2024-03-05T16:11:24,579 Created temporary directory: /tmp/pip-build-tracker-tb3dmrz7 2024-03-05T16:11:24,581 Initialized build tracking at /tmp/pip-build-tracker-tb3dmrz7 2024-03-05T16:11:24,581 Created build tracker: /tmp/pip-build-tracker-tb3dmrz7 2024-03-05T16:11:24,581 Entered build tracker: /tmp/pip-build-tracker-tb3dmrz7 2024-03-05T16:11:24,583 Created temporary directory: /tmp/pip-wheel-l_tr5ji6 2024-03-05T16:11:24,586 Created temporary directory: /tmp/pip-ephem-wheel-cache-bbdmg9s9 2024-03-05T16:11:24,607 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-03-05T16:11:24,611 2 location(s) to search for versions of uncalled4: 2024-03-05T16:11:24,611 * https://pypi.org/simple/uncalled4/ 2024-03-05T16:11:24,611 * https://www.piwheels.org/simple/uncalled4/ 2024-03-05T16:11:24,612 Fetching project page and analyzing links: https://pypi.org/simple/uncalled4/ 2024-03-05T16:11:24,612 Getting page https://pypi.org/simple/uncalled4/ 2024-03-05T16:11:24,614 Found index url https://pypi.org/simple/ 2024-03-05T16:11:24,830 Fetched page https://pypi.org/simple/uncalled4/ as application/vnd.pypi.simple.v1+json 2024-03-05T16:11:24,831 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 2024-03-05T16:11:24,832 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 2024-03-05T16:11:24,833 Fetching project page and analyzing links: https://www.piwheels.org/simple/uncalled4/ 2024-03-05T16:11:24,834 Getting page https://www.piwheels.org/simple/uncalled4/ 2024-03-05T16:11:24,835 Found index url https://www.piwheels.org/simple/ 2024-03-05T16:11:25,623 Fetched page https://www.piwheels.org/simple/uncalled4/ as text/html 2024-03-05T16:11:25,625 Skipping link: not a file: https://www.piwheels.org/simple/uncalled4/ 2024-03-05T16:11:25,626 Skipping link: not a file: https://pypi.org/simple/uncalled4/ 2024-03-05T16:11:25,666 Given no hashes to check 1 links for project 'uncalled4': discarding no candidates 2024-03-05T16:11:25,704 Collecting uncalled4==4.0.0 2024-03-05T16:11:25,708 Created temporary directory: /tmp/pip-unpack-104mdf6s 2024-03-05T16:11:26,060 Downloading uncalled4-4.0.0.tar.gz (19.2 MB) 2024-03-05T16:11:35,320 Added uncalled4==4.0.0 from https://files.pythonhosted.org/packages/bc/fd/a714f3b65dee9941ca73910515fd77bda3b6813c5832df5d4392221ad64b/uncalled4-4.0.0.tar.gz to build tracker '/tmp/pip-build-tracker-tb3dmrz7' 2024-03-05T16:11:35,322 Running setup.py (path:/tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/setup.py) egg_info for package uncalled4 2024-03-05T16:11:35,323 Created temporary directory: /tmp/pip-pip-egg-info-lihkthz5 2024-03-05T16:11:35,324 Preparing metadata (setup.py): started 2024-03-05T16:11:35,325 Running command python setup.py egg_info 2024-03-05T16:11:36,213 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-03-05T16:11:36,214 !! 2024-03-05T16:11:36,215 ******************************************************************************** 2024-03-05T16:11:36,216 Requirements should be satisfied by a PEP 517 installer. 2024-03-05T16:11:36,216 If you are using pip, you can try `pip install --use-pep517`. 2024-03-05T16:11:36,217 ******************************************************************************** 2024-03-05T16:11:36,218 !! 2024-03-05T16:11:36,219 dist.fetch_build_eggs(dist.setup_requires) 2024-03-05T16:11:38,886 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'build_backend' 2024-03-05T16:11:38,887 warnings.warn(msg) 2024-03-05T16:11:38,971 running egg_info 2024-03-05T16:11:38,973 creating /tmp/pip-pip-egg-info-lihkthz5/uncalled4.egg-info 2024-03-05T16:11:38,998 writing /tmp/pip-pip-egg-info-lihkthz5/uncalled4.egg-info/PKG-INFO 2024-03-05T16:11:39,001 writing dependency_links to /tmp/pip-pip-egg-info-lihkthz5/uncalled4.egg-info/dependency_links.txt 2024-03-05T16:11:39,003 writing entry points to /tmp/pip-pip-egg-info-lihkthz5/uncalled4.egg-info/entry_points.txt 2024-03-05T16:11:39,004 writing requirements to /tmp/pip-pip-egg-info-lihkthz5/uncalled4.egg-info/requires.txt 2024-03-05T16:11:39,005 writing top-level names to /tmp/pip-pip-egg-info-lihkthz5/uncalled4.egg-info/top_level.txt 2024-03-05T16:11:39,007 writing manifest file '/tmp/pip-pip-egg-info-lihkthz5/uncalled4.egg-info/SOURCES.txt' 2024-03-05T16:11:39,124 reading manifest file '/tmp/pip-pip-egg-info-lihkthz5/uncalled4.egg-info/SOURCES.txt' 2024-03-05T16:11:39,126 reading manifest template 'MANIFEST.in' 2024-03-05T16:11:39,176 adding license file 'LICENSE' 2024-03-05T16:11:39,182 writing manifest file '/tmp/pip-pip-egg-info-lihkthz5/uncalled4.egg-info/SOURCES.txt' 2024-03-05T16:11:39,292 Preparing metadata (setup.py): finished with status 'done' 2024-03-05T16:11:39,296 Source in /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606 has version 4.0.0, which satisfies requirement uncalled4==4.0.0 from https://files.pythonhosted.org/packages/bc/fd/a714f3b65dee9941ca73910515fd77bda3b6813c5832df5d4392221ad64b/uncalled4-4.0.0.tar.gz 2024-03-05T16:11:39,297 Removed uncalled4==4.0.0 from https://files.pythonhosted.org/packages/bc/fd/a714f3b65dee9941ca73910515fd77bda3b6813c5832df5d4392221ad64b/uncalled4-4.0.0.tar.gz from build tracker '/tmp/pip-build-tracker-tb3dmrz7' 2024-03-05T16:11:39,303 Created temporary directory: /tmp/pip-unpack-pp2byhs3 2024-03-05T16:11:39,304 Created temporary directory: /tmp/pip-unpack-7q0cy9di 2024-03-05T16:11:39,317 Building wheels for collected packages: uncalled4 2024-03-05T16:11:39,321 Created temporary directory: /tmp/pip-wheel-crx227sw 2024-03-05T16:11:39,321 Building wheel for uncalled4 (setup.py): started 2024-03-05T16:11:39,323 Destination directory: /tmp/pip-wheel-crx227sw 2024-03-05T16:11:39,323 Running command python setup.py bdist_wheel 2024-03-05T16:11:40,157 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-03-05T16:11:40,158 !! 2024-03-05T16:11:40,159 ******************************************************************************** 2024-03-05T16:11:40,159 Requirements should be satisfied by a PEP 517 installer. 2024-03-05T16:11:40,160 If you are using pip, you can try `pip install --use-pep517`. 2024-03-05T16:11:40,161 ******************************************************************************** 2024-03-05T16:11:40,162 !! 2024-03-05T16:11:40,163 dist.fetch_build_eggs(dist.setup_requires) 2024-03-05T16:11:40,378 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'build_backend' 2024-03-05T16:11:40,379 warnings.warn(msg) 2024-03-05T16:11:40,527 running bdist_wheel 2024-03-05T16:11:40,630 running build 2024-03-05T16:11:40,631 running build_py 2024-03-05T16:11:40,659 creating build 2024-03-05T16:11:40,660 creating build/lib.linux-armv7l-cpython-311 2024-03-05T16:11:40,661 creating build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-05T16:11:40,662 copying src/uncalled4/__main__.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-05T16:11:40,665 copying src/uncalled4/signal_processor.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-05T16:11:40,667 copying src/uncalled4/config.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-05T16:11:40,669 copying src/uncalled4/argparse.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-05T16:11:40,671 copying src/uncalled4/tracks.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-05T16:11:40,674 copying src/uncalled4/align.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-05T16:11:40,676 copying src/uncalled4/ref_index.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-05T16:11:40,679 copying src/uncalled4/pore_model.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-05T16:11:40,681 copying src/uncalled4/train.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-05T16:11:40,683 copying src/uncalled4/read_index.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-05T16:11:40,686 copying src/uncalled4/moves.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-05T16:11:40,687 copying src/uncalled4/__init__.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-05T16:11:40,689 copying src/uncalled4/params.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-05T16:11:40,691 copying src/uncalled4/__about__.py -> build/lib.linux-armv7l-cpython-311/uncalled4 2024-03-05T16:11:40,693 creating build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-05T16:11:40,694 copying src/uncalled4/vis/trackplot.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-05T16:11:40,697 copying src/uncalled4/vis/sigplot.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-05T16:11:40,699 copying src/uncalled4/vis/refplot.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-05T16:11:40,701 copying src/uncalled4/vis/browser.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-05T16:11:40,703 copying src/uncalled4/vis/dotplot.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-05T16:11:40,706 copying src/uncalled4/vis/__init__.py -> build/lib.linux-armv7l-cpython-311/uncalled4/vis 2024-03-05T16:11:40,708 creating build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-05T16:11:40,709 copying src/uncalled4/io/model_trainer.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-05T16:11:40,712 copying src/uncalled4/io/eventalign.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-05T16:11:40,714 copying src/uncalled4/io/m6anet.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-05T16:11:40,716 copying src/uncalled4/io/bam.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-05T16:11:40,719 copying src/uncalled4/io/tsv.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-05T16:11:40,721 copying src/uncalled4/io/tombo.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-05T16:11:40,723 copying src/uncalled4/io/__init__.py -> build/lib.linux-armv7l-cpython-311/uncalled4/io 2024-03-05T16:11:40,726 creating build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-03-05T16:11:40,727 copying src/uncalled4/stats/layerstats.py -> build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-03-05T16:11:40,729 copying src/uncalled4/stats/readstats.py -> build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-03-05T16:11:40,731 copying src/uncalled4/stats/refstats.py -> build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-03-05T16:11:40,732 copying src/uncalled4/stats/__init__.py -> build/lib.linux-armv7l-cpython-311/uncalled4/stats 2024-03-05T16:11:40,734 running egg_info 2024-03-05T16:11:40,784 writing src/uncalled4.egg-info/PKG-INFO 2024-03-05T16:11:40,788 writing dependency_links to src/uncalled4.egg-info/dependency_links.txt 2024-03-05T16:11:40,789 writing entry points to src/uncalled4.egg-info/entry_points.txt 2024-03-05T16:11:40,791 writing requirements to src/uncalled4.egg-info/requires.txt 2024-03-05T16:11:40,792 writing top-level names to src/uncalled4.egg-info/top_level.txt 2024-03-05T16:11:40,825 reading manifest file 'src/uncalled4.egg-info/SOURCES.txt' 2024-03-05T16:11:40,829 reading manifest template 'MANIFEST.in' 2024-03-05T16:11:40,877 adding license file 'LICENSE' 2024-03-05T16:11:40,885 writing manifest file 'src/uncalled4.egg-info/SOURCES.txt' 2024-03-05T16:11:40,888 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.__pycache__' is absent from the `packages` configuration. 2024-03-05T16:11:40,889 !! 2024-03-05T16:11:40,890 ******************************************************************************** 2024-03-05T16:11:40,891 ############################ 2024-03-05T16:11:40,891 # Package would be ignored # 2024-03-05T16:11:40,892 ############################ 2024-03-05T16:11:40,892 Python recognizes 'uncalled4.__pycache__' as an importable package[^1], 2024-03-05T16:11:40,892 but it is absent from setuptools' `packages` configuration. 2024-03-05T16:11:40,893 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-05T16:11:40,894 package, please make sure that 'uncalled4.__pycache__' is explicitly added 2024-03-05T16:11:40,894 to the `packages` configuration field. 2024-03-05T16:11:40,895 Alternatively, you can also rely on setuptools' discovery methods 2024-03-05T16:11:40,895 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-05T16:11:40,896 instead of `find_packages(...)`/`find:`). 2024-03-05T16:11:40,897 You can read more about "package discovery" on setuptools documentation page: 2024-03-05T16:11:40,897 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-05T16:11:40,898 If you don't want 'uncalled4.__pycache__' to be distributed and are 2024-03-05T16:11:40,899 already explicitly excluding 'uncalled4.__pycache__' via 2024-03-05T16:11:40,899 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-05T16:11:40,900 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-05T16:11:40,900 combination with a more fine grained `package-data` configuration. 2024-03-05T16:11:40,901 You can read more about "package data files" on setuptools documentation page: 2024-03-05T16:11:40,902 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-05T16:11:40,904 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-05T16:11:40,905 even if it does not contain any `.py` files. 2024-03-05T16:11:40,905 On the other hand, currently there is no concept of package data 2024-03-05T16:11:40,906 directory, all directories are treated like packages. 2024-03-05T16:11:40,906 ******************************************************************************** 2024-03-05T16:11:40,907 !! 2024-03-05T16:11:40,908 check.warn(importable) 2024-03-05T16:11:40,908 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.io.__pycache__' is absent from the `packages` configuration. 2024-03-05T16:11:40,909 !! 2024-03-05T16:11:40,910 ******************************************************************************** 2024-03-05T16:11:40,911 ############################ 2024-03-05T16:11:40,911 # Package would be ignored # 2024-03-05T16:11:40,912 ############################ 2024-03-05T16:11:40,912 Python recognizes 'uncalled4.io.__pycache__' as an importable package[^1], 2024-03-05T16:11:40,913 but it is absent from setuptools' `packages` configuration. 2024-03-05T16:11:40,914 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-05T16:11:40,915 package, please make sure that 'uncalled4.io.__pycache__' is explicitly added 2024-03-05T16:11:40,915 to the `packages` configuration field. 2024-03-05T16:11:40,917 Alternatively, you can also rely on setuptools' discovery methods 2024-03-05T16:11:40,917 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-05T16:11:40,918 instead of `find_packages(...)`/`find:`). 2024-03-05T16:11:40,920 You can read more about "package discovery" on setuptools documentation page: 2024-03-05T16:11:40,921 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-05T16:11:40,923 If you don't want 'uncalled4.io.__pycache__' to be distributed and are 2024-03-05T16:11:40,925 already explicitly excluding 'uncalled4.io.__pycache__' via 2024-03-05T16:11:40,926 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-05T16:11:40,927 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-05T16:11:40,927 combination with a more fine grained `package-data` configuration. 2024-03-05T16:11:40,928 You can read more about "package data files" on setuptools documentation page: 2024-03-05T16:11:40,930 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-05T16:11:40,933 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-05T16:11:40,934 even if it does not contain any `.py` files. 2024-03-05T16:11:40,934 On the other hand, currently there is no concept of package data 2024-03-05T16:11:40,935 directory, all directories are treated like packages. 2024-03-05T16:11:40,936 ******************************************************************************** 2024-03-05T16:11:40,937 !! 2024-03-05T16:11:40,938 check.warn(importable) 2024-03-05T16:11:40,938 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.models' is absent from the `packages` configuration. 2024-03-05T16:11:40,939 !! 2024-03-05T16:11:40,940 ******************************************************************************** 2024-03-05T16:11:40,941 ############################ 2024-03-05T16:11:40,941 # Package would be ignored # 2024-03-05T16:11:40,942 ############################ 2024-03-05T16:11:40,943 Python recognizes 'uncalled4.models' as an importable package[^1], 2024-03-05T16:11:40,943 but it is absent from setuptools' `packages` configuration. 2024-03-05T16:11:40,946 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-05T16:11:40,948 package, please make sure that 'uncalled4.models' is explicitly added 2024-03-05T16:11:40,949 to the `packages` configuration field. 2024-03-05T16:11:40,950 Alternatively, you can also rely on setuptools' discovery methods 2024-03-05T16:11:40,951 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-05T16:11:40,951 instead of `find_packages(...)`/`find:`). 2024-03-05T16:11:40,952 You can read more about "package discovery" on setuptools documentation page: 2024-03-05T16:11:40,953 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-05T16:11:40,955 If you don't want 'uncalled4.models' to be distributed and are 2024-03-05T16:11:40,955 already explicitly excluding 'uncalled4.models' via 2024-03-05T16:11:40,955 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-05T16:11:40,956 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-05T16:11:40,957 combination with a more fine grained `package-data` configuration. 2024-03-05T16:11:40,958 You can read more about "package data files" on setuptools documentation page: 2024-03-05T16:11:40,959 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-05T16:11:40,960 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-05T16:11:40,961 even if it does not contain any `.py` files. 2024-03-05T16:11:40,962 On the other hand, currently there is no concept of package data 2024-03-05T16:11:40,962 directory, all directories are treated like packages. 2024-03-05T16:11:40,963 ******************************************************************************** 2024-03-05T16:11:40,964 !! 2024-03-05T16:11:40,965 check.warn(importable) 2024-03-05T16:11:40,965 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.models.tombo' is absent from the `packages` configuration. 2024-03-05T16:11:40,965 !! 2024-03-05T16:11:40,966 ******************************************************************************** 2024-03-05T16:11:40,967 ############################ 2024-03-05T16:11:40,968 # Package would be ignored # 2024-03-05T16:11:40,968 ############################ 2024-03-05T16:11:40,969 Python recognizes 'uncalled4.models.tombo' as an importable package[^1], 2024-03-05T16:11:40,969 but it is absent from setuptools' `packages` configuration. 2024-03-05T16:11:40,970 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-05T16:11:40,971 package, please make sure that 'uncalled4.models.tombo' is explicitly added 2024-03-05T16:11:40,971 to the `packages` configuration field. 2024-03-05T16:11:40,976 Alternatively, you can also rely on setuptools' discovery methods 2024-03-05T16:11:40,976 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-05T16:11:40,976 instead of `find_packages(...)`/`find:`). 2024-03-05T16:11:40,977 You can read more about "package discovery" on setuptools documentation page: 2024-03-05T16:11:40,978 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-05T16:11:40,979 If you don't want 'uncalled4.models.tombo' to be distributed and are 2024-03-05T16:11:40,980 already explicitly excluding 'uncalled4.models.tombo' via 2024-03-05T16:11:40,981 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-05T16:11:40,982 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-05T16:11:40,982 combination with a more fine grained `package-data` configuration. 2024-03-05T16:11:40,984 You can read more about "package data files" on setuptools documentation page: 2024-03-05T16:11:40,985 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-05T16:11:40,987 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-05T16:11:40,987 even if it does not contain any `.py` files. 2024-03-05T16:11:40,988 On the other hand, currently there is no concept of package data 2024-03-05T16:11:40,989 directory, all directories are treated like packages. 2024-03-05T16:11:40,990 ******************************************************************************** 2024-03-05T16:11:40,991 !! 2024-03-05T16:11:40,992 check.warn(importable) 2024-03-05T16:11:40,992 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.stats.__pycache__' is absent from the `packages` configuration. 2024-03-05T16:11:40,993 !! 2024-03-05T16:11:40,994 ******************************************************************************** 2024-03-05T16:11:40,994 ############################ 2024-03-05T16:11:40,995 # Package would be ignored # 2024-03-05T16:11:40,996 ############################ 2024-03-05T16:11:41,008 Python recognizes 'uncalled4.stats.__pycache__' as an importable package[^1], 2024-03-05T16:11:41,037 but it is absent from setuptools' `packages` configuration. 2024-03-05T16:11:41,051 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-05T16:11:41,051 package, please make sure that 'uncalled4.stats.__pycache__' is explicitly added 2024-03-05T16:11:41,052 to the `packages` configuration field. 2024-03-05T16:11:41,053 Alternatively, you can also rely on setuptools' discovery methods 2024-03-05T16:11:41,054 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-05T16:11:41,055 instead of `find_packages(...)`/`find:`). 2024-03-05T16:11:41,056 You can read more about "package discovery" on setuptools documentation page: 2024-03-05T16:11:41,058 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-05T16:11:41,059 If you don't want 'uncalled4.stats.__pycache__' to be distributed and are 2024-03-05T16:11:41,059 already explicitly excluding 'uncalled4.stats.__pycache__' via 2024-03-05T16:11:41,060 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-05T16:11:41,060 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-05T16:11:41,061 combination with a more fine grained `package-data` configuration. 2024-03-05T16:11:41,062 You can read more about "package data files" on setuptools documentation page: 2024-03-05T16:11:41,063 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-05T16:11:41,065 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-05T16:11:41,065 even if it does not contain any `.py` files. 2024-03-05T16:11:41,066 On the other hand, currently there is no concept of package data 2024-03-05T16:11:41,066 directory, all directories are treated like packages. 2024-03-05T16:11:41,067 ******************************************************************************** 2024-03-05T16:11:41,068 !! 2024-03-05T16:11:41,068 check.warn(importable) 2024-03-05T16:11:41,069 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.vis.__pycache__' is absent from the `packages` configuration. 2024-03-05T16:11:41,069 !! 2024-03-05T16:11:41,070 ******************************************************************************** 2024-03-05T16:11:41,071 ############################ 2024-03-05T16:11:41,071 # Package would be ignored # 2024-03-05T16:11:41,072 ############################ 2024-03-05T16:11:41,072 Python recognizes 'uncalled4.vis.__pycache__' as an importable package[^1], 2024-03-05T16:11:41,073 but it is absent from setuptools' `packages` configuration. 2024-03-05T16:11:41,074 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-05T16:11:41,075 package, please make sure that 'uncalled4.vis.__pycache__' is explicitly added 2024-03-05T16:11:41,075 to the `packages` configuration field. 2024-03-05T16:11:41,076 Alternatively, you can also rely on setuptools' discovery methods 2024-03-05T16:11:41,077 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-05T16:11:41,077 instead of `find_packages(...)`/`find:`). 2024-03-05T16:11:41,079 You can read more about "package discovery" on setuptools documentation page: 2024-03-05T16:11:41,080 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-05T16:11:41,081 If you don't want 'uncalled4.vis.__pycache__' to be distributed and are 2024-03-05T16:11:41,082 already explicitly excluding 'uncalled4.vis.__pycache__' via 2024-03-05T16:11:41,083 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-05T16:11:41,083 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-05T16:11:41,084 combination with a more fine grained `package-data` configuration. 2024-03-05T16:11:41,085 You can read more about "package data files" on setuptools documentation page: 2024-03-05T16:11:41,087 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-05T16:11:41,089 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-05T16:11:41,090 even if it does not contain any `.py` files. 2024-03-05T16:11:41,091 On the other hand, currently there is no concept of package data 2024-03-05T16:11:41,092 directory, all directories are treated like packages. 2024-03-05T16:11:41,092 ******************************************************************************** 2024-03-05T16:11:41,093 !! 2024-03-05T16:11:41,094 check.warn(importable) 2024-03-05T16:11:41,095 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'uncalled4.vis.assets' is absent from the `packages` configuration. 2024-03-05T16:11:41,095 !! 2024-03-05T16:11:41,097 ******************************************************************************** 2024-03-05T16:11:41,098 ############################ 2024-03-05T16:11:41,098 # Package would be ignored # 2024-03-05T16:11:41,099 ############################ 2024-03-05T16:11:41,100 Python recognizes 'uncalled4.vis.assets' as an importable package[^1], 2024-03-05T16:11:41,100 but it is absent from setuptools' `packages` configuration. 2024-03-05T16:11:41,102 This leads to an ambiguous overall configuration. If you want to distribute this 2024-03-05T16:11:41,103 package, please make sure that 'uncalled4.vis.assets' is explicitly added 2024-03-05T16:11:41,103 to the `packages` configuration field. 2024-03-05T16:11:41,105 Alternatively, you can also rely on setuptools' discovery methods 2024-03-05T16:11:41,105 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-03-05T16:11:41,106 instead of `find_packages(...)`/`find:`). 2024-03-05T16:11:41,107 You can read more about "package discovery" on setuptools documentation page: 2024-03-05T16:11:41,109 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-03-05T16:11:41,110 If you don't want 'uncalled4.vis.assets' to be distributed and are 2024-03-05T16:11:41,110 already explicitly excluding 'uncalled4.vis.assets' via 2024-03-05T16:11:41,111 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-03-05T16:11:41,112 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-03-05T16:11:41,113 combination with a more fine grained `package-data` configuration. 2024-03-05T16:11:41,114 You can read more about "package data files" on setuptools documentation page: 2024-03-05T16:11:41,115 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-03-05T16:11:41,118 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-03-05T16:11:41,118 even if it does not contain any `.py` files. 2024-03-05T16:11:41,119 On the other hand, currently there is no concept of package data 2024-03-05T16:11:41,120 directory, all directories are treated like packages. 2024-03-05T16:11:41,120 ******************************************************************************** 2024-03-05T16:11:41,122 !! 2024-03-05T16:11:41,123 check.warn(importable) 2024-03-05T16:11:41,123 creating build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,124 copying src/uncalled4/__pycache__/__about__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,125 copying src/uncalled4/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,126 copying src/uncalled4/__pycache__/__main__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,126 copying src/uncalled4/__pycache__/align.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,127 copying src/uncalled4/__pycache__/aln.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,127 copying src/uncalled4/__pycache__/aln_track.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,128 copying src/uncalled4/__pycache__/argparse.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,129 copying src/uncalled4/__pycache__/config.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,129 copying src/uncalled4/__pycache__/dtw.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,130 copying src/uncalled4/__pycache__/index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,131 copying src/uncalled4/__pycache__/layers.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,131 copying src/uncalled4/__pycache__/moves.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,131 copying src/uncalled4/__pycache__/params.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,132 copying src/uncalled4/__pycache__/pore_model.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,132 copying src/uncalled4/__pycache__/read_index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,133 copying src/uncalled4/__pycache__/ref_index.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,133 copying src/uncalled4/__pycache__/signal_processor.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,134 copying src/uncalled4/__pycache__/tracks.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,134 copying src/uncalled4/__pycache__/train.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/__pycache__ 2024-03-05T16:11:41,134 creating build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-03-05T16:11:41,135 copying src/uncalled4/models/README.txt -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-03-05T16:11:41,136 copying src/uncalled4/models/dna_r10.4.1_400bps_9mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-03-05T16:11:41,136 copying src/uncalled4/models/dna_r9.4.1_400bps_6mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-03-05T16:11:41,136 copying src/uncalled4/models/presets.tsv -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-03-05T16:11:41,137 copying src/uncalled4/models/rna_r9.4.1_70bps_5mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models 2024-03-05T16:11:41,137 creating build/lib.linux-armv7l-cpython-311/uncalled4/models/tombo 2024-03-05T16:11:41,138 copying src/uncalled4/models/tombo/dna_r9.4.1_400bps_6mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models/tombo 2024-03-05T16:11:41,138 copying src/uncalled4/models/tombo/rna_r9.4.1_70bps_5mer.npz -> build/lib.linux-armv7l-cpython-311/uncalled4/models/tombo 2024-03-05T16:11:41,139 creating build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-05T16:11:41,139 copying src/uncalled4/vis/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-05T16:11:41,140 copying src/uncalled4/vis/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-05T16:11:41,140 copying src/uncalled4/vis/__pycache__/__init__.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-05T16:11:41,141 copying src/uncalled4/vis/__pycache__/browser.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-05T16:11:41,142 copying src/uncalled4/vis/__pycache__/browser.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-05T16:11:41,142 copying src/uncalled4/vis/__pycache__/browser.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-05T16:11:41,143 copying src/uncalled4/vis/__pycache__/dotplot.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-05T16:11:41,143 copying src/uncalled4/vis/__pycache__/dotplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-05T16:11:41,144 copying src/uncalled4/vis/__pycache__/dotplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-05T16:11:41,144 copying src/uncalled4/vis/__pycache__/refplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-05T16:11:41,144 copying src/uncalled4/vis/__pycache__/sigplot.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-05T16:11:41,145 copying src/uncalled4/vis/__pycache__/sigplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-05T16:11:41,145 copying src/uncalled4/vis/__pycache__/sigplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-05T16:11:41,146 copying src/uncalled4/vis/__pycache__/trackplot.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-05T16:11:41,146 copying src/uncalled4/vis/__pycache__/trackplot.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/__pycache__ 2024-03-05T16:11:41,147 creating build/lib.linux-armv7l-cpython-311/uncalled4/vis/assets 2024-03-05T16:11:41,147 copying src/uncalled4/vis/assets/.browser.js.swp -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/assets 2024-03-05T16:11:41,147 copying src/uncalled4/vis/assets/browser.css -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/assets 2024-03-05T16:11:41,148 copying src/uncalled4/vis/assets/browser.js -> build/lib.linux-armv7l-cpython-311/uncalled4/vis/assets 2024-03-05T16:11:41,148 creating build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-05T16:11:41,149 copying src/uncalled4/io/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-05T16:11:41,149 copying src/uncalled4/io/__pycache__/bam.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-05T16:11:41,150 copying src/uncalled4/io/__pycache__/eventalign.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-05T16:11:41,150 copying src/uncalled4/io/__pycache__/guppy.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-05T16:11:41,151 copying src/uncalled4/io/__pycache__/m6anet.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-05T16:11:41,151 copying src/uncalled4/io/__pycache__/model.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-05T16:11:41,152 copying src/uncalled4/io/__pycache__/model_trainer.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-05T16:11:41,152 copying src/uncalled4/io/__pycache__/sqlite.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-05T16:11:41,153 copying src/uncalled4/io/__pycache__/tombo.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-05T16:11:41,155 copying src/uncalled4/io/__pycache__/tsv.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/io/__pycache__ 2024-03-05T16:11:41,157 creating build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-05T16:11:41,157 copying src/uncalled4/stats/__pycache__/__init__.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-05T16:11:41,160 copying src/uncalled4/stats/__pycache__/__init__.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-05T16:11:41,161 copying src/uncalled4/stats/__pycache__/__init__.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-05T16:11:41,163 copying src/uncalled4/stats/__pycache__/_dtwstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-05T16:11:41,166 copying src/uncalled4/stats/__pycache__/_dtwstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-05T16:11:41,168 copying src/uncalled4/stats/__pycache__/_readstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-05T16:11:41,170 copying src/uncalled4/stats/__pycache__/_readstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-05T16:11:41,172 copying src/uncalled4/stats/__pycache__/_refstats.cpython-37.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-05T16:11:41,174 copying src/uncalled4/stats/__pycache__/_refstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-05T16:11:41,176 copying src/uncalled4/stats/__pycache__/dtwstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-05T16:11:41,178 copying src/uncalled4/stats/__pycache__/layerstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-05T16:11:41,180 copying src/uncalled4/stats/__pycache__/layerstats.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-05T16:11:41,182 copying src/uncalled4/stats/__pycache__/refstats.cpython-38.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-05T16:11:41,184 copying src/uncalled4/stats/__pycache__/refstats.cpython-39.pyc -> build/lib.linux-armv7l-cpython-311/uncalled4/stats/__pycache__ 2024-03-05T16:11:41,189 running build_ext 2024-03-05T16:11:41,765 building '_uncalled4' extension 2024-03-05T16:11:41,787 creating build/temp.linux-armv7l-cpython-311 2024-03-05T16:11:41,787 creating build/temp.linux-armv7l-cpython-311/src 2024-03-05T16:11:41,788 creating build/temp.linux-armv7l-cpython-311/src/cpp 2024-03-05T16:11:41,789 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-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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 2024-03-05T16:11:47,827 In file included from src/cpp/dtw.hpp:7, 2024-03-05T16:11:47,828 from src/cpp/config.hpp:30, 2024-03-05T16:11:47,829 from src/cpp/config.cpp:1: 2024-03-05T16:11:47,830 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:11:47,830 src/cpp/intervals.hpp:110:20: required from here 2024-03-05T16:11:47,831 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:11:47,832 192 | struct PyArray { 2024-03-05T16:11:47,832 | ^~~~~~~ 2024-03-05T16:11:48,063 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:11:48,064 src/cpp/read_buffer.hpp:99:38: required from here 2024-03-05T16:11:48,065 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:11:48,155 In file included from src/cpp/aln.hpp:11, 2024-03-05T16:11:48,156 from src/cpp/dtw.hpp:9: 2024-03-05T16:11:48,157 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-05T16:11:48,158 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T16:11:48,158 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-05T16:11:48,159 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-05T16:11:48,160 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T16:11:48,161 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-05T16:11:48,187 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-05T16:11:48,187 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] 2024-03-05T16:11:48,188 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-05T16:11:48,188 | ~~^~~~~~~~~~ 2024-03-05T16:11:48,189 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-05T16:11:48,190 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] 2024-03-05T16:11:48,190 158 | normalize({0, events.size(), scale, shift}); 2024-03-05T16:11:48,191 | ~~~~~~~~~~~^~ 2024-03-05T16:11:48,261 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:11:48,262 src/cpp/event_detector.hpp:211:39: required from here 2024-03-05T16:11:48,263 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:11:48,263 192 | struct PyArray { 2024-03-05T16:11:48,264 | ^~~~~~~ 2024-03-05T16:11:48,385 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-03-05T16:11:48,386 src/cpp/aln.hpp:187:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-03-05T16:11:48,387 187 | i64 ref; 2024-03-05T16:11:48,388 | ^~~ 2024-03-05T16:11:48,391 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-03-05T16:11:48,392 src/cpp/aln.hpp:279:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-03-05T16:11:48,393 279 | int len,dist; 2024-03-05T16:11:48,393 | ^~~~ 2024-03-05T16:11:48,404 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:11:48,405 src/cpp/aln.hpp:383:23: required from here 2024-03-05T16:11:48,405 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:11:48,406 192 | struct PyArray { 2024-03-05T16:11:48,407 | ^~~~~~~ 2024-03-05T16:11:48,484 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:11:48,484 src/cpp/dtw.hpp:395:26: required from here 2024-03-05T16:11:48,485 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:12:05,829 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-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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 2024-03-05T16:12:11,577 In file included from src/cpp/dtw.hpp:7, 2024-03-05T16:12:11,577 from src/cpp/dtw.cpp:1: 2024-03-05T16:12:11,578 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:12:11,579 src/cpp/intervals.hpp:110:20: required from here 2024-03-05T16:12:11,580 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:12:11,581 192 | struct PyArray { 2024-03-05T16:12:11,581 | ^~~~~~~ 2024-03-05T16:12:11,814 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:12:11,814 src/cpp/read_buffer.hpp:99:38: required from here 2024-03-05T16:12:11,815 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:12:11,906 In file included from src/cpp/aln.hpp:11, 2024-03-05T16:12:11,907 from src/cpp/dtw.hpp:9: 2024-03-05T16:12:11,907 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-05T16:12:11,908 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T16:12:11,908 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-05T16:12:11,909 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-05T16:12:11,909 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T16:12:11,910 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-05T16:12:11,938 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-05T16:12:11,939 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] 2024-03-05T16:12:11,939 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-05T16:12:11,940 | ~~^~~~~~~~~~ 2024-03-05T16:12:11,941 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-05T16:12:11,942 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] 2024-03-05T16:12:11,942 158 | normalize({0, events.size(), scale, shift}); 2024-03-05T16:12:11,943 | ~~~~~~~~~~~^~ 2024-03-05T16:12:12,017 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:12:12,017 src/cpp/event_detector.hpp:211:39: required from here 2024-03-05T16:12:12,018 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:12:12,019 192 | struct PyArray { 2024-03-05T16:12:12,019 | ^~~~~~~ 2024-03-05T16:12:12,143 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-03-05T16:12:12,144 src/cpp/aln.hpp:187:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-03-05T16:12:12,144 187 | i64 ref; 2024-03-05T16:12:12,145 | ^~~ 2024-03-05T16:12:12,150 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-03-05T16:12:12,151 src/cpp/aln.hpp:279:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-03-05T16:12:12,151 279 | int len,dist; 2024-03-05T16:12:12,152 | ^~~~ 2024-03-05T16:12:12,164 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:12:12,165 src/cpp/aln.hpp:383:23: required from here 2024-03-05T16:12:12,166 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:12:12,167 192 | struct PyArray { 2024-03-05T16:12:12,168 | ^~~~~~~ 2024-03-05T16:12:12,249 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:12:12,249 src/cpp/dtw.hpp:395:26: required from here 2024-03-05T16:12:12,250 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:12:12,272 src/cpp/dtw.cpp: In function ‘pybind11::array_t get_guided_bands(pybind11::array_t&, pybind11::array_t&, pybind11::array_t&, size_t, i32)’: 2024-03-05T16:12:12,273 src/cpp/dtw.cpp:21:26: warning: unused variable ‘b’ [-Wunused-variable] 2024-03-05T16:12:12,273 21 | size_t i = 0, j = 0, b = 0; 2024-03-05T16:12:12,274 | ^ 2024-03-05T16:12:12,279 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:12:12,280 src/cpp/dtw.cpp:64:30: required from here 2024-03-05T16:12:12,280 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:12:12,281 192 | struct PyArray { 2024-03-05T16:12:12,281 | ^~~~~~~ 2024-03-05T16:12:12,289 src/cpp/dtw.cpp: In function ‘AlnDF read_to_ref_moves(const AlnDF&, pybind11::array_t, pybind11::array_t, i32, i32, bool)’: 2024-03-05T16:12:12,290 src/cpp/dtw.cpp:98:18: warning: variable ‘fill’ set but not used [-Wunused-but-set-variable] 2024-03-05T16:12:12,290 98 | auto fill = backfill_na ? samps : Interval(); 2024-03-05T16:12:12,291 | ^~~~ 2024-03-05T16:13:10,082 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-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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 2024-03-05T16:13:15,814 In file included from src/cpp/intervals.hpp:11, 2024-03-05T16:13:15,815 from src/cpp/event_detector.hpp:13, 2024-03-05T16:13:15,816 from src/cpp/event_detector.cpp:15: 2024-03-05T16:13:15,816 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:13:15,817 src/cpp/intervals.hpp:110:20: required from here 2024-03-05T16:13:15,818 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:13:15,819 192 | struct PyArray { 2024-03-05T16:13:15,819 | ^~~~~~~ 2024-03-05T16:13:15,840 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:13:15,841 src/cpp/read_buffer.hpp:99:38: required from here 2024-03-05T16:13:15,841 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:13:15,939 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-05T16:13:15,940 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T16:13:15,941 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-05T16:13:15,942 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-05T16:13:15,942 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T16:13:15,943 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-05T16:13:15,973 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-05T16:13:15,974 src/cpp/event_detector.hpp:147:39: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘i32’ {aka ‘int’} [-Wsign-compare] 2024-03-05T16:13:15,975 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-05T16:13:15,975 | ~~^~~~~~~~~~ 2024-03-05T16:13:15,976 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-05T16:13:15,977 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] 2024-03-05T16:13:15,977 158 | normalize({0, events.size(), scale, shift}); 2024-03-05T16:13:15,978 | ~~~~~~~~~~~^~ 2024-03-05T16:13:16,063 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:13:16,064 src/cpp/event_detector.hpp:211:39: required from here 2024-03-05T16:13:16,065 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:13:16,065 192 | struct PyArray { 2024-03-05T16:13:16,066 | ^~~~~~~ 2024-03-05T16:13:16,141 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:13:16,142 src/cpp/event_detector.cpp:242:30: required from here 2024-03-05T16:13:16,143 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:13:42,893 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-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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 2024-03-05T16:13:48,609 In file included from src/cpp/intervals.hpp:11, 2024-03-05T16:13:48,610 from src/cpp/intervals.cpp:2: 2024-03-05T16:13:48,610 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:13:48,611 src/cpp/intervals.hpp:110:20: required from here 2024-03-05T16:13:48,611 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:13:48,612 192 | struct PyArray { 2024-03-05T16:13:48,613 | ^~~~~~~ 2024-03-05T16:13:50,826 src/cpp/intervals.hpp: In instantiation of ‘ValArray IntervalIndex::to_runlen() const [with T = int]’: 2024-03-05T16:13:50,827 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]’ 2024-03-05T16:13:50,827 src/cpp/intervals.cpp:7:31: required from here 2024-03-05T16:13:50,828 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] 2024-03-05T16:13:50,829 348 | while (gap >= MAX_LEN_I16) { 2024-03-05T16:13:50,829 | ~~~~^~~~~~~~~~~~~~ 2024-03-05T16:14:22,914 In file included from /usr/include/c++/12/vector:70, 2024-03-05T16:14:22,914 from src/cpp/intervals.hpp:6: 2024-03-05T16:14:22,915 /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 >]’: 2024-03-05T16:14:22,915 /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 2024-03-05T16:14:22,916 439 | vector<_Tp, _Alloc>:: 2024-03-05T16:14:22,917 | ^~~~~~~~~~~~~~~~~~~ 2024-03-05T16:14:23,010 In file included from /usr/include/c++/12/vector:64: 2024-03-05T16:14:23,011 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-05T16:14:23,011 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-05T16:14:23,012 inlined from ‘void IntervalIndex::append(T, T) [with T = long long int]’ at src/cpp/intervals.hpp:261:15, 2024-03-05T16:14:23,012 inlined from ‘IntervalIndex IntervalIndex::mirror() const [with T = long long int]’ at src/cpp/intervals.hpp:160:23: 2024-03-05T16:14:23,013 /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 2024-03-05T16:14:23,013 1287 | _M_realloc_insert(end(), __x); 2024-03-05T16:14:23,014 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-05T16:14:23,110 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-05T16:14:23,111 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-05T16:14:23,112 inlined from ‘IntervalIndex IntervalIndex::islice(size_t, size_t) const [with T = long long int]’ at src/cpp/intervals.hpp:235:23: 2024-03-05T16:14:23,112 /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 2024-03-05T16:14:23,113 1287 | _M_realloc_insert(end(), __x); 2024-03-05T16:14:23,114 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-05T16:14:23,115 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-05T16:14:23,115 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-05T16:14:23,116 inlined from ‘IntervalIndex IntervalIndex::islice(size_t, size_t) const [with T = long long int]’ at src/cpp/intervals.hpp:237:27: 2024-03-05T16:14:23,117 /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 2024-03-05T16:14:23,118 1287 | _M_realloc_insert(end(), __x); 2024-03-05T16:14:23,118 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-05T16:14:23,119 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-05T16:14:23,119 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-05T16:14:23,120 inlined from ‘IntervalIndex IntervalIndex::islice(size_t, size_t) const [with T = long long int]’ at src/cpp/intervals.hpp:242:19: 2024-03-05T16:14:23,121 /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 2024-03-05T16:14:23,122 1287 | _M_realloc_insert(end(), __x); 2024-03-05T16:14:23,122 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-05T16:14:23,353 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-05T16:14:23,354 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-05T16:14:23,355 inlined from ‘IntervalIndex IntervalIndex::get_union(IntervalIndex) const [with T = long long int]’ at src/cpp/intervals.hpp:202:27: 2024-03-05T16:14:23,355 /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 2024-03-05T16:14:23,356 1287 | _M_realloc_insert(end(), __x); 2024-03-05T16:14:23,356 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-05T16:14:23,357 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-05T16:14:23,357 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-05T16:14:23,358 inlined from ‘IntervalIndex IntervalIndex::get_union(IntervalIndex) const [with T = long long int]’ at src/cpp/intervals.hpp:212:19: 2024-03-05T16:14:23,359 /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 2024-03-05T16:14:23,359 1287 | _M_realloc_insert(end(), __x); 2024-03-05T16:14:23,360 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-05T16:14:23,465 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-05T16:14:23,465 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-05T16:14:23,466 inlined from ‘IntervalIndex IntervalIndex::intersect(IntervalIndex) const [with T = long long int]’ at src/cpp/intervals.hpp:176:31: 2024-03-05T16:14:23,467 /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 2024-03-05T16:14:23,467 1287 | _M_realloc_insert(end(), __x); 2024-03-05T16:14:23,468 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-05T16:14:37,235 /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 >]’: 2024-03-05T16:14:37,236 /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 2024-03-05T16:14:37,236 439 | vector<_Tp, _Alloc>:: 2024-03-05T16:14:37,237 | ^~~~~~~~~~~~~~~~~~~ 2024-03-05T16:14:37,316 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’, 2024-03-05T16:14:37,316 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, 2024-03-05T16:14:37,317 inlined from ‘bool pybind11::detail::list_caster::load(pybind11::handle, bool) [with Type = std::vector, std::allocator > >; Value = std::pair]’ at /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/stl.h:180:28: 2024-03-05T16:14:37,318 /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 2024-03-05T16:14:37,318 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2024-03-05T16:14:37,319 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-05T16:14:37,544 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-05T16:14:37,544 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-05T16:14:37,545 inlined from ‘void IntervalIndex::append(T, T) [with T = long long int]’ at src/cpp/intervals.hpp:261:15, 2024-03-05T16:14:37,546 inlined from ‘void IntervalIndex::init_coords(std::vector >) [with T = long long int]’ at src/cpp/intervals.hpp:134:19, 2024-03-05T16:14:37,546 inlined from ‘IntervalIndex::IntervalIndex(std::vector >) [with T = long long int]’ at src/cpp/intervals.hpp:101:20, 2024-03-05T16:14:37,547 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-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:76:12, 2024-03-05T16:14:37,548 inlined from ‘pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>’ at /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:206:70, 2024-03-05T16:14:37,549 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-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/../cast.h:1480:37, 2024-03-05T16:14:37,549 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-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/../cast.h:1454:65, 2024-03-05T16:14:37,550 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-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:250:78, 2024-03-05T16:14:37,551 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-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:224:21: 2024-03-05T16:14:37,551 /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 2024-03-05T16:14:37,552 1287 | _M_realloc_insert(end(), __x); 2024-03-05T16:14:37,553 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-05T16:14:37,553 In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interval; _Alloc = std::allocator >]’, 2024-03-05T16:14:37,554 inlined from ‘void IntervalIndex::append(Interval) [with T = long long int]’ at src/cpp/intervals.hpp:253:25, 2024-03-05T16:14:37,555 inlined from ‘void IntervalIndex::append(T, T) [with T = long long int]’ at src/cpp/intervals.hpp:261:15, 2024-03-05T16:14:37,555 inlined from ‘void IntervalIndex::init_coords(std::vector >) [with T = long long int]’ at src/cpp/intervals.hpp:134:19, 2024-03-05T16:14:37,556 inlined from ‘IntervalIndex::IntervalIndex(std::vector >) [with T = long long int]’ at src/cpp/intervals.hpp:101:20, 2024-03-05T16:14:37,556 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-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:76:12, 2024-03-05T16:14:37,557 inlined from ‘pybind11::detail::initimpl::constructor, std::allocator > > >::execute > >(pybind11::class_ >&)::, std::allocator > >)>’ at /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/init.h:206:70, 2024-03-05T16:14:37,558 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-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/../cast.h:1480:37, 2024-03-05T16:14:37,559 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-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/detail/../cast.h:1454:65, 2024-03-05T16:14:37,560 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-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:254:75, 2024-03-05T16:14:37,560 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-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include/pybind11/pybind11.h:224:21: 2024-03-05T16:14:37,561 /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 2024-03-05T16:14:37,562 1287 | _M_realloc_insert(end(), __x); 2024-03-05T16:14:37,562 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2024-03-05T16:14:45,988 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-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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 2024-03-05T16:14:57,702 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-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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 2024-03-05T16:15:03,391 In file included from src/cpp/pore_model.hpp:36, 2024-03-05T16:15:03,391 from src/cpp/pore_model.cpp:1: 2024-03-05T16:15:03,392 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:15:03,393 src/cpp/intervals.hpp:110:20: required from here 2024-03-05T16:15:03,393 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:15:03,394 192 | struct PyArray { 2024-03-05T16:15:03,395 | ^~~~~~~ 2024-03-05T16:15:39,468 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-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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 2024-03-05T16:15:45,186 In file included from src/cpp/read_buffer.hpp:30, 2024-03-05T16:15:45,187 from src/cpp/pybinder.cpp:5: 2024-03-05T16:15:45,187 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:15:45,188 src/cpp/read_buffer.hpp:99:38: required from here 2024-03-05T16:15:45,189 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:15:45,189 192 | struct PyArray { 2024-03-05T16:15:45,190 | ^~~~~~~ 2024-03-05T16:15:45,221 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:15:45,221 src/cpp/intervals.hpp:110:20: required from here 2024-03-05T16:15:45,222 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:15:45,322 In file included from src/cpp/signal_processor.hpp:7, 2024-03-05T16:15:45,322 from src/cpp/pybinder.cpp:6: 2024-03-05T16:15:45,323 src/cpp/event_detector.hpp: In member function ‘size_t ProcessedRead::hard_mask(IntervalIndex)’: 2024-03-05T16:15:45,324 src/cpp/event_detector.hpp:64:78: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T16:15:45,325 64 | while (i < events.size() && (events[i].start + events[i].length) < c.start) i++; 2024-03-05T16:15:45,325 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2024-03-05T16:15:45,326 src/cpp/event_detector.hpp:65:57: warning: comparison of integer expressions of different signedness: ‘u32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T16:15:45,327 65 | while (i < events.size() && events[i].start < c.end) { 2024-03-05T16:15:45,372 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(NormVals)’: 2024-03-05T16:15:45,373 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] 2024-03-05T16:15:45,373 147 | for (size_t i = prms.start; i < prms.end; i++) { 2024-03-05T16:15:45,374 | ~~^~~~~~~~~~ 2024-03-05T16:15:45,374 src/cpp/event_detector.hpp: In member function ‘void ProcessedRead::normalize(float, float)’: 2024-03-05T16:15:45,375 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] 2024-03-05T16:15:45,376 158 | normalize({0, events.size(), scale, shift}); 2024-03-05T16:15:45,376 | ~~~~~~~~~~~^~ 2024-03-05T16:15:45,447 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:15:45,448 src/cpp/event_detector.hpp:211:39: required from here 2024-03-05T16:15:45,449 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:15:45,450 192 | struct PyArray { 2024-03-05T16:15:45,450 | ^~~~~~~ 2024-03-05T16:15:45,752 In file included from src/cpp/dtw.hpp:9, 2024-03-05T16:15:45,753 from src/cpp/pybinder.cpp:8: 2024-03-05T16:15:45,753 src/cpp/aln.hpp: In constructor ‘CmpDF::CmpDF(AlnDF&, AlnDF&, bool)’: 2024-03-05T16:15:45,754 src/cpp/aln.hpp:187:13: warning: unused variable ‘ref’ [-Wunused-variable] 2024-03-05T16:15:45,755 187 | i64 ref; 2024-03-05T16:15:45,755 | ^~~ 2024-03-05T16:15:45,759 src/cpp/aln.hpp: In member function ‘CmpDF::DistIter::Coefs CmpDF::DistIter::next_dist(int)’: 2024-03-05T16:15:45,759 src/cpp/aln.hpp:279:21: warning: unused variable ‘dist’ [-Wunused-variable] 2024-03-05T16:15:45,760 279 | int len,dist; 2024-03-05T16:15:45,760 | ^~~~ 2024-03-05T16:15:45,772 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:15:45,773 src/cpp/aln.hpp:383:23: required from here 2024-03-05T16:15:45,773 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:15:45,774 192 | struct PyArray { 2024-03-05T16:15:45,775 | ^~~~~~~ 2024-03-05T16:15:45,853 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:15:45,854 src/cpp/dtw.hpp:395:26: required from here 2024-03-05T16:15:45,854 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:15:45,897 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:15:45,898 src/cpp/eventalign.hpp:110:31: required from here 2024-03-05T16:15:45,899 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:15:49,616 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:15:49,616 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]’ 2024-03-05T16:15:49,617 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]’ 2024-03-05T16:15:49,618 src/cpp/pybinder.cpp:66:22: required from here 2024-03-05T16:15:49,619 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:15:49,647 In file included from src/cpp/pybinder.cpp:10: 2024-03-05T16:15:49,648 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]’: 2024-03-05T16:15:49,648 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]’ 2024-03-05T16:15:49,649 src/cpp/pybinder.cpp:66:22: required from here 2024-03-05T16:15:49,650 src/cpp/eventalign.hpp:76:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T16:15:49,650 76 | for (size_t j = samps.start+1; j < samps.end; j++) { 2024-03-05T16:15:49,651 | ~~^~~~~~~~~~~ 2024-03-05T16:15:49,821 src/cpp/util.hpp: In instantiation of ‘struct PyArray’: 2024-03-05T16:15:49,822 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]’ 2024-03-05T16:15:49,823 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]’ 2024-03-05T16:15:49,823 src/cpp/pybinder.cpp:67:22: required from here 2024-03-05T16:15:49,824 src/cpp/util.hpp:192:8: warning: ‘PyArray’ declared with greater visibility than the type of its field ‘PyArray::info’ [-Wattributes] 2024-03-05T16:15:49,825 192 | struct PyArray { 2024-03-05T16:15:49,825 | ^~~~~~~ 2024-03-05T16:15:49,850 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]’: 2024-03-05T16:15:49,851 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]’ 2024-03-05T16:15:49,852 src/cpp/pybinder.cpp:67:22: required from here 2024-03-05T16:15:49,852 src/cpp/eventalign.hpp:76:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-05T16:15:49,853 76 | for (size_t j = samps.start+1; j < samps.end; j++) { 2024-03-05T16:15:49,854 | ~~^~~~~~~~~~~ 2024-03-05T16:15:56,597 src/cpp/dtw.hpp: In instantiation of ‘std::vector BandedDTW::get_flat_mat() const [with ModelType = PoreModel]’: 2024-03-05T16:15:56,598 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]’ 2024-03-05T16:15:56,599 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]’ 2024-03-05T16:15:56,599 src/cpp/pybinder.cpp:66:22: required from here 2024-03-05T16:15:56,600 src/cpp/dtw.hpp:644:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-05T16:15:56,600 644 | if (q0 >= qry_size()) { 2024-03-05T16:15:56,601 | ~~~^~~~~~~~~~~~~ 2024-03-05T16:15:56,601 src/cpp/dtw.hpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-05T16:15:56,602 651 | if (r1 > ref_size()) { 2024-03-05T16:15:56,602 | ~~~^~~~~~~~~~~~ 2024-03-05T16:15:57,106 src/cpp/dtw.hpp: In instantiation of ‘std::vector BandedDTW::get_flat_mat() const [with ModelType = PoreModel]’: 2024-03-05T16:15:57,106 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]’ 2024-03-05T16:15:57,107 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]’ 2024-03-05T16:15:57,108 src/cpp/pybinder.cpp:67:22: required from here 2024-03-05T16:15:57,108 src/cpp/dtw.hpp:644:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-05T16:15:57,109 644 | if (q0 >= qry_size()) { 2024-03-05T16:15:57,110 | ~~~^~~~~~~~~~~~~ 2024-03-05T16:15:57,111 src/cpp/dtw.hpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-05T16:15:57,112 651 | if (r1 > ref_size()) { 2024-03-05T16:15:57,112 | ~~~^~~~~~~~~~~~ 2024-03-05T16:16:07,917 In file included from src/cpp/seq.hpp:32, 2024-03-05T16:16:07,918 from src/cpp/pybinder.cpp:7: 2024-03-05T16:16:07,918 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]’: 2024-03-05T16:16:07,919 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]’ 2024-03-05T16:16:07,920 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]’ 2024-03-05T16:16:07,921 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]’ 2024-03-05T16:16:07,921 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]’ 2024-03-05T16:16:07,923 src/cpp/pybinder.cpp:66:22: required from here 2024-03-05T16:16:07,923 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-05T16:16:07,924 507 | kmer = kmer_neighbor(kmer, BASE_BYTES[*iseq]); 2024-03-05T16:16:07,924 | ~~~~~~~~~~^ 2024-03-05T16:16:07,925 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]’: 2024-03-05T16:16:07,926 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]’ 2024-03-05T16:16:07,926 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]’ 2024-03-05T16:16:07,927 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]’ 2024-03-05T16:16:07,927 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]’ 2024-03-05T16:16:07,928 src/cpp/pybinder.cpp:66:22: required from here 2024-03-05T16:16:07,929 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-05T16:16:10,553 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]’: 2024-03-05T16:16:10,553 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]’ 2024-03-05T16:16:10,554 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]’ 2024-03-05T16:16:10,554 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]’ 2024-03-05T16:16:10,555 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]’ 2024-03-05T16:16:10,556 src/cpp/pybinder.cpp:67:22: required from here 2024-03-05T16:16:10,556 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-05T16:16:10,557 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]’: 2024-03-05T16:16:10,558 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]’ 2024-03-05T16:16:10,559 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]’ 2024-03-05T16:16:10,559 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]’ 2024-03-05T16:16:10,560 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]’ 2024-03-05T16:16:10,560 src/cpp/pybinder.cpp:67:22: required from here 2024-03-05T16:16:10,561 src/cpp/pore_model.hpp:507:50: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2024-03-05T16:16:17,727 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]’: 2024-03-05T16:16:17,727 src/cpp/pore_model.hpp:339:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = short unsigned int]’ 2024-03-05T16:16:17,728 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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]’ 2024-03-05T16:16:17,729 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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}]’ 2024-03-05T16:16:17,729 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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 = {}]’ 2024-03-05T16:16:17,730 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]’ 2024-03-05T16:16:17,731 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]’ 2024-03-05T16:16:17,732 src/cpp/pybinder.cpp:66:22: required from here 2024-03-05T16:16:17,732 src/cpp/pore_model.hpp:354:14: warning: variable ‘get_kmer’ set but not used [-Wunused-but-set-variable] 2024-03-05T16:16:17,733 354 | auto get_kmer = [&](size_t i) {return i;}; 2024-03-05T16:16:17,734 | ^~~~~~~~ 2024-03-05T16:16:18,431 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::fill_mat() [with ModelType = PoreModel]’: 2024-03-05T16:16:18,432 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]’ 2024-03-05T16:16:18,432 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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]’ 2024-03-05T16:16:18,433 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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&}]’ 2024-03-05T16:16:18,433 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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 = {}]’ 2024-03-05T16:16:18,434 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]’ 2024-03-05T16:16:18,435 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]’ 2024-03-05T16:16:18,436 src/cpp/pybinder.cpp:66:22: required from here 2024-03-05T16:16:18,436 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] 2024-03-05T16:16:18,437 443 | if (q >= 0 && q < qry_size() && in_range(r, ref_vals_)) { 2024-03-05T16:16:18,438 | ~~^~~~~~~~~~~~ 2024-03-05T16:16:18,438 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::traceback() [with ModelType = PoreModel]’: 2024-03-05T16:16:18,439 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]’ 2024-03-05T16:16:18,440 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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]’ 2024-03-05T16:16:18,440 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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&}]’ 2024-03-05T16:16:18,442 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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 = {}]’ 2024-03-05T16:16:18,442 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]’ 2024-03-05T16:16:18,443 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]’ 2024-03-05T16:16:18,444 src/cpp/pybinder.cpp:66:22: required from here 2024-03-05T16:16:18,444 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] 2024-03-05T16:16:18,445 507 | path_.push_back({path_ll.qry-offs+event_start_, path_ll.ref+offs}); 2024-03-05T16:16:18,446 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2024-03-05T16:16:19,231 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]’: 2024-03-05T16:16:19,231 src/cpp/pore_model.hpp:339:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = unsigned int]’ 2024-03-05T16:16:19,232 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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]’ 2024-03-05T16:16:19,233 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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}]’ 2024-03-05T16:16:19,233 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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 = {}]’ 2024-03-05T16:16:19,234 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]’ 2024-03-05T16:16:19,235 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]’ 2024-03-05T16:16:19,235 src/cpp/pybinder.cpp:67:22: required from here 2024-03-05T16:16:19,236 src/cpp/pore_model.hpp:354:14: warning: variable ‘get_kmer’ set but not used [-Wunused-but-set-variable] 2024-03-05T16:16:19,236 354 | auto get_kmer = [&](size_t i) {return i;}; 2024-03-05T16:16:19,237 | ^~~~~~~~ 2024-03-05T16:16:19,418 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::fill_mat() [with ModelType = PoreModel]’: 2024-03-05T16:16:19,419 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]’ 2024-03-05T16:16:19,420 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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]’ 2024-03-05T16:16:19,421 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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&}]’ 2024-03-05T16:16:19,421 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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 = {}]’ 2024-03-05T16:16:19,422 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]’ 2024-03-05T16:16:19,423 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]’ 2024-03-05T16:16:19,424 src/cpp/pybinder.cpp:67:22: required from here 2024-03-05T16:16:19,424 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] 2024-03-05T16:16:19,425 443 | if (q >= 0 && q < qry_size() && in_range(r, ref_vals_)) { 2024-03-05T16:16:19,425 | ~~^~~~~~~~~~~~ 2024-03-05T16:16:19,426 src/cpp/dtw.hpp: In instantiation of ‘void BandedDTW::traceback() [with ModelType = PoreModel]’: 2024-03-05T16:16:19,427 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]’ 2024-03-05T16:16:19,427 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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]’ 2024-03-05T16:16:19,428 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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&}]’ 2024-03-05T16:16:19,428 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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 = {}]’ 2024-03-05T16:16:19,429 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]’ 2024-03-05T16:16:19,430 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]’ 2024-03-05T16:16:19,431 src/cpp/pybinder.cpp:67:22: required from here 2024-03-05T16:16:19,431 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] 2024-03-05T16:16:19,432 507 | path_.push_back({path_ll.qry-offs+event_start_, path_ll.ref+offs}); 2024-03-05T16:16:19,433 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 2024-03-05T16:16:20,539 src/cpp/util.hpp: In instantiation of ‘T ValArray::mean() const [with T = float]’: 2024-03-05T16:16:20,540 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]’ 2024-03-05T16:16:20,540 src/cpp/pore_model.hpp:339:21: required from ‘PoreModel::PoreModel(PoreModelParams, pybind11::array_t, pybind11::array_t, bool) [with KmerType = short unsigned int]’ 2024-03-05T16:16:20,541 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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]’ 2024-03-05T16:16:20,541 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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}]’ 2024-03-05T16:16:20,542 /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/.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 = {}]’ 2024-03-05T16:16:20,543 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]’ 2024-03-05T16:16:20,543 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]’ 2024-03-05T16:16:20,544 src/cpp/pybinder.cpp:66:22: required from here 2024-03-05T16:16:20,545 src/cpp/util.hpp:144:14: warning: unused variable ‘sum’ [-Wunused-variable] 2024-03-05T16:16:20,545 144 | auto sum = super::sum(); 2024-03-05T16:16:20,546 | ^~~ 2024-03-05T16:16:20,547 src/cpp/util.hpp:145:14: warning: unused variable ‘len’ [-Wunused-variable] 2024-03-05T16:16:20,548 145 | auto len = super::size(); 2024-03-05T16:16:20,548 | ^~~ 2024-03-05T16:17:07,559 virtual memory exhausted: Cannot allocate memory 2024-03-05T16:17:07,671 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2024-03-05T16:17:07,821 ERROR: python setup.py bdist_wheel exited with 1 2024-03-05T16:17:07,835 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2024-03-05T16:17:07,835 exec(compile('"'"''"'"''"'"' 2024-03-05T16:17:07,835 # This is -- a caller that pip uses to run setup.py 2024-03-05T16:17:07,835 # 2024-03-05T16:17:07,835 # - It imports setuptools before invoking setup.py, to enable projects that directly 2024-03-05T16:17:07,835 # import from `distutils.core` to work with newer packaging standards. 2024-03-05T16:17:07,835 # - It provides a clear error message when setuptools is not installed. 2024-03-05T16:17:07,835 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2024-03-05T16:17:07,835 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2024-03-05T16:17:07,835 # manifest_maker: standard file '"'"'-c'"'"' not found". 2024-03-05T16:17:07,835 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2024-03-05T16:17:07,835 import os, sys, tokenize 2024-03-05T16:17:07,835 2024-03-05T16:17:07,835 try: 2024-03-05T16:17:07,835 import setuptools 2024-03-05T16:17:07,835 except ImportError as error: 2024-03-05T16:17:07,835 print( 2024-03-05T16:17:07,835 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2024-03-05T16:17:07,835 "the build environment.", 2024-03-05T16:17:07,835 file=sys.stderr, 2024-03-05T16:17:07,835 ) 2024-03-05T16:17:07,835 sys.exit(1) 2024-03-05T16:17:07,835 2024-03-05T16:17:07,835 __file__ = %r 2024-03-05T16:17:07,835 sys.argv[0] = __file__ 2024-03-05T16:17:07,835 2024-03-05T16:17:07,835 if os.path.exists(__file__): 2024-03-05T16:17:07,835 filename = __file__ 2024-03-05T16:17:07,835 with tokenize.open(__file__) as f: 2024-03-05T16:17:07,835 setup_py_code = f.read() 2024-03-05T16:17:07,835 else: 2024-03-05T16:17:07,835 filename = "" 2024-03-05T16:17:07,835 setup_py_code = "from setuptools import setup; setup()" 2024-03-05T16:17:07,835 2024-03-05T16:17:07,835 exec(compile(setup_py_code, filename, "exec")) 2024-03-05T16:17:07,835 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-crx227sw[/] 2024-03-05T16:17:07,835 [bold magenta]cwd[/]: /tmp/pip-wheel-l_tr5ji6/uncalled4_c95ccf7aca42485c953bd783aea38606/ 2024-03-05T16:17:07,836 Building wheel for uncalled4 (setup.py): finished with status 'error' 2024-03-05T16:17:07,838 ERROR: Failed building wheel for uncalled4 2024-03-05T16:17:07,839 Running setup.py clean for uncalled4 2024-03-05T16:17:07,840 Running command python setup.py clean 2024-03-05T16:17:08,732 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2024-03-05T16:17:08,732 !! 2024-03-05T16:17:08,733 ******************************************************************************** 2024-03-05T16:17:08,734 Requirements should be satisfied by a PEP 517 installer. 2024-03-05T16:17:08,735 If you are using pip, you can try `pip install --use-pep517`. 2024-03-05T16:17:08,736 ******************************************************************************** 2024-03-05T16:17:08,737 !! 2024-03-05T16:17:08,737 dist.fetch_build_eggs(dist.setup_requires) 2024-03-05T16:17:08,943 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'build_backend' 2024-03-05T16:17:08,944 warnings.warn(msg) 2024-03-05T16:17:09,099 running clean 2024-03-05T16:17:09,149 removing 'build/temp.linux-armv7l-cpython-311' (and everything under it) 2024-03-05T16:17:09,161 removing 'build/lib.linux-armv7l-cpython-311' (and everything under it) 2024-03-05T16:17:09,191 'build/bdist.linux-armv7l' does not exist -- can't clean it 2024-03-05T16:17:09,192 'build/scripts-3.11' does not exist -- can't clean it 2024-03-05T16:17:09,192 removing 'build' 2024-03-05T16:17:09,302 Failed to build uncalled4 2024-03-05T16:17:09,303 ERROR: Failed to build one or more wheels 2024-03-05T16:17:09,305 Exception information: 2024-03-05T16:17:09,305 Traceback (most recent call last): 2024-03-05T16:17:09,305 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2024-03-05T16:17:09,305 status = run_func(*args) 2024-03-05T16:17:09,305 ^^^^^^^^^^^^^^^ 2024-03-05T16:17:09,305 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 245, in wrapper 2024-03-05T16:17:09,305 return func(self, options, args) 2024-03-05T16:17:09,305 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2024-03-05T16:17:09,305 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2024-03-05T16:17:09,305 raise CommandError("Failed to build one or more wheels") 2024-03-05T16:17:09,305 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2024-03-05T16:17:09,309 Removed build tracker: '/tmp/pip-build-tracker-tb3dmrz7'