.gz (19.2 MB) 2024-03-21T19:01:24,005 Added uncalled4==4.0.1 from https://files.pythonhosted.org/packages/47/e3/f549652974d8e10f90214041a747af1d93d6b7be9e61720234b5c082eef8/uncalled4-4.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-7nbra8ty' 2024-03-21T19:01:24,006 Running setup.py (path:/tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/setup.py) egg_info for package uncalled4 2024-03-21T19:01:24,007 Created temporary directory: /tmp/pip-pip-egg-info-2lgkv50h 2024-03-21T19:01:24,008 Preparing metadata (setup.py): started 2024-03-21T19:01:24,009 Running command python setup.py egg_info 2024-03-21T19:01:24,893 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-03-21T19:01:24,893 !! 2024-03-21T19:01:24,894 ******************************************************************************** 2024-03-21T19:01:24,895 Requirements should be satisfied by a PEP 517 installer. 2024-03-21T19:01:24,896 If you are using pip, you can try `pip install --use-pep517`. 2024-03-21T19:01:24,896 ******************************************************************************** 2024-03-21T19:01:24,898 !! 2024-03-21T19:01:24,898 dist.fetch_build_eggs(dist.setup_requires) 2024-03-21T19:01:27,884 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'build_backend' 2024-03-21T19:01:27,885 warnings.warn(msg) 2024-03-21T19:01:27,974 running egg_info 2024-03-21T19:01:27,975 creating /tmp/pip-pip-egg-info-2lgkv50h/uncalled4.egg-info 2024-03-21T19:01:28,002 writing /tmp/pip-pip-egg-info-2lgkv50h/uncalled4.egg-info/PKG-INFO 2024-03-21T19:01:28,006 writing dependency_links to /tmp/pip-pip-egg-info-2lgkv50h/uncalled4.egg-info/dependency_links.txt 2024-03-21T19:01:28,007 writing entry points to /tmp/pip-pip-egg-info-2lgkv50h/uncalled4.egg-info/entry_points.txt 2024-03-21T19:01:28,008 writing requirements to /tmp/pip-pip-egg-info-2lgkv50h/uncalled4.egg-info/requires.txt 2024-03-21T19:01:28,010 writing top-level names to /tmp/pip-pip-egg-info-2lgkv50h/uncalled4.egg-info/top_level.txt 2024-03-21T19:01:28,011 writing manifest file '/tmp/pip-pip-egg-info-2lgkv50h/uncalled4.egg-info/SOURCES.txt' 2024-03-21T19:01:28,133 reading manifest file '/tmp/pip-pip-egg-info-2lgkv50h/uncalled4.egg-info/SOURCES.txt' 2024-03-21T19:01:28,135 reading manifest template 'MANIFEST.in' 2024-03-21T19:01:28,188 adding license file 'LICENSE' 2024-03-21T19:01:28,194 writing manifest file '/tmp/pip-pip-egg-info-2lgkv50h/uncalled4.egg-info/SOURCES.txt' 2024-03-21T19:01:28,305 Preparing metadata (setup.py): finished with status 'done' 2024-03-21T19:01:28,310 Source in /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b has version 4.0.1, which satisfies requirement uncalled4==4.0.1 from https://files.pythonhosted.org/packages/47/e3/f549652974d8e10f90214041a747af1d93d6b7be9e61720234b5c082eef8/uncalled4-4.0.1.tar.gz 2024-03-21T19:01:28,311 Removed uncalled4==4.0.1 from https://files.pythonhosted.org/packages/47/e3/f549652974d8e10f90214041a747af1d93d6b7be9e61720234b5c082eef8/uncalled4-4.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-7nbra8ty' 2024-03-21T19:01:28,316 Created temporary directory: /tmp/pip-unpack-7vbkwe1o 2024-03-21T19:01:28,318 Created temporary directory: /tmp/pip-unpack-xg5ok78l 2024-03-21T19:01:28,332 Building wheels for collected packages: uncalled4 2024-03-21T19:01:28,336 Created temporary directory: /tmp/pip-wheel-bsrbbm4h 2024-03-21T19:01:28,337 Building wheel for uncalled4 (setup.py): started 2024-03-21T19:01:28,338 Destination directory: /tmp/pip-wheel-bsrbbm4h 2024-03-21T19:01:28,339 Running command python setup.py bdist_wheel 2024-03-21T19:01:29,232 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-03-21T19:01:29,233 !! 2024-03-21T19:01:29,234 ******************************************************************************** 2024-03-21T19:01:29,234 Requirements should be satisfied by a PEP 517 installer. 2024-03-21T19:01:29,235 If you are using pip, you can try `pip install --use-pep517`. 2024-03-21T19:01:29,236 ******************************************************************************** 2024-03-21T19:01:29,237 !! 2024-03-21T19:01:29,237 dist.fetch_build_eggs(dist.setup_requires) 2024-03-21T19:01:29,455 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'build_backend' 2024-03-21T19:01:29,456 warnings.warn(msg) 2024-03-21T19:01:29,606 running bdist_wheel 2024-03-21T19:01:29,710 running build 2024-03-21T19:01:29,711 running build_py 2024-03-21T19:01:29,741 creating build 2024-03-21T19:01:29,742 creating build/lib.linux-armv7l-cpython-311 2024-03-21T19:01:29,742 creating build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-21T19:01:29,744 copying src/uncalled4/read_index.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-21T19:01:29,746 copying src/uncalled4/pore_model.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-21T19:01:29,749 copying src/uncalled4/ref_index.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-21T19:01:29,751 copying src/uncalled4/align.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-21T19:01:29,754 copying src/uncalled4/tracks.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-21T19:01:29,757 copying src/uncalled4/signal_processor.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-21T19:01:29,758 copying src/uncalled4/__about__.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-21T19:01:29,760 copying src/uncalled4/config.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-21T19:01:29,762 copying src/uncalled4/__init__.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-21T19:01:29,764 copying src/uncalled4/argparse.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-21T19:01:29,767 copying src/uncalled4/moves.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-21T19:01:29,768 copying src/uncalled4/train.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-21T19:01:29,770 copying src/uncalled4/params.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-21T19:01:29,772 copying src/uncalled4/__main__.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-21T19:01:29,775 creating build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-03-21T19:01:29,777 copying src/uncalled4/stats/refstats.py -> build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-03-21T19:01:29,779 copying src/uncalled4/stats/layerstats.py -> build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-03-21T19:01:29,780 copying src/uncalled4/stats/__init__.py -> build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-03-21T19:01:29,781 copying src/uncalled4/stats/readstats.py -> build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-03-21T19:01:29,784 creating build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-21T19:01:29,785 copying src/uncalled4/vis/browser.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-21T19:01:29,787 copying src/uncalled4/vis/refplot.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-21T19:01:29,789 copying src/uncalled4/vis/trackplot.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-21T19:01:29,791 copying src/uncalled4/vis/sigplot.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-21T19:01:29,793 copying src/uncalled4/vis/dotplot.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-21T19:01:29,796 copying src/uncalled4/vis/__init__.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-21T19:01:29,798 creating build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-21T19:01:29,799 copying src/uncalled4/io/tsv.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-21T19:01:29,801 copying src/uncalled4/io/tombo.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-21T19:01:29,804 copying src/uncalled4/io/m6anet.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-21T19:01:29,806 copying src/uncalled4/io/__init__.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-21T19:01:29,808 copying src/uncalled4/io/model_trainer.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-21T19:01:29,810 copying src/uncalled4/io/eventalign.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-21T19:01:29,812 copying src/uncalled4/io/bam.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-21T19:01:29,815 running egg_info 2024-03-21T19:01:29,868 writing src/uncalled4.egg-info/PKG-INFO 2024-03-21T19:01:29,871 writing dependency_links to src/uncalled4.egg-info/dependency_links.txt 2024-03-21T19:01:29,873 writing entry points to src/uncalled4.egg-info/entry_points.txt 2024-03-21T19:01:29,875 writing requirements to src/uncalled4.egg-info/requires.txt 2024-03-21T19:01:29,876 writing top-level names to src/uncalled4.egg-info/top_level.txt 2024-03-21T19:01:29,909 reading manifest file 'src/uncalled4.egg-info/SOURCES.txt' 2024-03-21T19:01:29,913 reading manifest template 'MANIFEST.in' 2024-03-21T19:01:29,965 adding license file 'LICENSE' 2024-03-21T19:01:29,972 writing manifest file 'src/uncalled4.egg-info/SOURCES.txt' 2024-03-21T19:01:29,975 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.__pycache__' is absent from the `packages` configuration. 2024-03-21T19:01:29,975 !! 2024-03-21T19:01:29,976 ******************************************************************************** 2024-03-21T19:01:29,977 ############################ 2024-03-21T19:01:29,977 # Package would be ignored # 2024-03-21T19:01:29,978 ############################ 2024-03-21T19:01:29,978 Python recognizes 'uncalled4.__pycache__' as an importable package[^1], 2024-03-21T19:01:29,978 but it is absent from setuptools' `packages` configuration. 2024-03-21T19:01:29,979 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-21T19:01:29,980 package, please make sure that 'uncalled4.__pycache__' is explicitly added 2024-03-21T19:01:29,980 to the `packages` configuration field. 2024-03-21T19:01:29,981 Alternatively, you can also rely on setuptools' discovery methods 2024-03-21T19:01:29,982 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-21T19:01:29,982 instead of `find_packages(...)`/`find:`). 2024-03-21T19:01:29,983 You can read more about "package discovery" on setuptools documentation page: 2024-03-21T19:01:29,984 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-21T19:01:29,985 If you don't want 'uncalled4.__pycache__' to be distributed and are 2024-03-21T19:01:29,985 already explicitly excluding 'uncalled4.__pycache__' via 2024-03-21T19:01:29,986 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-21T19:01:29,987 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-21T19:01:29,987 combination with a more fine grained `package-data` configuration. 2024-03-21T19:01:29,988 You can read more about "package data files" on setuptools documentation page: 2024-03-21T19:01:29,989 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-21T19:01:29,991 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-21T19:01:29,991 even if it does not contain any `.py` files. 2024-03-21T19:01:29,992 On the other hand, currently there is no concept of package data 2024-03-21T19:01:29,992 directory, all directories are treated like packages. 2024-03-21T19:01:29,993 ******************************************************************************** 2024-03-21T19:01:29,994 !! 2024-03-21T19:01:29,994 check.warn(importable) 2024-03-21T19:01:29,995 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.io.__pycache__' is absent from the `packages` configuration. 2024-03-21T19:01:29,995 !! 2024-03-21T19:01:29,996 ******************************************************************************** 2024-03-21T19:01:29,997 ############################ 2024-03-21T19:01:29,997 # Package would be ignored # 2024-03-21T19:01:29,998 ############################ 2024-03-21T19:01:29,998 Python recognizes 'uncalled4.io.__pycache__' as an importable package[^1], 2024-03-21T19:01:29,999 but it is absent from setuptools' `packages` configuration. 2024-03-21T19:01:30,000 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-21T19:01:30,000 package, please make sure that 'uncalled4.io.__pycache__' is explicitly added 2024-03-21T19:01:30,001 to the `packages` configuration field. 2024-03-21T19:01:30,002 Alternatively, you can also rely on setuptools' discovery methods 2024-03-21T19:01:30,003 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-21T19:01:30,003 instead of `find_packages(...)`/`find:`). 2024-03-21T19:01:30,004 You can read more about "package discovery" on setuptools documentation page: 2024-03-21T19:01:30,005 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-21T19:01:30,006 If you don't want 'uncalled4.io.__pycache__' to be distributed and are 2024-03-21T19:01:30,007 already explicitly excluding 'uncalled4.io.__pycache__' via 2024-03-21T19:01:30,007 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-21T19:01:30,008 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-21T19:01:30,008 combination with a more fine grained `package-data` configuration. 2024-03-21T19:01:30,009 You can read more about "package data files" on setuptools documentation page: 2024-03-21T19:01:30,010 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-21T19:01:30,011 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-21T19:01:30,012 even if it does not contain any `.py` files. 2024-03-21T19:01:30,012 On the other hand, currently there is no concept of package data 2024-03-21T19:01:30,013 directory, all directories are treated like packages. 2024-03-21T19:01:30,013 ******************************************************************************** 2024-03-21T19:01:30,014 !! 2024-03-21T19:01:30,015 check.warn(importable) 2024-03-21T19:01:30,015 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.models' is absent from the `packages` configuration. 2024-03-21T19:01:30,016 !! 2024-03-21T19:01:30,017 ******************************************************************************** 2024-03-21T19:01:30,017 ############################ 2024-03-21T19:01:30,018 # Package would be ignored # 2024-03-21T19:01:30,018 ############################ 2024-03-21T19:01:30,019 Python recognizes 'uncalled4.models' as an importable package[^1], 2024-03-21T19:01:30,019 but it is absent from setuptools' `packages` configuration. 2024-03-21T19:01:30,020 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-21T19:01:30,021 package, please make sure that 'uncalled4.models' is explicitly added 2024-03-21T19:01:30,021 to the `packages` configuration field. 2024-03-21T19:01:30,022 Alternatively, you can also rely on setuptools' discovery methods 2024-03-21T19:01:30,023 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-21T19:01:30,023 instead of `find_packages(...)`/`find:`). 2024-03-21T19:01:30,024 You can read more about "package discovery" on setuptools documentation page: 2024-03-21T19:01:30,026 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-21T19:01:30,027 If you don't want 'uncalled4.models' to be distributed and are 2024-03-21T19:01:30,028 already explicitly excluding 'uncalled4.models' via 2024-03-21T19:01:30,028 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-21T19:01:30,029 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-21T19:01:30,029 combination with a more fine grained `package-data` configuration. 2024-03-21T19:01:30,031 You can read more about "package data files" on setuptools documentation page: 2024-03-21T19:01:30,032 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-21T19:01:30,034 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-21T19:01:30,035 even if it does not contain any `.py` files. 2024-03-21T19:01:30,035 On the other hand, currently there is no concept of package data 2024-03-21T19:01:30,036 directory, all directories are treated like packages. 2024-03-21T19:01:30,037 ******************************************************************************** 2024-03-21T19:01:30,037 !! 2024-03-21T19:01:30,038 check.warn(importable) 2024-03-21T19:01:30,038 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.models.tombo' is absent from the `packages` configuration. 2024-03-21T19:01:30,039 !! 2024-03-21T19:01:30,040 ******************************************************************************** 2024-03-21T19:01:30,040 ############################ 2024-03-21T19:01:30,040 # Package would be ignored # 2024-03-21T19:01:30,041 ############################ 2024-03-21T19:01:30,041 Python recognizes 'uncalled4.models.tombo' as an importable package[^1], 2024-03-21T19:01:30,042 but it is absent from setuptools' `packages` configuration. 2024-03-21T19:01:30,042 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-21T19:01:30,043 package, please make sure that 'uncalled4.models.tombo' is explicitly added 2024-03-21T19:01:30,043 to the `packages` configuration field. 2024-03-21T19:01:30,044 Alternatively, you can also rely on setuptools' discovery methods 2024-03-21T19:01:30,045 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-21T19:01:30,045 instead of `find_packages(...)`/`find:`). 2024-03-21T19:01:30,046 You can read more about "package discovery" on setuptools documentation page: 2024-03-21T19:01:30,047 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-21T19:01:30,048 If you don't want 'uncalled4.models.tombo' to be distributed and are 2024-03-21T19:01:30,049 already explicitly excluding 'uncalled4.models.tombo' via 2024-03-21T19:01:30,050 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-21T19:01:30,050 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-21T19:01:30,051 combination with a more fine grained `package-data` configuration. 2024-03-21T19:01:30,052 You can read more about "package data files" on setuptools documentation page: 2024-03-21T19:01:30,053 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-21T19:01:30,055 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-21T19:01:30,055 even if it does not contain any `.py` files. 2024-03-21T19:01:30,056 On the other hand, currently there is no concept of package data 2024-03-21T19:01:30,056 directory, all directories are treated like packages. 2024-03-21T19:01:30,057 ******************************************************************************** 2024-03-21T19:01:30,058 !! 2024-03-21T19:01:30,059 check.warn(importable) 2024-03-21T19:01:30,059 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.stats.__pycache__' is absent from the `packages` configuration. 2024-03-21T19:01:30,060 !! 2024-03-21T19:01:30,061 ******************************************************************************** 2024-03-21T19:01:30,062 ############################ 2024-03-21T19:01:30,062 # Package would be ignored # 2024-03-21T19:01:30,063 ############################ 2024-03-21T19:01:30,063 Python recognizes 'uncalled4.stats.__pycache__' as an importable package[^1], 2024-03-21T19:01:30,064 but it is absent from setuptools' `packages` configuration. 2024-03-21T19:01:30,065 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-21T19:01:30,066 package, please make sure that 'uncalled4.stats.__pycache__' is explicitly added 2024-03-21T19:01:30,066 to the `packages` configuration field. 2024-03-21T19:01:30,068 Alternatively, you can also rely on setuptools' discovery methods 2024-03-21T19:01:30,069 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-21T19:01:30,072 instead of `find_packages(...)`/`find:`). 2024-03-21T19:01:30,074 You can read more about "package discovery" on setuptools documentation page: 2024-03-21T19:01:30,098 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-21T19:01:30,125 If you don't want 'uncalled4.stats.__pycache__' to be distributed and are 2024-03-21T19:01:30,125 already explicitly excluding 'uncalled4.stats.__pycache__' via 2024-03-21T19:01:30,126 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-21T19:01:30,126 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-21T19:01:30,127 combination with a more fine grained `package-data` configuration. 2024-03-21T19:01:30,128 You can read more about "package data files" on setuptools documentation page: 2024-03-21T19:01:30,129 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-21T19:01:30,130 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-21T19:01:30,131 even if it does not contain any `.py` files. 2024-03-21T19:01:30,132 On the other hand, currently there is no concept of package data 2024-03-21T19:01:30,132 directory, all directories are treated like packages. 2024-03-21T19:01:30,133 ******************************************************************************** 2024-03-21T19:01:30,134 !! 2024-03-21T19:01:30,134 check.warn(importable) 2024-03-21T19:01:30,135 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.vis.__pycache__' is absent from the `packages` configuration. 2024-03-21T19:01:30,135 !! 2024-03-21T19:01:30,137 ******************************************************************************** 2024-03-21T19:01:30,137 ############################ 2024-03-21T19:01:30,138 # Package would be ignored # 2024-03-21T19:01:30,139 ############################ 2024-03-21T19:01:30,139 Python recognizes 'uncalled4.vis.__pycache__' as an importable package[^1], 2024-03-21T19:01:30,140 but it is absent from setuptools' `packages` configuration. 2024-03-21T19:01:30,141 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-21T19:01:30,141 package, please make sure that 'uncalled4.vis.__pycache__' is explicitly added 2024-03-21T19:01:30,142 to the `packages` configuration field. 2024-03-21T19:01:30,143 Alternatively, you can also rely on setuptools' discovery methods 2024-03-21T19:01:30,144 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-21T19:01:30,144 instead of `find_packages(...)`/`find:`). 2024-03-21T19:01:30,146 You can read more about "package discovery" on setuptools documentation page: 2024-03-21T19:01:30,147 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-21T19:01:30,148 If you don't want 'uncalled4.vis.__pycache__' to be distributed and are 2024-03-21T19:01:30,148 already explicitly excluding 'uncalled4.vis.__pycache__' via 2024-03-21T19:01:30,149 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-21T19:01:30,149 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-21T19:01:30,150 combination with a more fine grained `package-data` configuration. 2024-03-21T19:01:30,151 You can read more about "package data files" on setuptools documentation page: 2024-03-21T19:01:30,152 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-21T19:01:30,154 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-21T19:01:30,154 even if it does not contain any `.py` files. 2024-03-21T19:01:30,155 On the other hand, currently there is no concept of package data 2024-03-21T19:01:30,155 directory, all directories are treated like packages. 2024-03-21T19:01:30,155 ******************************************************************************** 2024-03-21T19:01:30,156 !! 2024-03-21T19:01:30,157 check.warn(importable) 2024-03-21T19:01:30,158 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.vis.assets' is absent from the `packages` configuration. 2024-03-21T19:01:30,158 !! 2024-03-21T19:01:30,159 ******************************************************************************** 2024-03-21T19:01:30,160 ############################ 2024-03-21T19:01:30,160 # Package would be ignored # 2024-03-21T19:01:30,160 ############################ 2024-03-21T19:01:30,161 Python recognizes 'uncalled4.vis.assets' as an importable package[^1], 2024-03-21T19:01:30,161 but it is absent from setuptools' `packages` configuration. 2024-03-21T19:01:30,162 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-21T19:01:30,163 package, please make sure that 'uncalled4.vis.assets' is explicitly added 2024-03-21T19:01:30,163 to the `packages` configuration field. 2024-03-21T19:01:30,164 Alternatively, you can also rely on setuptools' discovery methods 2024-03-21T19:01:30,165 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-21T19:01:30,166 instead of `find_packages(...)`/`find:`). 2024-03-21T19:01:30,167 You can read more about "package discovery" on setuptools documentation page: 2024-03-21T19:01:30,168 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-21T19:01:30,169 If you don't want 'uncalled4.vis.assets' to be distributed and are 2024-03-21T19:01:30,170 already explicitly excluding 'uncalled4.vis.assets' via 2024-03-21T19:01:30,170 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-21T19:01:30,171 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-21T19:01:30,171 combination with a more fine grained `package-data` configuration. 2024-03-21T19:01:30,172 You can read more about "package data files" on setuptools documentation page: 2024-03-21T19:01:30,174 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-21T19:01:30,175 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-21T19:01:30,176 even if it does not contain any `.py` files. 2024-03-21T19:01:30,177 On the other hand, currently there is no concept of package data 2024-03-21T19:01:30,177 directory, all directories are treated like packages. 2024-03-21T19:01:30,178 ******************************************************************************** 2024-03-21T19:01:30,179 !! 2024-03-21T19:01:30,179 check.warn(importable) 2024-03-21T19:01:30,180 creating build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,180 copying src/uncalled4/__pycache__/__about__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,181 copying src/uncalled4/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,181 copying src/uncalled4/__pycache__/__main__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,182 copying src/uncalled4/__pycache__/align.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,183 copying src/uncalled4/__pycache__/aln.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,183 copying src/uncalled4/__pycache__/aln_track.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,184 copying src/uncalled4/__pycache__/argparse.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,184 copying src/uncalled4/__pycache__/config.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,185 copying src/uncalled4/__pycache__/dtw.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,185 copying src/uncalled4/__pycache__/index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,186 copying src/uncalled4/__pycache__/layers.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,186 copying src/uncalled4/__pycache__/moves.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,186 copying src/uncalled4/__pycache__/params.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,187 copying src/uncalled4/__pycache__/pore_model.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,188 copying src/uncalled4/__pycache__/read_index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,189 copying src/uncalled4/__pycache__/ref_index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,189 copying src/uncalled4/__pycache__/signal_processor.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,190 copying src/uncalled4/__pycache__/tracks.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,190 copying src/uncalled4/__pycache__/train.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-21T19:01:30,191 creating build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-03-21T19:01:30,191 copying src/uncalled4/models/README.txt -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-03-21T19:01:30,192 copying src/uncalled4/models/dna_r10.4.1_400bps_9mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-03-21T19:01:30,193 copying src/uncalled4/models/dna_r9.4.1_400bps_6mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-03-21T19:01:30,193 copying src/uncalled4/models/presets.tsv -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-03-21T19:01:30,194 copying src/uncalled4/models/rna_r9.4.1_70bps_5mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-03-21T19:01:30,194 creating build/lib.linux-armv7l-cpython-311/uncalled4/models/tombo 2024-03-21T19:01:30,195 copying src/uncalled4/models/tombo/dna_r9.4.1_400bps_6mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models/tombo 2024-03-21T19:01:30,195 copying src/uncalled4/models/tombo/rna_r9.4.1_70bps_5mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models/tombo 2024-03-21T19:01:30,196 creating build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-21T19:01:30,196 copying src/uncalled4/stats/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-21T19:01:30,197 copying src/uncalled4/stats/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-21T19:01:30,197 copying src/uncalled4/stats/__pycache__/__init__.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-21T19:01:30,198 copying src/uncalled4/stats/__pycache__/_dtwstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-21T19:01:30,199 copying src/uncalled4/stats/__pycache__/_dtwstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-21T19:01:30,199 copying src/uncalled4/stats/__pycache__/_readstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-21T19:01:30,200 copying src/uncalled4/stats/__pycache__/_readstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-21T19:01:30,200 copying src/uncalled4/stats/__pycache__/_refstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-21T19:01:30,201 copying src/uncalled4/stats/__pycache__/_refstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-21T19:01:30,201 copying src/uncalled4/stats/__pycache__/dtwstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-21T19:01:30,202 copying src/uncalled4/stats/__pycache__/layerstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-21T19:01:30,202 copying src/uncalled4/stats/__pycache__/layerstats.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-21T19:01:30,203 copying src/uncalled4/stats/__pycache__/refstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-21T19:01:30,203 copying src/uncalled4/stats/__pycache__/refstats.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-21T19:01:30,204 creating build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-21T19:01:30,205 copying src/uncalled4/vis/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-21T19:01:30,205 copying src/uncalled4/vis/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-21T19:01:30,206 copying src/uncalled4/vis/__pycache__/__init__.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-21T19:01:30,206 copying src/uncalled4/vis/__pycache__/browser.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-21T19:01:30,207 copying src/uncalled4/vis/__pycache__/browser.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-21T19:01:30,207 copying src/uncalled4/vis/__pycache__/browser.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-21T19:01:30,208 copying src/uncalled4/vis/__pycache__/dotplot.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-21T19:01:30,209 copying src/uncalled4/vis/__pycache__/dotplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-21T19:01:30,209 copying src/uncalled4/vis/__pycache__/dotplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-21T19:01:30,210 copying src/uncalled4/vis/__pycache__/refplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-21T19:01:30,211 copying src/uncalled4/vis/__pycache__/sigplot.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-21T19:01:30,214 copying src/uncalled4/vis/__pycache__/sigplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-21T19:01:30,216 copying src/uncalled4/vis/__pycache__/sigplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-21T19:01:30,218 copying src/uncalled4/vis/__pycache__/trackplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-21T19:01:30,221 copying src/uncalled4/vis/__pycache__/trackplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-21T19:01:30,223 creating build/lib.linux-armv7l-cpython-311/uncalled4/vis/assets 2024-03-21T19:01:30,224 copying src/uncalled4/vis/assets/.browser.js.swp -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/assets 2024-03-21T19:01:30,227 copying src/uncalled4/vis/assets/browser.css -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/assets 2024-03-21T19:01:30,229 copying src/uncalled4/vis/assets/browser.js -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/assets 2024-03-21T19:01:30,231 creating build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-21T19:01:30,232 copying src/uncalled4/io/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-21T19:01:30,234 copying src/uncalled4/io/__pycache__/bam.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-21T19:01:30,237 copying src/uncalled4/io/__pycache__/eventalign.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-21T19:01:30,239 copying src/uncalled4/io/__pycache__/guppy.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-21T19:01:30,241 copying src/uncalled4/io/__pycache__/m6anet.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-21T19:01:30,243 copying src/uncalled4/io/__pycache__/model.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-21T19:01:30,245 copying src/uncalled4/io/__pycache__/model_trainer.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-21T19:01:30,248 copying src/uncalled4/io/__pycache__/sqlite.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-21T19:01:30,250 copying src/uncalled4/io/__pycache__/tombo.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-21T19:01:30,252 copying src/uncalled4/io/__pycache__/tsv.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-21T19:01:30,257 running build_ext 2024-03-21T19:01:30,780 building '_uncalled4' extension 2024-03-21T19:01:30,803 creating build/temp.linux-armv7l-cpython-311 2024-03-21T19:01:30,804 creating build/temp.linux-armv7l-cpython-311/src 2024-03-21T19:01:30,804 creating build/temp.linux-armv7l-cpython-311/src/cpp 2024-03-21T19:01:30,805 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.11 -c src/cpp/config.cpp -o build/temp.linux-armv7l-cpython-311/src/cpp/config.o -std=c++11 -O3 -g 2024-03-21T19:01:36,602 In file included from src/cpp/dtw.hpp:7, 2024-03-21T19:01:36,603 from src/cpp/config.hpp:30, 2024-03-21T19:01:36,604 from src/cpp/config.cpp:1: 2024-03-21T19:01:36,605 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:01:36,605 src/cpp/intervals.hpp:110:20: required from here 2024-03-21T19:01:36,606 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:01:36,607 192 | struct PyArray { 2024-03-21T19:01:36,607 | ^~~~~~~ 2024-03-21T19:01:36,837 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:01:36,838 src/cpp/read_buffer.hpp:99:38: required from here 2024-03-21T19:01:36,838 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:01:36,929 In file included from src/cpp/aln.hpp:11, 2024-03-21T19:01:36,930 from src/cpp/dtw.hpp:9: 2024-03-21T19:01:36,931 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-21T19:01:36,932 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T19:01:36,932 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-21T19:01:36,934 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-21T19:01:36,934 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T19:01:36,935 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-21T19:01:36,959 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-21T19:01:36,960 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] 2024-03-21T19:01:36,960 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-21T19:01:36,961 | ~~^~~~~~~~~~ 2024-03-21T19:01:36,962 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-21T19:01:36,962 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] 2024-03-21T19:01:36,963 158 | normalize({0, events.size(), scale, shift}); 2024-03-21T19:01:36,963 | ~~~~~~~~~~~^~ 2024-03-21T19:01:37,035 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:01:37,036 src/cpp/event_detector.hpp:211:39: required from here 2024-03-21T19:01:37,037 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:01:37,038 192 | struct PyArray { 2024-03-21T19:01:37,038 | ^~~~~~~ 2024-03-21T19:01:37,161 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-03-21T19:01:37,161 src/cpp/aln.hpp:187:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-03-21T19:01:37,162 187 | i64 ref; 2024-03-21T19:01:37,163 | ^~~ 2024-03-21T19:01:37,167 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-03-21T19:01:37,167 src/cpp/aln.hpp:279:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-03-21T19:01:37,168 279 | int len,dist; 2024-03-21T19:01:37,169 | ^~~~ 2024-03-21T19:01:37,180 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:01:37,181 src/cpp/aln.hpp:383:23: required from here 2024-03-21T19:01:37,181 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:01:37,182 192 | struct PyArray { 2024-03-21T19:01:37,183 | ^~~~~~~ 2024-03-21T19:01:37,261 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:01:37,261 src/cpp/dtw.hpp:395:26: required from here 2024-03-21T19:01:37,262 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:01:54,742 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.11 -c src/cpp/dtw.cpp -o build/temp.linux-armv7l-cpython-311/src/cpp/dtw.o -std=c++11 -O3 -g 2024-03-21T19:02:00,532 In file included from src/cpp/dtw.hpp:7, 2024-03-21T19:02:00,533 from src/cpp/dtw.cpp:1: 2024-03-21T19:02:00,534 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:02:00,534 src/cpp/intervals.hpp:110:20: required from here 2024-03-21T19:02:00,535 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:02:00,535 192 | struct PyArray { 2024-03-21T19:02:00,536 | ^~~~~~~ 2024-03-21T19:02:00,775 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:02:00,776 src/cpp/read_buffer.hpp:99:38: required from here 2024-03-21T19:02:00,776 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:02:00,868 In file included from src/cpp/aln.hpp:11, 2024-03-21T19:02:00,868 from src/cpp/dtw.hpp:9: 2024-03-21T19:02:00,869 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-21T19:02:00,870 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T19:02:00,870 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-21T19:02:00,871 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-21T19:02:00,871 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T19:02:00,872 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-21T19:02:00,899 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-21T19:02:00,899 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] 2024-03-21T19:02:00,900 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-21T19:02:00,901 | ~~^~~~~~~~~~ 2024-03-21T19:02:00,902 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-21T19:02:00,902 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] 2024-03-21T19:02:00,903 158 | normalize({0, events.size(), scale, shift}); 2024-03-21T19:02:00,904 | ~~~~~~~~~~~^~ 2024-03-21T19:02:00,976 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:02:00,976 src/cpp/event_detector.hpp:211:39: required from here 2024-03-21T19:02:00,977 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:02:00,978 192 | struct PyArray { 2024-03-21T19:02:00,978 | ^~~~~~~ 2024-03-21T19:02:01,103 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-03-21T19:02:01,103 src/cpp/aln.hpp:187:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-03-21T19:02:01,104 187 | i64 ref; 2024-03-21T19:02:01,104 | ^~~ 2024-03-21T19:02:01,109 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-03-21T19:02:01,110 src/cpp/aln.hpp:279:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-03-21T19:02:01,111 279 | int len,dist; 2024-03-21T19:02:01,111 | ^~~~ 2024-03-21T19:02:01,123 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:02:01,124 src/cpp/aln.hpp:383:23: required from here 2024-03-21T19:02:01,125 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:02:01,125 192 | struct PyArray { 2024-03-21T19:02:01,126 | ^~~~~~~ 2024-03-21T19:02:01,204 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:02:01,205 src/cpp/dtw.hpp:395:26: required from here 2024-03-21T19:02:01,206 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:02:01,227 src/cpp/dtw.cpp: In function ‘pybind11::array_t get_guided_bands(pybind11::array_t&, pybind11::array_t&, pybind11::array_t&, size_t, i32)’: 2024-03-21T19:02:01,228 src/cpp/dtw.cpp:21:26: warning: unused variable ‘b’ [-Wunused-variable] 2024-03-21T19:02:01,228 21 | size_t i = 0, j = 0, b = 0; 2024-03-21T19:02:01,229 | ^ 2024-03-21T19:02:01,233 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:02:01,234 src/cpp/dtw.cpp:64:30: required from here 2024-03-21T19:02:01,234 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:02:01,235 192 | struct PyArray { 2024-03-21T19:02:01,235 | ^~~~~~~ 2024-03-21T19:02:01,241 src/cpp/dtw.cpp: In function ‘AlnDF read_to_ref_moves(const AlnDF&, pybind11::array_t, pybind11::array_t, i32, i32, bool)’: 2024-03-21T19:02:01,242 src/cpp/dtw.cpp:98:18: warning: variable ‘fill’ set but not used [-Wunused-but-set-variable] 2024-03-21T19:02:01,243 98 | auto fill = backfill_na ? samps : Interval(); 2024-03-21T19:02:01,243 | ^~~~ 2024-03-21T19:02:58,954 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.11 -c src/cpp/event_detector.cpp -o build/temp.linux-armv7l-cpython-311/src/cpp/event_detector.o -std=c++11 -O3 -g 2024-03-21T19:03:04,685 In file included from src/cpp/intervals.hpp:11, 2024-03-21T19:03:04,686 from src/cpp/event_detector.hpp:13, 2024-03-21T19:03:04,686 from src/cpp/event_detector.cpp:15: 2024-03-21T19:03:04,687 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:03:04,688 src/cpp/intervals.hpp:110:20: required from here 2024-03-21T19:03:04,688 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:03:04,689 192 | struct PyArray { 2024-03-21T19:03:04,689 | ^~~~~~~ 2024-03-21T19:03:04,713 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:03:04,714 src/cpp/read_buffer.hpp:99:38: required from here 2024-03-21T19:03:04,715 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:03:04,815 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-21T19:03:04,815 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T19:03:04,816 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-21T19:03:04,817 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-21T19:03:04,817 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T19:03:04,818 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-21T19:03:04,851 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-21T19:03:04,852 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] 2024-03-21T19:03:04,852 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-21T19:03:04,853 | ~~^~~~~~~~~~ 2024-03-21T19:03:04,854 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-21T19:03:04,854 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] 2024-03-21T19:03:04,855 158 | normalize({0, events.size(), scale, shift}); 2024-03-21T19:03:04,855 | ~~~~~~~~~~~^~ 2024-03-21T19:03:04,944 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:03:04,944 src/cpp/event_detector.hpp:211:39: required from here 2024-03-21T19:03:04,945 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:03:04,946 192 | struct PyArray { 2024-03-21T19:03:04,946 | ^~~~~~~ 2024-03-21T19:03:05,024 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:03:05,025 src/cpp/event_detector.cpp:242:30: required from here 2024-03-21T19:03:05,025 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:03:31,840 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.11 -c src/cpp/intervals.cpp -o build/temp.linux-armv7l-cpython-311/src/cpp/intervals.o -std=c++11 -O3 -g 2024-03-21T19:03:37,541 In file included from src/cpp/intervals.hpp:11, 2024-03-21T19:03:37,542 from src/cpp/intervals.cpp:2: 2024-03-21T19:03:37,543 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:03:37,544 src/cpp/intervals.hpp:110:20: required from here 2024-03-21T19:03:37,544 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:03:37,545 192 | struct PyArray { 2024-03-21T19:03:37,545 | ^~~~~~~ 2024-03-21T19:03:39,770 src/cpp/intervals.hpp: In instantiation of ‘ValArray IntervalIndex::to_runlen() const [with T = int]’: 2024-03-21T19:03:39,771 src/cpp/intervals.hpp:467:31: required from ‘static void IntervalIndex::pybind(pybind11::module_&, const std::string&) [with T = int; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:03:39,772 src/cpp/intervals.cpp:7:31: required from here 2024-03-21T19:03:39,772 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] 2024-03-21T19:03:39,773 348 | while (gap >= MAX_LEN_I16) { 2024-03-21T19:03:39,774 | ~~~~^~~~~~~~~~~~~~ 2024-03-21T19:04:11,909 In file included from /usr/include/c++/12/vector:70, 2024-03-21T19:04:11,909 from src/cpp/intervals.hpp:6: 2024-03-21T19:04:11,910 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Interval&}; _Tp = Interval; _Alloc = std::allocator >]’: 2024-03-21T19:04:11,911 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ changed in GCC 7.1 2024-03-21T19:04:11,911 439 | vector<_Tp, _Alloc>:: 2024-03-21T19:04:11,911 | ^~~~~~~~~~~~~~~~~~~ 2024-03-21T19:04:12,005 In file included from /usr/include/c++/12/vector:64: 2024-03-21T19:04:12,006 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-21T19:04:12,007 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-21T19:04:12,007 inlined from ‘void IntervalIndex::append(T, T) [with T = long long int]’ at src/cpp/intervals.hpp:261:15, 2024-03-21T19:04:12,008 inlined from ‘IntervalIndex IntervalIndex::mirror() const [with T = long long int]’ at src/cpp/intervals.hpp:160:23: 2024-03-21T19:04:12,008 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-21T19:04:12,009 1287 | _M_realloc_insert(end(), __x); 2024-03-21T19:04:12,009 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-21T19:04:12,106 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-21T19:04:12,106 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-21T19:04:12,107 inlined from ‘IntervalIndex IntervalIndex::islice(size_t, size_t) const [with T = long long int]’ at src/cpp/intervals.hpp:235:23: 2024-03-21T19:04:12,108 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-21T19:04:12,109 1287 | _M_realloc_insert(end(), __x); 2024-03-21T19:04:12,109 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-21T19:04:12,110 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-21T19:04:12,111 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-21T19:04:12,111 inlined from ‘IntervalIndex IntervalIndex::islice(size_t, size_t) const [with T = long long int]’ at src/cpp/intervals.hpp:237:27: 2024-03-21T19:04:12,112 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-21T19:04:12,113 1287 | _M_realloc_insert(end(), __x); 2024-03-21T19:04:12,113 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-21T19:04:12,114 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-21T19:04:12,115 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-21T19:04:12,115 inlined from ‘IntervalIndex IntervalIndex::islice(size_t, size_t) const [with T = long long int]’ at src/cpp/intervals.hpp:242:19: 2024-03-21T19:04:12,116 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-21T19:04:12,117 1287 | _M_realloc_insert(end(), __x); 2024-03-21T19:04:12,117 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-21T19:04:12,349 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-21T19:04:12,350 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-21T19:04:12,350 inlined from ‘IntervalIndex IntervalIndex::get_union(IntervalIndex) const [with T = long long int]’ at src/cpp/intervals.hpp:202:27: 2024-03-21T19:04:12,351 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-21T19:04:12,351 1287 | _M_realloc_insert(end(), __x); 2024-03-21T19:04:12,352 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-21T19:04:12,353 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-21T19:04:12,353 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-21T19:04:12,354 inlined from ‘IntervalIndex IntervalIndex::get_union(IntervalIndex) const [with T = long long int]’ at src/cpp/intervals.hpp:212:19: 2024-03-21T19:04:12,355 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-21T19:04:12,355 1287 | _M_realloc_insert(end(), __x); 2024-03-21T19:04:12,356 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-21T19:04:12,460 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-21T19:04:12,461 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-21T19:04:12,462 inlined from ‘IntervalIndex IntervalIndex::intersect(IntervalIndex) const [with T = long long int]’ at src/cpp/intervals.hpp:176:31: 2024-03-21T19:04:12,462 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-21T19:04:12,463 1287 | _M_realloc_insert(end(), __x); 2024-03-21T19:04:12,464 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-21T19:04:26,260 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: 2024-03-21T19:04:26,260 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ changed in GCC 7.1 2024-03-21T19:04:26,261 439 | vector<_Tp, _Alloc>:: 2024-03-21T19:04:26,262 | ^~~~~~~~~~~~~~~~~~~ 2024-03-21T19:04:26,341 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2024-03-21T19:04:26,341 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair; _Alloc = std::allocator >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2024-03-21T19:04:26,342 inlined from ‘bool pybind11::detail::list_caster::load(pybind11::handle, bool) [with Type = std::vector, std::allocator > >; Value = std::pair]’ at /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/stl.h:180:28: 2024-03-21T19:04:26,342 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-21T19:04:26,343 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2024-03-21T19:04:26,344 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-21T19:04:26,568 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-21T19:04:26,569 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-21T19:04:26,569 inlined from ‘void IntervalIndex::append(T, T) [with T = long long int]’ at src/cpp/intervals.hpp:261:15, 2024-03-21T19:04:26,570 inlined from ‘void IntervalIndex::init_coords(std::vector >) [with T = long long int]’ at src/cpp/intervals.hpp:134:19, 2024-03-21T19:04:26,571 inlined from ‘IntervalIndex::IntervalIndex(std::vector >) [with T = long long int]’ at src/cpp/intervals.hpp:101:20, 2024-03-21T19:04:26,571 inlined from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = IntervalIndex; Args = {std::vector, std::allocator > >}; typename std::enable_if::value, int>::type = 0]’ at /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:76:12, 2024-03-21T19:04:26,572 inlined from ‘pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>’ at /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:206:70, 2024-03-21T19:04:26,573 inlined from ‘Return pybind11::detail::argument_loader::call_impl(Func&&, pybind11::detail::index_sequence, Guard&&) && [with Return = void; Func = pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>&; unsigned int ...Is = {0, 1}; Guard = pybind11::detail::void_type; Args = {pybind11::detail::value_and_holder&, std::vector, std::allocator > >}]’ at /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/../cast.h:1480:37, 2024-03-21T19:04:26,574 inlined from ‘pybind11::detail::enable_if_t::value, pybind11::detail::void_type> pybind11::detail::argument_loader::call(Func&&) && [with Return = void; Guard = pybind11::detail::void_type; Func = pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>&; Args = {pybind11::detail::value_and_holder&, std::vector, std::allocator > >}]’ at /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/../cast.h:1454:65, 2024-03-21T19:04:26,575 inlined from ‘pybind11::cpp_function::initialize, std::allocator > > >::execute > >(pybind11::class_ >&)::, 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>(pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>&&, void (*)(pybind11::detail::value_and_holder&, std::vector, std::allocator > >), const pybind11::name&, const pybind11::is_method&, const pybind11::sibling&, const pybind11::detail::is_new_style_constructor&)::’ at /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:250:78, 2024-03-21T19:04:26,576 inlined from ‘static pybind11::handle pybind11::cpp_function::initialize, std::allocator > > >::execute > >(pybind11::class_ >&)::, 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>(pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>&&, void (*)(pybind11::detail::value_and_holder&, std::vector, std::allocator > >), const pybind11::name&, const pybind11::is_method&, const pybind11::sibling&, const pybind11::detail::is_new_style_constructor&)::::_FUN(pybind11::detail::function_call&)’ at /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:224:21: 2024-03-21T19:04:26,576 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-21T19:04:26,577 1287 | _M_realloc_insert(end(), __x); 2024-03-21T19:04:26,578 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-21T19:04:26,579 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-21T19:04:26,579 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-21T19:04:26,580 inlined from ‘void IntervalIndex::append(T, T) [with T = long long int]’ at src/cpp/intervals.hpp:261:15, 2024-03-21T19:04:26,580 inlined from ‘void IntervalIndex::init_coords(std::vector >) [with T = long long int]’ at src/cpp/intervals.hpp:134:19, 2024-03-21T19:04:26,581 inlined from ‘IntervalIndex::IntervalIndex(std::vector >) [with T = long long int]’ at src/cpp/intervals.hpp:101:20, 2024-03-21T19:04:26,582 inlined from ‘Class* pybind11::detail::initimpl::construct_or_initialize(Args&& ...) [with Class = IntervalIndex; Args = {std::vector, std::allocator > >}; typename std::enable_if::value, int>::type = 0]’ at /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:76:12, 2024-03-21T19:04:26,582 inlined from ‘pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>’ at /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:206:70, 2024-03-21T19:04:26,583 inlined from ‘Return pybind11::detail::argument_loader::call_impl(Func&&, pybind11::detail::index_sequence, Guard&&) && [with Return = void; Func = pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>&; unsigned int ...Is = {0, 1}; Guard = pybind11::detail::void_type; Args = {pybind11::detail::value_and_holder&, std::vector, std::allocator > >}]’ at /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/../cast.h:1480:37, 2024-03-21T19:04:26,584 inlined from ‘pybind11::detail::enable_if_t::value, pybind11::detail::void_type> pybind11::detail::argument_loader::call(Func&&) && [with Return = void; Guard = pybind11::detail::void_type; Func = pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>&; Args = {pybind11::detail::value_and_holder&, std::vector, std::allocator > >}]’ at /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/../cast.h:1454:65, 2024-03-21T19:04:26,585 inlined from ‘pybind11::cpp_function::initialize, std::allocator > > >::execute > >(pybind11::class_ >&)::, 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>(pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>&&, void (*)(pybind11::detail::value_and_holder&, std::vector, std::allocator > >), const pybind11::name&, const pybind11::is_method&, const pybind11::sibling&, const pybind11::detail::is_new_style_constructor&)::’ at /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:254:75, 2024-03-21T19:04:26,585 inlined from ‘static pybind11::handle pybind11::cpp_function::initialize, std::allocator > > >::execute > >(pybind11::class_ >&)::, 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>(pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>&&, void (*)(pybind11::detail::value_and_holder&, std::vector, std::allocator > >), const pybind11::name&, const pybind11::is_method&, const pybind11::sibling&, const pybind11::detail::is_new_style_constructor&)::::_FUN(pybind11::detail::function_call&)’ at /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:224:21: 2024-03-21T19:04:26,586 /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 2024-03-21T19:04:26,587 1287 | _M_realloc_insert(end(), __x); 2024-03-21T19:04:26,587 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-21T19:04:35,127 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.11 -c src/cpp/normalizer.cpp -o build/temp.linux-armv7l-cpython-311/src/cpp/normalizer.o -std=c++11 -O3 -g 2024-03-21T19:04:46,809 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.11 -c src/cpp/pore_model.cpp -o build/temp.linux-armv7l-cpython-311/src/cpp/pore_model.o -std=c++11 -O3 -g 2024-03-21T19:04:52,527 In file included from src/cpp/pore_model.hpp:36, 2024-03-21T19:04:52,528 from src/cpp/pore_model.cpp:1: 2024-03-21T19:04:52,529 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:04:52,529 src/cpp/intervals.hpp:110:20: required from here 2024-03-21T19:04:52,530 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:04:52,531 192 | struct PyArray { 2024-03-21T19:04:52,531 | ^~~~~~~ 2024-03-21T19:05:28,390 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPYBIND -I/tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include -I./src/cpp/ -I/usr/include/python3.11 -c src/cpp/pybinder.cpp -o build/temp.linux-armv7l-cpython-311/src/cpp/pybinder.o -std=c++11 -O3 -g 2024-03-21T19:05:34,147 In file included from src/cpp/read_buffer.hpp:30, 2024-03-21T19:05:34,148 from src/cpp/pybinder.cpp:5: 2024-03-21T19:05:34,148 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:05:34,149 src/cpp/read_buffer.hpp:99:38: required from here 2024-03-21T19:05:34,149 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:05:34,150 192 | struct PyArray { 2024-03-21T19:05:34,151 | ^~~~~~~ 2024-03-21T19:05:34,183 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:05:34,184 src/cpp/intervals.hpp:110:20: required from here 2024-03-21T19:05:34,184 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:05:34,286 In file included from src/cpp/signal_processor.hpp:7, 2024-03-21T19:05:34,287 from src/cpp/pybinder.cpp:6: 2024-03-21T19:05:34,287 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-21T19:05:34,288 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T19:05:34,289 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-21T19:05:34,290 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-21T19:05:34,290 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T19:05:34,291 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-21T19:05:34,338 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-21T19:05:34,339 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] 2024-03-21T19:05:34,339 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-21T19:05:34,340 | ~~^~~~~~~~~~ 2024-03-21T19:05:34,341 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-21T19:05:34,341 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] 2024-03-21T19:05:34,342 158 | normalize({0, events.size(), scale, shift}); 2024-03-21T19:05:34,343 | ~~~~~~~~~~~^~ 2024-03-21T19:05:34,416 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:05:34,417 src/cpp/event_detector.hpp:211:39: required from here 2024-03-21T19:05:34,417 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:05:34,418 192 | struct PyArray { 2024-03-21T19:05:34,418 | ^~~~~~~ 2024-03-21T19:05:34,723 In file included from src/cpp/dtw.hpp:9, 2024-03-21T19:05:34,724 from src/cpp/pybinder.cpp:8: 2024-03-21T19:05:34,725 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-03-21T19:05:34,725 src/cpp/aln.hpp:187:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-03-21T19:05:34,726 187 | i64 ref; 2024-03-21T19:05:34,726 | ^~~ 2024-03-21T19:05:34,731 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-03-21T19:05:34,732 src/cpp/aln.hpp:279:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-03-21T19:05:34,732 279 | int len,dist; 2024-03-21T19:05:34,733 | ^~~~ 2024-03-21T19:05:34,745 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:05:34,746 src/cpp/aln.hpp:383:23: required from here 2024-03-21T19:05:34,746 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:05:34,747 192 | struct PyArray { 2024-03-21T19:05:34,748 | ^~~~~~~ 2024-03-21T19:05:34,827 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:05:34,828 src/cpp/dtw.hpp:395:26: required from here 2024-03-21T19:05:34,829 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:05:34,873 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:05:34,873 src/cpp/eventalign.hpp:110:31: required from here 2024-03-21T19:05:34,874 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:05:38,630 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:05:38,630 src/cpp/eventalign.hpp:101:18: required from ‘std::string write_eventalign(Config&, ModelType&, std::string, bool, ProcessedRead, const std::string&, pybind11::array_t, bool, pybind11::array_t, pybind11::array_t, pybind11::array_t, pybind11::array_t) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string; typename ModelType::kmer_t = short unsigned int]’ 2024-03-21T19:05:38,631 src/cpp/pybinder.cpp:31:10: 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]’ 2024-03-21T19:05:38,631 src/cpp/pybinder.cpp:66:22: required from here 2024-03-21T19:05:38,632 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:05:38,663 In file included from src/cpp/pybinder.cpp:10: 2024-03-21T19:05:38,663 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]’: 2024-03-21T19:05:38,664 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]’ 2024-03-21T19:05:38,664 src/cpp/pybinder.cpp:66:22: required from here 2024-03-21T19:05:38,665 src/cpp/eventalign.hpp:76:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T19:05:38,665 76 | for (size_t j = samps.start+1; j < samps.end; j++) { 2024-03-21T19:05:38,666 | ~~^~~~~~~~~~~ 2024-03-21T19:05:38,841 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-21T19:05:38,842 src/cpp/eventalign.hpp:101:18: required from ‘std::string write_eventalign(Config&, ModelType&, std::string, bool, ProcessedRead, const std::string&, pybind11::array_t, bool, pybind11::array_t, pybind11::array_t, pybind11::array_t, pybind11::array_t) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string; typename ModelType::kmer_t = unsigned int]’ 2024-03-21T19:05:38,843 src/cpp/pybinder.cpp:31:10: required from ‘size_t pybind_model(pybind11::module_&, std::string) [with KmerType = unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:05:38,843 src/cpp/pybinder.cpp:67:22: required from here 2024-03-21T19:05:38,844 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-21T19:05:38,844 192 | struct PyArray { 2024-03-21T19:05:38,845 | ^~~~~~~ 2024-03-21T19:05:38,873 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]’: 2024-03-21T19:05:38,873 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]’ 2024-03-21T19:05:38,874 src/cpp/pybinder.cpp:67:22: required from here 2024-03-21T19:05:38,875 src/cpp/eventalign.hpp:76:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-21T19:05:38,876 76 | for (size_t j = samps.start+1; j < samps.end; j++) { 2024-03-21T19:05:38,876 | ~~^~~~~~~~~~~ 2024-03-21T19:05:45,684 src/cpp/dtw.hpp: In instantiation of ‘std::vector BandedDTW::get_flat_mat() const [with ModelType = PoreModel]’: 2024-03-21T19:05:45,685 src/cpp/dtw.hpp:734:9: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:05:45,686 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]’ 2024-03-21T19:05:45,686 src/cpp/pybinder.cpp:66:22: required from here 2024-03-21T19:05:45,687 src/cpp/dtw.hpp:644:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-21T19:05:45,687 644 | if (q0 >= qry_size()) { 2024-03-21T19:05:45,688 | ~~~^~~~~~~~~~~~~ 2024-03-21T19:05:45,689 src/cpp/dtw.hpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-21T19:05:45,689 651 | if (r1 > ref_size()) { 2024-03-21T19:05:45,690 | ~~~^~~~~~~~~~~~ 2024-03-21T19:05:46,197 src/cpp/dtw.hpp: In instantiation of ‘std::vector BandedDTW::get_flat_mat() const [with ModelType = PoreModel]’: 2024-03-21T19:05:46,197 src/cpp/dtw.hpp:734:9: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:05:46,198 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]’ 2024-03-21T19:05:46,199 src/cpp/pybinder.cpp:67:22: required from here 2024-03-21T19:05:46,199 src/cpp/dtw.hpp:644:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-21T19:05:46,200 644 | if (q0 >= qry_size()) { 2024-03-21T19:05:46,201 | ~~~^~~~~~~~~~~~~ 2024-03-21T19:05:46,201 src/cpp/dtw.hpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-21T19:05:46,202 651 | if (r1 > ref_size()) { 2024-03-21T19:05:46,203 | ~~~^~~~~~~~~~~~ 2024-03-21T19:05:57,063 In file included from src/cpp/seq.hpp:32, 2024-03-21T19:05:57,064 from src/cpp/pybinder.cpp:7: 2024-03-21T19:05:57,065 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]’: 2024-03-21T19:05:57,065 src/cpp/pore_model.hpp:496:32: required from ‘DestIter PoreModel::str_to_kmers(const std::string&, DestIter, bool, bool) const [with DestIter = short unsigned int*; KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:05:57,066 src/cpp/pore_model.hpp:480:21: required from ‘ValArray PoreModel::str_to_kmers(const std::string&, bool, bool) const [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:05:57,067 src/cpp/pore_model.hpp:672:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:05:57,068 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]’ 2024-03-21T19:05:57,068 src/cpp/pybinder.cpp:66:22: required from here 2024-03-21T19:05:57,069 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-21T19:05:57,069 507 | kmer = kmer_neighbor(kmer, BASE_BYTES[*iseq]); 2024-03-21T19:05:57,070 | ~~~~~~~~~~^ 2024-03-21T19:05:57,071 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]’: 2024-03-21T19:05:57,071 src/cpp/pore_model.hpp:498:32: required from ‘DestIter PoreModel::str_to_kmers(const std::string&, DestIter, bool, bool) const [with DestIter = short unsigned int*; KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:05:57,072 src/cpp/pore_model.hpp:480:21: required from ‘ValArray PoreModel::str_to_kmers(const std::string&, bool, bool) const [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:05:57,072 src/cpp/pore_model.hpp:672:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:05:57,073 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]’ 2024-03-21T19:05:57,074 src/cpp/pybinder.cpp:66:22: required from here 2024-03-21T19:05:57,074 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-21T19:05:59,712 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]’: 2024-03-21T19:05:59,713 src/cpp/pore_model.hpp:496:32: required from ‘DestIter PoreModel::str_to_kmers(const std::string&, DestIter, bool, bool) const [with DestIter = unsigned int*; KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:05:59,714 src/cpp/pore_model.hpp:480:21: required from ‘ValArray PoreModel::str_to_kmers(const std::string&, bool, bool) const [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:05:59,715 src/cpp/pore_model.hpp:672:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:05:59,715 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]’ 2024-03-21T19:05:59,716 src/cpp/pybinder.cpp:67:22: required from here 2024-03-21T19:05:59,717 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-21T19:05:59,718 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]’: 2024-03-21T19:05:59,718 src/cpp/pore_model.hpp:498:32: required from ‘DestIter PoreModel::str_to_kmers(const std::string&, DestIter, bool, bool) const [with DestIter = unsigned int*; KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:05:59,719 src/cpp/pore_model.hpp:480:21: required from ‘ValArray PoreModel::str_to_kmers(const std::string&, bool, bool) const [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:05:59,720 src/cpp/pore_model.hpp:672:15: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:05:59,721 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]’ 2024-03-21T19:05:59,721 src/cpp/pybinder.cpp:67:22: required from here 2024-03-21T19:05:59,722 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-21T19:06:06,929 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]’: 2024-03-21T19:06:06,929 src/cpp/pore_model.hpp:339:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = short unsigned int]’ 2024-03-21T19:06:06,930 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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]’ 2024-03-21T19:06:06,930 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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}]’ 2024-03-21T19:06:06,931 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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 = {}]’ 2024-03-21T19:06:06,932 src/cpp/pore_model.hpp:646:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:06:06,932 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]’ 2024-03-21T19:06:06,933 src/cpp/pybinder.cpp:66:22: required from here 2024-03-21T19:06:06,934 src/cpp/pore_model.hpp:354:14: warning: variable ‘get_kmer’ set but not used [-Wunused-but-set-variable] 2024-03-21T19:06:06,934 354 | auto get_kmer = [&](size_t i) {return i;}; 2024-03-21T19:06:06,935 | ^~~~~~~~ 2024-03-21T19:06:07,626 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::fill_mat() [with ModelType = PoreModel]’: 2024-03-21T19:06:07,627 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]’ 2024-03-21T19:06:07,628 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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]’ 2024-03-21T19:06:07,628 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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&}]’ 2024-03-21T19:06:07,629 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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 = {}]’ 2024-03-21T19:06:07,629 src/cpp/dtw.hpp:714:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:06:07,630 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]’ 2024-03-21T19:06:07,631 src/cpp/pybinder.cpp:66:22: required from here 2024-03-21T19:06:07,631 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] 2024-03-21T19:06:07,632 443 | if (q >= 0 && q < qry_size() && in_range(r, ref_vals_)) { 2024-03-21T19:06:07,633 | ~~^~~~~~~~~~~~ 2024-03-21T19:06:07,633 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::traceback() [with ModelType = PoreModel]’: 2024-03-21T19:06:07,634 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]’ 2024-03-21T19:06:07,635 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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]’ 2024-03-21T19:06:07,636 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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&}]’ 2024-03-21T19:06:07,636 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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 = {}]’ 2024-03-21T19:06:07,637 src/cpp/dtw.hpp:714:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:06:07,638 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]’ 2024-03-21T19:06:07,638 src/cpp/pybinder.cpp:66:22: required from here 2024-03-21T19:06:07,639 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] 2024-03-21T19:06:07,640 507 | path_.push_back({path_ll.qry-offs+event_start_, path_ll.ref+offs}); 2024-03-21T19:06:07,641 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2024-03-21T19:06:08,430 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]’: 2024-03-21T19:06:08,431 src/cpp/pore_model.hpp:339:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = unsigned int]’ 2024-03-21T19:06:08,432 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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]’ 2024-03-21T19:06:08,432 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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}]’ 2024-03-21T19:06:08,433 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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 = {}]’ 2024-03-21T19:06:08,434 src/cpp/pore_model.hpp:646:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:06:08,434 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]’ 2024-03-21T19:06:08,435 src/cpp/pybinder.cpp:67:22: required from here 2024-03-21T19:06:08,435 src/cpp/pore_model.hpp:354:14: warning: variable ‘get_kmer’ set but not used [-Wunused-but-set-variable] 2024-03-21T19:06:08,436 354 | auto get_kmer = [&](size_t i) {return i;}; 2024-03-21T19:06:08,437 | ^~~~~~~~ 2024-03-21T19:06:08,624 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::fill_mat() [with ModelType = PoreModel]’: 2024-03-21T19:06:08,625 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]’ 2024-03-21T19:06:08,626 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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]’ 2024-03-21T19:06:08,627 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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&}]’ 2024-03-21T19:06:08,627 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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 = {}]’ 2024-03-21T19:06:08,628 src/cpp/dtw.hpp:714:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:06:08,629 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]’ 2024-03-21T19:06:08,630 src/cpp/pybinder.cpp:67:22: required from here 2024-03-21T19:06:08,630 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] 2024-03-21T19:06:08,631 443 | if (q >= 0 && q < qry_size() && in_range(r, ref_vals_)) { 2024-03-21T19:06:08,631 | ~~^~~~~~~~~~~~ 2024-03-21T19:06:08,632 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::traceback() [with ModelType = PoreModel]’: 2024-03-21T19:06:08,633 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]’ 2024-03-21T19:06:08,633 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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]’ 2024-03-21T19:06:08,634 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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&}]’ 2024-03-21T19:06:08,635 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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 = {}]’ 2024-03-21T19:06:08,636 src/cpp/dtw.hpp:714:14: required from ‘static void BandedDTW::pybind_defs(pybind11::module_&, const std::string&) [with ModelType = PoreModel; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:06:08,636 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]’ 2024-03-21T19:06:08,637 src/cpp/pybinder.cpp:67:22: required from here 2024-03-21T19:06:08,638 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] 2024-03-21T19:06:08,638 507 | path_.push_back({path_ll.qry-offs+event_start_, path_ll.ref+offs}); 2024-03-21T19:06:08,639 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2024-03-21T19:06:09,757 src/cpp/util.hpp: In instantiation of ‘T ValArray::mean() const [with T = float]’: 2024-03-21T19:06:09,758 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]’ 2024-03-21T19:06:09,759 src/cpp/pore_model.hpp:339:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = short unsigned int]’ 2024-03-21T19:06:09,759 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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]’ 2024-03-21T19:06:09,760 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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}]’ 2024-03-21T19:06:09,760 /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/.eggs/pybind11-2.11.1-py3.11.egg/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 = {}]’ 2024-03-21T19:06:09,761 src/cpp/pore_model.hpp:646:14: required from ‘static void PoreModel::pybind(pybind11::module_&, const std::string&) [with KmerType = short unsigned int; std::string = std::__cxx11::basic_string]’ 2024-03-21T19:06:09,762 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]’ 2024-03-21T19:06:09,763 src/cpp/pybinder.cpp:66:22: required from here 2024-03-21T19:06:09,763 src/cpp/util.hpp:144:14: warning: unused variable ‘sum’ [-Wunused-variable] 2024-03-21T19:06:09,764 144 | auto sum = super::sum(); 2024-03-21T19:06:09,765 | ^~~ 2024-03-21T19:06:09,765 src/cpp/util.hpp:145:14: warning: unused variable ‘len’ [-Wunused-variable] 2024-03-21T19:06:09,766 145 | auto len = super::size(); 2024-03-21T19:06:09,767 | ^~~ 2024-03-21T19:06:56,985 virtual memory exhausted: Cannot allocate memory 2024-03-21T19:06:57,108 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2024-03-21T19:06:57,257 ERROR: python setup.py bdist_wheel exited with 1 2024-03-21T19:06:57,272 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2024-03-21T19:06:57,272 exec(compile('"'"''"'"''"'"' 2024-03-21T19:06:57,272 # This is -- a caller that pip uses to run setup.py 2024-03-21T19:06:57,272 # 2024-03-21T19:06:57,272 # - It imports setuptools before invoking setup.py, to enable projects that directly 2024-03-21T19:06:57,272 # import from `distutils.core` to work with newer packaging standards. 2024-03-21T19:06:57,272 # - It provides a clear error message when setuptools is not installed. 2024-03-21T19:06:57,272 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2024-03-21T19:06:57,272 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2024-03-21T19:06:57,272 # manifest_maker: standard file '"'"'-c'"'"' not found". 2024-03-21T19:06:57,272 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2024-03-21T19:06:57,272 import os, sys, tokenize 2024-03-21T19:06:57,272 2024-03-21T19:06:57,272 try: 2024-03-21T19:06:57,272 import setuptools 2024-03-21T19:06:57,272 except ImportError as error: 2024-03-21T19:06:57,272 print( 2024-03-21T19:06:57,272 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2024-03-21T19:06:57,272 "the build environment.", 2024-03-21T19:06:57,272 file=sys.stderr, 2024-03-21T19:06:57,272 ) 2024-03-21T19:06:57,272 sys.exit(1) 2024-03-21T19:06:57,272 2024-03-21T19:06:57,272 __file__ = %r 2024-03-21T19:06:57,272 sys.argv[0] = __file__ 2024-03-21T19:06:57,272 2024-03-21T19:06:57,272 if os.path.exists(__file__): 2024-03-21T19:06:57,272 filename = __file__ 2024-03-21T19:06:57,272 with tokenize.open(__file__) as f: 2024-03-21T19:06:57,272 setup_py_code = f.read() 2024-03-21T19:06:57,272 else: 2024-03-21T19:06:57,272 filename = "" 2024-03-21T19:06:57,272 setup_py_code = "from setuptools import setup; setup()" 2024-03-21T19:06:57,272 2024-03-21T19:06:57,272 exec(compile(setup_py_code, filename, "exec")) 2024-03-21T19:06:57,272 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-bsrbbm4h[/] 2024-03-21T19:06:57,273 [bold magenta]cwd[/]: /tmp/pip-wheel-mxbmlf6w/uncalled4_bc2d832398b04b7eac7661e6300a179b/ 2024-03-21T19:06:57,274 Building wheel for uncalled4 (setup.py): finished with status 'error' 2024-03-21T19:06:57,275 ERROR: Failed building wheel for uncalled4 2024-03-21T19:06:57,277 Running setup.py clean for uncalled4 2024-03-21T19:06:57,278 Running command python setup.py clean 2024-03-21T19:06:58,219 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-03-21T19:06:58,220 !! 2024-03-21T19:06:58,221 ******************************************************************************** 2024-03-21T19:06:58,222 Requirements should be satisfied by a PEP 517 installer. 2024-03-21T19:06:58,222 If you are using pip, you can try `pip install --use-pep517`. 2024-03-21T19:06:58,223 ******************************************************************************** 2024-03-21T19:06:58,224 !! 2024-03-21T19:06:58,224 dist.fetch_build_eggs(dist.setup_requires) 2024-03-21T19:06:58,444 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'build_backend' 2024-03-21T19:06:58,444 warnings.warn(msg) 2024-03-21T19:06:58,607 running clean 2024-03-21T19:06:58,659 removing 'build/temp.linux-armv7l-cpython-311' (and everything under it) 2024-03-21T19:06:58,672 removing 'build/lib.linux-armv7l-cpython-311' (and everything under it) 2024-03-21T19:06:58,704 'build/bdist.linux-armv7l' does not exist -- can't clean it 2024-03-21T19:06:58,705 'build/scripts-3.11' does not exist -- can't clean it 2024-03-21T19:06:58,705 removing 'build' 2024-03-21T19:06:58,816 Failed to build uncalled4 2024-03-21T19:06:58,817 ERROR: Failed to build one or more wheels 2024-03-21T19:06:58,818 Exception information: 2024-03-21T19:06:58,818 Traceback (most recent call last): 2024-03-21T19:06:58,818 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2024-03-21T19:06:58,818 status = run_func(*args) 2024-03-21T19:06:58,818 ^^^^^^^^^^^^^^^ 2024-03-21T19:06:58,818 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 245, in wrapper 2024-03-21T19:06:58,818 return func(self, options, args) 2024-03-21T19:06:58,818 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2024-03-21T19:06:58,818 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2024-03-21T19:06:58,818 raise CommandError("Failed to build one or more wheels") 2024-03-21T19:06:58,818 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2024-03-21T19:06:58,822 Removed build tracker: '/tmp/pip-build-tracker-7nbra8ty'